[112] | 1 | %'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch) |
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[2] | 2 | %------------------------------------------------------------------------ |
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[309] | 3 | % provides an interface for the software menucivx |
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[2] | 4 | % function varargout = civ(varargin) |
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[309] | 5 | % provides an interface for the software menucivx |
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[2] | 6 | % |
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| 7 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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[282] | 8 | % Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr |
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[2] | 9 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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[112] | 10 | % This file is part of the toolbox UVMAT. |
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| 11 | % |
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[2] | 12 | % UVMAT is free software; you can redistribute it and/or modify |
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| 13 | % it under the terms of the GNU General Public License as published by |
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| 14 | % the Free Software Foundation; either version 2 of the License, or |
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| 15 | % (at your option) any later version. |
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[112] | 16 | % |
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[2] | 17 | % UVMAT is distributed in the hope that it will be useful, |
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| 18 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 19 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 20 | % GNU General Public License (file UVMAT/COPYING.txt) for more details. |
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| 21 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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| 22 | function varargout = civ(varargin) |
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[273] | 23 | %TODO: search range |
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[2] | 24 | |
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[317] | 25 | % Last Modified by GUIDE v2.5 04-Dec-2011 18:52:13 |
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[2] | 26 | % Begin initialization code - DO NOT EDIT |
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| 27 | gui_Singleton = 1; |
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| 28 | gui_State = struct('gui_Name', mfilename, ... |
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[112] | 29 | 'gui_Singleton', gui_Singleton, ... |
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| 30 | 'gui_OpeningFcn', @civ_OpeningFcn, ... |
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| 31 | 'gui_OutputFcn', @civ_OutputFcn, ... |
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| 32 | 'gui_LayoutFcn', [] , ... |
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| 33 | 'gui_Callback', []); |
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[2] | 34 | if nargin && ischar(varargin{1}) |
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| 35 | gui_State.gui_Callback = str2func(varargin{1}); |
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| 36 | end |
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| 37 | |
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| 38 | if nargout |
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| 39 | [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); |
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| 40 | else |
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| 41 | gui_mainfcn(gui_State, varargin{:}); |
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| 42 | end |
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| 43 | % End initialization code - DO NOT EDIT |
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| 44 | |
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[12] | 45 | %------------------------------------------------------------------------ |
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[2] | 46 | % --- Executes just before civ is made visible. |
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[298] | 47 | function civ_OpeningFcn(hObject, eventdata, handles, fileinput) |
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[12] | 48 | %------------------------------------------------------------------------ |
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[2] | 49 | % This function has no output args, see OutputFcn. |
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[298] | 50 | |
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| 51 | %% General settings |
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[2] | 52 | handles.output = hObject; |
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[298] | 53 | guidata(hObject, handles); % Update handles structure |
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[309] | 54 | set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display) |
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[252] | 55 | |
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[298] | 56 | %% Adjust the GUI according to the binaries available in PARAM.xml |
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[276] | 57 | path_civ=fileparts(which('civ')); %path to civ |
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[298] | 58 | addpath (path_civ) ; %add the path to civ, (useful in case of change of working directory after civ has been s opened in the working directory) |
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[273] | 59 | errormsg=[];%default error message |
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| 60 | xmlfile='PARAM.xml'; |
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| 61 | if exist(xmlfile,'file') |
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| 62 | try |
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| 63 | t=xmltree(xmlfile); |
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| 64 | sparam=convert(t); |
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| 65 | catch |
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| 66 | errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr}; |
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| 67 | end |
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| 68 | else |
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| 69 | errormsg=[xmlfile ' not found: path to civx binaries undefined']; |
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| 70 | end |
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| 71 | if ~isempty(errormsg) |
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[301] | 72 | msgbox_uvmat('WARNING',errormsg); |
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[273] | 73 | end |
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| 74 | test_batch=0;%default: ,no batch mode available |
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| 75 | if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode') |
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| 76 | test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod |
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| 77 | end |
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| 78 | if test_batch==0 |
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| 79 | set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated) |
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| 80 | set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated) |
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| 81 | end |
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| 82 | if isfield(sparam.RunParam,'CivBin') |
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| 83 | if ~exist(sparam.RunParam.CivBin,'file') |
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[276] | 84 | sparam.RunParam.CivBin=fullfile(path_civ,sparam.RunParam.CivBin); |
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[273] | 85 | end |
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| 86 | else |
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| 87 | sparam.RunParam.CivBin=''; |
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| 88 | end |
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| 89 | |
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[298] | 90 | %% load the list of previously browsed files in the upper bar menu Open/ |
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[296] | 91 | dir_perso=prefdir; % path to the directory .matlab for personal data |
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| 92 | profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab |
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| 93 | if exist(profil_perso,'file') |
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| 94 | h=load (profil_perso); |
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| 95 | if isfield(h,'MenuFile') |
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| 96 | for ifile=1:min(length(h.MenuFile),5) |
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| 97 | eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});']) |
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| 98 | end |
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| 99 | end |
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[273] | 100 | end |
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| 101 | |
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[298] | 102 | %% prepare the GUI with parameters from the input file if opened from uvmat |
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| 103 | if exist('fileinput','var')% && isfield(param,'RootName') && ~isempty(param.RootName) |
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| 104 | errormsg=display_file_name(handles,fileinput); |
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| 105 | if ~isempty(errormsg) |
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| 106 | msgbox_uvmat('ERROR',errormsg) |
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[112] | 107 | end |
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[2] | 108 | end |
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| 109 | |
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[12] | 110 | %------------------------------------------------------------------------ |
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[2] | 111 | % --- Outputs from this function are returned to the command line. |
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| 112 | function varargout = civ_OutputFcn(hObject, eventdata, handles) |
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[12] | 113 | %------------------------------------------------------------------------ |
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[2] | 114 | % Get default command line output from handles structure |
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| 115 | varargout{1} = handles.output; |
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| 116 | |
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[307] | 117 | %------------------------------------------------------------------------ |
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[309] | 118 | % --- Function activated by the Open/Browse... option in the upper menu bar. |
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[307] | 119 | function MenuBrowse_Callback(hObject, eventdata, handles) |
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| 120 | %------------------------------------------------------------------------ |
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| 121 | %get the current input root file name to initiate the browser |
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| 122 | filebase=get(handles.RootName,'String'); |
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| 123 | oldfile=''; %default |
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[309] | 124 | if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name |
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[307] | 125 | dir_perso=prefdir; |
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| 126 | profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); |
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| 127 | if exist(profil_perso,'file') |
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| 128 | h=load (profil_perso); |
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| 129 | if isfield(h,'filebase')&& ischar(h.filebase) |
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| 130 | oldfile=h.filebase; |
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| 131 | end |
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| 132 | if isfield(h,'RootPath') && ischar(h.RootPath) |
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| 133 | oldfile=h.RootPath; |
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| 134 | end |
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| 135 | end |
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| 136 | else |
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| 137 | oldfile=filebase; |
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| 138 | end |
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| 139 | ind_opening=1;%default |
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| 140 | browse.incr_pair=[0 0]; %default |
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| 141 | menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)'; |
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[309] | 142 | '*.xml', '.xml files '; ... |
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| 143 | '*.civ', '.civ files '; ... |
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| 144 | '*.png','.png image files'; ... |
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| 145 | '*.jpg',' jpeg image files'; ... |
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| 146 | '*.tif','.tif image files'; ... |
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| 147 | '*.avi;*.AVI','.avi movie files'; ... |
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| 148 | '*.nc','.netcdf files'; ... |
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| 149 | '*.*', 'All Files (*.*)'}; |
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[307] | 150 | [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile); |
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| 151 | fileinput=[PathName FileName];%complete file name |
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| 152 | sizf=size(fileinput); |
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| 153 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
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[2] | 154 | |
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[307] | 155 | %% prepare the GUI with parameters from the input file if opened from uvmat |
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| 156 | errormsg=display_file_name(handles,fileinput); |
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[309] | 157 | if ~isempty(errormsg) |
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| 158 | msgbox_uvmat('ERROR',erromsg) |
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| 159 | end |
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[2] | 160 | |
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[307] | 161 | [path,name,ext]=fileparts(fileinput); |
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| 162 | testeditxml=0; |
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| 163 | if isequal(ext,'.xml') |
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| 164 | testeditxml=1; |
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| 165 | t_browse=xmltree(fileinput); |
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| 166 | head_element=get(t_browse,1); |
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| 167 | if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc') |
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| 168 | testeditxml=0; |
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| 169 | end |
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| 170 | end |
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| 171 | if testeditxml==1 || isequal(ext,'.xls') |
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| 172 | heditxml=editxml({fileinput}); |
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| 173 | set(heditxml,'Tag','browser') |
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| 174 | waitfor(heditxml,'Tag','idle') |
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| 175 | if ~ishandle(heditxml) |
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| 176 | return |
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| 177 | end |
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| 178 | attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes'); |
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| 179 | set(handles.browse,'UserData',fileinput)% store for future opening with browser |
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| 180 | fileinput=get(attr,'UserData'); |
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| 181 | if ~exist(fileinput,'file') |
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| 182 | return |
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| 183 | end |
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| 184 | end |
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| 185 | [RootPath,RootFile,str1,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput); |
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[309] | 186 | % filebase=fullfile(RootPath,RootFile); |
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[307] | 187 | num_i1=str2double(str1); |
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| 188 | if isnan(num_i1),num_i1=1;end |
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| 189 | num_i2=str2double(str2); |
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| 190 | if isnan(num_i2),num_i2=num_i1;end |
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| 191 | num_j1=stra2num(str_a); |
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| 192 | if isnan(num_j1),num_j1=1;end |
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| 193 | num_j2=stra2num(str_b); |
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| 194 | if isnan(num_j2),num_j2=num_j1;end |
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| 195 | if isequal(get(handles.ListCompareMode,'Value'),1) |
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| 196 | browse=[];%initialisation |
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| 197 | else |
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| 198 | browse=get(handlesRootName,'UserData'); |
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| 199 | end |
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| 200 | browse.num_i1=num_i1; |
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| 201 | browse.num_i2=num_i2; |
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| 202 | browse.num_j1=num_j1; |
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| 203 | browse.num_j2=num_j2; |
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| 204 | if length(ext)>1 && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat |
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| 205 | browse.nom_type_ima=nom_type; |
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| 206 | browse.ext_ima=ext; |
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| 207 | set(handles.ImaExt,'String',ext) |
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| 208 | end |
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| 209 | set(handles.ImaDoc,'String',ext); |
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| 210 | |
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| 211 | set(handles.RootName,'UserData',browse);% store information from browser |
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| 212 | |
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[309] | 213 | %------------------------------------------------------------------------ |
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[273] | 214 | % --- Open again the file whose name has been recorded in MenuFile_1 |
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| 215 | function MenuFile_1_Callback(hObject, eventdata, handles) |
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[12] | 216 | %------------------------------------------------------------------------ |
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[273] | 217 | fileinput=get(handles.MenuFile_1,'Label'); |
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[298] | 218 | errormsg=display_file_name(handles,fileinput); |
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| 219 | if ~isempty(errormsg) |
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| 220 | msgbox_uvmat('ERROR',erromsg) |
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| 221 | end |
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[273] | 222 | |
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| 223 | % ----------------------------------------------------------------------- |
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| 224 | % --- Open again the file whose name has been recorded in MenuFile_2 |
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| 225 | function MenuFile_2_Callback(hObject, eventdata, handles) |
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| 226 | %------------------------------------------------------------------------ |
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| 227 | fileinput=get(handles.MenuFile_2,'Label'); |
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[298] | 228 | errormsg=display_file_name(handles,fileinput); |
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| 229 | if ~isempty(errormsg) |
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| 230 | msgbox_uvmat('ERROR',erromsg) |
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| 231 | end |
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[309] | 232 | |
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[273] | 233 | % ----------------------------------------------------------------------- |
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| 234 | % --- Open again the file whose name has been recorded in MenuFile_3 |
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| 235 | function MenuFile_3_Callback(hObject, eventdata, handles) |
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| 236 | %------------------------------------------------------------------------ |
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| 237 | fileinput=get(handles.MenuFile_3,'Label'); |
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[298] | 238 | errormsg=display_file_name(handles,fileinput); |
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| 239 | if ~isempty(errormsg) |
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| 240 | msgbox_uvmat('ERROR',erromsg) |
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| 241 | end |
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[309] | 242 | |
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[273] | 243 | % ----------------------------------------------------------------------- |
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| 244 | % --- Open again the file whose name has been recorded in MenuFile_4 |
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| 245 | function MenuFile_4_Callback(hObject, eventdata, handles) |
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| 246 | %------------------------------------------------------------------------ |
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| 247 | fileinput=get(handles.MenuFile_4,'Label'); |
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[298] | 248 | errormsg=display_file_name(handles,fileinput); |
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| 249 | if ~isempty(errormsg) |
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| 250 | msgbox_uvmat('ERROR',erromsg) |
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| 251 | end |
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[309] | 252 | |
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[273] | 253 | % ----------------------------------------------------------------------- |
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| 254 | % --- Open again the file whose name has been recorded in MenuFile_5 |
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| 255 | function MenuFile_5_Callback(hObject, eventdata, handles) |
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| 256 | %------------------------------------------------------------------------ |
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| 257 | fileinput=get(handles.MenuFile_5,'Label'); |
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[298] | 258 | errormsg=display_file_name(handles,fileinput); |
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| 259 | if ~isempty(errormsg) |
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| 260 | msgbox_uvmat('ERROR',erromsg) |
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| 261 | end |
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[2] | 262 | |
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[309] | 263 | % ----------------------------------------------------------------------- |
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| 264 | % --- Prepare the GUI for the compiled CivX program |
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| 265 | function MenuCivX_Callback(hObject, eventdata, handles) |
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| 266 | set(handles.MenuMatlab,'checked','off') |
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| 267 | set(handles.MenuCivX,'checked','on') |
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| 268 | %set(handles.thresh_patch1,'Visible','off') |
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| 269 | % set(handles.thresh_text1,'Visible','off') |
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[316] | 270 | set(handles.num_MaxDiff,'Visible','off') |
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| 271 | set(handles.title_MaxDiff,'Visible','off') |
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[309] | 272 | set(handles.num_Rho,'Style','edit') |
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| 273 | set(handles.num_Rho,'String','1') |
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| 274 | set(handles.BATCH,'Enable','on') |
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| 275 | % ----------------------------------------------------------------------- |
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| 276 | |
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| 277 | % ----------------------------------------------------------------------- |
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| 278 | % --- Prepare the GUI for the Matlab PIV program |
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| 279 | function MenuMatlab_Callback(hObject, eventdata, handles) |
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| 280 | % ----------------------------------------------------------------------- |
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| 281 | set(handles.MenuMatlab,'checked','on') |
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| 282 | set(handles.MenuCivX,'checked','off') |
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[316] | 283 | % if get(handles.CheckPatch1,'Value') |
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| 284 | set(handles.num_MaxDiff,'Visible','on') |
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| 285 | set(handles.title_MaxDiff,'Visible','on') |
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| 286 | |
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| 287 | % end |
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[309] | 288 | set(handles.num_Rho,'Style','popupmenu') |
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| 289 | set(handles.num_Rho,'Value',1) |
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| 290 | set(handles.num_Rho,'String',{'1';'2'}) |
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| 291 | set(handles.BATCH,'Enable','off') |
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| 292 | |
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| 293 | % ----------------------------------------------------------------------- |
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| 294 | % --- Open the help html file |
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| 295 | function MenuHelp_Callback(hObject, eventdata, handles) |
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| 296 | % ----------------------------------------------------------------------- |
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| 297 | path_civ=fileparts(which ('civ')); |
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| 298 | helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html'); |
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| 299 | if isempty(dir(helpfile)) |
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| 300 | msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package') |
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| 301 | else |
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| 302 | addpath (fullfile(path_civ,'uvmat_doc')) |
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| 303 | web([helpfile '#civ']) |
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| 304 | end |
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| 305 | |
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[12] | 306 | %------------------------------------------------------------------------ |
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[309] | 307 | % --- Function activated when a new filebase (image series) is introduced |
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[71] | 308 | function RootName_Callback(hObject, eventdata, handles) |
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[12] | 309 | %------------------------------------------------------------------------ |
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[273] | 310 | filebase=get(handles.RootName,'String'); |
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[298] | 311 | errormsg=display_file_name(handles,filebase); |
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| 312 | if ~isempty(errormsg) |
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| 313 | msgbox_uvmat('ERROR',erromsg) |
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| 314 | end |
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[309] | 315 | |
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[273] | 316 | %------------------------------------------------------------------------ |
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[309] | 317 | % --- general function activated for an input file series |
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[298] | 318 | function errormsg=display_file_name(handles,fileinput) |
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[273] | 319 | %------------------------------------------------------------------------ |
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[282] | 320 | set(handles.ListCompareMode,'Visible','on') |
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[298] | 321 | errormsg='';%default empty error message |
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[273] | 322 | |
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[298] | 323 | %% enable RUN, BATCH button and 'status' display |
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| 324 | set(handles.RUN, 'Enable','On') |
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| 325 | set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color |
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| 326 | set(handles.BATCH,'Enable','On') |
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| 327 | set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color |
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| 328 | if isfield(handles,'status') |
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| 329 | set(handles.status,'Value',0); %suppress the 'status' display |
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| 330 | status_Callback([], [], handles) |
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[2] | 331 | end |
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| 332 | |
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[298] | 333 | %% determine nomenclature types and extension of the input files |
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| 334 | ext_ima='';%default |
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| 335 | nom_type_ima='';%default |
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| 336 | nom_type_nc=''; |
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| 337 | [RootPath,FileName,i1_str,i2_str,j1_str,j2_str,ext_input,nom_type_input,subdir]=name2display(fileinput); |
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| 338 | RootName=fullfile(RootPath,FileName); |
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| 339 | set(handles.RootName,'String',RootName) |
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[309] | 340 | set(handles.RootName,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
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[313] | 341 | i1=str2double(i1_str); |
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| 342 | i2=str2double(i2_str); |
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| 343 | j1=str2double(j1_str); |
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| 344 | j2=str2double(j2_str); |
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| 345 | num_ref_i=i1;%efaulmt ref index |
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| 346 | num_ref_j=j1; |
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[300] | 347 | browse.incr_pair=[0 0];%default |
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[307] | 348 | |
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| 349 | % form=imformats(ext_input(2:end)); |
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| 350 | if ~isempty(ext_input)&&(~isempty(imformats(ext_input(2:end)))||strcmpi(ext_input,'.avi'))% if the extension corresponds to an image or movie format recognized by Matlab |
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[298] | 351 | ext_ima=ext_input; |
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| 352 | nom_type_ima=nom_type_input; |
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| 353 | else %case of netcdf input file, look for corresponding images |
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| 354 | nom_type_nc=nom_type_input; |
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[313] | 355 | if ~isnan(i2) |
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| 356 | num_ref_i=floor((num_ref_i+i2)/2);% reference image number corresponding to the file |
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| 357 | browse.incr_pair(1)=i2-i1; |
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[300] | 358 | browse.incr_pair(2)=0; |
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| 359 | end |
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[298] | 360 | %TODO: read the image name in the netcdf file (if documented) |
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| 361 | %look for double image series '_i_j' |
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| 362 | dirima=dir([RootName '_' i1_str '_' j1_str '.*']); |
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| 363 | if isempty(dirima) |
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| 364 | % look for images series with sub marker '_' |
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| 365 | dirima=dir([RootName '_*' i1_str '.*']); |
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| 366 | if isempty(dirima) |
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| 367 | % look for other images series |
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| 368 | dirima=dir([RootName '*' i1_str '.*']); |
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| 369 | if isempty(dirima) |
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| 370 | % look for other images series witth letter appendix |
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| 371 | appendix=char(96+j1_str); |
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| 372 | dirima=dir([RootName '*' i1_str appendix '.*']); |
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| 373 | end |
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| 374 | end |
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[2] | 375 | end |
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[298] | 376 | for ilist=1:numel(dirima) |
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[313] | 377 | [pp,ff,i1_str,i2_str,j1_str,j2_str,ext_list,nom_type_list]=name2display(dirima(ilist).name); |
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[298] | 378 | form=imformats(ext_list(2:end)); |
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| 379 | if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab |
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| 380 | ext_ima=ext_list; |
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| 381 | nom_type_ima=nom_type_list; |
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[313] | 382 | i1=str2double(i1_str); |
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| 383 | j1=str2double(j1_str); |
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| 384 | i2=str2double(i2_str); |
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| 385 | j2=str2double(j2_str); |
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[298] | 386 | % set the range of fields (1:1 by default) and selected pair |
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[313] | 387 | if isequal(i2,i1)||isnan(i2) |
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| 388 | num_ref_i=i1; |
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[298] | 389 | else |
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[313] | 390 | num_ref_i=floor((i1+i2)/2); |
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| 391 | browse.incr_pair(1)=i2-i1; |
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[298] | 392 | browse.incr_pair(2)=0; |
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| 393 | end |
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[313] | 394 | if isequal(j1,j2)||isnan(j2) |
---|
| 395 | if isnan(j1) |
---|
[298] | 396 | num_ref_j=1; |
---|
| 397 | else |
---|
[313] | 398 | num_ref_j=j1; |
---|
[298] | 399 | end |
---|
| 400 | else |
---|
[313] | 401 | num_ref_j=floor((j1+j2)/2); |
---|
| 402 | browse.incr_pair(2)=j2-j1; |
---|
[298] | 403 | end |
---|
| 404 | break |
---|
| 405 | end |
---|
| 406 | end |
---|
[2] | 407 | end |
---|
[300] | 408 | |
---|
[298] | 409 | %% look for an image documentation file |
---|
| 410 | ext_imadoc='';%default |
---|
| 411 | if exist([RootName '.xml'],'file') |
---|
| 412 | ext_imadoc='.xml'; |
---|
| 413 | elseif exist([RootName '.civxml'],'file') |
---|
| 414 | ext_imadoc='.civxml'; |
---|
| 415 | elseif exist([RootName '.civ'],'file') |
---|
| 416 | ext_imadoc='.civ'; |
---|
| 417 | elseif exist([RootName '.avi'],'file') |
---|
| 418 | ext_imadoc='.avi'; |
---|
| 419 | elseif exist([RootName '.AVI'],'file') |
---|
| 420 | ext_imadoc='.AVI'; |
---|
| 421 | end |
---|
| 422 | set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used |
---|
| 423 | set(handles.ImaDoc,'BackgroundColor',[1 1 0]) |
---|
| 424 | drawnow |
---|
[2] | 425 | %%%%%%%% read image documentation file %%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
[84] | 426 | mode=''; %default |
---|
[298] | 427 | time=[]; |
---|
| 428 | TimeUnit='frame'; %default |
---|
| 429 | CoordUnit='px';%default |
---|
| 430 | pxcmx_search=[];%default |
---|
| 431 | pxcmy_search=[];%default |
---|
[128] | 432 | if isequal(ext_imadoc,'.civxml')%TO ABANDON |
---|
[298] | 433 | [nbfield,nbfield2,time]=read_civxml([RootName '.civxml']); |
---|
[2] | 434 | mode='pair j1-j2'; |
---|
| 435 | if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat |
---|
[112] | 436 | nom_type_ima='_i_j'; |
---|
[2] | 437 | end |
---|
[128] | 438 | elseif isequal(ext_imadoc,'.xml') |
---|
[298] | 439 | [XmlData,warntext]=imadoc2struct([RootName '.xml']); |
---|
[2] | 440 | ext_ima_read=[]; |
---|
| 441 | nom_type_read=[]; |
---|
[12] | 442 | if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file |
---|
[2] | 443 | [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName); |
---|
[298] | 444 | fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file, |
---|
[45] | 445 | if ~exist(fullname,'file') |
---|
[12] | 446 | msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist']) |
---|
| 447 | end |
---|
[2] | 448 | end |
---|
[84] | 449 | if isfield(XmlData,'Time') |
---|
[85] | 450 | time=XmlData.Time; |
---|
[84] | 451 | nbfield=size(time,1); |
---|
[122] | 452 | nbfield2=size(time,2); |
---|
[127] | 453 | %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml |
---|
[122] | 454 | if isequal(nbfield,1) && ~isequal(nbfield2,1)% .Time is a line vector |
---|
[301] | 455 | if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once')) |
---|
[84] | 456 | time=time'; |
---|
[122] | 457 | nbfield=nbfield2; |
---|
| 458 | nbfield2=1; |
---|
[84] | 459 | end |
---|
| 460 | end |
---|
| 461 | end |
---|
[71] | 462 | if isfield(XmlData,'TimeUnit') |
---|
| 463 | TimeUnit=XmlData.TimeUnit; |
---|
[2] | 464 | end |
---|
| 465 | pxcmx_search=1; |
---|
| 466 | pxcmy_search=1; |
---|
| 467 | if isfield(XmlData,'GeometryCalib') |
---|
| 468 | tsai=XmlData.GeometryCalib; |
---|
[112] | 469 | if isfield(tsai,'f') && isfield(tsai,'Tz') && isfield(tsai,'dpx') && isfield(tsai,'dpy')&& isfield(tsai,'R') |
---|
| 470 | rot2D=tsai.R(1:2,[1,2]); |
---|
| 471 | pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx); |
---|
| 472 | pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy); |
---|
[2] | 473 | end |
---|
[112] | 474 | if isfield(tsai,'CoordUnit') |
---|
| 475 | CoordUnit=tsai.CoordUnit; |
---|
[2] | 476 | end |
---|
[112] | 477 | end |
---|
[128] | 478 | elseif strcmp(ext_imadoc,'.civ')% case of .civ image documentation file |
---|
[298] | 479 | [error,time,TimeUnit,mode,npx,npy]=read_imatext([RootName '.civ']); |
---|
| 480 | if error==2, msgbox_uvmat('WARNING',['no file ' RootName '.civ']); |
---|
[112] | 481 | elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
---|
| 482 | end |
---|
[128] | 483 | nom_type_ima='001a'; |
---|
| 484 | elseif strcmpi(ext_imadoc,'.avi') |
---|
[112] | 485 | nom_type_ima='*'; |
---|
[128] | 486 | ext_ima=ext_imadoc; |
---|
[282] | 487 | set(handles.ListPairMode,'Value',1); |
---|
| 488 | set(handles.ListPairMode,'String',{'series(Di)'}) |
---|
[112] | 489 | dt=0.04;%default |
---|
[298] | 490 | if exist([RootName ext_imadoc],'file')==2 |
---|
| 491 | info=aviinfo([RootName ext_imadoc]);%read infos on the avi movie |
---|
[112] | 492 | dt=1/info.FramesPerSecond;%time interval between successive frames |
---|
| 493 | nbfield=info.NumFrames;%number of frames |
---|
| 494 | end |
---|
| 495 | time=(dt*(0:nbfield-1))';%list of image times |
---|
[2] | 496 | end |
---|
| 497 | if isempty(time) |
---|
| 498 | set(handles.ImaDoc,'String',''); %xml file not used for timing |
---|
| 499 | end |
---|
[298] | 500 | set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box to yellow color |
---|
[2] | 501 | |
---|
[120] | 502 | |
---|
[298] | 503 | %% timing display |
---|
| 504 | %show the reference image edit box if relevant (not needed for movies or in the absence of time information |
---|
| 505 | if ~isempty(time) |
---|
[2] | 506 | if size(time,1)+size(time,2)>=3 % if there are at least two time values to define dt |
---|
| 507 | nbfield=size(time,1); |
---|
| 508 | nbfield2=size(time,2); |
---|
[273] | 509 | set(handles.ImaDoc,'UserData',time); %store the set of times |
---|
[71] | 510 | set(handles.dt_unit,'String',['dt in m' TimeUnit]); |
---|
| 511 | set(handles.TimeUnit,'String',TimeUnit); |
---|
[2] | 512 | set(handles.nb_field,'String',num2str(nbfield)); |
---|
| 513 | set(handles.nb_field2,'String',num2str(nbfield2)); |
---|
| 514 | end |
---|
| 515 | end |
---|
[71] | 516 | set(handles.CoordUnit,'String',CoordUnit) |
---|
[273] | 517 | set(handles.SearchRange,'UserData',[pxcmx_search pxcmy_search]); |
---|
[71] | 518 | set(handles.ImaExt,'String',ext_ima) |
---|
[298] | 519 | set(handles.ref_i,'String',num2str(num_ref_i)) |
---|
| 520 | set(handles.first_i,'String',num2str(num_ref_i)); |
---|
| 521 | set(handles.last_i,'String',num2str(num_ref_i));% |
---|
| 522 | set(handles.ref_j,'String',num2str(num_ref_j)) |
---|
| 523 | set(handles.first_j,'String',num2str(num_ref_j)); |
---|
| 524 | set(handles.last_j,'String',num2str(num_ref_j));% |
---|
[2] | 525 | |
---|
[298] | 526 | %% set the civ options depending on the input file content |
---|
| 527 | ind_opening=0;%default |
---|
| 528 | if isequal(ext_input,'.nc') |
---|
| 529 | browse.nom_type_nc=nom_type_input; |
---|
| 530 | ind_opening=2;% propose 'fix' as the default option |
---|
| 531 | Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','absolut_time_T0','fix','patch','civ2','fix2'); |
---|
[315] | 532 | if isfield(Data,'Txt') |
---|
| 533 | msgbox_uvmat('ERROR',Data.Txt) |
---|
| 534 | return |
---|
| 535 | end |
---|
[298] | 536 | if ~isempty(Data.CivStage)%test for civ files |
---|
| 537 | ind_opening=Data.CivStage; |
---|
| 538 | set(handles.ListPairMode,'Value',3) |
---|
| 539 | end |
---|
| 540 | end |
---|
| 541 | ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'}; |
---|
| 542 | for index = 1:ind_opening |
---|
| 543 | set(handles.(ListOptions{index}),'value',0) |
---|
| 544 | end |
---|
[300] | 545 | for index = ind_opening+1 |
---|
[298] | 546 | set(handles.(ListOptions{index}),'value',1) |
---|
| 547 | end |
---|
| 548 | update_CivOptions(handles) |
---|
| 549 | |
---|
| 550 | |
---|
[273] | 551 | %% set the menus of image pairs and default selection for civ %%%%%%%%%%%%%%%%%%% |
---|
[177] | 552 | test_ima_i=numel(nom_type_ima)>1 && isempty(regexp(nom_type_ima(2:end),'\D','once'));%images with single indexing |
---|
[122] | 553 | if test_ima_i || isequal(nom_type_nc,'_i1-i2')||~(exist('nbfield2','var')&&(nbfield2~=1)) |
---|
[282] | 554 | set(handles.ListPairMode,'Value',1) |
---|
| 555 | set(handles.ListPairMode,'String',{'series(Di)'}) |
---|
[2] | 556 | elseif (nbfield==1)% simple series in j |
---|
[282] | 557 | set(handles.ListPairMode,'Value',1) |
---|
| 558 | set(handles.ListPairMode,'String',{'series(Dj)'}) |
---|
[2] | 559 | else |
---|
[282] | 560 | set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice |
---|
[122] | 561 | if nbfield2 <= 10 |
---|
[282] | 562 | set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' for small burst |
---|
[2] | 563 | end |
---|
| 564 | end |
---|
| 565 | |
---|
[298] | 566 | %% update the subdirectory display |
---|
[300] | 567 | listot=dir(RootPath);%directory of RootPath |
---|
[273] | 568 | idir=0; |
---|
| 569 | listdir={''};%default |
---|
[300] | 570 | % get the list of existing civ subdirectories in the path of theinput root file |
---|
[273] | 571 | for ilist=1:length(listot) |
---|
| 572 | if listot(ilist).isdir |
---|
| 573 | name=listot(ilist).name; |
---|
| 574 | if ~isequal(name,'.') && ~isequal(name,'..') |
---|
| 575 | idir=idir+1; |
---|
| 576 | listdir{idir,1}=listot(ilist).name; |
---|
| 577 | end |
---|
| 578 | end |
---|
| 579 | end |
---|
[298] | 580 | Value=find(strcmp(subdir,listdir));%search the index of subdir in the cell listdir |
---|
[300] | 581 | if isempty(Value)% if the input subdir is not found |
---|
| 582 | ValueCiv1=get(handles.ListSubdirCiv1,'Value');%read the currrently selected dir name |
---|
[298] | 583 | if ValueCiv1>numel(listdir) |
---|
| 584 | ValueCiv1=1; |
---|
| 585 | end |
---|
[300] | 586 | set(handles.txt_SubdirCiv1,'String',listdir{ValueCiv1}) |
---|
[298] | 587 | ValueCiv2=get(handles.ListSubdirCiv2,'Value'); |
---|
| 588 | if ValueCiv2>numel(listdir) |
---|
| 589 | ValueCiv2=1; |
---|
| 590 | end |
---|
[300] | 591 | set(handles.txt_SubdirCiv2,'String',listdir{ValueCiv2}) |
---|
[298] | 592 | else |
---|
[301] | 593 | ValueCiv1=Value; |
---|
| 594 | ValueCiv2=Value; |
---|
[300] | 595 | set(handles.txt_SubdirCiv1,'String',listdir{Value}) |
---|
| 596 | set(handles.txt_SubdirCiv2,'String',listdir{Value}) |
---|
[298] | 597 | end |
---|
[301] | 598 | set(handles.ListSubdirCiv1,'Value',ValueCiv1) |
---|
| 599 | set(handles.ListSubdirCiv2,'Value',ValueCiv2) |
---|
[282] | 600 | set(handles.ListSubdirCiv1,'String',[listdir;'new...']) |
---|
[289] | 601 | set(handles.ListSubdirCiv2,'String',[listdir;'new...']) |
---|
[273] | 602 | if isempty(listdir) |
---|
[300] | 603 | set(handles.txt_SubdirCiv1,'String','CIV') |
---|
| 604 | set(handles.txt_SubdirCiv2,'String','CIV') |
---|
[273] | 605 | end |
---|
| 606 | |
---|
[300] | 607 | %% store info |
---|
| 608 | browse.nom_type_ima=nom_type_ima; |
---|
| 609 | set(handles.RootName,'UserData',browse)% store the nomenclature type |
---|
[273] | 610 | |
---|
[298] | 611 | %% list the possible index pairs, depending on the option set in ListPairMode |
---|
| 612 | ListPairMode_Callback([], [], handles) |
---|
| 613 | |
---|
| 614 | %% store the root input filename for future opening |
---|
| 615 | profil_perso=fullfile(prefdir,'uvmat_perso.mat'); |
---|
| 616 | % RootPath=fileparts(RootName); |
---|
| 617 | if exist(profil_perso,'file') |
---|
| 618 | save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat |
---|
| 619 | else |
---|
| 620 | txt=ver('MATLAB'); |
---|
| 621 | Release=txt.Release; |
---|
| 622 | relnumb=str2double(Release(3:4)); |
---|
| 623 | if relnumb >= 14 |
---|
| 624 | save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat |
---|
| 625 | else |
---|
| 626 | save (profil_perso,'RootPath'); %store the root name for future opening of uvmat |
---|
| 627 | end |
---|
| 628 | end |
---|
[309] | 629 | set(handles.RootName,'BackgroundColor',[1 1 1]) |
---|
[298] | 630 | |
---|
[12] | 631 | %------------------------------------------------------------------------ |
---|
[309] | 632 | % --- Executes on carriage return on the subdir checkciv1 edit window |
---|
| 633 | function txt_SubdirCiv1_Callback(hObject, eventdata, handles) |
---|
[12] | 634 | %------------------------------------------------------------------------ |
---|
[309] | 635 | subdir=get(handles.txt_SubdirCiv1,'String'); |
---|
| 636 | menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update |
---|
| 637 | ichoice=find(strcmp(subdir,menu_str),1); |
---|
| 638 | if isempty(ichoice) |
---|
| 639 | ilist=numel(menu_str); %select 'new...' in the menu |
---|
[2] | 640 | else |
---|
[309] | 641 | ilist=ichoice; |
---|
[2] | 642 | end |
---|
[309] | 643 | set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu |
---|
| 644 | if get(handles.CheckCiv1,'Value')% if Civ1 is performed |
---|
| 645 | set(handles.txt_SubdirCiv2,'String',subdir);% set by default civ2 directory the same as civ1 |
---|
| 646 | set(handles.ListSubdirCiv2,'Value',ilist) |
---|
| 647 | else % if Civ1 data already exist |
---|
| 648 | find_netcpair_civ1(handles); %update the list of available pairs from netcdf files in the new directory |
---|
[112] | 649 | end |
---|
[2] | 650 | |
---|
[12] | 651 | %------------------------------------------------------------------------ |
---|
[309] | 652 | % --- Executes on carriage return on the subdir checkciv1 edit window |
---|
| 653 | function txt_SubdirCiv2_Callback(hObject, eventdata, handles) |
---|
[12] | 654 | %------------------------------------------------------------------------ |
---|
[309] | 655 | subdir=get(handles.txt_SubdirCiv1,'String'); |
---|
| 656 | menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update |
---|
| 657 | ichoice=find(strcmp(subdir,menu_str),1); |
---|
| 658 | if isempty(ichoice) |
---|
| 659 | ilist=numel(menu_str); %select 'new...' in the menu |
---|
[2] | 660 | else |
---|
[309] | 661 | ilist=ichoice; |
---|
[2] | 662 | end |
---|
[309] | 663 | set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu |
---|
| 664 | %update the list of available pairs from netcdf files in the new directory |
---|
| 665 | if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value') |
---|
| 666 | find_netcpair_civ2(handles); |
---|
[2] | 667 | end |
---|
| 668 | |
---|
[309] | 669 | %------------------------------------------------------------------------ |
---|
| 670 | % --- Executes on button press in CheckCiv1. |
---|
| 671 | function CheckCiv1_Callback(hObject, eventdata, handles) |
---|
| 672 | %------------------------------------------------------------------------ |
---|
| 673 | update_CivOptions(handles) |
---|
[2] | 674 | |
---|
[309] | 675 | %------------------------------------------------------------------------ |
---|
| 676 | % --- Executes on button press in CheckFix1. |
---|
| 677 | function CheckFix1_Callback(hObject, eventdata, handles) |
---|
| 678 | %------------------------------------------------------------------------ |
---|
| 679 | update_CivOptions(handles) |
---|
[2] | 680 | |
---|
[309] | 681 | %------------------------------------------------------------------------ |
---|
| 682 | % --- Executes on button press in CheckPatch1. |
---|
| 683 | function CheckPatch1_Callback(hObject, eventdata, handles) |
---|
| 684 | %------------------------------------------------------------------------ |
---|
| 685 | update_CivOptions(handles) |
---|
[2] | 686 | |
---|
[309] | 687 | %------------------------------------------------------------------------ |
---|
| 688 | % --- Executes on button press in CheckCiv2. |
---|
| 689 | function CheckCiv2_Callback(hObject, eventdata, handles) |
---|
| 690 | %------------------------------------------------------------------------ |
---|
| 691 | update_CivOptions(handles) |
---|
[301] | 692 | |
---|
[309] | 693 | %------------------------------------------------------------------------ |
---|
| 694 | % --- Executes on button press in CheckFix2. |
---|
| 695 | function CheckFix2_Callback(hObject, eventdata, handles) |
---|
| 696 | %------------------------------------------------------------------------ |
---|
| 697 | update_CivOptions(handles) |
---|
[301] | 698 | |
---|
[309] | 699 | %------------------------------------------------------------------------ |
---|
| 700 | % --- Executes on button press in CheckPatch2. |
---|
| 701 | function CheckPatch2_Callback(hObject, eventdata, handles) |
---|
| 702 | %------------------------------------------------------------------------ |
---|
| 703 | update_CivOptions(handles) |
---|
[300] | 704 | |
---|
[12] | 705 | %------------------------------------------------------------------------ |
---|
[309] | 706 | % --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2 |
---|
| 707 | function update_CivOptions(handles) |
---|
[12] | 708 | %------------------------------------------------------------------------ |
---|
[309] | 709 | checkbox=zeros(1,6); |
---|
| 710 | checkbox(1)=get(handles.CheckCiv1,'Value'); |
---|
| 711 | checkbox(2)=get(handles.CheckFix1,'Value'); |
---|
| 712 | checkbox(3)=get(handles.CheckPatch1,'Value'); |
---|
| 713 | checkbox(4)=get(handles.CheckCiv2,'Value'); |
---|
| 714 | checkbox(5)=get(handles.CheckFix2,'Value'); |
---|
| 715 | checkbox(6)=get(handles.CheckPatch2,'Value'); |
---|
| 716 | ind_selected=find(checkbox,1); |
---|
| 717 | if ~isempty(ind_selected) |
---|
| 718 | RootName=get(handles.RootName,'String'); |
---|
| 719 | if isempty(RootName) |
---|
| 720 | msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...') |
---|
[270] | 721 | return |
---|
| 722 | end |
---|
[2] | 723 | end |
---|
[309] | 724 | set(handles.PairIndices,'Visible','on') |
---|
| 725 | set(handles.txt_SubdirCiv1,'Visible','on') |
---|
| 726 | set(handles.ListSubdirCiv1,'Visible','on') |
---|
| 727 | find_netcpair_civ1(handles) % select the available netcdf files |
---|
| 728 | if max(checkbox(4:6))% case of civ2 pair choice needed |
---|
| 729 | set(handles.TitlePairCiv2,'Visible','on') |
---|
| 730 | set(handles.TitleSubdirCiv2,'Visible','on') |
---|
| 731 | set(handles.txt_SubdirCiv2,'Visible','on') |
---|
| 732 | set(handles.ListSubdirCiv2,'Visible','on') |
---|
| 733 | set(handles.ListPairCiv2,'Visible','on') |
---|
| 734 | find_netcpair_civ2(handles) % select the available netcdf files |
---|
| 735 | else |
---|
| 736 | set(handles.TitleSubdirCiv2,'Visible','off') |
---|
| 737 | set(handles.txt_SubdirCiv2,'Visible','off') |
---|
| 738 | set(handles.ListSubdirCiv2,'Visible','off') |
---|
| 739 | set(handles.ListPairCiv2,'Visible','off') |
---|
[2] | 740 | end |
---|
[309] | 741 | options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'}; |
---|
| 742 | for ilist=1:length(options) |
---|
| 743 | if checkbox(ilist) |
---|
| 744 | set(handles.(options{ilist}),'Visible','on') |
---|
[2] | 745 | else |
---|
[309] | 746 | set(handles.(options{ilist}),'Visible','off') |
---|
[112] | 747 | end |
---|
[2] | 748 | end |
---|
| 749 | |
---|
[12] | 750 | %------------------------------------------------------------------------ |
---|
[177] | 751 | % --- Executes on button press in RUN: processing on local computer |
---|
[67] | 752 | function RUN_Callback(hObject, eventdata, handles) |
---|
| 753 | %------------------------------------------------------------------------ |
---|
[73] | 754 | set(handles.RUN, 'Enable','Off') |
---|
| 755 | set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784]) |
---|
[67] | 756 | batch=0; |
---|
[229] | 757 | errormsg=launch_jobs(hObject, eventdata, handles,batch); |
---|
[73] | 758 | set(handles.RUN, 'Enable','On') |
---|
| 759 | set(handles.RUN,'BackgroundColor',[1 0 0]) |
---|
[36] | 760 | |
---|
[177] | 761 | % start status callback to visualise results |
---|
[229] | 762 | if ~isempty(errormsg) |
---|
| 763 | display(errormsg) |
---|
| 764 | msgbox_uvmat('ERROR',errormsg) |
---|
[282] | 765 | elseif isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3) |
---|
[225] | 766 | set(handles.status,'Value',1);%suppress status display |
---|
| 767 | status_Callback(hObject, eventdata, handles) |
---|
[178] | 768 | end |
---|
[177] | 769 | |
---|
[12] | 770 | %------------------------------------------------------------------------ |
---|
[2] | 771 | % --- Executes on button press in BATCH: remote processing |
---|
| 772 | function BATCH_Callback(hObject, eventdata, handles) |
---|
[177] | 773 | % ----------------------------------------------------------------------- |
---|
[73] | 774 | set(handles.BATCH, 'Enable','Off') |
---|
| 775 | set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784]) |
---|
[67] | 776 | batch=1; |
---|
[229] | 777 | errormsg=launch_jobs(hObject, eventdata, handles, batch); |
---|
[73] | 778 | set(handles.BATCH, 'Enable','On') |
---|
| 779 | set(handles.BATCH,'BackgroundColor',[1 0 0]) |
---|
[67] | 780 | |
---|
[177] | 781 | % start status callback to visualise results |
---|
[229] | 782 | if ~isempty(errormsg) |
---|
| 783 | display(errormsg) |
---|
| 784 | msgbox_uvmat('ERROR',errormsg) |
---|
| 785 | elseif isfield(handles,'status') |
---|
| 786 | set(handles.status,'Value',1);%suppress status display |
---|
| 787 | status_Callback(hObject, eventdata, handles) |
---|
[178] | 788 | end |
---|
[227] | 789 | |
---|
[309] | 790 | %------------------------------------------------------------------- |
---|
| 791 | % --- Executes on button press in status. |
---|
| 792 | function status_Callback(hObject, eventdata, handles) |
---|
| 793 | %------------------------------------------------------------------- |
---|
| 794 | val=get(handles.status,'Value'); |
---|
| 795 | if val==0 |
---|
| 796 | set(handles.status,'BackgroundColor',[0 1 0]) |
---|
| 797 | hfig=findobj(allchild(0),'name','civ_status'); |
---|
| 798 | if ~isempty(hfig) |
---|
| 799 | delete(hfig) |
---|
| 800 | end |
---|
| 801 | return |
---|
| 802 | end |
---|
| 803 | set(handles.status,'BackgroundColor',[1 1 0]) |
---|
| 804 | drawnow |
---|
| 805 | listtype={'civ1','fix1','patch1','civ2','fix2','patch2'}; |
---|
| 806 | Param.CheckCiv1=get(handles.CheckCiv1,'Value'); |
---|
| 807 | Param.CheckFix1=get(handles.CheckFix1,'Value'); |
---|
| 808 | Param.CheckPatch1=get(handles.CheckPatch1,'Value'); |
---|
| 809 | Param.CheckCiv2=get(handles.CheckCiv2,'Value'); |
---|
| 810 | Param.CheckFix2=get(handles.CheckFix2,'Value'); |
---|
| 811 | Param.CheckPatch2=get(handles.CheckPatch2,'Value'); |
---|
| 812 | box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2]; |
---|
| 813 | |
---|
| 814 | option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test) |
---|
| 815 | filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV |
---|
| 816 | test_new=0; |
---|
| 817 | if ~isfield(filecell,'nc') |
---|
| 818 | test_new=1; |
---|
| 819 | [ref_i,ref_j,errormsg]=find_ref_indices(handles); |
---|
| 820 | if ~isempty(errormsg) |
---|
| 821 | msgbox_uvmat('ERROR',errormsg) |
---|
| 822 | return |
---|
| 823 | end |
---|
| 824 | filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status |
---|
| 825 | end |
---|
| 826 | if ~isequal(box_test(4:6),[0 0 0]) |
---|
| 827 | civ_files=filecell.nc.civ2;%case of civ2 operations |
---|
| 828 | else |
---|
| 829 | civ_files=filecell.nc.civ1; |
---|
| 830 | end |
---|
| 831 | [root,filename,ext]=fileparts(civ_files{1}); |
---|
| 832 | [rootroot,subdir,extdir]=fileparts(root); |
---|
| 833 | hfig=findobj(allchild(0),'name','civ_status'); |
---|
| 834 | if isempty(hfig) |
---|
| 835 | hfig=figure('DeleteFcn',@stop_status); |
---|
| 836 | set(hfig,'name','civ_status') |
---|
| 837 | hlist=uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', @open_view_field,'tag','list'); |
---|
| 838 | uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...'); |
---|
| 839 | uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]); |
---|
| 840 | uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','OK','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI); |
---|
| 841 | BarPosition=[0.05 0.81 0.01 0.05]; |
---|
| 842 | hwaitbar=uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar'); |
---|
| 843 | drawnow |
---|
| 844 | end |
---|
| 845 | % datnum=[]; |
---|
| 846 | Tabchar={}; |
---|
| 847 | nbfiles=numel(civ_files); |
---|
| 848 | count=0; |
---|
| 849 | testrecent=0; |
---|
| 850 | while count<nbfiles |
---|
| 851 | count=0; |
---|
| 852 | datnum=zeros(1,nbfiles); |
---|
| 853 | for ifile=1:nbfiles |
---|
| 854 | detect=exist(civ_files{ifile},'file'); % check the existence of the file |
---|
| 855 | option=0; |
---|
| 856 | if detect==0 |
---|
| 857 | option_str='not created'; |
---|
| 858 | else |
---|
| 859 | datfile=dir(civ_files{ifile}); |
---|
| 860 | if isfield(datfile,'datenum') |
---|
| 861 | datnum(ifile)=datfile.datenum;%only available in recent matlab versions |
---|
| 862 | testrecent=1; |
---|
| 863 | end |
---|
| 864 | filefound(ifile)={datfile.name}; |
---|
| 865 | lastfield=''; |
---|
| 866 | % check the content netcdf file |
---|
[316] | 867 | Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix'); |
---|
| 868 | option_list={'civ1','fix1','patch1','civ2','fix2','patch2'}; |
---|
| 869 | if ~isempty(Data.CivStage) |
---|
| 870 | option=Data.CivStage; |
---|
[309] | 871 | else |
---|
[316] | 872 | if ~isempty(Data.patch2) && isequal(Data.patch2,1) |
---|
| 873 | option=6; |
---|
| 874 | % option_str='patch2'; |
---|
| 875 | elseif ~isempty(Data.fix2) && isequal(Data.fix2,1) |
---|
| 876 | option=5; |
---|
| 877 | % option_str='fix2'; |
---|
| 878 | elseif ~isempty(Data.civ2) && isequal(Data.civ2,1); |
---|
| 879 | option=4; |
---|
| 880 | % option_str='civ2'; |
---|
| 881 | elseif ~isempty(Data.patch) && isequal(Data.patch,1); |
---|
| 882 | option=3; |
---|
| 883 | % option_str='patch1'; |
---|
| 884 | elseif ~isempty(Data.fix) && isequal(Data.fix,1); |
---|
| 885 | option=2; |
---|
| 886 | % option_str='fix1'; |
---|
| 887 | else |
---|
| 888 | option=1; |
---|
| 889 | % option_str='civ1'; |
---|
| 890 | end |
---|
[309] | 891 | end |
---|
[316] | 892 | option_str=option_list{option}; |
---|
[309] | 893 | end |
---|
| 894 | if option >= option_civ |
---|
| 895 | count=count+1; |
---|
| 896 | end |
---|
| 897 | [rr,filename,ext]=fileparts(civ_files{ifile}); |
---|
| 898 | Tabchar{ifile,1}=[fullfile([subdir extdir],filename) ext '...' option_str]; |
---|
| 899 | end |
---|
| 900 | datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files |
---|
| 901 | if isempty(datnum) |
---|
| 902 | if testrecent |
---|
| 903 | message='no civ result created yet'; |
---|
| 904 | else |
---|
| 905 | message=''; |
---|
| 906 | end |
---|
| 907 | else |
---|
| 908 | datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files |
---|
| 909 | [first,ind]=min(datnum); |
---|
| 910 | [last,indlast]=max(datnum); |
---|
| 911 | if test_new |
---|
| 912 | message='existing file status, no processing launched yet'; |
---|
| 913 | else |
---|
| 914 | message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification: ' cell2mat(filefound(ind)) ' : ' datestr(first)];... |
---|
| 915 | ['latest modification: ' cell2mat(filefound(indlast)) ' : ' datestr(last)]}; |
---|
| 916 | end |
---|
| 917 | end |
---|
| 918 | hfig=findobj(allchild(0),'name','civ_status'); |
---|
| 919 | if isempty(hfig)% the status list has been deleted |
---|
| 920 | return |
---|
| 921 | else |
---|
| 922 | hlist=findobj(hfig,'tag','list'); |
---|
| 923 | hmsgbox=findobj(hfig,'tag','msgbox'); |
---|
| 924 | hwaitbar=findobj(hfig,'tag','waitbar'); |
---|
| 925 | set(hlist,'String',Tabchar) |
---|
| 926 | set(hmsgbox,'String', message) |
---|
| 927 | if count>0 && ~test_new |
---|
| 928 | BarPosition(3)=0.9*count/nbfiles; |
---|
| 929 | set(hwaitbar,'Position',BarPosition) |
---|
| 930 | end |
---|
| 931 | end |
---|
| 932 | set(hlist,'UserData',rootroot) |
---|
[314] | 933 | if count<10||(nbfiles-count)<10 |
---|
[312] | 934 | pause(.5)% wait 0.5 seconds for next check |
---|
| 935 | else |
---|
| 936 | pause(10)% wait 10 seconds for next check |
---|
| 937 | end |
---|
[309] | 938 | end |
---|
| 939 | |
---|
[67] | 940 | %------------------------------------------------------------------------ |
---|
[309] | 941 | % --- Main lauch command, called by RUN and BATCH |
---|
[229] | 942 | function errormsg=launch_jobs(hObject, eventdata, handles, batch) |
---|
[67] | 943 | %----------------------------------------------------------------------- |
---|
[229] | 944 | errormsg='';%default |
---|
[313] | 945 | |
---|
| 946 | %% read the input parameters from the GUI civ |
---|
[309] | 947 | Param=read_GUI(handles.civ); |
---|
[272] | 948 | |
---|
[133] | 949 | %% check the selected list of operations: |
---|
[289] | 950 | operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'}; |
---|
[282] | 951 | box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2]; |
---|
[180] | 952 | index_first=find(box_test==1,1); |
---|
| 953 | if isempty(index_first) |
---|
[229] | 954 | errormsg='no selected operation'; |
---|
[2] | 955 | return |
---|
| 956 | end |
---|
[180] | 957 | index_last=find(box_test==1,1,'last'); |
---|
[159] | 958 | box_used=box_test(index_first : index_last); |
---|
[2] | 959 | [box_missing,ind_missing]=min(box_used); |
---|
[180] | 960 | if isequal(box_missing,0); %there is a missing step in the sequence of operations |
---|
[229] | 961 | errormsg=['missing' cell2mat(operations(ind_missing))]; |
---|
[2] | 962 | return |
---|
| 963 | end |
---|
| 964 | |
---|
[272] | 965 | %% check mask if selecetd |
---|
| 966 | %could be included in get_mask callback ? |
---|
[282] | 967 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
[315] | 968 | maskname=get(handles.txt_Mask,'String'); |
---|
[12] | 969 | if ~exist(maskname,'file') |
---|
| 970 | get_mask_civ1_Callback(hObject, eventdata, handles); |
---|
| 971 | end |
---|
[2] | 972 | end |
---|
[282] | 973 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
[315] | 974 | maskname=get(handles.txt_Mask,'String'); |
---|
[12] | 975 | if ~exist(maskname,'file') |
---|
| 976 | get_mask_fix1_Callback(hObject, eventdata, handles); |
---|
| 977 | end |
---|
[2] | 978 | end |
---|
[282] | 979 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
[276] | 980 | maskname=get(handles.txt_Mask,'String'); |
---|
[12] | 981 | if ~exist(maskname,'file') |
---|
[112] | 982 | get_mask_civ2_Callback(hObject, eventdata, handles); |
---|
[12] | 983 | end |
---|
[2] | 984 | end |
---|
[282] | 985 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
[315] | 986 | maskname=get(handles.txt_Mask,'String'); |
---|
[12] | 987 | if ~exist(maskname,'file') |
---|
[112] | 988 | get_mask_fix2_Callback(hObject, eventdata, handles); |
---|
[12] | 989 | end |
---|
[2] | 990 | end |
---|
| 991 | |
---|
[177] | 992 | %% reinitialise status callback |
---|
[178] | 993 | if isfield(handles,'status') |
---|
[180] | 994 | set(handles.status,'Value',0);%suppress status display |
---|
| 995 | status_Callback(hObject, eventdata, handles) |
---|
[178] | 996 | end |
---|
[133] | 997 | |
---|
[272] | 998 | %% read the PARAM.xml file to get the binaries (and batch_mode if batch) |
---|
[276] | 999 | path_civ=fileparts(which('civ')); %path to the source directory of uvmat |
---|
[112] | 1000 | xmlfile='PARAM.xml'; |
---|
[133] | 1001 | if exist(xmlfile,'file')% search parameter xml file in the whole matlab path |
---|
[54] | 1002 | t=xmltree(xmlfile); |
---|
[67] | 1003 | s=convert(t); |
---|
[272] | 1004 | else |
---|
| 1005 | errormsg=['no file ' xmlfile]; |
---|
| 1006 | return |
---|
[2] | 1007 | end |
---|
[272] | 1008 | test_interp=0; %eviter les variables test_ (LG) |
---|
[127] | 1009 | if batch |
---|
[67] | 1010 | if isfield(s,'BatchParam') |
---|
[284] | 1011 | Param.xml=s.BatchParam; |
---|
| 1012 | if isfield(Param.xml,'BatchMode') |
---|
| 1013 | batch_mode=Param.xml.BatchMode; |
---|
[257] | 1014 | if ~ismember(batch_mode,{'sge','oar'}) |
---|
| 1015 | errormsg=['batch mode ' batch_mode ' not supported by UVMAT']; |
---|
| 1016 | return |
---|
| 1017 | end |
---|
[67] | 1018 | end |
---|
| 1019 | else |
---|
[229] | 1020 | errormsg='no batch civ binaries defined in PARAM.xml'; |
---|
[67] | 1021 | return |
---|
| 1022 | end |
---|
[257] | 1023 | else % run |
---|
[67] | 1024 | if isfield(s,'RunParam') |
---|
[284] | 1025 | Param.xml=s.RunParam; |
---|
[67] | 1026 | else |
---|
[225] | 1027 | msgbox_uvmat('ERROR','no run civ binaries defined in PARAM.xml') |
---|
[67] | 1028 | return |
---|
| 1029 | end |
---|
[225] | 1030 | end |
---|
[238] | 1031 | |
---|
[272] | 1032 | %% check batch mode supported |
---|
| 1033 | if batch |
---|
| 1034 | switch batch_mode |
---|
| 1035 | case 'sge' |
---|
| 1036 | test_command='qstat'; |
---|
| 1037 | case 'oar' |
---|
[290] | 1038 | test_command='oarstat'; |
---|
[272] | 1039 | end |
---|
| 1040 | [s,w]=system(test_command); |
---|
| 1041 | if ~isequal(s,0) |
---|
| 1042 | msgbox_uvmat('ERROR',[batch_mode ' batch system not available']) |
---|
| 1043 | return |
---|
| 1044 | end |
---|
| 1045 | end |
---|
| 1046 | |
---|
| 1047 | %% check if the binaries exist |
---|
[309] | 1048 | if isequal(get(handles.MenuMatlab,'checked'),'on') |
---|
[273] | 1049 | CivMode='Matlab'; |
---|
| 1050 | else |
---|
| 1051 | CivMode='CivX'; |
---|
| 1052 | end |
---|
[280] | 1053 | binary_list={}; |
---|
[257] | 1054 | switch CivMode |
---|
[280] | 1055 | case 'CivX' |
---|
| 1056 | binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'}; |
---|
| 1057 | case 'CivAll' |
---|
[289] | 1058 | binary_list={'Civ'}; |
---|
[257] | 1059 | case 'Matlab' |
---|
| 1060 | if batch |
---|
[309] | 1061 | % vérifier MenuMatlab installé sur le cluster |
---|
[272] | 1062 | % difficile a faire a priori |
---|
[257] | 1063 | end |
---|
[225] | 1064 | end |
---|
[309] | 1065 | for bin_name=binary_list %loop on the list of binaries |
---|
| 1066 | if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list |
---|
[284] | 1067 | if ~exist(Param.xml.(bin_name{1}),'file')%look for the full path if the file name has been defined with a relative path in PARAM.xml |
---|
[289] | 1068 | fullname=fullfile(path_civ,Param.xml.(bin_name{1})); |
---|
[280] | 1069 | if exist(fullname,'file') |
---|
[284] | 1070 | Param.xml.(bin_name{1})=fullname; |
---|
[280] | 1071 | else |
---|
[284] | 1072 | msgbox_uvmat('ERROR',['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist']) |
---|
[280] | 1073 | return |
---|
| 1074 | end |
---|
| 1075 | else |
---|
[284] | 1076 | [path,name,ext]=fileparts(Param.xml.(bin_name{1})); |
---|
[280] | 1077 | currentdir=pwd; |
---|
| 1078 | cd(path); |
---|
| 1079 | binpath=pwd;%path of the binary |
---|
[284] | 1080 | Param.xml.(bin_name{1})=fullfile(binpath,[name ext]); |
---|
[280] | 1081 | cd(currentdir); |
---|
| 1082 | end |
---|
| 1083 | |
---|
| 1084 | end |
---|
| 1085 | end |
---|
[272] | 1086 | display('files OK, processing...') |
---|
[2] | 1087 | |
---|
[313] | 1088 | %% set the list of files and check them |
---|
| 1089 | display('checking the files...') |
---|
| 1090 | [ref_i,ref_j,errormsg]=find_ref_indices(handles); |
---|
| 1091 | if ~isempty(errormsg) |
---|
| 1092 | return |
---|
| 1093 | end |
---|
| 1094 | [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,xx,yy,compare]=... |
---|
| 1095 | set_civ_filenames(handles,ref_i,ref_j,box_test); |
---|
| 1096 | Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention) |
---|
| 1097 | set(handles.civ,'UserData',filecell);%store for futur use of status callback |
---|
| 1098 | if isempty(filecell)% (error message displayed in fct set_civ_filenames) |
---|
| 1099 | return |
---|
| 1100 | end |
---|
| 1101 | nbfield=numel(i1_civ1); |
---|
| 1102 | nbslice=numel(j1_civ1); |
---|
[2] | 1103 | |
---|
[133] | 1104 | %% MAIN LOOP |
---|
[273] | 1105 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
[269] | 1106 | batch_file_list=[]; |
---|
[309] | 1107 | |
---|
[2] | 1108 | for ifile=1:nbfield |
---|
| 1109 | for j=1:nbslice |
---|
[257] | 1110 | % initiate system command |
---|
| 1111 | switch CivMode |
---|
| 1112 | case 'CivX' |
---|
| 1113 | if isunix % check: necessaire aussi en RUN? |
---|
[272] | 1114 | cmd=['#!/bin/bash \n '... |
---|
| 1115 | '#$ -cwd \n '... |
---|
| 1116 | 'hostname && date \n '... |
---|
| 1117 | 'umask 002 \n'];%allow writting access to created files for user group |
---|
| 1118 | else |
---|
| 1119 | cmd=[]; |
---|
[257] | 1120 | end |
---|
| 1121 | case 'CivAll' |
---|
| 1122 | CivAllxml=xmltree;% xml contents, all parameters |
---|
| 1123 | CivAllCmd=''; |
---|
| 1124 | CivAllxml=set(CivAllxml,1,'name','CivDoc'); |
---|
[2] | 1125 | end |
---|
[313] | 1126 | |
---|
[272] | 1127 | % define output file name |
---|
[282] | 1128 | if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1 |
---|
[272] | 1129 | OutputFile=filecell.nc.civ2{ifile,j}; |
---|
| 1130 | else |
---|
| 1131 | OutputFile=filecell.nc.civ1{ifile,j}; |
---|
| 1132 | end |
---|
| 1133 | OutputFile=regexprep(OutputFile,'.nc',''); |
---|
[309] | 1134 | |
---|
[282] | 1135 | if Param.CheckCiv1 |
---|
[272] | 1136 | % read image-dependent parameters |
---|
[315] | 1137 | Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j}; |
---|
| 1138 | Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j}; |
---|
[313] | 1139 | if size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j) |
---|
| 1140 | Param.Civ1.Dt=(time(i2_civ1(ifile),j2_civ1(j))-time(i1_civ1(ifile),j1_civ1(j))); |
---|
[315] | 1141 | Param.Civ1.Time=((time(i2_civ1(ifile),j2_civ1(j))+time(i1_civ1(ifile),j1_civ1(j)))/2); |
---|
[301] | 1142 | else |
---|
| 1143 | Param.Civ1.Dt=1; |
---|
[315] | 1144 | Param.Civ1.Time=0; |
---|
[301] | 1145 | end |
---|
[313] | 1146 | Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE? |
---|
[315] | 1147 | Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);% |
---|
| 1148 | ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size |
---|
| 1149 | Param.Civ1.ImageWidth=ImageInfo.Width; |
---|
| 1150 | Param.Civ1.ImageHeight=ImageInfo.Height; |
---|
| 1151 | Param.Civ1.ImageBitDepth=ImageInfo.BitDepth; |
---|
[272] | 1152 | % read mask parameters |
---|
[284] | 1153 | if Param.Civ1.CheckMask % the lines below should be changed with the new gui |
---|
[315] | 1154 | if ~exist(Param.Civ1.Mask,'file') |
---|
| 1155 | maskbase=[filecell.filebase '_' Param.Civ1.Mask]; % |
---|
| 1156 | nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); % |
---|
[313] | 1157 | i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1; |
---|
[315] | 1158 | Param.Civ1.Mask=name_generator(maskbase,i1_mask,1,'.png','_i'); |
---|
[2] | 1159 | end |
---|
| 1160 | end |
---|
[313] | 1161 | % read grid parameters |
---|
[284] | 1162 | if Param.Civ1.CheckGrid |
---|
[315] | 1163 | if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid') |
---|
| 1164 | nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); % |
---|
[137] | 1165 | if ~isnan(nbslice_grid) |
---|
[313] | 1166 | i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1; |
---|
[315] | 1167 | Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')]; |
---|
[285] | 1168 | if ~exist(Param.Civ1.GridName,'file') |
---|
[112] | 1169 | msgbox_uvmat('ERROR','grid file absent for civ1') |
---|
[2] | 1170 | end |
---|
[315] | 1171 | elseif ~exist(Param.Civ1.Grid,'file') |
---|
[2] | 1172 | msgbox_uvmat('ERROR','grid file absent for civ1') |
---|
| 1173 | end |
---|
| 1174 | end |
---|
| 1175 | end |
---|
[257] | 1176 | |
---|
[285] | 1177 | % send command |
---|
[257] | 1178 | switch CivMode |
---|
| 1179 | case 'CivX' |
---|
[284] | 1180 | cmd=[cmd... |
---|
| 1181 | cmd_civ1(filecell.nc.civ1{ifile,j},Param) '\n']; |
---|
[257] | 1182 | case 'CivAll' |
---|
| 1183 | CivAllCmd=[CivAllCmd ' civ1 ']; |
---|
[284] | 1184 | str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1); |
---|
[257] | 1185 | fieldnames=fields(str); |
---|
| 1186 | [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1'); |
---|
| 1187 | for ilist=1:length(fieldnames) |
---|
| 1188 | val=eval(['str.' fieldnames{ilist}]); |
---|
| 1189 | if ischar(val) |
---|
| 1190 | [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist}); |
---|
| 1191 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
| 1192 | end |
---|
[112] | 1193 | end |
---|
[2] | 1194 | end |
---|
| 1195 | end |
---|
| 1196 | |
---|
[282] | 1197 | if Param.CheckFix1 |
---|
[309] | 1198 | switch CivMode |
---|
[257] | 1199 | case 'CivX' |
---|
[285] | 1200 | cmd=[cmd... |
---|
| 1201 | cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n']; |
---|
[313] | 1202 | case 'CivAll'%to abandon |
---|
[257] | 1203 | fix1.inputFileName=filecell.nc.civ1{ifile,j} ; |
---|
[272] | 1204 | fix1.fi1=num2str(param.fix1.flagindex1(1)); |
---|
| 1205 | fix1.fi2=num2str(param.fix1.flagindex1(2)); |
---|
| 1206 | fix1.fi3=num2str(param.fix1.flagindex1(3)); |
---|
| 1207 | fix1.threshC=num2str(param.fix1.thresh_vecC1); |
---|
| 1208 | fix1.threshV=num2str(param.fix1.thresh_vel1); |
---|
[257] | 1209 | fieldnames=fields(fix1); |
---|
| 1210 | [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1'); |
---|
| 1211 | for ilist=1:length(fieldnames) |
---|
| 1212 | val=eval(['fix1.' fieldnames{ilist}]); |
---|
| 1213 | if ischar(val) |
---|
| 1214 | [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist}); |
---|
| 1215 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
| 1216 | end |
---|
| 1217 | end |
---|
| 1218 | CivAllCmd=[CivAllCmd ' fix1 ']; |
---|
[112] | 1219 | end |
---|
| 1220 | end |
---|
| 1221 | |
---|
[282] | 1222 | %CheckPatch1 |
---|
| 1223 | if Param.CheckPatch1==1 |
---|
[257] | 1224 | switch CivMode |
---|
| 1225 | case 'CivX' |
---|
[286] | 1226 | cmd=[cmd... |
---|
| 1227 | cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n']; |
---|
[257] | 1228 | case 'CivAll' |
---|
| 1229 | patch1.inputFileName=filecell.nc.civ1{ifile,j} ; |
---|
| 1230 | patch1.nopt=subdomain_patch1; |
---|
| 1231 | patch1.maxdiff=thresh_patch1; |
---|
| 1232 | patch1.ro=rho_patch1; |
---|
| 1233 | test_grid=get(handles.get_gridpatch1,'Value'); |
---|
| 1234 | if test_grid |
---|
| 1235 | patch1.gridflag='y'; |
---|
| 1236 | gridname=get(handles.grid_patch1,'String'); |
---|
| 1237 | if isequal(gridname(end-3:end),'grid') |
---|
| 1238 | nbslice_grid=str2double(gridname(1:end-4)); % |
---|
| 1239 | if ~isnan(nbslice_grid) |
---|
[313] | 1240 | i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1; |
---|
| 1241 | patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; |
---|
[257] | 1242 | if ~exist(patch1.gridPatch,'file') |
---|
| 1243 | msgbox_uvmat('ERROR','grid file absent for patch1') |
---|
| 1244 | end |
---|
| 1245 | elseif exist(gridname,'file') |
---|
| 1246 | patch1.gridPatch=gridname; |
---|
| 1247 | else |
---|
[112] | 1248 | msgbox_uvmat('ERROR','grid file absent for patch1') |
---|
| 1249 | end |
---|
[2] | 1250 | end |
---|
[257] | 1251 | else |
---|
| 1252 | patch1.gridPatch='none'; |
---|
| 1253 | patch1.gridflag='n'; |
---|
| 1254 | patch1.m=nx_patch1; |
---|
| 1255 | patch1.n=ny_patch1; |
---|
[2] | 1256 | end |
---|
[257] | 1257 | patch1.convectFlow='n'; |
---|
| 1258 | fieldnames=fields(patch1); |
---|
| 1259 | [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1'); |
---|
| 1260 | for ilist=1:length(fieldnames) |
---|
| 1261 | val=eval(['patch1.' fieldnames{ilist}]); |
---|
| 1262 | if ischar(val) |
---|
| 1263 | [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist}); |
---|
| 1264 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
| 1265 | end |
---|
[112] | 1266 | end |
---|
[257] | 1267 | CivAllCmd=[CivAllCmd ' patch1 ']; |
---|
[112] | 1268 | end |
---|
[2] | 1269 | end |
---|
[282] | 1270 | if Param.CheckCiv2==1 |
---|
[315] | 1271 | Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j}; |
---|
| 1272 | Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j}; |
---|
[313] | 1273 | if size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j) |
---|
| 1274 | Param.Civ2.Dt=num2str(time(i2_civ2(ifile),j2_civ2(j))-time(i1_civ2(ifile),j1_civ2(j))); |
---|
[315] | 1275 | Param.Civ2.Time=num2str((time(i2_civ2(ifile),j2_civ2(j))+time(i1_civ2(ifile),j1_civ2(j)))/2); |
---|
[301] | 1276 | else |
---|
| 1277 | Param.Civ2.Dt=1; |
---|
[315] | 1278 | Param.Civ2.Time=0; |
---|
[309] | 1279 | end |
---|
[313] | 1280 | Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc); |
---|
| 1281 | Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc); |
---|
[290] | 1282 | Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j}; |
---|
| 1283 | Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc' |
---|
[315] | 1284 | |
---|
| 1285 | % mask |
---|
[287] | 1286 | if Param.Civ2.CheckMask |
---|
[315] | 1287 | if ~exist(Param.Civ2.Mask,'file') |
---|
| 1288 | maskbase=[filecell.filebase '_' Param.Civ2.Mask]; % |
---|
| 1289 | nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); % |
---|
[313] | 1290 | i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1; |
---|
[315] | 1291 | Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i'); |
---|
[2] | 1292 | end |
---|
| 1293 | end |
---|
[315] | 1294 | %grid |
---|
| 1295 | if Param.Civ2.CheckGrid |
---|
| 1296 | if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid') |
---|
| 1297 | nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); % |
---|
| 1298 | if ~isnan(nbslice_grid) |
---|
| 1299 | i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1; |
---|
| 1300 | Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; |
---|
| 1301 | end |
---|
[2] | 1302 | end |
---|
| 1303 | end |
---|
[315] | 1304 | ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size |
---|
| 1305 | Param.Civ2.ImageWidth=ImageInfo.Width; |
---|
| 1306 | Param.Civ2.ImageHeight=ImageInfo.Height; |
---|
| 1307 | Param.Civ2.ImageBitDepth=ImageInfo.BitDepth; |
---|
| 1308 | % TODO: case of movie |
---|
[257] | 1309 | switch CivMode |
---|
| 1310 | case 'CivX' |
---|
[309] | 1311 | cmd=[cmd... |
---|
[290] | 1312 | cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n']; |
---|
[257] | 1313 | case 'CivAll' |
---|
| 1314 | CivAllCmd=[CivAllCmd ' civ2 ']; |
---|
[290] | 1315 | str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2); |
---|
[257] | 1316 | fieldnames=fields(str); |
---|
| 1317 | [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2'); |
---|
| 1318 | for ilist=1:length(fieldnames) |
---|
| 1319 | val=eval(['str.' fieldnames{ilist}]); |
---|
| 1320 | if ischar(val) |
---|
| 1321 | [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist}); |
---|
| 1322 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
| 1323 | end |
---|
[2] | 1324 | end |
---|
| 1325 | end |
---|
[112] | 1326 | end |
---|
| 1327 | |
---|
[282] | 1328 | % CheckFix2 |
---|
| 1329 | if Param.CheckFix2==1 |
---|
[257] | 1330 | switch CivMode |
---|
| 1331 | case 'CivX' |
---|
[291] | 1332 | cmd=[cmd... |
---|
| 1333 | cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n']; |
---|
[257] | 1334 | case 'CivAll' |
---|
| 1335 | fix2.inputFileName=filecell.nc.civ2{ifile,j} ; |
---|
| 1336 | fix2.fi1=num2str(flagindex2(1)); |
---|
| 1337 | fix2.fi2=num2str(flagindex2(2)); |
---|
| 1338 | fix2.fi3=num2str(flagindex2(3)); |
---|
| 1339 | fix2.threshC=num2str(thresh_vec2C); |
---|
| 1340 | fix2.threshV=num2str(thresh_vel2); |
---|
| 1341 | fieldnames=fields(fix2); |
---|
| 1342 | [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2'); |
---|
| 1343 | for ilist=1:length(fieldnames) |
---|
| 1344 | val=eval(['fix2.' fieldnames{ilist}]); |
---|
| 1345 | if ischar(val) |
---|
| 1346 | [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist}); |
---|
| 1347 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
| 1348 | end |
---|
| 1349 | end |
---|
| 1350 | CivAllCmd=[CivAllCmd ' fix2 ']; |
---|
[112] | 1351 | end |
---|
| 1352 | end |
---|
| 1353 | |
---|
[282] | 1354 | %CheckPatch2 |
---|
| 1355 | if Param.CheckPatch2==1 |
---|
[313] | 1356 | |
---|
[257] | 1357 | switch CivMode |
---|
[313] | 1358 | |
---|
[257] | 1359 | case 'CivX' |
---|
[291] | 1360 | cmd=[cmd... |
---|
| 1361 | cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n']; |
---|
[313] | 1362 | |
---|
[257] | 1363 | case 'CivAll' |
---|
| 1364 | patch2.inputFileName=filecell.nc.civ1{ifile,j} ; |
---|
| 1365 | patch2.nopt=subdomain_patch2; |
---|
| 1366 | patch2.maxdiff=thresh_patch2; |
---|
| 1367 | patch2.ro=rho_patch2; |
---|
| 1368 | test_grid=get(handles.get_gridpatch2,'Value'); |
---|
| 1369 | if test_grid |
---|
| 1370 | patch2.gridflag='y'; |
---|
| 1371 | gridname=get(handles.grid_patch2,'String'); |
---|
| 1372 | if isequal(gridname(end-3:end),'grid') |
---|
| 1373 | nbslice_grid=str2double(gridname(1:end-4)); % |
---|
| 1374 | if ~isnan(nbslice_grid) |
---|
[313] | 1375 | i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1; |
---|
| 1376 | patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; |
---|
[257] | 1377 | if ~exist(patch2.gridPatch,'file') |
---|
| 1378 | msgbox_uvmat('ERROR','grid file absent for patch2') |
---|
| 1379 | end |
---|
| 1380 | elseif exist(gridname,'file') |
---|
| 1381 | patch2.gridPatch=gridname; |
---|
| 1382 | else |
---|
[112] | 1383 | msgbox_uvmat('ERROR','grid file absent for patch2') |
---|
[12] | 1384 | end |
---|
[2] | 1385 | end |
---|
[257] | 1386 | else |
---|
| 1387 | patch2.gridPatch='none'; |
---|
| 1388 | patch2.gridflag='n'; |
---|
| 1389 | patch2.m=nx_patch2; |
---|
| 1390 | patch2.n=ny_patch2; |
---|
[2] | 1391 | end |
---|
[257] | 1392 | patch2.convectFlow='n'; |
---|
| 1393 | fieldnames=fields(patch2); |
---|
| 1394 | [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2'); |
---|
| 1395 | for ilist=1:length(fieldnames) |
---|
| 1396 | val=eval(['patch2.' fieldnames{ilist}]); |
---|
| 1397 | if ischar(val) |
---|
| 1398 | [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist}); |
---|
| 1399 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
| 1400 | end |
---|
[112] | 1401 | end |
---|
[257] | 1402 | CivAllCmd=[CivAllCmd ' patch2 ']; |
---|
[112] | 1403 | end |
---|
[12] | 1404 | end |
---|
[309] | 1405 | |
---|
[257] | 1406 | switch CivMode |
---|
[313] | 1407 | |
---|
[257] | 1408 | case {'CivX','CivAll'} |
---|
| 1409 | if isequal(CivMode,'CivAll') |
---|
[272] | 1410 | save(CivAllxml,[OutputFile '.xml']); |
---|
| 1411 | cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml ' CivAllCmd ' >' OutputFile '.log' '\n']; |
---|
[313] | 1412 | end |
---|
[272] | 1413 | % create the .bat file used in run or batch |
---|
| 1414 | filename_bat=[OutputFile '.bat']; |
---|
[257] | 1415 | [fid,message]=fopen(filename_bat,'w'); |
---|
| 1416 | if isequal(fid,-1) |
---|
| 1417 | msgbox_uvmat('ERROR', ['creation of .bat file: ' message]) |
---|
| 1418 | return |
---|
[238] | 1419 | end |
---|
[257] | 1420 | fprintf(fid,cmd); |
---|
[313] | 1421 | fclose(fid); |
---|
[279] | 1422 | if isunix |
---|
| 1423 | system(['chmod +x ' filename_bat]); |
---|
[313] | 1424 | end |
---|
[269] | 1425 | batch_file_list{length(batch_file_list)+1}=filename_bat; |
---|
| 1426 | |
---|
[257] | 1427 | case 'Matlab' |
---|
| 1428 | drawnow |
---|
[263] | 1429 | if ~strcmp(compare,'stereo PIV') |
---|
[309] | 1430 | [Data,erromsg]=civ_matlab(Param,filecell.nc.civ1{ifile,j}); |
---|
[263] | 1431 | if isempty(errormsg) |
---|
| 1432 | display([filecell.nc.civ1{ifile,j} ' written']) |
---|
| 1433 | else |
---|
| 1434 | msgbox_uvmat('ERROR',errormsg) |
---|
[309] | 1435 | end |
---|
[263] | 1436 | end |
---|
[257] | 1437 | end |
---|
[112] | 1438 | end |
---|
[2] | 1439 | end |
---|
[134] | 1440 | |
---|
[313] | 1441 | if batch |
---|
| 1442 | switch batch_mode |
---|
| 1443 | |
---|
[269] | 1444 | case 'sge' |
---|
| 1445 | for p=1:length(batch_file_list) |
---|
| 1446 | cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}]; |
---|
| 1447 | display(cmd);eval(cmd); |
---|
[314] | 1448 | end |
---|
[279] | 1449 | case 'oar_old' |
---|
| 1450 | for p=1:length(batch_file_list) |
---|
| 1451 | oar_command=['!oarsub -n CIVX -q nicejob '... |
---|
| 1452 | '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')... |
---|
| 1453 | '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00" ' batch_file_list{p}]; |
---|
| 1454 | display(oar_command);eval(oar_command); |
---|
[314] | 1455 | end |
---|
| 1456 | case 'oar' |
---|
| 1457 | |
---|
| 1458 | oar_modes={'oar-dispatch','mpilauncher'}; |
---|
| 1459 | text={'Batch processing on servcalcul3 LEGI';... |
---|
| 1460 | 'Please choose one of the followint modes';... |
---|
| 1461 | '* oar-dispatch : jobs in a container';... |
---|
| 1462 | '* mpilauncher : one single job using several cores';... |
---|
| 1463 | '**********************************'... |
---|
| 1464 | }; |
---|
| 1465 | [S,v]=listdlg('PromptString',text,'ListString',oar_modes,... |
---|
| 1466 | 'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode'); |
---|
| 1467 | switch oar_modes{S} |
---|
| 1468 | |
---|
| 1469 | case 'oar-dispatch' %oar-dispatch.pl |
---|
| 1470 | filename_joblist=fullfile(Rootbat,'job_list.txt'); |
---|
| 1471 | fid=fopen(filename_joblist,'w'); |
---|
| 1472 | walltime_onejob=600;%seconds |
---|
| 1473 | for p=1:length(batch_file_list) |
---|
| 1474 | oar_command=['oarsub -n CIVX '... |
---|
| 1475 | '-E ' regexprep(batch_file_list{p},'\.bat\>','.errors') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.log ')... |
---|
| 1476 | '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '" ' batch_file_list{p}]; |
---|
| 1477 | fprintf(fid,[oar_command '\n']); |
---|
| 1478 | end |
---|
| 1479 | fclose(fid); |
---|
| 1480 | ncores=36; |
---|
| 1481 | oar_command=['oarsub -t container -n civx-container '... |
---|
| 1482 | '-l /core=' num2str(ncores)... |
---|
| 1483 | ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13)... |
---|
| 1484 | ' "oar-dispatch -f ' filename_joblist '"']; |
---|
| 1485 | filename_oarcommand=fullfile(Rootbat,'oar_command'); |
---|
| 1486 | fid=fopen(filename_oarcommand,'w'); |
---|
[313] | 1487 | fprintf(fid,[oar_command '\n']); |
---|
[314] | 1488 | fclose(fid); |
---|
| 1489 | display(oar_command); |
---|
| 1490 | eval(['! . ' filename_oarcommand]) |
---|
| 1491 | case 'mpilauncher' |
---|
| 1492 | filename_joblist=fullfile(Rootbat,'job_list.txt'); |
---|
| 1493 | fid=fopen(filename_joblist,'w'); |
---|
| 1494 | |
---|
| 1495 | for p=1:length(batch_file_list) |
---|
| 1496 | fprintf(fid,[batch_file_list{p} '\n']); |
---|
| 1497 | end |
---|
| 1498 | fclose(fid) |
---|
| 1499 | text_oarscript=[... |
---|
| 1500 | '#!/bin/bash \n'... |
---|
| 1501 | '#OAR -n Mylauncher \n'... |
---|
| 1502 | '#OAR -l node=4/core=5,walltime=0:15:00 \n'... |
---|
| 1503 | '#OAR -E stderrfile.log \n'... |
---|
| 1504 | '#OAR -O stdoutfile.log \n'... |
---|
| 1505 | '# ========================================================= \n'... |
---|
| 1506 | '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'... |
---|
| 1507 | '# application for coriolis PIV post-processing. \n'... |
---|
| 1508 | '# OAR uses oarshmost wrapper to propagate the user environement. \n'... |
---|
| 1509 | '# This wrapper assert that the user has the same environment on all the \n'... |
---|
| 1510 | '# allocated nodes (basic behavior needed by most MPI applications). \n'... |
---|
| 1511 | '# \n'... |
---|
| 1512 | '# REQUIREMENT: \n'... |
---|
| 1513 | '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'... |
---|
| 1514 | '# If a different location is used, change the line following the comment "Bidouille" \n'... |
---|
| 1515 | '# ========================================================= \n'... |
---|
| 1516 | '# USER should only modify these 2 lines \n'... |
---|
| 1517 | 'WORKDIR=' pwd ' \n'... |
---|
| 1518 | 'COMMANDE="mpilauncher -f ' filename_joblist '" \n'... |
---|
| 1519 | '# ========================================================= \n'... |
---|
| 1520 | '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'... |
---|
| 1521 | 'echo "job starting on: "`hostname` \n'... |
---|
| 1522 | 'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'... |
---|
| 1523 | 'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'... |
---|
| 1524 | '#========== Bidouille ============== \n'... |
---|
| 1525 | 'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...% 'cd $WORKDIR \n'... |
---|
| 1526 | 'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'... |
---|
| 1527 | 'echo "I run: $CMD" \n'... |
---|
| 1528 | '$CMD \n'... |
---|
| 1529 | 'echo "job ending" \n'... |
---|
| 1530 | ]; |
---|
| 1531 | % oarsub -S ./oar.sub |
---|
| 1532 | filename_oarscript=fullfile(Rootbat,'oar_command'); |
---|
| 1533 | fid=fopen(filename_oarscript,'w'); |
---|
| 1534 | fprintf(fid,[text_oarscript]); |
---|
| 1535 | fclose(fid); |
---|
| 1536 | eval(['!chmod +x ' filename_oarscript]); |
---|
| 1537 | eval(['!oarsub -S ' filename_oarscript]); |
---|
| 1538 | end |
---|
[269] | 1539 | end |
---|
| 1540 | else |
---|
| 1541 | if ~isequal(CivMode,'Matlab') |
---|
| 1542 | filename_superbat=fullfile(Rootbat,'job_list.bat'); |
---|
| 1543 | fid=fopen(filename_superbat,'w'); |
---|
| 1544 | if fid==-1 |
---|
| 1545 | msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat]) |
---|
| 1546 | return |
---|
| 1547 | end |
---|
| 1548 | for p=1:length(batch_file_list) |
---|
| 1549 | if isunix |
---|
| 1550 | fprintf(fid,['sh ' batch_file_list{p} '\n']); |
---|
| 1551 | else |
---|
| 1552 | fprintf(fid,['@call "' regexprep(filename_bat,'\\','\\\\') '"' '\n']); |
---|
[265] | 1553 | end |
---|
[269] | 1554 | end |
---|
| 1555 | fclose(fid); |
---|
| 1556 | if(isunix) |
---|
| 1557 | system(['chmod +x ' filename_superbat]); |
---|
| 1558 | end |
---|
| 1559 | system([filename_superbat ' &']);% execute main commmand |
---|
[313] | 1560 | end |
---|
[265] | 1561 | end |
---|
| 1562 | |
---|
[2] | 1563 | |
---|
[137] | 1564 | %% save interface state |
---|
[2] | 1565 | if isfield(filecell,'nc') |
---|
| 1566 | if isfield(filecell.nc,'civ2') |
---|
| 1567 | fileresu=filecell.nc.civ2{1,1}; |
---|
| 1568 | else |
---|
| 1569 | fileresu=filecell.nc.civ1{1,1}; |
---|
| 1570 | end |
---|
| 1571 | end |
---|
| 1572 | [RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu); |
---|
| 1573 | namedoc=fullfile(RootPath,subdir,RootFile); |
---|
[112] | 1574 | detect=1; |
---|
[2] | 1575 | while detect==1 |
---|
| 1576 | namefigfull=[namedoc '.fig']; |
---|
| 1577 | hh=dir(namefigfull); |
---|
| 1578 | if ~isempty(hh) |
---|
| 1579 | detect=1; |
---|
| 1580 | namedoc=[namedoc '.0']; |
---|
| 1581 | else |
---|
| 1582 | detect=0; |
---|
| 1583 | end |
---|
| 1584 | end |
---|
| 1585 | saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml) |
---|
| 1586 | |
---|
[273] | 1587 | %Save info in personal profile (initiate browser next time) TODO |
---|
| 1588 | MenuFile={}; |
---|
| 1589 | dir_perso=prefdir; |
---|
| 1590 | profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); |
---|
| 1591 | if exist(profil_perso,'file') |
---|
| 1592 | hh=load (profil_perso); |
---|
| 1593 | if isfield(hh,'MenuFile') |
---|
| 1594 | MenuFile=hh.MenuFile; |
---|
| 1595 | end |
---|
[289] | 1596 | if isfield(filecell.nc,'civ2') |
---|
| 1597 | MenuFile=[filecell.nc.civ2{1,1}; MenuFile]; |
---|
| 1598 | else |
---|
| 1599 | MenuFile=[filecell.nc.civ1{1,1}; MenuFile]; |
---|
| 1600 | end |
---|
[273] | 1601 | save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat |
---|
| 1602 | else |
---|
| 1603 | MenuFile=filecell.ima1.civ1(1,1); |
---|
| 1604 | save (profil_perso,'MenuFile') |
---|
| 1605 | end |
---|
| 1606 | |
---|
[227] | 1607 | %------------------------------------------------------------------------ |
---|
| 1608 | % --- determine the list of reference indices of processing file |
---|
| 1609 | function [ref_i,ref_j,errormsg]=find_ref_indices(handles) |
---|
| 1610 | %------------------------------------------------------------------------ |
---|
| 1611 | errormsg=''; %default error message |
---|
| 1612 | first_i=str2double(get(handles.first_i,'String'));%first index i |
---|
| 1613 | last_i=str2double(get(handles.last_i,'String'));%last index i |
---|
| 1614 | incr_i=str2double(get(handles.incr_i,'String'));% increment |
---|
| 1615 | if isequal(get(handles.first_j,'Visible'),'on') |
---|
| 1616 | first_j=str2double(get(handles.first_j,'String'));%first index j |
---|
| 1617 | last_j=str2double(get(handles.last_j,'String'));%last index j |
---|
| 1618 | incr_j=str2double(get(handles.incr_j,'String'));% increment |
---|
| 1619 | else |
---|
| 1620 | first_j=1; |
---|
| 1621 | last_j=1; |
---|
| 1622 | incr_j=1; |
---|
| 1623 | end |
---|
| 1624 | ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair) |
---|
| 1625 | ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair) |
---|
| 1626 | if isnan(first_i)||isnan(first_j) |
---|
| 1627 | errormsg='first field number not defined'; |
---|
| 1628 | elseif isnan(last_i)||isnan(last_j) |
---|
| 1629 | errormsg='last field number not defined'; |
---|
| 1630 | elseif isnan(incr_i)||isnan(incr_j) |
---|
| 1631 | errormsg='increment in field number not defined'; |
---|
| 1632 | elseif last_i < first_i || last_j < first_j |
---|
| 1633 | errormsg='last field number must be larger than the first one'; |
---|
| 1634 | end |
---|
[134] | 1635 | |
---|
[227] | 1636 | %------------------------------------------------------------------------ |
---|
| 1637 | % --- determine the list of filenames and indices needed for launch_job |
---|
[263] | 1638 | function [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2,compare]=... |
---|
[282] | 1639 | set_civ_filenames(handles,ref_i,ref_j,checkbox) |
---|
[12] | 1640 | %------------------------------------------------------------------------ |
---|
[85] | 1641 | filecell=[];%default |
---|
[136] | 1642 | |
---|
| 1643 | %% get the root names nomenclature and numbers |
---|
[71] | 1644 | filebase=get(handles.RootName,'String'); |
---|
[136] | 1645 | |
---|
| 1646 | if isempty(filebase)||isequal(filebase,'') |
---|
[298] | 1647 | msgbox_uvmat('ERROR','please open an image with the upper menu option Open/Browse...') |
---|
[136] | 1648 | return |
---|
| 1649 | end |
---|
| 1650 | |
---|
[137] | 1651 | %filebase=regexprep(filebase,'\.fsnet','fsnet');% temporary fix for cluster Coriolis |
---|
[136] | 1652 | filecell.filebase=filebase; |
---|
| 1653 | |
---|
[273] | 1654 | browse=get(handles.RootName,'UserData'); |
---|
[282] | 1655 | compare_list=get(handles.ListCompareMode,'String'); |
---|
| 1656 | val=get(handles.ListCompareMode,'Value'); |
---|
[2] | 1657 | compare=compare_list{val}; |
---|
| 1658 | if strcmp(compare,'displacement') |
---|
| 1659 | mode='displacement'; |
---|
| 1660 | else |
---|
[282] | 1661 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 1662 | mode_value=get(handles.ListPairMode,'Value'); |
---|
[2] | 1663 | mode=mode_list{mode_value}; |
---|
| 1664 | end |
---|
[137] | 1665 | %time=get(handles.RootName,'UserData'); %get the set of times |
---|
[71] | 1666 | ext_ima=get(handles.ImaExt,'String'); |
---|
[2] | 1667 | nom_type_nc=browse.nom_type_nc; |
---|
[122] | 1668 | if isfield(browse,'nom_type_ima') |
---|
| 1669 | nom_type_ima2=browse.nom_type_ima; |
---|
| 1670 | end |
---|
| 1671 | if isempty(nom_type_ima2),nom_type_ima2='1';end; %default |
---|
| 1672 | if isempty(nom_type_nc),nom_type_nc='_i1-i2';end; %default |
---|
[2] | 1673 | [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=... |
---|
[227] | 1674 | find_pair_indices(handles,ref_i,ref_j,mode); |
---|
[282] | 1675 | %determine the new filebase for 'displacement' ListPairMode (comparison of two series) |
---|
[2] | 1676 | filebase_B=filebase;% root name of the second field series for stereo |
---|
| 1677 | if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV') |
---|
[127] | 1678 | % test_disp=1; |
---|
[2] | 1679 | nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series |
---|
| 1680 | [Path2,Name2]=fileparts(filebase_B); |
---|
| 1681 | Path1=Path2; |
---|
[71] | 1682 | Name1=get(handles.RootName_1,'String');% root name of the first field series for stereo |
---|
[2] | 1683 | filebase_A=fullfile(Path1,Name1); |
---|
| 1684 | if length(Name1)>6 |
---|
| 1685 | Name1=Name1(end-5:end); |
---|
| 1686 | end |
---|
| 1687 | if length(Name2)>6 |
---|
| 1688 | Name2=Name2(end-5:end); |
---|
| 1689 | end |
---|
| 1690 | filebase_AB=fullfile(Path2,[Name2 '-' Name1]); |
---|
| 1691 | else |
---|
[127] | 1692 | % test_disp=0; |
---|
[2] | 1693 | filebase_A=filebase; |
---|
| 1694 | nom_type_ima1=nom_type_ima2; |
---|
| 1695 | filebase_AB=filebase; |
---|
| 1696 | end |
---|
| 1697 | if strcmp(compare,'displacement') |
---|
[112] | 1698 | filebase_ima1=filebase_A; |
---|
| 1699 | filebase_ima2=filebase_B; |
---|
| 1700 | filebase_nc=filebase_AB; %root name for the result of civ2 |
---|
[2] | 1701 | else |
---|
[112] | 1702 | filebase_ima1=filebase_B; |
---|
| 1703 | filebase_ima2=filebase_B; |
---|
| 1704 | filebase_nc=filebase_B; |
---|
| 1705 | end |
---|
[2] | 1706 | |
---|
| 1707 | %determine reference files for fix: |
---|
| 1708 | file_ref_fix1={};%default |
---|
| 1709 | file_ref_fix2={}; |
---|
| 1710 | nbfield=length(num1_civ1); |
---|
| 1711 | nbslice=length(num_a_civ1); |
---|
[282] | 1712 | if checkbox(2)==1% fix1 performed |
---|
[2] | 1713 | ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback |
---|
| 1714 | if ~isempty(ref) |
---|
[137] | 1715 | first_i=str2double(get(handles.first_i,'String')); |
---|
| 1716 | last_i=str2double(get(handles.last_i,'String')); |
---|
| 1717 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
| 1718 | first_j=str2double(get(handles.first_j,'String')); |
---|
| 1719 | last_j=str2double(get(handles.last_j,'String')); |
---|
| 1720 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
[127] | 1721 | num_i_ref=first_i:incr_i:last_i; |
---|
| 1722 | num_j_ref=first_j:incr_j:last_j; |
---|
[2] | 1723 | if isequal(mode,'displacement') |
---|
| 1724 | num_i1=num_i_ref; |
---|
| 1725 | num_i2=num_i_ref; |
---|
| 1726 | num_j1=num_j_ref; |
---|
| 1727 | num_j2=num_j_ref; |
---|
| 1728 | elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2') |
---|
| 1729 | num_i1=num_i_ref; |
---|
| 1730 | num_i2=num_i1; |
---|
| 1731 | num_j1=ref.num_a*ones(size(num_i_ref)); |
---|
| 1732 | num_j2=ref.num_b*ones(size(num_i_ref)); |
---|
| 1733 | elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)') |
---|
| 1734 | delta1=floor((ref.num2-ref.num1)/2); |
---|
| 1735 | delta2=ceil((ref.num2-ref.num1)/2); |
---|
| 1736 | num_i1=num_i_ref-delta1*ones(size(num_i_ref)); |
---|
| 1737 | num_i2=num_i_ref+delta2*ones(size(num_i_ref)); |
---|
| 1738 | if isempty(ref.num_a) |
---|
| 1739 | ref.num_a=1; |
---|
| 1740 | end |
---|
| 1741 | num_j1=ref.num_a*ones(size(num_i1)); |
---|
| 1742 | num_j2=num_j1; |
---|
| 1743 | elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)') |
---|
| 1744 | delta1=floor((ref.num_b-ref.num_a)/2); |
---|
| 1745 | delta2=ceil((ref.num_b-ref.num_a)/2); |
---|
| 1746 | num_i1=ref.num1*ones(size(num_i_ref)); |
---|
| 1747 | num_i2=num_i1; |
---|
| 1748 | num_j1=num_j_ref-delta1*ones(size(num_j_ref)); |
---|
| 1749 | num_j2=num_j_ref+delta2*ones(size(num_j_ref)); |
---|
| 1750 | end |
---|
| 1751 | for ifile=1:nbfield |
---|
| 1752 | for j=1:nbslice |
---|
| 1753 | file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);% |
---|
| 1754 | file_ref_fix1(ifile,j)={file_ref}; |
---|
| 1755 | if ~exist(file_ref,'file') |
---|
| 1756 | msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1']) |
---|
[12] | 1757 | filecell=[]; |
---|
[2] | 1758 | return |
---|
| 1759 | end |
---|
| 1760 | end |
---|
| 1761 | end |
---|
| 1762 | end |
---|
| 1763 | end |
---|
| 1764 | |
---|
[282] | 1765 | %determine reference files for checkfix2: |
---|
| 1766 | if checkbox(5)==1% fix2 performed |
---|
[2] | 1767 | ref=get(handles.ref_fix2,'UserData'); |
---|
| 1768 | if ~isempty(ref) |
---|
[127] | 1769 | first_i=str2double(get(handles.first_i,'String')); |
---|
| 1770 | last_i=str2double(get(handles.last_i,'String')); |
---|
| 1771 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
| 1772 | first_j=str2double(get(handles.first_j,'String')); |
---|
| 1773 | last_j=str2double(get(handles.last_j,'String')); |
---|
| 1774 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
[229] | 1775 | num_i_ref=first_i:incr_i:last_i; |
---|
| 1776 | num_j_ref=first_j:incr_j:last_j; |
---|
[2] | 1777 | if isequal(mode,'displacement') |
---|
| 1778 | num_i1=num_i_ref; |
---|
| 1779 | num_i2=num_i_ref; |
---|
| 1780 | num_j1=num_j_ref; |
---|
| 1781 | num_j2=num_j_ref; |
---|
| 1782 | elseif isequal(mode,'pair j1-j2') |
---|
| 1783 | num_i1=num_i_ref; |
---|
| 1784 | num_i2=num_i1; |
---|
| 1785 | num_j1=ref.num_a; |
---|
| 1786 | num_j2=ref.num_b; |
---|
| 1787 | elseif isequal(mode,'series(Di)') |
---|
| 1788 | delta1=floor((ref.num2-ref.num1)/2); |
---|
| 1789 | delta2=ceil((ref.num2-ref.num1)/2); |
---|
| 1790 | num_i1=num_i_ref-delta1*ones(size(num_i_ref)); |
---|
| 1791 | num_i2=num_i_ref+delta2*ones(size(num_i_ref)); |
---|
| 1792 | num_j1=ref.num_a*ones(size(num_i1)); |
---|
| 1793 | num_j2=num_j1; |
---|
| 1794 | elseif isequal(mode,'series(Dj)') |
---|
| 1795 | delta1=floor((ref.num_b-ref.num_a)/2); |
---|
| 1796 | delta2=ceil((ref.num_b-ref.num_a)/2); |
---|
| 1797 | num_i1=ref.num1*ones(size(num_i_ref)); |
---|
| 1798 | num_i2=num_i1; |
---|
| 1799 | num_j1=num_j_ref-delta1*ones(size(num_j_ref)); |
---|
| 1800 | num_j2=num_j_ref+delta2*ones(size(num_j_ref)); |
---|
| 1801 | end |
---|
| 1802 | for ifile=1:nbfield |
---|
| 1803 | for j=1:nbslice |
---|
| 1804 | file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);% |
---|
| 1805 | file_ref_fix2(ifile,j)={file_ref}; |
---|
| 1806 | if ~exist(file_ref,'file') |
---|
| 1807 | msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2']) |
---|
[122] | 1808 | filecell={}; |
---|
[2] | 1809 | return |
---|
| 1810 | end |
---|
| 1811 | end |
---|
| 1812 | end |
---|
| 1813 | end |
---|
| 1814 | end |
---|
| 1815 | |
---|
| 1816 | %check dir |
---|
[289] | 1817 | subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data |
---|
| 1818 | subdir_civ2=get(handles.txt_SubdirCiv2,'String'); |
---|
[174] | 1819 | if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir |
---|
[2] | 1820 | if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir |
---|
[266] | 1821 | % currentdir=pwd;%store the current working directory |
---|
[2] | 1822 | [Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ) |
---|
| 1823 | if ~exist(Path_ima,'dir') |
---|
[12] | 1824 | msgbox_uvmat('ERROR',['path to images ' Path_ima ' not found']) |
---|
[122] | 1825 | filecell={}; |
---|
[2] | 1826 | return |
---|
| 1827 | end |
---|
[127] | 1828 | [xx,message]=fileattrib(Path_ima); |
---|
[122] | 1829 | if ~isempty(message) && ~isequal(message.UserWrite,1) |
---|
[112] | 1830 | msgbox_uvmat('ERROR',['No writting access to ' Path_ima]) |
---|
[122] | 1831 | filecell={}; |
---|
[266] | 1832 | % cd(currentdir); |
---|
[112] | 1833 | return |
---|
[2] | 1834 | end |
---|
| 1835 | |
---|
| 1836 | %check the existence of the netcdf and image files involved |
---|
[282] | 1837 | % %%%%%%%%%%%% case CheckCiv1 activated %%%%%%%%%%%%% |
---|
| 1838 | if checkbox(1)==1; |
---|
[112] | 1839 | detect=1; |
---|
[127] | 1840 | vers=0; |
---|
| 1841 | subdir_civ1_new=subdir_civ1; |
---|
[153] | 1842 | while detect==1 %create a new subdir if the netcdf files already exist |
---|
[122] | 1843 | for ifile=1:nbfield |
---|
[112] | 1844 | for j=1:nbslice |
---|
[122] | 1845 | filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new); |
---|
[112] | 1846 | detect=exist(filename,'file')==2; |
---|
| 1847 | if detect% if a netcdf file already exists |
---|
[137] | 1848 | indstr=regexp(subdir_civ1_new,'\D'); |
---|
| 1849 | if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number |
---|
| 1850 | vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1; |
---|
| 1851 | subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)]; |
---|
[127] | 1852 | else |
---|
| 1853 | vers=vers+1; |
---|
[137] | 1854 | subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)]; |
---|
[127] | 1855 | end |
---|
[137] | 1856 | subdir_civ2=subdir_civ1_new; |
---|
[112] | 1857 | break |
---|
| 1858 | end |
---|
| 1859 | filecell.nc.civ1(ifile,j)={filename}; |
---|
| 1860 | end |
---|
| 1861 | if detect% if a netcdf file already exists |
---|
| 1862 | break |
---|
| 1863 | end |
---|
| 1864 | end |
---|
[134] | 1865 | |
---|
[289] | 1866 | %create the new txt_SubdirCiv1 |
---|
[127] | 1867 | if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir') |
---|
[263] | 1868 | % cd(Path_ima); |
---|
| 1869 | [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new)); |
---|
[134] | 1870 | |
---|
[128] | 1871 | if ~strcmp(msg1,'') |
---|
| 1872 | msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation |
---|
[122] | 1873 | filecell={}; |
---|
| 1874 | return |
---|
[163] | 1875 | elseif isunix |
---|
[266] | 1876 | [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
[128] | 1877 | if ~strcmp(msg2,'') |
---|
[266] | 1878 | msgbox_uvmat('ERROR',['pb of permission for ' fullfile(Path_ima,subdir_civ1_new) ': ' msg2])%error message for directory creation |
---|
[128] | 1879 | filecell={}; |
---|
| 1880 | return |
---|
| 1881 | end |
---|
[112] | 1882 | end |
---|
[263] | 1883 | % cd(currentdir); |
---|
[112] | 1884 | end |
---|
| 1885 | if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series |
---|
| 1886 | for ifile=1:nbfield |
---|
| 1887 | for j=1:nbslice |
---|
[122] | 1888 | filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);% |
---|
[112] | 1889 | detect=exist(filename,'file')==2; |
---|
[2] | 1890 | if detect% if a netcdf file already exists |
---|
[137] | 1891 | indstr=regexp(subdir_civ1_new,'\D'); |
---|
| 1892 | if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number |
---|
| 1893 | vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1; |
---|
| 1894 | subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)]; |
---|
[127] | 1895 | else |
---|
| 1896 | vers=vers+1; |
---|
[137] | 1897 | subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)]; |
---|
[127] | 1898 | end |
---|
| 1899 | subdir_civ2=subdir_civ1; |
---|
| 1900 | break |
---|
[2] | 1901 | end |
---|
[112] | 1902 | filecell.ncA.civ1(ifile,j)={filename}; |
---|
| 1903 | end |
---|
| 1904 | if detect% if a netcdf file already exists |
---|
| 1905 | break |
---|
| 1906 | end |
---|
| 1907 | end |
---|
[289] | 1908 | %create the new txt_SubdirCiv1 |
---|
[263] | 1909 | if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir') |
---|
| 1910 | % cd(Path_ima); |
---|
| 1911 | [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new)); |
---|
| 1912 | % cd(currentdir); |
---|
[252] | 1913 | if ~strcmp(msg1,'') |
---|
[128] | 1914 | msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1]) |
---|
[263] | 1915 | % cd(currentdir) |
---|
[122] | 1916 | filecell={}; |
---|
| 1917 | return |
---|
[128] | 1918 | else |
---|
[266] | 1919 | [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
[128] | 1920 | if ~strcmp(msg2,'') |
---|
| 1921 | msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation |
---|
[263] | 1922 | % cd(currentdir) |
---|
[128] | 1923 | filecell={}; |
---|
| 1924 | return |
---|
| 1925 | end |
---|
[112] | 1926 | end |
---|
| 1927 | end |
---|
| 1928 | end |
---|
| 1929 | end |
---|
[127] | 1930 | subdir_civ1=subdir_civ1_new; |
---|
[2] | 1931 | % get image names |
---|
| 1932 | for ifile=1:nbfield |
---|
[112] | 1933 | for j=1:nbslice |
---|
[2] | 1934 | filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1); |
---|
| 1935 | idetect(j)=exist(filename,'file')==2; |
---|
| 1936 | filecell.ima1.civ1(ifile,j)={filename}; %first image |
---|
| 1937 | filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2); |
---|
| 1938 | idetect_1(j)=exist(filename,'file')==2; |
---|
| 1939 | filecell.ima2.civ1(ifile,j)={filename};%second image |
---|
[112] | 1940 | end |
---|
| 1941 | [idetectmin,indexj]=min(idetect); |
---|
| 1942 | if idetectmin==0, |
---|
| 1943 | msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found']) |
---|
[122] | 1944 | filecell={}; |
---|
[266] | 1945 | % cd(currentdir) |
---|
[112] | 1946 | return |
---|
| 1947 | end |
---|
| 1948 | [idetectmin,indexj]=min(idetect_1); |
---|
| 1949 | if idetectmin==0, |
---|
| 1950 | msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found']) |
---|
[122] | 1951 | filecell={}; |
---|
[266] | 1952 | %cd(currentdir) |
---|
[112] | 1953 | return |
---|
| 1954 | end |
---|
| 1955 | end |
---|
| 1956 | if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)')) |
---|
| 1957 | for ifile=1:nbfield |
---|
| 1958 | for j=1:nbslice |
---|
| 1959 | filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1); |
---|
| 1960 | idetect(j)=exist(filename,'file')==2; |
---|
| 1961 | filecell.imaA1.civ1(ifile,j)={filename} ;%first image |
---|
| 1962 | filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2); |
---|
| 1963 | idetect_1(j)=exist(filename,'file')==2; |
---|
| 1964 | filecell.imaA2.civ1(ifile,j)={filename};%second image |
---|
| 1965 | end |
---|
[2] | 1966 | [idetectmin,indexj]=min(idetect); |
---|
[112] | 1967 | if idetectmin==0, |
---|
| 1968 | msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found']) |
---|
[122] | 1969 | filecell={}; |
---|
[266] | 1970 | % cd(currentdir) |
---|
[2] | 1971 | return |
---|
[112] | 1972 | end |
---|
[2] | 1973 | [idetectmin,indexj]=min(idetect_1); |
---|
[112] | 1974 | if idetectmin==0, |
---|
| 1975 | msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found']) |
---|
[122] | 1976 | filecell={}; |
---|
[266] | 1977 | % cd(currentdir) |
---|
[2] | 1978 | return |
---|
[112] | 1979 | end |
---|
| 1980 | end |
---|
[2] | 1981 | end |
---|
[112] | 1982 | |
---|
[282] | 1983 | %%%%%%%%%%%%% checkfix1 or checkpatch1 activated but no checkciv1 %%%%%%%%%%%%% |
---|
| 1984 | elseif (checkbox(2)==1 || checkbox(3)==1); |
---|
[2] | 1985 | for ifile=1:nbfield |
---|
| 1986 | for j=1:nbslice |
---|
| 1987 | filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',... |
---|
[112] | 1988 | nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);% |
---|
| 1989 | detect=exist(filename,'file')==2; |
---|
[122] | 1990 | if detect==0 |
---|
| 1991 | msgbox_uvmat('ERROR',[filename ' not found']) |
---|
| 1992 | filecell={}; |
---|
[266] | 1993 | % cd(currentdir) |
---|
[122] | 1994 | return |
---|
| 1995 | end |
---|
[2] | 1996 | filecell.nc.civ1(ifile,j)={filename}; |
---|
| 1997 | end |
---|
| 1998 | end |
---|
| 1999 | if strcmp(compare,'stereo PIV') |
---|
[112] | 2000 | for ifile=1:nbfield |
---|
| 2001 | for j=1:nbslice |
---|
| 2002 | filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);% |
---|
| 2003 | filecell.ncA.civ1(ifile,j)={filename}; |
---|
| 2004 | if ~exist(filename,'file') |
---|
| 2005 | msgbox_uvmat('ERROR',['input file ' filename ' not found']) |
---|
| 2006 | set(handles.RUN, 'Enable','On') |
---|
| 2007 | set(handles.RUN,'BackgroundColor',[1 0 0]) |
---|
[122] | 2008 | filecell={}; |
---|
[266] | 2009 | %cd(currentdir) |
---|
[112] | 2010 | return |
---|
[2] | 2011 | end |
---|
| 2012 | end |
---|
[112] | 2013 | end |
---|
[2] | 2014 | end |
---|
| 2015 | end |
---|
| 2016 | |
---|
[282] | 2017 | %%%%%%%%%%%%% if checkciv2 performed with pairs different than checkciv1 %%%%%%%%%%%%% |
---|
[2] | 2018 | testdiff=0; |
---|
[282] | 2019 | if (checkbox(4)==1)&&... |
---|
| 2020 | ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1)) |
---|
[2] | 2021 | testdiff=1; |
---|
[112] | 2022 | detect=1; |
---|
[127] | 2023 | vers=0; |
---|
| 2024 | subdir_civ2_new=subdir_civ2; |
---|
[2] | 2025 | while detect==1 %create a new subdir if the netcdf files already exist |
---|
[112] | 2026 | for ifile=1:nbfield |
---|
| 2027 | for j=1:nbslice |
---|
[127] | 2028 | filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2_new);% |
---|
[112] | 2029 | detect=exist(filename,'file')==2; |
---|
| 2030 | if detect% if a netcdf file already exists |
---|
[127] | 2031 | indstr=regexp(subdir_civ2,'\D'); |
---|
| 2032 | if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number |
---|
| 2033 | vers=str2double(subdir_civ2(indstr(end)+1:end))+1; |
---|
| 2034 | subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)]; |
---|
| 2035 | else |
---|
| 2036 | vers=vers+1; |
---|
| 2037 | subdir_civ2_new=[subdir_civ1 '_' num2str(vers)]; |
---|
| 2038 | end |
---|
[112] | 2039 | break |
---|
| 2040 | end |
---|
| 2041 | filecell.nc.civ2(ifile,j)={filename}; |
---|
| 2042 | end |
---|
| 2043 | if detect% if a netcdf file already exists |
---|
| 2044 | break |
---|
| 2045 | end |
---|
| 2046 | end |
---|
[128] | 2047 | %create the new subdir_civ2_new |
---|
| 2048 | if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir') |
---|
[174] | 2049 | [xx,m2]=mkdir(fullfile(Path_ima,subdir_civ2_new)); |
---|
[266] | 2050 | [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
[112] | 2051 | if ~isequal(m2,'') |
---|
[266] | 2052 | msgbox_uvmat('ERROR',['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2]) |
---|
[122] | 2053 | filecell={}; |
---|
[266] | 2054 | % cd(currentdir) |
---|
[122] | 2055 | return |
---|
[112] | 2056 | end |
---|
| 2057 | end |
---|
| 2058 | if strcmp(compare,'stereo PIV')%check second nc series |
---|
| 2059 | for ifile=1:nbfield |
---|
| 2060 | for j=1:nbslice |
---|
| 2061 | filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',... |
---|
[122] | 2062 | nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2_new);% |
---|
[112] | 2063 | detect=exist(filename,'file')==2; |
---|
[2] | 2064 | if detect% if a netcdf file already exists |
---|
[127] | 2065 | indstr=regexp(subdir_civ2,'\D'); |
---|
| 2066 | if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number |
---|
| 2067 | vers=str2double(subdir_civ2(indstr(end)+1:end))+1; |
---|
| 2068 | subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)]; |
---|
| 2069 | else |
---|
| 2070 | vers=vers+1; |
---|
| 2071 | subdir_civ2_new=[subdir_civ1 '_' num2str(vers)]; |
---|
| 2072 | end |
---|
[112] | 2073 | break |
---|
[2] | 2074 | end |
---|
[112] | 2075 | filecell.ncA.civ2(ifile,j)={filename}; |
---|
| 2076 | end |
---|
| 2077 | if detect% if a netcdf file already exists |
---|
| 2078 | break |
---|
| 2079 | end |
---|
| 2080 | end |
---|
[122] | 2081 | subdir_civ2=subdir_civ2_new; |
---|
[289] | 2082 | %create the new txt_SubdirCiv1 |
---|
[127] | 2083 | if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir') |
---|
| 2084 | [xx,m2]=mkdir(subdir_civ2_new); |
---|
[266] | 2085 | [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
[112] | 2086 | if ~isequal(m2,'') |
---|
[266] | 2087 | msgbox_uvmat('ERROR', ['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])%error message for directory creation |
---|
| 2088 | % cd(currentdir) |
---|
[122] | 2089 | filecell={}; |
---|
| 2090 | return |
---|
[112] | 2091 | end |
---|
| 2092 | end |
---|
| 2093 | end |
---|
| 2094 | end |
---|
[127] | 2095 | subdir_civ2=subdir_civ2_new; |
---|
[2] | 2096 | end |
---|
[266] | 2097 | %cd(currentdir);%come back to the current working directory |
---|
[2] | 2098 | |
---|
[282] | 2099 | %%%%%%%%%%%%% if checkciv2 results are obtained or used %%%%%%%%%%%%% |
---|
| 2100 | if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2 |
---|
| 2101 | %check source netcdf file of checkciv1 estimates |
---|
| 2102 | if checkbox(1)==0; %no civ1 performed |
---|
[2] | 2103 | for ifile=1:nbfield |
---|
| 2104 | for j=1:nbslice |
---|
| 2105 | filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',... |
---|
| 2106 | nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);% |
---|
| 2107 | filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file |
---|
| 2108 | if ~exist(filename,'file') |
---|
| 2109 | msgbox_uvmat('ERROR',['input file ' filename ' not found']) |
---|
[122] | 2110 | filecell={}; |
---|
[2] | 2111 | return |
---|
| 2112 | end |
---|
| 2113 | if ~testdiff % civ2 or patch2 are written in the same file as civ1 |
---|
[282] | 2114 | if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated |
---|
[248] | 2115 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2'); |
---|
| 2116 | if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files |
---|
[2] | 2117 | msgbox_uvmat('ERROR',['no civ2 data in ' filename]) |
---|
[12] | 2118 | filecell=[]; |
---|
[2] | 2119 | return |
---|
[248] | 2120 | elseif isempty(Data.civ2)||isequal(Data.civ2,0) |
---|
| 2121 | msgbox_uvmat('ERROR',['no civ2 data in ' filename]) |
---|
| 2122 | filecell=[]; |
---|
| 2123 | return |
---|
[112] | 2124 | end |
---|
[282] | 2125 | elseif checkbox(3)==0; %check the existence of patch if it is not calculated |
---|
[275] | 2126 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch'); |
---|
[248] | 2127 | if ~isempty(Data.CivStage) |
---|
| 2128 | if Data.CivStage<3 %test for civ files |
---|
| 2129 | msgbox_uvmat('ERROR',['no patch data in ' filename]) |
---|
| 2130 | filecell=[]; |
---|
| 2131 | return |
---|
| 2132 | end |
---|
| 2133 | elseif isempty(Data.patch)||isequal(Data.patch,0) |
---|
[2] | 2134 | msgbox_uvmat('ERROR',['no patch data in ' filename]) |
---|
[12] | 2135 | filecell=[]; |
---|
[2] | 2136 | return |
---|
| 2137 | end |
---|
[112] | 2138 | end |
---|
[2] | 2139 | end |
---|
| 2140 | end |
---|
| 2141 | end |
---|
| 2142 | if strcmp(compare,'stereo PIV') |
---|
| 2143 | for ifile=1:nbfield |
---|
| 2144 | for j=1:nbslice |
---|
| 2145 | filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',... |
---|
| 2146 | nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);% |
---|
| 2147 | filecell.ncA.civ2(ifile,j)={filename}; |
---|
| 2148 | if ~exist(filename,'file') |
---|
| 2149 | msgbox_uvmat('ERROR',['input file ' filename ' not found']) |
---|
| 2150 | set(handles.RUN, 'Enable','On') |
---|
| 2151 | set(handles.RUN,'BackgroundColor',[1 0 0]) |
---|
| 2152 | return |
---|
| 2153 | end |
---|
| 2154 | end |
---|
| 2155 | end |
---|
| 2156 | end |
---|
| 2157 | end |
---|
[112] | 2158 | |
---|
| 2159 | detect=1; |
---|
[282] | 2160 | % while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data |
---|
[112] | 2161 | for ifile=1:nbfield |
---|
| 2162 | for j=1:nbslice |
---|
| 2163 | filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',... |
---|
[2] | 2164 | nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2); |
---|
[112] | 2165 | detect=exist(filename,'file')==2; |
---|
| 2166 | filecell.nc.civ2(ifile,j)={filename}; |
---|
[2] | 2167 | end |
---|
[112] | 2168 | end |
---|
[282] | 2169 | %get first image names for checkciv2 |
---|
| 2170 | if checkbox(1)==1 && isequal(num1_civ1,num1_civ2) && isequal(num_a_civ1,num_a_civ2) |
---|
[2] | 2171 | filecell.ima1.civ2=filecell.ima1.civ1; |
---|
[282] | 2172 | elseif checkbox(4)==1 |
---|
[2] | 2173 | for ifile=1:nbfield |
---|
| 2174 | for j=1:nbslice |
---|
| 2175 | filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1); |
---|
| 2176 | idetect_2(j)=exist(filename,'file')==2; |
---|
| 2177 | filecell.ima1.civ2(ifile,j)={filename};%first image |
---|
| 2178 | end |
---|
[112] | 2179 | [idetectmin,indexj]=min(idetect_2); |
---|
[2] | 2180 | if idetectmin==0, |
---|
[112] | 2181 | msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found']) |
---|
| 2182 | filecell=[]; |
---|
| 2183 | return |
---|
[2] | 2184 | end |
---|
| 2185 | end |
---|
| 2186 | end |
---|
| 2187 | |
---|
[282] | 2188 | %get second image names for checkciv2 |
---|
| 2189 | if checkbox(1)==1 && isequal(num2_civ1,num2_civ2) && isequal(num_b_civ1,num_b_civ2) |
---|
[2] | 2190 | filecell.ima2.civ2=filecell.ima2.civ1; |
---|
[282] | 2191 | elseif checkbox(4)==1 |
---|
[2] | 2192 | for ifile=1:nbfield |
---|
| 2193 | for j=1:nbslice |
---|
| 2194 | filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2); |
---|
| 2195 | idetect_3(j)=exist(filename,'file')==2; |
---|
| 2196 | filecell.ima2.civ2(ifile,j)={filename};%first image |
---|
| 2197 | end |
---|
[112] | 2198 | [idetectmin,indexj]=min(idetect_3); |
---|
[2] | 2199 | if idetectmin==0, |
---|
[112] | 2200 | msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found']) |
---|
| 2201 | filecell=[]; |
---|
| 2202 | return |
---|
[2] | 2203 | end |
---|
| 2204 | end |
---|
| 2205 | end |
---|
| 2206 | end |
---|
[282] | 2207 | if (checkbox(5) || checkbox(6)) && ~checkbox(4) % need to read an existing netcdf civ2 file |
---|
[2] | 2208 | if ~testdiff |
---|
| 2209 | filecell.nc.civ2=filecell.nc.civ1;% file already checked |
---|
[112] | 2210 | else % check the civ2 files |
---|
[2] | 2211 | for ifile=1:nbfield |
---|
| 2212 | for j=1:nbslice |
---|
| 2213 | filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',... |
---|
[112] | 2214 | nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);% |
---|
[2] | 2215 | filecell.nc.civ2(ifile,j)={filename}; |
---|
| 2216 | if ~exist(filename,'file') |
---|
| 2217 | msgbox_uvmat('ERROR',['input file ' filename ' not found']) |
---|
[12] | 2218 | filecell=[]; |
---|
[2] | 2219 | return |
---|
| 2220 | else |
---|
[248] | 2221 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2'); |
---|
| 2222 | if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files |
---|
| 2223 | msgbox_uvmat('ERROR',['no civ2 data in ' filename]) |
---|
| 2224 | filecell=[]; |
---|
| 2225 | return |
---|
| 2226 | elseif isempty(Data.civ2)||isequal(Data.civ2,0) |
---|
[2] | 2227 | msgbox_uvmat('ERROR',['no civ2 data in ' filename]) |
---|
[12] | 2228 | filecell=[]; |
---|
[2] | 2229 | return |
---|
| 2230 | end |
---|
| 2231 | end |
---|
| 2232 | end |
---|
| 2233 | end |
---|
| 2234 | end |
---|
| 2235 | end |
---|
| 2236 | |
---|
| 2237 | %%%%%%%%%%%%% if stereo fields are calculated by PATCH %%%%%%%%%%%%% |
---|
| 2238 | if strcmp(compare,'stereo PIV') |
---|
[282] | 2239 | if checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1) |
---|
[2] | 2240 | for ifile=1:nbfield |
---|
| 2241 | for j=1:nbslice |
---|
| 2242 | filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',... |
---|
| 2243 | nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);% |
---|
| 2244 | filecell.st(ifile,j)={filename}; |
---|
| 2245 | end |
---|
| 2246 | end |
---|
| 2247 | end |
---|
[282] | 2248 | if checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1) |
---|
[2] | 2249 | for ifile=1:nbfield |
---|
| 2250 | for j=1:nbslice |
---|
| 2251 | filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',... |
---|
| 2252 | nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);% |
---|
| 2253 | filecell.st(ifile,j)={filename}; |
---|
| 2254 | end |
---|
| 2255 | end |
---|
[112] | 2256 | end |
---|
[2] | 2257 | end |
---|
[289] | 2258 | set(handles.txt_SubdirCiv1,'String',subdir_civ1);%update the edit box |
---|
| 2259 | set(handles.txt_SubdirCiv2,'String',subdir_civ2);%update the edit box |
---|
[2] | 2260 | browse.nom_type_nc=nom_type_nc; |
---|
[273] | 2261 | set(handles.RootName,'UserData',browse); %update the nomenclature type for uvmat |
---|
[2] | 2262 | |
---|
| 2263 | |
---|
| 2264 | %COPY IMAGES TO THE FORMAT .png IF NEEDED |
---|
[45] | 2265 | if isequal(nom_type_ima1,'*')%case of movie files |
---|
| 2266 | nom_type_imanew1='_i'; |
---|
[2] | 2267 | else |
---|
| 2268 | nom_type_imanew1=nom_type_ima1; |
---|
| 2269 | end |
---|
[45] | 2270 | if isequal(nom_type_ima2,'*')%case of movie files |
---|
| 2271 | nom_type_imanew2='_i'; |
---|
[2] | 2272 | else |
---|
| 2273 | nom_type_imanew2=nom_type_ima2; |
---|
| 2274 | end |
---|
| 2275 | if ~isequal(ext_ima,'.png') |
---|
[45] | 2276 | %%type of image file |
---|
| 2277 | type_ima1='none';%default |
---|
| 2278 | movieobject1=[];%default |
---|
[133] | 2279 | if strcmpi(ext_ima,'.avi') |
---|
[45] | 2280 | hhh=which('mmreader'); |
---|
| 2281 | if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab) |
---|
| 2282 | type_ima1='movie'; |
---|
| 2283 | movieobject1=mmreader([filebase_ima2 ext_ima]); |
---|
| 2284 | else |
---|
| 2285 | type_ima1='avi'; |
---|
| 2286 | end |
---|
[133] | 2287 | elseif ischar(ext_ima) && ~isempty(ext_ima(2:end)) |
---|
[112] | 2288 | form=imformats(ext_ima(2:end)); |
---|
| 2289 | if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab |
---|
| 2290 | if isequal(nom_type_ima1,'*'); |
---|
| 2291 | type_ima1='multimage';%image series in a single image file |
---|
| 2292 | else |
---|
| 2293 | type_ima1='image'; |
---|
| 2294 | end |
---|
| 2295 | end |
---|
[45] | 2296 | end |
---|
| 2297 | type_ima2='none';%default |
---|
| 2298 | movieobject2=[]; |
---|
[133] | 2299 | if strcmpi(ext_ima,'.avi') |
---|
[45] | 2300 | hhh=which('mmreader'); |
---|
| 2301 | if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab) |
---|
| 2302 | type_ima2='movie'; |
---|
| 2303 | movieobject2=mmreader([filebase_ima2 ext_ima]); |
---|
| 2304 | else |
---|
| 2305 | type_ima2='avi'; |
---|
| 2306 | end |
---|
[133] | 2307 | elseif ischar(ext_ima) && ~isempty(ext_ima(2:end)) |
---|
[112] | 2308 | form=imformats(ext_ima(2:end)); |
---|
| 2309 | if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab |
---|
| 2310 | if isequal(nom_type_ima1,'*'); |
---|
| 2311 | type_ima2='multimage';%image series in a single image file |
---|
| 2312 | else |
---|
| 2313 | type_ima2='image'; |
---|
| 2314 | end |
---|
| 2315 | end |
---|
[45] | 2316 | end |
---|
[71] | 2317 | %npxy=get(handles.ImaExt,'UserData'); |
---|
[112] | 2318 | % % if numel(npxy)<2 |
---|
| 2319 | % |
---|
| 2320 | % filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ImaExt,nom_type_ima1); |
---|
| 2321 | % A=imread(filename); |
---|
| 2322 | % npxy=size(A); |
---|
| 2323 | % % end |
---|
| 2324 | % npy=npxy(1); |
---|
| 2325 | % npx=npxy(2); |
---|
[282] | 2326 | if checkbox(1) %if civ1 is performed |
---|
[224] | 2327 | h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar |
---|
[112] | 2328 | for ifile=1:nbfield |
---|
[2] | 2329 | waitbar(ifile/nbfield); |
---|
| 2330 | for j=1:nbslice |
---|
[112] | 2331 | filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1); |
---|
| 2332 | if ~exist(filename,'file') |
---|
| 2333 | A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,num1_civ1(ifile),movieobject1); |
---|
| 2334 | imwrite(A,filename,'BitDepth',16); |
---|
| 2335 | end |
---|
| 2336 | filecell.ima1.civ1(ifile,j)={filename}; |
---|
| 2337 | filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2); |
---|
| 2338 | if ~exist(filename,'file') |
---|
| 2339 | A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,num2_civ1(ifile),movieobject2); |
---|
| 2340 | imwrite(A,filename,'BitDepth',16); |
---|
| 2341 | end |
---|
| 2342 | filecell.ima2.civ1(ifile,j)={filename}; |
---|
[2] | 2343 | end |
---|
| 2344 | end |
---|
| 2345 | close(h) |
---|
| 2346 | end |
---|
[282] | 2347 | if checkbox(4) %if civ2 is performed |
---|
[229] | 2348 | h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar |
---|
[2] | 2349 | for ifile=1:nbfield |
---|
| 2350 | waitbar(ifile/nbfield); |
---|
| 2351 | for j=1:nbslice |
---|
[112] | 2352 | filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1); |
---|
| 2353 | if ~exist(filename,'file') |
---|
| 2354 | A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,num1_civ2(ifile)); |
---|
| 2355 | imwrite(A,filename,'BitDepth',16); |
---|
| 2356 | end |
---|
| 2357 | filecell.ima1.civ2(ifile,j)={filename}; |
---|
| 2358 | filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2); |
---|
| 2359 | if ~exist(filename,'file') |
---|
| 2360 | A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,num2_civ2(ifile)); |
---|
| 2361 | imwrite(A,filename,'BitDepth',16); |
---|
| 2362 | end |
---|
| 2363 | filecell.ima2.civ2(ifile,j)={filename}; |
---|
[2] | 2364 | end |
---|
| 2365 | end |
---|
| 2366 | close(h); |
---|
| 2367 | end |
---|
| 2368 | end |
---|
| 2369 | |
---|
[12] | 2370 | %------------------------------------------------------------------------ |
---|
[227] | 2371 | % --- determine the list of index pairs of processing file |
---|
| 2372 | function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=... |
---|
| 2373 | find_pair_indices(handles,ref_i,ref_j,mode) |
---|
| 2374 | %------------------------------------------------------------------------ |
---|
| 2375 | |
---|
[282] | 2376 | list_civ1=get(handles.ListPairCiv1,'String'); |
---|
| 2377 | index_civ1=get(handles.ListPairCiv1,'Value'); |
---|
[227] | 2378 | str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1 |
---|
| 2379 | if isempty(str_civ1)||isequal(str_civ1,'') |
---|
| 2380 | msgbox_uvmat('ERROR','no image pair selected for civ1') |
---|
| 2381 | return |
---|
| 2382 | end |
---|
[282] | 2383 | list_civ2=get(handles.ListPairCiv2,'String'); |
---|
| 2384 | index_civ2=get(handles.ListPairCiv2,'Value'); |
---|
[227] | 2385 | if index_civ2>length(list_civ2) |
---|
| 2386 | list_civ2=list_civ1; |
---|
| 2387 | index_civ2=index_civ1; |
---|
| 2388 | end |
---|
| 2389 | str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2 |
---|
| 2390 | |
---|
| 2391 | if isequal (mode,'series(Di)') |
---|
| 2392 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
| 2393 | num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers |
---|
| 2394 | num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i)); |
---|
| 2395 | num_a_civ1=ref_j; |
---|
| 2396 | num_b_civ1=ref_j; |
---|
[229] | 2397 | num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i)); |
---|
[227] | 2398 | num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i)); |
---|
| 2399 | num_a_civ2=ref_j; |
---|
| 2400 | num_b_civ2=ref_j; |
---|
| 2401 | |
---|
| 2402 | % adjust the first and last field number |
---|
| 2403 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
| 2404 | if isnan(lastfield) |
---|
| 2405 | indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1)); |
---|
| 2406 | else |
---|
| 2407 | indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1)); |
---|
| 2408 | end |
---|
| 2409 | if length(indsel)>=1 |
---|
| 2410 | firstind=indsel(1); |
---|
| 2411 | lastind=indsel(end); |
---|
| 2412 | set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields |
---|
| 2413 | set(handles.last_i,'String',num2str(ref_i(lastind))) |
---|
| 2414 | ref_i=ref_i(indsel); |
---|
| 2415 | num1_civ1=num1_civ1(indsel); |
---|
| 2416 | num1_civ2=num1_civ2(indsel); |
---|
| 2417 | num2_civ1=num2_civ1(indsel); |
---|
| 2418 | num2_civ2=num2_civ2(indsel); |
---|
| 2419 | end |
---|
| 2420 | elseif isequal (mode,'series(Dj)') |
---|
| 2421 | lastfield_j=str2double(get(handles.nb_field2,'String')); |
---|
| 2422 | num1_civ1=ref_i;% set of first image numbers |
---|
| 2423 | num2_civ1=ref_i; |
---|
| 2424 | num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j)); |
---|
| 2425 | num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j)); |
---|
| 2426 | num1_civ2=ref_i; |
---|
| 2427 | num2_civ2=ref_i; |
---|
| 2428 | num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j)); |
---|
| 2429 | num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j)); |
---|
| 2430 | % adjust the first and last field number |
---|
| 2431 | if isnan(lastfield_j) |
---|
| 2432 | indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1)); |
---|
| 2433 | else |
---|
| 2434 | indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1)); |
---|
| 2435 | end |
---|
| 2436 | if length(indsel)>=1 |
---|
| 2437 | firstind=indsel(1); |
---|
| 2438 | lastind=indsel(end); |
---|
| 2439 | set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields |
---|
| 2440 | set(handles.last_j,'String',num2str(ref_j(lastind))) |
---|
| 2441 | ref_j=ref_j(indsel); |
---|
| 2442 | num_a_civ1=num_a_civ1(indsel); |
---|
| 2443 | num_b_civ1=num_b_civ1(indsel); |
---|
| 2444 | num_a_civ2=num_a_civ2(indsel); |
---|
| 2445 | num_b_civ2=num_b_civ2(indsel); |
---|
| 2446 | end |
---|
| 2447 | elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) |
---|
[282] | 2448 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
[227] | 2449 | num1_civ1=ref_i; |
---|
| 2450 | num2_civ1=ref_i; |
---|
| 2451 | num_a_civ1=displ_num(1,index_civ1); |
---|
| 2452 | num_b_civ1=displ_num(2,index_civ1); |
---|
| 2453 | num1_civ2=ref_i; |
---|
| 2454 | num2_civ2=ref_i; |
---|
| 2455 | num_a_civ2=displ_num(1,index_civ2); |
---|
| 2456 | num_b_civ2=displ_num(2,index_civ2); |
---|
| 2457 | elseif isequal(mode,'displacement') |
---|
| 2458 | num1_civ1=ref_i; |
---|
| 2459 | num2_civ1=ref_i; |
---|
| 2460 | num_a_civ1=ref_j; |
---|
| 2461 | num_b_civ1=ref_j; |
---|
| 2462 | num1_civ2=ref_i; |
---|
| 2463 | num2_civ2=ref_i; |
---|
| 2464 | num_a_civ2=ref_j; |
---|
| 2465 | num_b_civ2=ref_j; |
---|
| 2466 | end |
---|
| 2467 | |
---|
| 2468 | %------------------------------------------------------------------------ |
---|
[309] | 2469 | % --- Executes on button press in ListCompareMode. |
---|
| 2470 | function ListCompareMode_Callback(hObject, eventdata, handles) |
---|
[12] | 2471 | %------------------------------------------------------------------------ |
---|
[309] | 2472 | test=get(handles.ListCompareMode,'Value'); |
---|
| 2473 | if test==2 || test==3 % case 'dispalcemen' or 'stereo PIV' |
---|
| 2474 | filebase=get(handles.RootName,'String'); |
---|
| 2475 | browse=get(handlesRootName,'Userdata'); |
---|
| 2476 | browse.nom_type_ima1=browse.nom_type_ima; |
---|
| 2477 | set(handlesRootName,'UserData',browse); |
---|
| 2478 | set(handles.sub_txt,'Visible','on') |
---|
| 2479 | set(handles.RootName_1,'Visible','On');%mkes the second file input window visible |
---|
| 2480 | mode_store=get(handles.ListPairMode,'String');%get the present 'mode' |
---|
| 2481 | set(handles.ListCompareMode,'UserData',mode_store);%store the mode display |
---|
| 2482 | set(handles.ListPairMode,'Visible','off') |
---|
| 2483 | if test==2 |
---|
| 2484 | set(handles.ListPairMode,'Visible','off') |
---|
| 2485 | set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default |
---|
| 2486 | else |
---|
| 2487 | set(handles.ListPairMode,'Visible','on') |
---|
| 2488 | set(handles.ListPairMode,'Value',3) % mode 'Matlab' selected for stereo |
---|
| 2489 | end |
---|
| 2490 | |
---|
| 2491 | %% menuopen an image file with the browser |
---|
| 2492 | ind_opening=1;%default |
---|
| 2493 | browse.incr_pair=[0 0]; %default |
---|
| 2494 | oldfile=get(handles.RootName,'String'); |
---|
| 2495 | menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)'; |
---|
| 2496 | '*.xml', '.xml files '; ... |
---|
| 2497 | '*.civ', '.civ files '; ... |
---|
| 2498 | '*.png','.png image files'; ... |
---|
| 2499 | '*.jpg',' jpeg image files'; ... |
---|
| 2500 | '*.tif','.tif image files'; ... |
---|
| 2501 | '*.avi;*.AVI','.avi movie files'; ... |
---|
| 2502 | '*.nc','.netcdf files'; ... |
---|
| 2503 | '*.*', 'All Files (*.*)'}; |
---|
| 2504 | [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file of the second series',oldfile); |
---|
| 2505 | fileinput=[PathName FileName];%complete file name |
---|
| 2506 | sizf=size(fileinput); |
---|
| 2507 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
| 2508 | [path,name,ext]=fileparts(fileinput); |
---|
| 2509 | [path1]=fileparts(filebase); |
---|
| 2510 | if isunix |
---|
| 2511 | [status,path]=system(['readlink ' path]); |
---|
| 2512 | [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths |
---|
| 2513 | end |
---|
| 2514 | if ~strcmp(path1,path) |
---|
| 2515 | msgbox_uvmat('ERROR','The second image series must be in the same directory as the first one') |
---|
| 2516 | return |
---|
| 2517 | end |
---|
| 2518 | % set(handles.RootName_1,'String',name); |
---|
| 2519 | [RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,subdir]=name2display(name); |
---|
| 2520 | set(handles.RootName_1,'String',RootFile); |
---|
| 2521 | browse=get(handlesRootName,'UserData'); |
---|
| 2522 | browse.nom_type_ima_1=nom_type; |
---|
| 2523 | set(handlesRootName,'UserData',browse) |
---|
| 2524 | |
---|
| 2525 | %check image extension |
---|
| 2526 | if ~strcmp(ext,get(handles.ImaExt,'String')) |
---|
| 2527 | msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one') |
---|
| 2528 | return |
---|
| 2529 | end |
---|
| 2530 | |
---|
| 2531 | %% check coincidence of image sizes |
---|
| 2532 | % ref_i=get(handles.ref_i,'string'); |
---|
| 2533 | % ref_j=get(handles.ref_j,'string'); |
---|
| 2534 | % [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]); |
---|
| 2535 | % A=imread(filecell.ima1.checkciv1{1}); |
---|
| 2536 | % A_1=imread(fileinput); |
---|
| 2537 | % npxy=size(A); |
---|
| 2538 | % npxy_1=size(A_1); |
---|
| 2539 | % if ~isequal(size(A),size(A_1)) |
---|
| 2540 | % msgbox_uvmat('ERROR','The two input image series do not have the same size') |
---|
| 2541 | % return |
---|
| 2542 | % end |
---|
| 2543 | else |
---|
| 2544 | set(handles.ListPairMode,'Visible','on') |
---|
| 2545 | set(handles.RootName_1,'Visible','Off'); |
---|
| 2546 | set(handles.sub_txt,'Visible','off') |
---|
| 2547 | set(handles.RootName_1,'String',[]); |
---|
| 2548 | mode_store=get(handles.ListCompareMode,'UserData'); |
---|
| 2549 | set(handles.ListPairMode,'Value',1) |
---|
| 2550 | set(handles.ListPairMode,'String',mode_store) |
---|
| 2551 | set(handles.test_stereo1,'Value',0) |
---|
| 2552 | set(handles.CheckStereo,'Value',0) |
---|
| 2553 | set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default |
---|
| 2554 | end |
---|
| 2555 | if test==3 && get(handles.CheckPatch1,'Value') |
---|
| 2556 | set(handles.test_stereo1,'Visible','on') |
---|
| 2557 | else |
---|
| 2558 | set(handles.test_stereo1,'Visible','off') |
---|
| 2559 | end |
---|
| 2560 | if test==3 && get(handles.CheckPatch2,'Value') |
---|
| 2561 | set(handles.CheckStereo,'Visible','on') |
---|
| 2562 | else |
---|
| 2563 | set(handles.CheckStereo,'Visible','off') |
---|
| 2564 | end |
---|
| 2565 | mode_Callback(hObject, eventdata, handles) |
---|
[2] | 2566 | |
---|
[309] | 2567 | |
---|
| 2568 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 2569 | % Callbacks in the uipanel Pair Indices |
---|
| 2570 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
[12] | 2571 | %------------------------------------------------------------------------ |
---|
[309] | 2572 | % --- Executes on button press in ListPairMode. |
---|
| 2573 | function ListPairMode_Callback(hObject, eventdata, handles) |
---|
[12] | 2574 | %------------------------------------------------------------------------ |
---|
[309] | 2575 | compare_list=get(handles.ListCompareMode,'String'); |
---|
| 2576 | val=get(handles.ListCompareMode,'Value'); |
---|
| 2577 | compare=compare_list{val}; |
---|
| 2578 | if strcmp(compare,'displacement') |
---|
| 2579 | mode='displacement'; |
---|
| 2580 | else |
---|
| 2581 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2582 | if ischar(mode_list) |
---|
| 2583 | mode_list={mode_list}; |
---|
| 2584 | end |
---|
| 2585 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2586 | mode=mode_list{mode_value}; |
---|
| 2587 | end |
---|
| 2588 | displ_num=[];%default |
---|
| 2589 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 2590 | % last_i=str2num(get(handles.last_i,'String')); |
---|
| 2591 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
| 2592 | siztime=size(time); |
---|
| 2593 | nbfield=siztime(1); |
---|
| 2594 | nbfield2=siztime(2); |
---|
| 2595 | indchosen=1; %%first pair selected by default |
---|
| 2596 | %displ_num used to define the indices of the civ pairs |
---|
| 2597 | % in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices |
---|
| 2598 | % are relative to the reference indices ref_i and ref_j respectively. |
---|
| 2599 | if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2') |
---|
| 2600 | dt=1; |
---|
| 2601 | displ=''; |
---|
| 2602 | index=0; |
---|
| 2603 | numlist_a=[]; |
---|
| 2604 | numlist_B=[]; |
---|
| 2605 | %get all the time intervals in bursts |
---|
| 2606 | displ_dt=1;%default |
---|
| 2607 | nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10 |
---|
| 2608 | for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode |
---|
| 2609 | for numod_b=(numod_a+1):nbfield2 |
---|
| 2610 | index=index+1; |
---|
| 2611 | numlist_a(index)=numod_a; |
---|
| 2612 | numlist_b(index)=numod_b; |
---|
| 2613 | if ~isempty(time) |
---|
| 2614 | dt(numod_a,numod_b)=time(ref_i,numod_b)-time(ref_i,numod_a);%first time interval dt |
---|
| 2615 | displ_dt(index)=dt(numod_a,numod_b); |
---|
| 2616 | else |
---|
| 2617 | displ_dt(index)=1; |
---|
| 2618 | end |
---|
| 2619 | end |
---|
| 2620 | end |
---|
| 2621 | [dtsort,indsort]=sort(displ_dt); |
---|
| 2622 | if ~isempty(numlist_a) |
---|
| 2623 | displ_num(1,:)=numlist_a(indsort); |
---|
| 2624 | displ_num(2,:)=numlist_b(indsort); |
---|
| 2625 | end |
---|
| 2626 | displ_num(3,:)=0; |
---|
| 2627 | displ_num(4,:)=0; |
---|
| 2628 | set(handles.jtext,'Visible','Off') |
---|
| 2629 | set(handles.first_j,'Visible','Off') |
---|
| 2630 | set(handles.last_j,'Visible','Off') |
---|
| 2631 | set(handles.incr_j,'Visible','Off') |
---|
| 2632 | set(handles.nb_field2,'Visible','Off') |
---|
| 2633 | set(handles.ref_j,'Visible','Off') |
---|
| 2634 | elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') |
---|
| 2635 | index=1:200; |
---|
| 2636 | displ_num(1,index)=-floor(index/2); |
---|
| 2637 | displ_num(2,index)=ceil(index/2); |
---|
| 2638 | displ_num(3:4,index)=zeros(2,200); |
---|
| 2639 | % for index=1:min(nbfield2-1,200) |
---|
| 2640 | % displ_num(1,index)=-floor(index/2); |
---|
| 2641 | % displ_num(2,index)=ceil(index/2); |
---|
| 2642 | % displ_num(3,index)=0; |
---|
| 2643 | % displ_num(4,index)=0; |
---|
| 2644 | % end |
---|
| 2645 | set(handles.jtext,'Visible','On') |
---|
| 2646 | set(handles.first_j,'Visible','On') |
---|
| 2647 | set(handles.last_j,'Visible','On') |
---|
| 2648 | set(handles.incr_j,'Visible','On') |
---|
| 2649 | set(handles.nb_field2,'Visible','On') |
---|
| 2650 | set(handles.ref_j,'Visible','On') |
---|
| 2651 | if nbfield > 1 |
---|
| 2652 | set(handles.itext,'Visible','On') |
---|
| 2653 | set(handles.first_i,'Visible','On') |
---|
| 2654 | set(handles.last_i,'Visible','On') |
---|
| 2655 | set(handles.incr_i,'Visible','On') |
---|
| 2656 | set(handles.nb_field,'Visible','On') |
---|
| 2657 | set(handles.ref_i,'Visible','On') |
---|
| 2658 | else |
---|
| 2659 | set(handles.itext,'Visible','Off') |
---|
| 2660 | set(handles.first_i,'Visible','Off') |
---|
| 2661 | set(handles.last_i,'Visible','Off') |
---|
| 2662 | set(handles.incr_i,'Visible','Off') |
---|
| 2663 | set(handles.nb_field,'Visible','Off') |
---|
| 2664 | set(handles.ref_i,'Visible','Off') |
---|
| 2665 | end |
---|
| 2666 | elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') |
---|
| 2667 | index=1:200; |
---|
| 2668 | displ_num(1:2,index)=zeros(2,200); |
---|
| 2669 | displ_num(3,index)=-floor(index/2); |
---|
| 2670 | displ_num(4,index)=ceil(index/2); |
---|
| 2671 | % for index=1:200%min(nbfield-1,200) |
---|
| 2672 | % displ_num(1,index)=0; |
---|
| 2673 | % displ_num(2,index)=0; |
---|
| 2674 | % displ_num(3,index)=-floor(index/2); |
---|
| 2675 | % displ_num(4,index)=ceil(index/2); |
---|
| 2676 | % end |
---|
| 2677 | set(handles.itext,'Visible','On') |
---|
| 2678 | set(handles.first_i,'Visible','On') |
---|
| 2679 | set(handles.last_i,'Visible','On') |
---|
| 2680 | set(handles.incr_i,'Visible','On') |
---|
| 2681 | set(handles.nb_field,'Visible','On') |
---|
| 2682 | set(handles.ref_i,'Visible','On') |
---|
| 2683 | if nbfield2 > 1 |
---|
| 2684 | set(handles.jtext,'Visible','On') |
---|
| 2685 | set(handles.first_j,'Visible','On') |
---|
| 2686 | set(handles.last_j,'Visible','On') |
---|
| 2687 | set(handles.incr_j,'Visible','On') |
---|
| 2688 | set(handles.nb_field2,'Visible','On') |
---|
| 2689 | set(handles.ref_j,'Visible','On') |
---|
| 2690 | else |
---|
| 2691 | set(handles.jtext,'Visible','Off') |
---|
| 2692 | set(handles.first_j,'Visible','Off') |
---|
| 2693 | set(handles.last_j,'Visible','Off') |
---|
| 2694 | set(handles.incr_j,'Visible','Off') |
---|
| 2695 | set(handles.nb_field2,'Visible','Off') |
---|
| 2696 | set(handles.ref_j,'Visible','Off') |
---|
| 2697 | end |
---|
| 2698 | elseif isequal(mode,'displacement')%the pairs have the same indices |
---|
| 2699 | displ_num(1,1)=0; |
---|
| 2700 | displ_num(2,1)=0; |
---|
| 2701 | displ_num(3,1)=0; |
---|
| 2702 | displ_num(4,1)=0; |
---|
| 2703 | if nbfield > 1 |
---|
| 2704 | set(handles.itext,'Visible','On') |
---|
| 2705 | set(handles.first_i,'Visible','On') |
---|
| 2706 | set(handles.last_i,'Visible','On') |
---|
| 2707 | set(handles.incr_i,'Visible','On') |
---|
| 2708 | set(handles.nb_field,'Visible','On') |
---|
| 2709 | set(handles.ref_i,'Visible','On') |
---|
| 2710 | else |
---|
| 2711 | set(handles.itext,'Visible','Off') |
---|
| 2712 | set(handles.first_i,'Visible','Off') |
---|
| 2713 | set(handles.last_i,'Visible','Off') |
---|
| 2714 | set(handles.incr_i,'Visible','Off') |
---|
| 2715 | set(handles.nb_field,'Visible','Off') |
---|
| 2716 | set(handles.ref_i,'Visible','Off') |
---|
| 2717 | end |
---|
| 2718 | if nbfield2 > 1 |
---|
| 2719 | set(handles.jtext,'Visible','On') |
---|
| 2720 | set(handles.first_j,'Visible','On') |
---|
| 2721 | set(handles.last_j,'Visible','On') |
---|
| 2722 | set(handles.incr_j,'Visible','On') |
---|
| 2723 | set(handles.nb_field2,'Visible','On') |
---|
| 2724 | set(handles.ref_j,'Visible','On') |
---|
| 2725 | else |
---|
| 2726 | set(handles.jtext,'Visible','Off') |
---|
| 2727 | set(handles.first_j,'Visible','Off') |
---|
| 2728 | set(handles.last_j,'Visible','Off') |
---|
| 2729 | set(handles.incr_j,'Visible','Off') |
---|
| 2730 | set(handles.nb_field2,'Visible','Off') |
---|
| 2731 | set(handles.ref_j,'Visible','Off') |
---|
| 2732 | end |
---|
| 2733 | end |
---|
| 2734 | set(handles.ListPairCiv1,'UserData',displ_num); |
---|
| 2735 | find_netcpair_civ1( handles) |
---|
| 2736 | find_netcpair_civ2(handles) |
---|
[2] | 2737 | |
---|
[12] | 2738 | %------------------------------------------------------------------------ |
---|
[309] | 2739 | % --- Executes on selection change in ListPairCiv1. |
---|
| 2740 | function ListPairCiv1_Callback(hObject, eventdata, handles) |
---|
[12] | 2741 | %------------------------------------------------------------------------ |
---|
[309] | 2742 | %reproduce by default the chosen pair in the checkciv2 menu |
---|
| 2743 | list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs |
---|
| 2744 | index_pair=get(handles.ListPairCiv1,'Value'); |
---|
| 2745 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
| 2746 | % num_a=displ_num(1,index_pair); |
---|
| 2747 | % num_b=displ_num(2,index_pair); |
---|
| 2748 | list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs |
---|
| 2749 | if index_pair<=length(list_pair2) |
---|
| 2750 | set(handles.ListPairCiv2,'Value',index_pair); |
---|
| 2751 | end |
---|
[2] | 2752 | |
---|
[309] | 2753 | %update first_i and last_i according to the chosen image pairs |
---|
| 2754 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2755 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2756 | mode=mode_list{mode_value}; |
---|
| 2757 | if isequal(mode,'series(Di)') |
---|
| 2758 | first_i=str2double(get(handles.first_i,'String')); |
---|
| 2759 | last_i=str2double(get(handles.last_i,'String')); |
---|
| 2760 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
| 2761 | num1=first_i:incr_i:last_i; |
---|
| 2762 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
| 2763 | if ~isnan(lastfield) |
---|
| 2764 | test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ... |
---|
| 2765 | (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield); |
---|
| 2766 | num1=num1(test_find); |
---|
| 2767 | end |
---|
| 2768 | set(handles.first_i,'String',num2str(num1(1))); |
---|
| 2769 | set(handles.last_i,'String',num2str(num1(end))); |
---|
| 2770 | elseif isequal(mode,'series(Dj)') |
---|
| 2771 | first_j=str2double(get(handles.first_j,'String')); |
---|
| 2772 | last_j=str2double(get(handles.last_j,'String')); |
---|
| 2773 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
| 2774 | num_j=first_j:incr_j:last_j; |
---|
| 2775 | lastfield2=str2double(get(handles.nb_field2,'String')); |
---|
| 2776 | if ~isnan(lastfield2) |
---|
| 2777 | test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... |
---|
| 2778 | (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); |
---|
| 2779 | num1=num_j(test_find); |
---|
| 2780 | end |
---|
| 2781 | set(handles.first_j,'String',num2str(num1(1))); |
---|
| 2782 | set(handles.last_j,'String',num2str(num1(end))); |
---|
| 2783 | end |
---|
| 2784 | |
---|
[12] | 2785 | %------------------------------------------------------------------------ |
---|
[309] | 2786 | % --- Executes on selection change in ListPairCiv2. |
---|
| 2787 | function ListPairCiv2_Callback(hObject, eventdata, handles) |
---|
[12] | 2788 | %------------------------------------------------------------------------ |
---|
[309] | 2789 | index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu |
---|
[2] | 2790 | |
---|
[309] | 2791 | %update first_i and last_i according to the chosen image pairs |
---|
| 2792 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2793 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2794 | mode=mode_list{mode_value}; |
---|
| 2795 | if isequal(mode,'series(Di)') |
---|
| 2796 | first_i=str2double(get(handles.first_i,'String')); |
---|
| 2797 | last_i=str2double(get(handles.last_i,'String')); |
---|
| 2798 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
| 2799 | num1=first_i:incr_i:last_i; |
---|
| 2800 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
| 2801 | if ~isnan(lastfield) |
---|
| 2802 | test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ... |
---|
| 2803 | (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield); |
---|
| 2804 | num1=num1(test_find); |
---|
| 2805 | end |
---|
| 2806 | set(handles.first_i,'String',num2str(num1(1))); |
---|
| 2807 | set(handles.last_i,'String',num2str(num1(end))); |
---|
| 2808 | elseif isequal(mode,'series(Dj)') |
---|
| 2809 | first_j=str2double(get(handles.first_j,'String')); |
---|
| 2810 | last_j=str2double(get(handles.last_j,'String')); |
---|
| 2811 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
| 2812 | num_j=first_j:incr_j:last_j; |
---|
| 2813 | lastfield2=str2double(get(handles.nb_field2,'String')); |
---|
| 2814 | if ~isnan(lastfield2) |
---|
| 2815 | test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... |
---|
| 2816 | (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); |
---|
| 2817 | num1=num_j(test_find); |
---|
| 2818 | end |
---|
| 2819 | set(handles.first_j,'String',num2str(num1(1))); |
---|
| 2820 | set(handles.last_j,'String',num2str(num1(end))); |
---|
| 2821 | end |
---|
| 2822 | |
---|
[12] | 2823 | %------------------------------------------------------------------------ |
---|
[309] | 2824 | function ref_i_Callback(hObject, eventdata, handles) |
---|
[12] | 2825 | %------------------------------------------------------------------------ |
---|
[309] | 2826 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2827 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2828 | mode=mode_list{mode_value}; |
---|
| 2829 | find_netcpair_civ1(handles);% update the menu of pairs depending on the available netcdf files |
---|
| 2830 | if isequal(mode,'series(Di)') || ...% we do patch2 only |
---|
| 2831 | (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) |
---|
| 2832 | find_netcpair_civ2( handles); |
---|
| 2833 | end |
---|
[2] | 2834 | |
---|
[12] | 2835 | %------------------------------------------------------------------------ |
---|
[309] | 2836 | function ref_j_Callback(hObject, eventdata, handles) |
---|
[12] | 2837 | %------------------------------------------------------------------------ |
---|
[309] | 2838 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2839 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2840 | mode=mode_list{mode_value}; |
---|
| 2841 | if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)') |
---|
| 2842 | find_netcpair_civ1(handles);% update the menu of pairs depending on the available netcdf files |
---|
| 2843 | end |
---|
| 2844 | if isequal(mode,'series(Dj)') || ... |
---|
| 2845 | (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) |
---|
| 2846 | find_netcpair_civ2(handles); |
---|
| 2847 | end |
---|
| 2848 | % |
---|
[12] | 2849 | %------------------------------------------------------------------------ |
---|
[309] | 2850 | % determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of |
---|
| 2851 | % the field series set by first_i, incr, last_i |
---|
| 2852 | function find_netcpair_civ1(handles) |
---|
[12] | 2853 | %------------------------------------------------------------------------ |
---|
[309] | 2854 | set(gcf,'Pointer','watch') |
---|
| 2855 | %nomenclature types |
---|
| 2856 | filebase=get(handles.RootName,'String'); |
---|
| 2857 | [filepath,Nme,ext_dir]=fileparts(filebase); |
---|
| 2858 | browse=get(handles.RootName,'UserData'); |
---|
| 2859 | compare_list=get(handles.ListCompareMode,'String'); |
---|
| 2860 | val=get(handles.ListCompareMode,'Value'); |
---|
| 2861 | compare=compare_list{val}; |
---|
| 2862 | if strcmp(compare,'displacement') |
---|
| 2863 | mode='displacement'; |
---|
| 2864 | else |
---|
| 2865 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2866 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2867 | if isempty(mode_list) |
---|
| 2868 | return |
---|
| 2869 | end |
---|
| 2870 | mode=mode_list{mode_value}; |
---|
| 2871 | end |
---|
[289] | 2872 | |
---|
[309] | 2873 | % nomenclature type of the .nc files |
---|
| 2874 | nom_type_ima=[];%default |
---|
| 2875 | if isfield(browse,'nom_type_ima') |
---|
| 2876 | nom_type_ima=browse.nom_type_ima; |
---|
| 2877 | end |
---|
| 2878 | |
---|
| 2879 | %determine nom_type_nc: |
---|
| 2880 | nom_type_nc=[];%default |
---|
| 2881 | if isfield(browse,'nom_type_nc') |
---|
| 2882 | nom_type_nc=browse.nom_type_nc; |
---|
| 2883 | end |
---|
| 2884 | if isempty(nom_type_nc) |
---|
| 2885 | [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)')); |
---|
| 2886 | end |
---|
| 2887 | browse.nom_type_nc=nom_type_nc; |
---|
| 2888 | set(handles.RootName,'UserData',browse) |
---|
| 2889 | |
---|
| 2890 | %reads .nc subdirectoy and image numbers from the interface |
---|
| 2891 | subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data |
---|
| 2892 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 2893 | if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') |
---|
| 2894 | ref_j=0; |
---|
| 2895 | else |
---|
| 2896 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
| 2897 | end |
---|
| 2898 | time=get(handles.ImaDoc,'UserData');%get the set of times |
---|
| 2899 | if isempty(time) |
---|
| 2900 | time=[0 1]; |
---|
| 2901 | end |
---|
| 2902 | dt_unit=1000;%default |
---|
| 2903 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
| 2904 | |
---|
| 2905 | %eliminate the first pairs inconsistent with the position |
---|
| 2906 | if isempty(displ_num) |
---|
| 2907 | nbpair=0; |
---|
| 2908 | else |
---|
| 2909 | nbpair=length(displ_num(1,:));%nbre of displayed pairs |
---|
| 2910 | if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') |
---|
| 2911 | nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index |
---|
| 2912 | elseif isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
| 2913 | nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index |
---|
| 2914 | end |
---|
| 2915 | end |
---|
| 2916 | nbpair=min(200,nbpair);%limit the number of displayed pairs to 200 |
---|
| 2917 | |
---|
| 2918 | %look for existing processed pairs involving the field at the middle of the series if checkciv1 will not |
---|
| 2919 | % be performed, while the result is needed for next steps. |
---|
| 2920 | displ_pair={''}; |
---|
| 2921 | select=ones(size(1:nbpair));%flag for displayed pairs =1 for display |
---|
| 2922 | testpair=0; |
---|
| 2923 | |
---|
| 2924 | %% case with no Civ1 operation, netcdf files need to exist for reading |
---|
| 2925 | if ~get(handles.CheckCiv1,'Value') % |
---|
| 2926 | if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir') |
---|
| 2927 | msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']); |
---|
| 2928 | set(handles.ListPairCiv1,'String',{}); |
---|
| 2929 | return |
---|
| 2930 | end |
---|
| 2931 | for ipair=1:nbpair |
---|
| 2932 | filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,... |
---|
| 2933 | ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1); |
---|
| 2934 | select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist |
---|
| 2935 | end |
---|
| 2936 | % case of no displayed pair |
---|
| 2937 | if isequal(select,zeros(size(1:nbpair))) |
---|
| 2938 | if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0]) |
---|
| 2939 | num_i1=ref_i-floor(browse.incr_pair(1)/2); |
---|
| 2940 | num_i2=ref_i+ceil(browse.incr_pair(1)/2); |
---|
| 2941 | num_j1=ref_j-floor(browse.incr_pair(2)/2); |
---|
| 2942 | num_j2=ref_j+ceil(browse.incr_pair(2)/2); |
---|
| 2943 | filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1); |
---|
| 2944 | select(1)=exist(filename,'file')==2; |
---|
| 2945 | testpair=1; |
---|
| 2946 | else |
---|
| 2947 | if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
| 2948 | msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]); |
---|
| 2949 | else |
---|
| 2950 | msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1]); |
---|
| 2951 | end |
---|
| 2952 | set(handles.ListPairCiv1,'String',{''}); |
---|
| 2953 | %COMPLETER CAS STEREO |
---|
| 2954 | return |
---|
| 2955 | end |
---|
| 2956 | end |
---|
| 2957 | end |
---|
| 2958 | |
---|
| 2959 | %% determine the menu display in .ListPairCiv1 |
---|
| 2960 | % the menu depends on the mode defined in ListPairMode_callback through the array displ_num: |
---|
| 2961 | % displ_num(1,:)=indices j1 |
---|
| 2962 | % displ_num(2,:)=indices j2 |
---|
| 2963 | % displ_num(3,:)=indices i1 |
---|
| 2964 | % displ_num(4,:)=indices i2 |
---|
| 2965 | % in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices |
---|
| 2966 | % are relative to the reference indices ref_i and ref_j respectively. |
---|
| 2967 | if isequal(mode,'series(Di)') |
---|
| 2968 | if testpair |
---|
| 2969 | displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; |
---|
| 2970 | else |
---|
| 2971 | for ipair=1:nbpair |
---|
| 2972 | if select(ipair) |
---|
| 2973 | displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))]; |
---|
| 2974 | if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) |
---|
| 2975 | dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt |
---|
| 2976 | displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; |
---|
| 2977 | end |
---|
| 2978 | else |
---|
| 2979 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
| 2980 | end |
---|
| 2981 | end |
---|
| 2982 | end |
---|
| 2983 | elseif isequal(mode,'series(Dj)') |
---|
| 2984 | if testpair |
---|
| 2985 | displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; |
---|
| 2986 | else |
---|
| 2987 | for ipair=1:nbpair |
---|
| 2988 | if select(ipair) |
---|
| 2989 | displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))]; |
---|
| 2990 | if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) |
---|
| 2991 | dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt |
---|
| 2992 | displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; |
---|
| 2993 | end |
---|
| 2994 | else |
---|
| 2995 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
| 2996 | end |
---|
| 2997 | end |
---|
| 2998 | end |
---|
| 2999 | elseif isequal(mode,'pair j1-j2')%case of pairs |
---|
| 3000 | for ipair=1:nbpair |
---|
| 3001 | if select(ipair) |
---|
| 3002 | dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt |
---|
| 3003 | displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ... |
---|
| 3004 | ' :dt= ' num2str(dt*1000)]; |
---|
| 3005 | else |
---|
| 3006 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
| 3007 | end |
---|
| 3008 | end |
---|
| 3009 | elseif isequal(mode,'displacement') |
---|
| 3010 | displ_pair={'Di=Dj=0'}; |
---|
| 3011 | end |
---|
| 3012 | set(handles.ListPairCiv1,'String',displ_pair'); |
---|
| 3013 | |
---|
| 3014 | %% determine the default selection in the pair menu |
---|
| 3015 | ichoice=find(select,1);% index of selected pair |
---|
| 3016 | if (isempty(ichoice) || ichoice < 1); ichoice=1; end; |
---|
| 3017 | initial=get(handles.ListPairCiv1,'Value');%initial choice of pair |
---|
| 3018 | if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1)) |
---|
| 3019 | set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu |
---|
| 3020 | end |
---|
| 3021 | initial=get(handles.ListPairCiv2,'Value'); |
---|
| 3022 | if initial>length(displ_pair')%|~isequal(select(initial),1) |
---|
| 3023 | if ichoice <= length(displ_pair') |
---|
| 3024 | set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2 |
---|
| 3025 | else |
---|
| 3026 | set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2 |
---|
| 3027 | end |
---|
| 3028 | end |
---|
| 3029 | set(handles.ListPairCiv2,'String',displ_pair'); |
---|
| 3030 | set(gcf,'Pointer','arrow') |
---|
| 3031 | |
---|
[289] | 3032 | %------------------------------------------------------------------------ |
---|
[309] | 3033 | % determine the menu for checkciv2 pairs depending on the existing netcdf file at the |
---|
| 3034 | %middle of the series set by first_i, incr, last_i |
---|
| 3035 | function find_netcpair_civ2(handles) |
---|
[289] | 3036 | %------------------------------------------------------------------------ |
---|
[309] | 3037 | set(gcf,'Pointer','watch') |
---|
| 3038 | %nomenclature types |
---|
| 3039 | filebase=get(handles.RootName,'String'); |
---|
| 3040 | [filepath,Nme,ext_dir]=fileparts(filebase); |
---|
| 3041 | browse=get(handles.RootName,'UserData'); |
---|
| 3042 | compare_list=get(handles.ListCompareMode,'String'); |
---|
| 3043 | val=get(handles.ListCompareMode,'Value'); |
---|
| 3044 | compare=compare_list{val}; |
---|
| 3045 | if strcmp(compare,'displacement') |
---|
| 3046 | mode='displacement'; |
---|
| 3047 | else |
---|
| 3048 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 3049 | if isempty(mode_list) |
---|
| 3050 | msgbox_uvmat('ERROR','please enter an input image or netcdf file') |
---|
[289] | 3051 | return |
---|
| 3052 | end |
---|
[309] | 3053 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 3054 | mode=mode_list{mode_value}; |
---|
[2] | 3055 | end |
---|
[309] | 3056 | |
---|
| 3057 | % nomenclature type of the .nc files |
---|
| 3058 | nom_type_ima='ima_num';%default |
---|
| 3059 | if isfield(browse,'nom_type_ima') |
---|
| 3060 | nom_type_ima=browse.nom_type_ima; |
---|
| 3061 | end |
---|
| 3062 | nom_type_nc='_i1-i2';%default |
---|
| 3063 | if isfield(browse,'nom_type_nc') |
---|
| 3064 | nom_type_nc=browse.nom_type_nc; |
---|
| 3065 | end |
---|
| 3066 | if isequal(nom_type_ima,'png_old') || isequal(nom_type_ima,'netc_old')|| isequal(nom_type_ima,'raw_SMD')|| isequal(nom_type_nc,'netc_old') |
---|
| 3067 | nom_type_nc='netc_old';%nom_type for the netcdf files |
---|
| 3068 | elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none') |
---|
| 3069 | nom_type_nc='none'; |
---|
| 3070 | elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_i1-i2') |
---|
| 3071 | nom_type_nc='_i1-i2'; |
---|
[289] | 3072 | else |
---|
[309] | 3073 | if isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)') |
---|
| 3074 | nom_type_nc='_i1-i2_j'; % PIV in volume |
---|
[289] | 3075 | else |
---|
[309] | 3076 | nom_type_nc='_i_j1-j2'; |
---|
[289] | 3077 | end |
---|
| 3078 | end |
---|
[309] | 3079 | browse.nom_type_nc=nom_type_nc; |
---|
| 3080 | set(handles.RootName,'UserData',browse) |
---|
[2] | 3081 | |
---|
[309] | 3082 | %reads .nc subdirectory and image numbers from the interface |
---|
| 3083 | subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data |
---|
| 3084 | subdir_civ2=get(handles.txt_SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data |
---|
| 3085 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 3086 | if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') |
---|
| 3087 | ref_j=0; |
---|
| 3088 | else |
---|
| 3089 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
| 3090 | end |
---|
| 3091 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
| 3092 | if isempty(time) |
---|
| 3093 | time=[0 1];%default |
---|
| 3094 | end |
---|
| 3095 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
| 3096 | |
---|
| 3097 | %eliminate the first pairs inconsistent with the position |
---|
| 3098 | if isempty(displ_num) |
---|
| 3099 | nbpair=0; |
---|
| 3100 | else |
---|
| 3101 | nbpair=length(displ_num(1,:));%nbre of displayed pairs |
---|
| 3102 | if isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)') |
---|
| 3103 | nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index |
---|
| 3104 | elseif isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
| 3105 | nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index |
---|
| 3106 | end |
---|
| 3107 | end |
---|
| 3108 | nbpair=min(200,nbpair);%limit the number of displayed pairs to 200 |
---|
| 3109 | |
---|
| 3110 | %% look for existing processed pairs at the reference indices if Civ1 will not |
---|
| 3111 | % be performed, while the result is needed for next steps. |
---|
| 3112 | displ_pair={''}; %default |
---|
| 3113 | select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs |
---|
| 3114 | if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value') |
---|
| 3115 | if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir') |
---|
| 3116 | errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist']) |
---|
| 3117 | set(handles.ListPairCiv2,'Value',1); |
---|
| 3118 | set(handles.ListPairCiv2,'String',{''}); |
---|
| 3119 | return |
---|
| 3120 | end |
---|
| 3121 | for ipair=1:nbpair |
---|
| 3122 | filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,... |
---|
| 3123 | ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1); |
---|
| 3124 | select(ipair)=exist(filename,'file')==2; |
---|
| 3125 | end |
---|
| 3126 | if isequal(select,zeros(size(1:nbpair))) |
---|
| 3127 | if isfield(browse,'incr_pair') |
---|
| 3128 | num_i1=ref_i-floor(browse.incr_pair(1)/2); |
---|
| 3129 | num_i2=ref_i+floor((browse.incr_pair(1)+1)/2); |
---|
| 3130 | num_j1=ref_j-floor(browse.incr_pair(2)/2); |
---|
| 3131 | num_j2=ref_j+floor((browse.incr_pair(2)+1)/2); |
---|
| 3132 | filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2); |
---|
| 3133 | select(1)=exist(filename,'file')==2; |
---|
| 3134 | else |
---|
| 3135 | if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
| 3136 | errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2]) |
---|
| 3137 | else |
---|
| 3138 | errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2]) |
---|
| 3139 | end |
---|
| 3140 | set(handles.ListPairCiv2,'Value',1); |
---|
| 3141 | set(handles.ListPairCiv2,'String',{''}); |
---|
| 3142 | return |
---|
| 3143 | end |
---|
| 3144 | end |
---|
| 3145 | end |
---|
| 3146 | if isequal(mode,'series(Di)') |
---|
| 3147 | for ipair=1:nbpair |
---|
| 3148 | if select(ipair) |
---|
| 3149 | displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ]; |
---|
| 3150 | if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) |
---|
| 3151 | dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt |
---|
| 3152 | displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; |
---|
| 3153 | end |
---|
| 3154 | else |
---|
| 3155 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
| 3156 | end |
---|
| 3157 | end |
---|
| 3158 | elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index |
---|
| 3159 | for ipair=1:nbpair |
---|
| 3160 | if select(ipair) |
---|
| 3161 | displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ]; |
---|
| 3162 | if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) |
---|
| 3163 | dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt |
---|
| 3164 | displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; |
---|
| 3165 | end |
---|
| 3166 | else |
---|
| 3167 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
| 3168 | end |
---|
| 3169 | end |
---|
| 3170 | elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs |
---|
| 3171 | for ipair=1:nbpair |
---|
| 3172 | if select(ipair) |
---|
| 3173 | dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt |
---|
| 3174 | displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ... |
---|
| 3175 | ' :dt= ' num2str(dt*1000)]; |
---|
| 3176 | else |
---|
| 3177 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
| 3178 | end |
---|
| 3179 | end |
---|
| 3180 | elseif isequal(mode,'displacement') |
---|
| 3181 | displ_pair={'Di=Dj=0'}; |
---|
| 3182 | end |
---|
| 3183 | val=get(handles.ListPairCiv2,'Value'); |
---|
| 3184 | ichoice=find(select,1); |
---|
| 3185 | if (isempty(ichoice) || ichoice < 1); ichoice=1; end; |
---|
| 3186 | if get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0 |
---|
| 3187 | val=ichoice;% first valid pair proposed by default in the menu |
---|
| 3188 | end |
---|
| 3189 | if val>length(displ_pair') |
---|
| 3190 | set(handles.ListPairCiv2,'Value',1);% first valid pair proposed by default in the menu |
---|
| 3191 | else |
---|
| 3192 | set(handles.ListPairCiv2,'Value',val); |
---|
| 3193 | end |
---|
| 3194 | set(handles.ListPairCiv2,'String',displ_pair'); |
---|
| 3195 | set(gcf,'Pointer','arrow') |
---|
| 3196 | |
---|
[315] | 3197 | %------------------------------------------------------------------- |
---|
| 3198 | % --- |
---|
| 3199 | function closeview_field(gcbo,eventdata) |
---|
| 3200 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
| 3201 | if ~isempty(hview_field) |
---|
| 3202 | delete(hview_field) |
---|
| 3203 | end |
---|
| 3204 | |
---|
| 3205 | |
---|
| 3206 | %------------------------------------------------------------------------ |
---|
| 3207 | % call 'view_field.fig' to display the field selected in the list of 'status' |
---|
| 3208 | function open_view_field(hObject, eventdata) |
---|
| 3209 | %------------------------------------------------------------------------ |
---|
| 3210 | list=get(hObject,'String'); |
---|
| 3211 | index=get(hObject,'Value'); |
---|
| 3212 | rootroot=get(hObject,'UserData'); |
---|
| 3213 | filename=list{index}; |
---|
| 3214 | ind_dot=strfind(filename,'...'); |
---|
| 3215 | filename=filename(1:ind_dot-1); |
---|
| 3216 | filename=fullfile(rootroot,filename); |
---|
| 3217 | delete(get(hObject,'parent'))%delete the display figure to stop the check process |
---|
| 3218 | if exist(filename,'file')%visualise the vel field if it exists |
---|
| 3219 | uvmat(filename) |
---|
| 3220 | set(gcbo,'Value',1) |
---|
| 3221 | end |
---|
[309] | 3222 | |
---|
[315] | 3223 | %------------------------------------------------------------------------ |
---|
| 3224 | % launched by pressing OK on the status figure |
---|
| 3225 | function close_GUI(hObject, eventdata) |
---|
| 3226 | %------------------------------------------------------------------------ |
---|
| 3227 | delete(gcbf) |
---|
| 3228 | |
---|
| 3229 | %------------------------------------------------------------------------ |
---|
| 3230 | % launched by deleting the status figure |
---|
| 3231 | function stop_status(hObject, eventdata) |
---|
| 3232 | %------------------------------------------------------------------------ |
---|
| 3233 | hciv=findobj(allchild(0),'tag','civ'); |
---|
| 3234 | hhciv=guidata(hciv); |
---|
| 3235 | set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ |
---|
| 3236 | set(hhciv.status,'BackgroundColor',[0 1 0]) |
---|
[309] | 3237 | |
---|
| 3238 | |
---|
| 3239 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 3240 | % Callbacks in the uipanel Reference Indices |
---|
| 3241 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
[12] | 3242 | %------------------------------------------------------------------------ |
---|
| 3243 | function first_i_Callback(hObject, eventdata, handles) |
---|
| 3244 | %------------------------------------------------------------------------ |
---|
[137] | 3245 | first_i=str2double(get(handles.first_i,'String')); |
---|
[12] | 3246 | set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index |
---|
| 3247 | ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt) |
---|
[2] | 3248 | |
---|
[12] | 3249 | %------------------------------------------------------------------------ |
---|
| 3250 | function first_j_Callback(hObject, eventdata, handles) |
---|
| 3251 | %------------------------------------------------------------------------ |
---|
| 3252 | first_j=str2num(get(handles.first_j,'String')); |
---|
| 3253 | set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index |
---|
| 3254 | ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt) |
---|
[2] | 3255 | |
---|
[309] | 3256 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 3257 | % Callbacks in the uipanel Civ1 |
---|
| 3258 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
[12] | 3259 | %------------------------------------------------------------------------ |
---|
[287] | 3260 | % --- Executes on button press in SearchRange: determine the search range num_Searchx,num_Searchy |
---|
[273] | 3261 | function SearchRange_Callback(hObject, eventdata, handles) |
---|
[12] | 3262 | %------------------------------------------------------------------------ |
---|
[2] | 3263 | %determine pair numbers |
---|
[273] | 3264 | if strcmp(get(handles.umin,'Visible'),'off') |
---|
| 3265 | set(handles.u_title,'Visible','on') |
---|
| 3266 | set(handles.v_title,'Visible','on') |
---|
| 3267 | set(handles.umin,'Visible','on') |
---|
| 3268 | set(handles.umax,'Visible','on') |
---|
| 3269 | set(handles.vmin,'Visible','on') |
---|
| 3270 | set(handles.vmax,'Visible','on') |
---|
| 3271 | set(handles.CoordUnit,'Visible','on') |
---|
| 3272 | set(handles.TimeUnit,'Visible','on') |
---|
| 3273 | set(handles.slash_title,'Visible','on') |
---|
| 3274 | set(handles.min_title,'Visible','on') |
---|
| 3275 | set(handles.max_title,'Visible','on') |
---|
| 3276 | set(handles.unit_title,'Visible','on') |
---|
| 3277 | else |
---|
| 3278 | get_search_range(hObject, eventdata, handles) |
---|
[2] | 3279 | end |
---|
| 3280 | |
---|
[12] | 3281 | %------------------------------------------------------------------------ |
---|
[287] | 3282 | % --- determine the search range num_Searchx,num_Searchy and shift |
---|
[273] | 3283 | function get_search_range(hObject, eventdata, handles) |
---|
| 3284 | umin=str2double(get(handles.umin,'String')); |
---|
| 3285 | umax=str2double(get(handles.umax,'String')); |
---|
| 3286 | vmin=str2double(get(handles.umin,'String')); |
---|
| 3287 | vmax=str2double(get(handles.vmax,'String')); |
---|
| 3288 | %switch min_title and max_title in case of error |
---|
| 3289 | if umax<=umin |
---|
| 3290 | umin_old=umin; |
---|
| 3291 | umin=umax; |
---|
| 3292 | umax=umin_old; |
---|
| 3293 | set(handles.umin,'String', num2str(umin)) |
---|
| 3294 | set(handles.umax,'String', num2str(umax)) |
---|
| 3295 | end |
---|
| 3296 | if vmax<=vmin |
---|
| 3297 | vmin_old=vmin; |
---|
| 3298 | vmin=vmax; |
---|
| 3299 | vmax=vmin_old; |
---|
| 3300 | set(handles.vmin,'String', num2str(vmin)) |
---|
| 3301 | set(handles.vmax,'String', num2str(vmax)) |
---|
| 3302 | end |
---|
| 3303 | if ~(isnan(umin)||isnan(umax)||isnan(vmin)||isnan(vmax)) |
---|
[282] | 3304 | list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs |
---|
| 3305 | index=get(handles.ListPairCiv1,'Value'); |
---|
| 3306 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
[273] | 3307 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
| 3308 | pxcm_xy=get(handles.SearchRange,'UserData'); |
---|
| 3309 | pxcmx=pxcm_xy(1); |
---|
| 3310 | pxcmy=pxcm_xy(2); |
---|
[282] | 3311 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 3312 | mode_value=get(handles.ListPairMode,'Value'); |
---|
[273] | 3313 | mode=mode_list{mode_value}; |
---|
| 3314 | if isequal (mode, 'series(Di)' ) |
---|
| 3315 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 3316 | num1=ref_i-floor(index/2);% first image numbers |
---|
| 3317 | num2=ref_i+ceil(index/2); |
---|
| 3318 | num_a=1; |
---|
| 3319 | num_b=1; |
---|
| 3320 | elseif isequal (mode, 'series(Dj)') |
---|
| 3321 | num1=1; |
---|
| 3322 | num2=1; |
---|
| 3323 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
| 3324 | num_a=ref_j-floor(index/2);% first image numbers |
---|
| 3325 | num_b=ref_j+ceil(index/2); |
---|
| 3326 | elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) |
---|
| 3327 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 3328 | num1=ref_i; |
---|
| 3329 | num2=ref_i; |
---|
| 3330 | num_a=displ_num(1,index); |
---|
| 3331 | num_b=displ_num(2,index); |
---|
| 3332 | end |
---|
| 3333 | dt=time(num2,num_b)-time(num1,num_a); |
---|
[282] | 3334 | ibx=str2double(get(handles.num_Bx,'String')); |
---|
| 3335 | iby=str2double(get(handles.num_By,'String')); |
---|
[273] | 3336 | umin=dt*pxcmx*umin; |
---|
| 3337 | umax=dt*pxcmx*umax; |
---|
| 3338 | vmin=dt*pxcmy*vmin; |
---|
| 3339 | vmax=dt*pxcmy*vmax; |
---|
| 3340 | shiftx=round((umin+umax)/2); |
---|
| 3341 | shifty=round((vmin+vmax)/2); |
---|
| 3342 | isx=(umax+2-shiftx)*2+ibx; |
---|
| 3343 | isx=2*ceil(isx/2)+1; |
---|
| 3344 | isy=(vmax+2-shifty)*2+iby; |
---|
| 3345 | isy=2*ceil(isy/2)+1; |
---|
[282] | 3346 | set(handles.num_Shiftx,'String',num2str(shiftx)); |
---|
| 3347 | set(handles.num_Shifty,'String',num2str(shifty)); |
---|
[287] | 3348 | set(handles.num_Searchx,'String',num2str(isx)); |
---|
| 3349 | set(handles.num_Searchy,'String',num2str(isy)); |
---|
[273] | 3350 | end |
---|
| 3351 | |
---|
[315] | 3352 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 3353 | % Callbacks in the uipanel Fix1 |
---|
| 3354 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
[12] | 3355 | %------------------------------------------------------------------------ |
---|
[282] | 3356 | % --- Executes on button press in CheckMask. |
---|
[2] | 3357 | function get_mask_fix1_Callback(hObject, eventdata, handles) |
---|
[12] | 3358 | %------------------------------------------------------------------------ |
---|
[282] | 3359 | maskval=get(handles.CheckMask,'Value'); |
---|
[2] | 3360 | if isequal(maskval,0) |
---|
[315] | 3361 | set(handles.txt_Mask,'String','') |
---|
[2] | 3362 | else |
---|
[112] | 3363 | mask_displ='no mask'; %default |
---|
| 3364 | filebase=get(handles.RootName,'String'); |
---|
| 3365 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
| 3366 | if isequal(flag_mask,1) |
---|
| 3367 | mask_displ=[num2str(nbslice) 'mask']; |
---|
[282] | 3368 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
[71] | 3369 | filebase_a=get(handles.RootName_1,'String'); |
---|
[2] | 3370 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
[229] | 3371 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
[2] | 3372 | mask_displ='no mask'; |
---|
| 3373 | end |
---|
[112] | 3374 | end |
---|
| 3375 | if isequal(mask_displ,'no mask') |
---|
| 3376 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
| 3377 | {'*.png', ' (*.png)'; |
---|
[12] | 3378 | '*.png', '.png files '; ... |
---|
| 3379 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3380 | 'Pick a mask file *.png',filebase); |
---|
[112] | 3381 | mask_displ=fullfile(PathName,FileName); |
---|
| 3382 | if ~exist(mask_displ,'file') |
---|
| 3383 | mask_displ='no mask'; |
---|
| 3384 | end |
---|
[12] | 3385 | end |
---|
[112] | 3386 | if isequal(mask_displ,'no mask') |
---|
[282] | 3387 | set(handles.CheckMask,'Value',0) |
---|
| 3388 | set(handles.CheckMask,'Value',0) |
---|
| 3389 | set(handles.CheckMask,'Value',0) |
---|
[112] | 3390 | else |
---|
[282] | 3391 | %set(handles.CheckMask,'Value',1) |
---|
| 3392 | set(handles.CheckMask,'Value',1) |
---|
[112] | 3393 | end |
---|
[276] | 3394 | set(handles.txt_Mask,'String',mask_displ) |
---|
[315] | 3395 | set(handles.txt_Mask,'String',mask_displ) |
---|
| 3396 | set(handles.txt_Mask,'String',mask_displ) |
---|
[12] | 3397 | end |
---|
| 3398 | |
---|
| 3399 | %------------------------------------------------------------------------ |
---|
[282] | 3400 | % --- Executes on button press in CheckMask: select box for mask option |
---|
[2] | 3401 | function get_mask_civ2_Callback(hObject, eventdata, handles) |
---|
[12] | 3402 | %------------------------------------------------------------------------ |
---|
[282] | 3403 | maskval=get(handles.CheckMask,'Value'); |
---|
[2] | 3404 | if isequal(maskval,0) |
---|
[276] | 3405 | set(handles.txt_Mask,'String','') |
---|
[2] | 3406 | else |
---|
[112] | 3407 | mask_displ='no mask'; %default |
---|
| 3408 | filebase=get(handles.RootName,'String'); |
---|
| 3409 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
| 3410 | if isequal(flag_mask,1) |
---|
| 3411 | mask_displ=[num2str(nbslice) 'mask']; |
---|
[282] | 3412 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
[71] | 3413 | filebase_a=get(handles.RootName_1,'String'); |
---|
[2] | 3414 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
[229] | 3415 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
[2] | 3416 | mask_displ='no mask'; |
---|
| 3417 | end |
---|
[112] | 3418 | end |
---|
| 3419 | if isequal(mask_displ,'no mask') |
---|
| 3420 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
| 3421 | {'*.png', ' (*.png)'; |
---|
[12] | 3422 | '*.png', '.png files '; ... |
---|
| 3423 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3424 | 'Pick a mask file *.png',filebase); |
---|
[112] | 3425 | mask_displ=fullfile(PathName,FileName); |
---|
| 3426 | if ~exist(mask_displ,'file') |
---|
| 3427 | mask_displ='no mask'; |
---|
| 3428 | end |
---|
[12] | 3429 | end |
---|
[112] | 3430 | if isequal(mask_displ,'no mask') |
---|
[282] | 3431 | set(handles.CheckMask,'Value',0) |
---|
| 3432 | set(handles.CheckMask,'Value',0) |
---|
[112] | 3433 | else |
---|
[282] | 3434 | set(handles.CheckMask,'Value',1) |
---|
[112] | 3435 | end |
---|
[276] | 3436 | set(handles.txt_Mask,'String',mask_displ) |
---|
[315] | 3437 | set(handles.txt_Mask,'String',mask_displ) |
---|
[12] | 3438 | end |
---|
| 3439 | |
---|
| 3440 | %------------------------------------------------------------------------ |
---|
[282] | 3441 | % --- Executes on button press in CheckMask. |
---|
[2] | 3442 | function get_mask_fix2_Callback(hObject, eventdata, handles) |
---|
[12] | 3443 | %------------------------------------------------------------------------ |
---|
[282] | 3444 | maskval=get(handles.CheckMask,'Value'); |
---|
[2] | 3445 | if isequal(maskval,0) |
---|
[315] | 3446 | set(handles.txt_Mask,'String','') |
---|
[2] | 3447 | else |
---|
[12] | 3448 | mask_displ='no mask'; %default |
---|
[71] | 3449 | filebase=get(handles.RootName,'String'); |
---|
[12] | 3450 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
| 3451 | if isequal(flag_mask,1) |
---|
[112] | 3452 | mask_displ=[num2str(nbslice) 'mask']; |
---|
[282] | 3453 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
[112] | 3454 | filebase_a=get(handles.RootName_1,'String'); |
---|
| 3455 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
[229] | 3456 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
[112] | 3457 | mask_displ='no mask'; |
---|
| 3458 | end |
---|
[12] | 3459 | end |
---|
| 3460 | if isequal(mask_displ,'no mask') |
---|
| 3461 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
[112] | 3462 | {'*.png', ' (*.png)'; |
---|
| 3463 | '*.png', '.png files '; ... |
---|
| 3464 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3465 | 'Pick a mask file *.png',filebase); |
---|
| 3466 | mask_displ=fullfile(PathName,FileName); |
---|
[12] | 3467 | if ~exist(mask_displ,'file') |
---|
[2] | 3468 | mask_displ='no mask'; |
---|
| 3469 | end |
---|
[12] | 3470 | end |
---|
| 3471 | if isequal(mask_displ,'no mask') |
---|
[282] | 3472 | set(handles.CheckMask,'Value',0) |
---|
[112] | 3473 | end |
---|
[315] | 3474 | set(handles.txt_Mask,'String',mask_displ) |
---|
[2] | 3475 | end |
---|
| 3476 | |
---|
[12] | 3477 | %------------------------------------------------------------------------ |
---|
| 3478 | % --- function called to look for mask files |
---|
[2] | 3479 | function [nbslice, flag_mask]=get_mask(filebase,handles) |
---|
[12] | 3480 | %------------------------------------------------------------------------ |
---|
[112] | 3481 | %detect mask files, images with appropriate file base |
---|
[2] | 3482 | %[filebase '_' xx 'mask'], xx=nbslice |
---|
| 3483 | %flag_mask=1 indicates detection |
---|
| 3484 | |
---|
| 3485 | flag_mask=0;%default |
---|
| 3486 | nbslice=1; |
---|
| 3487 | |
---|
[289] | 3488 | % subdir=get(handles.txt_SubdirCiv1,'String'); |
---|
[2] | 3489 | [Path,Name]=fileparts(filebase); |
---|
[12] | 3490 | if ~isdir(Path) |
---|
| 3491 | msgbox_uvmat('ERROR','no path for input files') |
---|
| 3492 | return |
---|
| 3493 | end |
---|
[272] | 3494 | % currentdir=pwd; |
---|
| 3495 | % cd(Path);%move in the dir of the root name filebase |
---|
| 3496 | maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files |
---|
| 3497 | % cd(currentdir);%come back to the current working directory |
---|
[12] | 3498 | if ~isempty(maskfiles) |
---|
[112] | 3499 | % msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat') |
---|
| 3500 | % else |
---|
[2] | 3501 | flag_mask=1; |
---|
| 3502 | maskname=maskfiles(1).name;% take the first mask file in the list |
---|
| 3503 | [Path2,Name,ext]=fileparts(maskname); |
---|
| 3504 | Namedouble=double(Name); |
---|
| 3505 | val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters |
---|
| 3506 | ind_mask=findstr('mask',Name); |
---|
| 3507 | i=ind_mask-1; |
---|
[137] | 3508 | while val(i)==0 && i>0 |
---|
[112] | 3509 | i=i-1; |
---|
[2] | 3510 | end |
---|
[137] | 3511 | nbslice=str2double(Name(i+1:ind_mask-1)); |
---|
| 3512 | if ~isnan(nbslice) && Name(i)=='_' |
---|
[112] | 3513 | flag_mask=1; |
---|
[2] | 3514 | else |
---|
[112] | 3515 | msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2]) |
---|
| 3516 | return |
---|
| 3517 | nbslice=1; |
---|
[2] | 3518 | end |
---|
[112] | 3519 | end |
---|
[2] | 3520 | |
---|
[12] | 3521 | %------------------------------------------------------------------------ |
---|
| 3522 | % --- function called to look for grid files |
---|
[2] | 3523 | function [nbslice, flag_mask]=get_grid(filebase,handles) |
---|
[12] | 3524 | %------------------------------------------------------------------------ |
---|
[2] | 3525 | flag_mask=0;%default |
---|
| 3526 | nbslice=1; |
---|
| 3527 | [Path,Name]=fileparts(filebase); |
---|
| 3528 | currentdir=pwd; |
---|
| 3529 | cd(Path);%move in the dir of the root name filebase |
---|
| 3530 | maskfiles=dir([Name '_*grid_*.grid']);%look for mask files |
---|
| 3531 | cd(currentdir);%come back to the current working directory |
---|
| 3532 | if ~isempty(maskfiles) |
---|
| 3533 | flag_mask=1; |
---|
| 3534 | maskname=maskfiles(1).name;% take the first mask file in the list |
---|
| 3535 | [Path2,Name,ext]=fileparts(maskname); |
---|
| 3536 | Namedouble=double(Name); |
---|
| 3537 | val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters |
---|
| 3538 | ind_mask=findstr('grid',Name); |
---|
| 3539 | i=ind_mask-1; |
---|
[137] | 3540 | while val(i)==0 && i>0 |
---|
[112] | 3541 | i=i-1; |
---|
[2] | 3542 | end |
---|
[137] | 3543 | nbslice=str2double(Name(i+1:ind_mask-1)); |
---|
| 3544 | if ~isnan(nbslice) && Name(i)=='_' |
---|
[112] | 3545 | flag_mask=1; |
---|
[2] | 3546 | else |
---|
[112] | 3547 | msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2]) |
---|
| 3548 | return |
---|
| 3549 | nbslice=1; |
---|
[2] | 3550 | end |
---|
[12] | 3551 | end |
---|
[2] | 3552 | |
---|
[12] | 3553 | %------------------------------------------------------------------------ |
---|
| 3554 | % --- transform numbers to letters |
---|
[122] | 3555 | function str=num2stra(num,nom_type) |
---|
[12] | 3556 | %------------------------------------------------------------------------ |
---|
[122] | 3557 | if isempty(nom_type) |
---|
| 3558 | str=''; |
---|
| 3559 | elseif strcmp(nom_type(end),'a') |
---|
[2] | 3560 | str=char(96+num); |
---|
[122] | 3561 | elseif strcmp(nom_type(end),'A') |
---|
| 3562 | str=char(96+num); |
---|
| 3563 | elseif isempty(nom_type(2:end))%a single index |
---|
[2] | 3564 | str=''; |
---|
| 3565 | else |
---|
| 3566 | str=num2str(num); |
---|
| 3567 | end |
---|
[12] | 3568 | |
---|
| 3569 | %------------------------------------------------------------------------ |
---|
[282] | 3570 | % --- Executes on button press in ListSubdirCiv1. |
---|
| 3571 | function ListSubdirCiv1_Callback(hObject, eventdata, handles) |
---|
[12] | 3572 | %------------------------------------------------------------------------ |
---|
[282] | 3573 | list_subdir_civ1=get(handles.ListSubdirCiv1,'String'); |
---|
| 3574 | val=get(handles.ListSubdirCiv1,'Value'); |
---|
[273] | 3575 | subdir=list_subdir_civ1{val}; |
---|
| 3576 | if strcmp(subdir,'new...') |
---|
[301] | 3577 | if get(handles.CheckCiv1,'Value') |
---|
| 3578 | subdir='CIV'; %default subdirectory |
---|
| 3579 | else |
---|
| 3580 | msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation') |
---|
| 3581 | return |
---|
| 3582 | end |
---|
[2] | 3583 | end |
---|
[289] | 3584 | set(handles.txt_SubdirCiv1,'String',subdir); |
---|
[301] | 3585 | find_netcpair_civ1(handles) |
---|
[2] | 3586 | |
---|
[12] | 3587 | %------------------------------------------------------------------------ |
---|
[289] | 3588 | % --- Executes on button press in ListSubdirCiv2. |
---|
| 3589 | function ListSubdirCiv2_Callback(hObject, eventdata, handles) |
---|
[12] | 3590 | %------------------------------------------------------------------------ |
---|
[289] | 3591 | list_subdir_civ2=get(handles.ListSubdirCiv2,'String'); |
---|
| 3592 | val=get(handles.ListSubdirCiv2,'Value'); |
---|
[273] | 3593 | subdir=list_subdir_civ2{val}; |
---|
| 3594 | if strcmp(subdir,'new...') |
---|
[301] | 3595 | if get(handles.CheckCiv2,'Value') |
---|
| 3596 | subdir='CIV'; %default subdirectory |
---|
| 3597 | else |
---|
| 3598 | msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation') |
---|
| 3599 | return |
---|
| 3600 | end |
---|
[2] | 3601 | end |
---|
[289] | 3602 | set(handles.txt_SubdirCiv2,'String',subdir); |
---|
[2] | 3603 | |
---|
[12] | 3604 | %------------------------------------------------------------------------ |
---|
[282] | 3605 | % --- Executes on button press in CheckGrid. |
---|
| 3606 | function CheckGrid_Callback(hObject, eventdata, handles) |
---|
[12] | 3607 | %------------------------------------------------------------------------ |
---|
[276] | 3608 | value=get(hObject,'Value'); |
---|
| 3609 | hparent=get(hObject,'parent'); |
---|
| 3610 | hchildren=get(hparent,'children'); |
---|
[315] | 3611 | handle_txtbox=findobj(hchildren,'tag','txt_Grid'); |
---|
[276] | 3612 | handle_dx=findobj(hchildren,'tag','num_Dx'); |
---|
| 3613 | handle_dy=findobj(hchildren,'tag','num_Dy'); |
---|
[315] | 3614 | handle_title_dx=findobj(hchildren,'tag','title_Dx'); |
---|
| 3615 | handle_title_dy=findobj(hchildren,'tag','title_Dy'); |
---|
[2] | 3616 | testgrid=0; |
---|
[276] | 3617 | filegrid=''; |
---|
[2] | 3618 | if value |
---|
[112] | 3619 | filebase=get(handles.RootName,'String'); |
---|
[276] | 3620 | [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name |
---|
[2] | 3621 | if isequal(flag_grid,1) |
---|
[112] | 3622 | filegrid=[num2str(nbslice) 'grid']; |
---|
| 3623 | testgrid=1; |
---|
[276] | 3624 | else % browse for a grid |
---|
| 3625 | filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData |
---|
| 3626 | if exist(filegrid,'file') |
---|
| 3627 | filebase=filegrid; |
---|
| 3628 | end |
---|
[2] | 3629 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
[112] | 3630 | {'*.grid', ' (*.grid)'; |
---|
| 3631 | '*.grid', '.grid files '; ... |
---|
| 3632 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3633 | 'Pick a file',filebase); |
---|
[2] | 3634 | filegrid=fullfile(PathName,FileName); |
---|
[276] | 3635 | set(hObject,'UserData',filegrid);%store for future use |
---|
[2] | 3636 | if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file')) |
---|
| 3637 | testgrid=1; |
---|
| 3638 | end |
---|
[112] | 3639 | end |
---|
[2] | 3640 | end |
---|
| 3641 | if testgrid |
---|
[276] | 3642 | set(handle_dx,'Visible','off'); |
---|
| 3643 | set(handle_dy,'Visible','off'); |
---|
[315] | 3644 | set(handle_title_dy,'Visible','off'); |
---|
| 3645 | set(handle_title_dx,'Visible','off'); |
---|
[276] | 3646 | set(handle_txtbox,'Visible','on') |
---|
| 3647 | set(handle_txtbox,'String',filegrid) |
---|
[112] | 3648 | else |
---|
[276] | 3649 | set(hObject,'Value',0); |
---|
[315] | 3650 | set(handle_dx,'Visible','on'); |
---|
[276] | 3651 | set(handle_dy,'Visible','on'); |
---|
[315] | 3652 | set(handle_title_dy,'Visible','on'); |
---|
| 3653 | set(handle_title_dx,'Visible','on'); |
---|
[276] | 3654 | set(handle_txtbox,'Visible','off') |
---|
[2] | 3655 | end |
---|
| 3656 | |
---|
[282] | 3657 | %% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame |
---|
[315] | 3658 | PanelName=get(hparent,'tag') |
---|
| 3659 | if strcmp(PanelName,'Civ1') |
---|
[282] | 3660 | hchildren=get(handles.Civ2,'children'); |
---|
[315] | 3661 | handle_checkbox=findobj(hchildren,'tag','CheckGrid'); |
---|
| 3662 | handle_txtbox=findobj(hchildren,'tag','txt_Grid'); |
---|
[276] | 3663 | handle_dx=findobj(hchildren,'tag','num_Dx'); |
---|
| 3664 | handle_dy=findobj(hchildren,'tag','num_Dy'); |
---|
[315] | 3665 | handle_title_dx=findobj(hchildren,'tag','title_Dx'); |
---|
| 3666 | handle_title_dy=findobj(hchildren,'tag','title_Dy'); |
---|
[276] | 3667 | set(handle_checkbox,'UserData',filegrid);%store for future use |
---|
| 3668 | if testgrid |
---|
| 3669 | set(handle_checkbox,'Value',1); |
---|
| 3670 | set(handle_dx,'Visible','off'); |
---|
| 3671 | set(handle_dy,'Visible','off'); |
---|
[315] | 3672 | set(handle_title_dx,'Visible','off'); |
---|
| 3673 | set(handle_title_dy,'Visible','off'); |
---|
[276] | 3674 | set(handle_txtbox,'Visible','on') |
---|
| 3675 | set(handle_txtbox,'String',filegrid) |
---|
[315] | 3676 | % else |
---|
| 3677 | % set(handle_checkbox,'Value',0); |
---|
| 3678 | % set(handles.CheckGrid,'Value',0); |
---|
| 3679 | % set(handle_dx,'Visible','on'); |
---|
| 3680 | % set(handle_dy,'Visible','on'); |
---|
| 3681 | % set(handle_title_dx,'Visible','on'); |
---|
| 3682 | % set(handle_title_dy,'Visible','on'); |
---|
| 3683 | % set(handle_txtbox,'Visible','off') |
---|
[276] | 3684 | end |
---|
| 3685 | end |
---|
[12] | 3686 | %------------------------------------------------------------------------ |
---|
[282] | 3687 | % --- Executes on button press in CheckMask. |
---|
| 3688 | function CheckMask_Callback(hObject, eventdata, handles) |
---|
[276] | 3689 | %------------------------------------------------------------------------ |
---|
| 3690 | value=get(hObject,'Value'); |
---|
[315] | 3691 | hparent=get(hObject,'parent'); |
---|
| 3692 | parent_tag=get(hparent,'Tag'); |
---|
| 3693 | hchildren=get(hparent,'children'); |
---|
| 3694 | handle_txtbox=findobj(hchildren,'tag','txt_Mask'); |
---|
| 3695 | % handle_dx=findobj(hchildren,'tag','num_Dx'); |
---|
| 3696 | % handle_dy=findobj(hchildren,'tag','num_Dy'); |
---|
[276] | 3697 | testmask=0; |
---|
| 3698 | if value |
---|
| 3699 | filebase=get(handles.RootName,'String'); |
---|
| 3700 | [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name |
---|
| 3701 | if isequal(flag_mask,1) |
---|
| 3702 | filemask=[num2str(nbslice) 'mask']; |
---|
| 3703 | testmask=1; |
---|
| 3704 | else % browse for a mask |
---|
[315] | 3705 | filemask=get(hObject,'UserData');%look for previous mask name stored as UserData |
---|
[276] | 3706 | if exist(filemask,'file') |
---|
| 3707 | filebase=filemask; |
---|
| 3708 | end |
---|
[315] | 3709 | [FileName, PathName] = uigetfile( ... |
---|
[276] | 3710 | {'*.png', ' (*.png)'; |
---|
| 3711 | '*.png', '.png files '; ... |
---|
| 3712 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3713 | 'Pick a mask file *.png',filebase); |
---|
| 3714 | filemask=fullfile(PathName,FileName); |
---|
[315] | 3715 | set(hObject,'UserData',filemask);%store for future use |
---|
[276] | 3716 | if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file')) |
---|
| 3717 | testmask=1; |
---|
| 3718 | end |
---|
| 3719 | end |
---|
| 3720 | end |
---|
| 3721 | if testmask |
---|
[316] | 3722 | % stage=4;%default |
---|
| 3723 | if strcmp(parent_tag,'Civ1') |
---|
| 3724 | set(handles.txt_Mask,'Visible','on') |
---|
| 3725 | set(handles.txt_Mask,'String',filemask) |
---|
| 3726 | set(handles.CheckMask,'Value',1) |
---|
[315] | 3727 | end |
---|
[316] | 3728 | % switch parent_tag |
---|
| 3729 | % % case 'Fix1' |
---|
| 3730 | % % stage=2; |
---|
| 3731 | % case 'Civ2' |
---|
| 3732 | % stage=3; |
---|
| 3733 | % % case 'Fix2' |
---|
| 3734 | % % stage=4; |
---|
| 3735 | % end |
---|
| 3736 | % set(handles.txt_Mask(stage:end),'Visible','on') |
---|
| 3737 | % set(handles.txt_Mask(stage:end),'String',filemask) |
---|
| 3738 | % set(handles.CheckMask(stage:end),'Value',1) |
---|
[276] | 3739 | else |
---|
[315] | 3740 | set(hObject,'Value',0); |
---|
| 3741 | set(handle_txtbox,'Visible','off') |
---|
[276] | 3742 | end |
---|
| 3743 | |
---|
[2] | 3744 | |
---|
| 3745 | % --- Executes on button press in get_gridpatch1. |
---|
| 3746 | function get_gridpatch1_Callback(hObject, eventdata, handles) |
---|
| 3747 | % hObject handle to get_gridpatch1 (see GCBO) |
---|
[309] | 3748 | % eventdata reserved - to be defined in a future version of MENUMATLAB |
---|
[2] | 3749 | % handles structure with handles and user data (see GUIDATA) |
---|
| 3750 | |
---|
[71] | 3751 | filebase=get(handles.RootName,'String'); |
---|
[2] | 3752 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
[112] | 3753 | {'*.grid', ' (*.grid)'; |
---|
| 3754 | '*.grid', '.grid files '; ... |
---|
| 3755 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3756 | 'Pick a file',filebase); |
---|
[2] | 3757 | filegrid=fullfile(PathName,FileName); |
---|
| 3758 | set(handles.grid_patch1,'string',filegrid); |
---|
| 3759 | % set(handles.grid_patch2,'string',filegrid |
---|
| 3760 | |
---|
[12] | 3761 | %------------------------------------------------------------------------ |
---|
[2] | 3762 | % --- Executes on button press in get_gridpatch2. |
---|
| 3763 | function get_gridpatch2_Callback(hObject, eventdata, handles) |
---|
[12] | 3764 | %------------------------------------------------------------------------ |
---|
[2] | 3765 | |
---|
| 3766 | |
---|
[12] | 3767 | %------------------------------------------------------------------------ |
---|
[309] | 3768 | % --- STEREO Interp |
---|
| 3769 | function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB) |
---|
[12] | 3770 | %------------------------------------------------------------------------ |
---|
[309] | 3771 | namelog=[filename_nc(1:end-3) '_stinterp.log']; |
---|
| 3772 | cmd=[stinterpBin ' -f1 ' filename_A_nc ' -f2 ' filename_B_nc ' -f ' filename_nc ... |
---|
| 3773 | ' -m ' nx_patch ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ' -c1 ' xmlA ' -c2 ' xmlB ' -xy x -Nfy 1024 > ' namelog ' 2>&1']; % redirect standard output to the log file |
---|
[273] | 3774 | |
---|
[12] | 3775 | %------------------------------------------------------------------------ |
---|
[2] | 3776 | %--read images and convert them to the uint16 format used for PIV |
---|
[45] | 3777 | function A=read_image(filename,type_ima,num,movieobject) |
---|
[12] | 3778 | %------------------------------------------------------------------------ |
---|
[2] | 3779 | %num is the view number needed for an avi movie |
---|
[45] | 3780 | switch type_ima |
---|
| 3781 | case 'movie' |
---|
| 3782 | A=read(movieobject,num); |
---|
| 3783 | case 'avi' |
---|
[112] | 3784 | mov=aviread(filename,num); |
---|
| 3785 | A=frame2im(mov(1)); |
---|
[45] | 3786 | case 'multimage' |
---|
| 3787 | A=imread(filename,num); |
---|
[112] | 3788 | case 'image' |
---|
[45] | 3789 | A=imread(filename); |
---|
| 3790 | end |
---|
| 3791 | siz=size(A); |
---|
| 3792 | if length(siz)==3;%color images |
---|
[2] | 3793 | A=sum(double(A),3); |
---|
| 3794 | A=uint16(A); |
---|
| 3795 | end |
---|
| 3796 | |
---|
| 3797 | |
---|
[12] | 3798 | %------------------------------------------------------------------------ |
---|
[2] | 3799 | % --- Executes on button press in get_ref_fix1. |
---|
| 3800 | function get_ref_fix1_Callback(hObject, eventdata, handles) |
---|
[12] | 3801 | %------------------------------------------------------------------------ |
---|
[71] | 3802 | filebase=get(handles.RootName,'String'); |
---|
[2] | 3803 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
[112] | 3804 | {'*.nc', ' (*.nc)'; |
---|
| 3805 | '*.nc', 'netcdf files '; ... |
---|
| 3806 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3807 | 'Pick a file',filebase); |
---|
| 3808 | |
---|
[2] | 3809 | fileinput=[PathName FileName]; |
---|
| 3810 | sizf=size(fileinput); |
---|
[122] | 3811 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
[2] | 3812 | [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); |
---|
| 3813 | ref.filebase=fullfile(Path,File); |
---|
| 3814 | ref.num_a=stra2num(str_a); |
---|
| 3815 | ref.num_b=stra2num(str_b); |
---|
[89] | 3816 | ref.num1=str2double(field_count); |
---|
| 3817 | ref.num2=str2double(str2); |
---|
[2] | 3818 | browse=[];%initialisation |
---|
| 3819 | if ~isequal(ref.ext,'.nc') |
---|
| 3820 | msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') |
---|
| 3821 | return |
---|
| 3822 | end |
---|
| 3823 | set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']); |
---|
| 3824 | set(handles.ref_fix1,'UserData',ref) |
---|
| 3825 | menu_field{1}='civ1'; |
---|
| 3826 | Data=nc2struct(fileinput,[]); |
---|
[45] | 3827 | if isfield(Data,'patch') && isequal(Data.patch,1) |
---|
[2] | 3828 | menu_field{2}='filter1'; |
---|
| 3829 | end |
---|
[45] | 3830 | if isfield(Data,'civ2') && isequal(Data.civ2,1) |
---|
[2] | 3831 | menu_field{3}='civ2'; |
---|
| 3832 | end |
---|
[45] | 3833 | if isfield(Data,'patch2') && isequal(Data.patch2,1) |
---|
[2] | 3834 | menu_field{4}='filter2'; |
---|
| 3835 | end |
---|
| 3836 | set(handles.field_ref1,'String',menu_field); |
---|
| 3837 | set(handles.field_ref1,'Value',length(menu_field)); |
---|
[287] | 3838 | set(handles.num_MinVel,'Value',2); |
---|
| 3839 | set(handles.num_MinVel,'String','1');%default threshold |
---|
[2] | 3840 | set(handles.ref_fix1,'Enable','on') |
---|
[12] | 3841 | |
---|
| 3842 | %------------------------------------------------------------------------ |
---|
[2] | 3843 | % --- Executes on button press in get_ref_fix2. |
---|
| 3844 | function get_ref_fix2_Callback(hObject, eventdata, handles) |
---|
[12] | 3845 | %------------------------------------------------------------------------ |
---|
[2] | 3846 | if isequal(get(handles.get_ref_fix2,'Value'),1) |
---|
[71] | 3847 | filebase=get(handles.RootName,'String'); |
---|
[2] | 3848 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
[112] | 3849 | {'*.nc', ' (*.nc)'; |
---|
| 3850 | '*.nc', 'netcdf files '; ... |
---|
| 3851 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3852 | 'Pick a file',filebase); |
---|
[2] | 3853 | fileinput=[PathName FileName]; |
---|
| 3854 | sizf=size(fileinput); |
---|
[45] | 3855 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
[2] | 3856 | [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); |
---|
| 3857 | ref.filebase=fullfile(Path,File); |
---|
| 3858 | ref.num_a=stra2num(str_a); |
---|
| 3859 | ref.num_b=stra2num(str_b); |
---|
| 3860 | ref.num1=str2num(field_count); |
---|
| 3861 | ref.num2=str2num(str2); |
---|
| 3862 | browse=[];%initialisation |
---|
| 3863 | if ~isequal(ref.ext,'.nc') |
---|
| 3864 | msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') |
---|
| 3865 | return |
---|
| 3866 | end |
---|
| 3867 | set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']); |
---|
[112] | 3868 | set(handles.ref_fix2,'UserData',ref) |
---|
[2] | 3869 | menu_field{1}='civ1'; |
---|
| 3870 | Data=nc2struct(fileinput,[]); |
---|
[301] | 3871 | if isfield(Data,'patch') && isequal(Data.patch,1) |
---|
[2] | 3872 | menu_field{2}='filter1'; |
---|
| 3873 | end |
---|
[301] | 3874 | if isfield(Data,'civ2') && isequal(Data.civ2,1) |
---|
[2] | 3875 | menu_field{3}='civ2'; |
---|
| 3876 | end |
---|
[301] | 3877 | if isfield(Data,'patch2') && isequal(Data.patch2,1) |
---|
[2] | 3878 | menu_field{4}='filter2'; |
---|
| 3879 | end |
---|
| 3880 | set(handles.field_ref2,'String',menu_field); |
---|
| 3881 | set(handles.field_ref2,'Value',length(menu_field)); |
---|
[287] | 3882 | set(handles.num_MinVel,'Value',2); |
---|
| 3883 | set(handles.num_MinVel,'String','1');%default threshold |
---|
[2] | 3884 | set(handles.ref_fix2,'Enable','on') |
---|
| 3885 | set(handles.ref_fix2,'Visible','on') |
---|
| 3886 | set(handles.field_ref2,'Visible','on') |
---|
| 3887 | else |
---|
| 3888 | set(handles.ref_fix2,'Visible','off') |
---|
| 3889 | set(handles.field_ref2,'Visible','off') |
---|
| 3890 | end |
---|
| 3891 | |
---|
[12] | 3892 | %------------------------------------------------------------------------ |
---|
[2] | 3893 | function ref_fix1_Callback(hObject, eventdata, handles) |
---|
[12] | 3894 | %------------------------------------------------------------------------ |
---|
[287] | 3895 | set(handles.num_MinVel,'Value',1); |
---|
[12] | 3896 | set(handles.field_ref1,'Value',1) |
---|
| 3897 | set(handles.field_ref1,'String',{' '}) |
---|
| 3898 | set(handles.ref_fix1,'UserData',[]); |
---|
| 3899 | set(handles.ref_fix1,'String',''); |
---|
| 3900 | set(handles.thresh_vel1,'String','0'); |
---|
[112] | 3901 | |
---|
[12] | 3902 | %------------------------------------------------------------------------ |
---|
[2] | 3903 | function ref_fix2_Callback(hObject, eventdata, handles) |
---|
[12] | 3904 | %------------------------------------------------------------------------ |
---|
[287] | 3905 | set(handles.num_MinVel,'Value',1); |
---|
[12] | 3906 | set(handles.field_ref2,'Value',1) |
---|
| 3907 | set(handles.field_ref2,'String',{' '}) |
---|
| 3908 | set(handles.ref_fix2,'UserData',[]); |
---|
| 3909 | set(handles.ref_fix2,'String',''); |
---|
[287] | 3910 | set(handles.num_MinVel,'String','0'); |
---|
[2] | 3911 | |
---|
[12] | 3912 | %------------------------------------------------------------------------ |
---|
[2] | 3913 | % --- Executes on button press in test_stereo1. |
---|
| 3914 | function test_stereo1_Callback(hObject, eventdata, handles) |
---|
[12] | 3915 | %------------------------------------------------------------------------ |
---|
[2] | 3916 | if isequal(get(handles.test_stereo1,'Value'),0) |
---|
| 3917 | set(handles.subdomain_patch1,'Visible','on') |
---|
| 3918 | set(handles.rho_patch1,'Visible','on') |
---|
| 3919 | else |
---|
| 3920 | set(handles.subdomain_patch1,'Visible','off') |
---|
| 3921 | set(handles.rho_patch1,'Visible','off') |
---|
| 3922 | end |
---|
| 3923 | |
---|
[12] | 3924 | %------------------------------------------------------------------------ |
---|
[282] | 3925 | % --- Executes on button press in CheckStereo. |
---|
[273] | 3926 | function StereoCheck_Callback(hObject, eventdata, handles) |
---|
[12] | 3927 | %------------------------------------------------------------------------ |
---|
[282] | 3928 | if isequal(get(handles.CheckStereo,'Value'),0) |
---|
[274] | 3929 | set(handles.num_SubdomainSize,'Visible','on') |
---|
[292] | 3930 | set(handles.num_SmoothingParam,'Visible','on') |
---|
[2] | 3931 | else |
---|
[274] | 3932 | set(handles.num_SubdomainSize,'Visible','off') |
---|
[292] | 3933 | set(handles.num_SmoothingParam,'Visible','off') |
---|
[2] | 3934 | end |
---|
| 3935 | |
---|
[12] | 3936 | %------------------------------------------------------------------------ |
---|
[225] | 3937 | % --- Executes on button press in TestCiv1: display image correlation function |
---|
[150] | 3938 | function TestCiv1_Callback(hObject, eventdata, handles) |
---|
[224] | 3939 | %------------------------------------------------------------------------ |
---|
[233] | 3940 | set(handles.TestCiv1,'BackgroundColor',[1 1 0]) |
---|
| 3941 | drawnow |
---|
[309] | 3942 | if get(handles.TestCiv1,'Value') |
---|
[227] | 3943 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 3944 | if strcmp(get(handles.ref_j,'Visible'),'on') |
---|
| 3945 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
| 3946 | else |
---|
| 3947 | ref_j=1;%default |
---|
| 3948 | end |
---|
[315] | 3949 | [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=... |
---|
[273] | 3950 | set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]); |
---|
[224] | 3951 | Data.ListVarName={'ny','nx','A'}; |
---|
[315] | 3952 | Data.VarDimName= {'ny','nx',{'ny','nx'}}; |
---|
[224] | 3953 | Data.A=imread(filecell.ima1.civ1{1}); |
---|
| 3954 | Data.ny=[size(Data.A,1) 1]; |
---|
| 3955 | Data.nx=[1 size(Data.A,2)]; |
---|
[309] | 3956 | par_civ1=read_GUI(handles.Civ1); |
---|
[315] | 3957 | par_civ1.ImageWidth=size(Data.A,1); |
---|
| 3958 | par_civ1.ImageHeight=size(Data.A,2); |
---|
| 3959 | par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation |
---|
[246] | 3960 | Param.Civ1=par_civ1; |
---|
[315] | 3961 | Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV |
---|
[231] | 3962 | hview_field=view_field(Data); |
---|
| 3963 | set(0,'CurrentFigure',hview_field) |
---|
| 3964 | hhview_field=guihandles(hview_field); |
---|
| 3965 | set(hview_field,'CurrentAxes',hhview_field.axes3) |
---|
| 3966 | ViewData=get(hview_field,'UserData'); |
---|
| 3967 | ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field |
---|
[224] | 3968 | ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field |
---|
[315] | 3969 | ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory |
---|
| 3970 | ViewData.axes3.Y=Grid.Civ1_Y; |
---|
[231] | 3971 | set(hview_field,'UserData',ViewData) |
---|
[224] | 3972 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
| 3973 | if isempty(corrfig) |
---|
| 3974 | corrfig=figure; |
---|
| 3975 | set(corrfig,'tag','corrfig') |
---|
| 3976 | set(corrfig,'name','image correlation') |
---|
| 3977 | set(corrfig,'DeleteFcn',{@closeview_field})% |
---|
| 3978 | end |
---|
[233] | 3979 | set(handles.TestCiv1,'BackgroundColor',[1 0 0]) |
---|
[224] | 3980 | else |
---|
| 3981 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
| 3982 | if ~isempty(corrfig) |
---|
| 3983 | delete(corrfig) |
---|
| 3984 | end |
---|
| 3985 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
| 3986 | if ~isempty(hview_field) |
---|
| 3987 | delete(hview_field) |
---|
| 3988 | end |
---|
[150] | 3989 | end |
---|
[71] | 3990 | |
---|
[150] | 3991 | |
---|
[252] | 3992 | %------------------------------------------------------------------------ |
---|
[315] | 3993 | % --- Executes on button press in CheckThreshold. |
---|
| 3994 | function CheckThreshold_Callback(hObject, eventdata, handles) |
---|
[252] | 3995 | %------------------------------------------------------------------------ |
---|
[315] | 3996 | huipanel=get(hObject,'parent'); |
---|
| 3997 | obj(1)=findobj(huipanel,'Tag','num_MinIma'); |
---|
| 3998 | obj(2)=findobj(huipanel,'Tag','num_MaxIma'); |
---|
| 3999 | obj(3)=findobj(huipanel,'Tag','title_Threshold'); |
---|
| 4000 | if get(hObject,'Value') |
---|
| 4001 | set(obj,'Visible','on') |
---|
| 4002 | else |
---|
| 4003 | set(obj,'Visible','off') |
---|
| 4004 | end |
---|
[220] | 4005 | |
---|
[315] | 4006 | |
---|
[252] | 4007 | %------------------------------------------------------------------------ |
---|
[282] | 4008 | % % --- Executes on button press in ListPairMode. |
---|
[273] | 4009 | % function CivMode_Callback(hObject, eventdata, handles) |
---|
| 4010 | % %------------------------------------------------------------------------ |
---|
[282] | 4011 | % Listprog=get(handles.ListPairMode,'String'); |
---|
| 4012 | % index=get(handles.ListPairMode,'Value'); |
---|
[273] | 4013 | % prog=Listprog{index}; |
---|
| 4014 | % switch prog |
---|
[309] | 4015 | % case 'MenuCivX' |
---|
[273] | 4016 | % set(handles.thresh_patch1,'Visible','off') |
---|
| 4017 | % set(handles.thresh_text1,'Visible','off') |
---|
[274] | 4018 | % set(handles.num_MaxDiff,'Visible','off') |
---|
[316] | 4019 | % set(handles.title_MaxDiff,'Visible','off') |
---|
[282] | 4020 | % set(handles.num_Rho,'Style','edit') |
---|
| 4021 | % set(handles.num_Rho,'String','1') |
---|
[273] | 4022 | % set(handles.BATCH,'Enable','on') |
---|
| 4023 | % case 'CivAll' |
---|
[282] | 4024 | % if get(handles.CheckPatch1,'Value') |
---|
[273] | 4025 | % set(handles.thresh_patch1,'Visible','on') |
---|
| 4026 | % set(handles.thresh_text1,'Visible','on') |
---|
| 4027 | % end |
---|
[282] | 4028 | % set(handles.num_Rho,'Style','edit') |
---|
| 4029 | % set(handles.num_Rho,'String','1') |
---|
[273] | 4030 | % set(handles.BATCH,'Enable','on') |
---|
| 4031 | % case 'CivUvmat' |
---|
| 4032 | % |
---|
| 4033 | % end |
---|
| 4034 | |
---|
[309] | 4035 | %------------------------------------------------------------------------ |
---|
[284] | 4036 | function cmd=cmd_civ1(filename,Param) |
---|
| 4037 | %------------------------------------------------------------------------ |
---|
| 4038 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
| 4039 | %changes : filename_cmx -> filename ( no extension ) |
---|
[309] | 4040 | filename=regexprep(filename,'.nc',''); %file name for the result |
---|
[284] | 4041 | if isequal(Param.Civ1.Dt,'0') |
---|
| 4042 | Param.Civ1.Dt='1' ;%case of 'displacement' mode |
---|
| 4043 | end |
---|
[315] | 4044 | Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png',''); |
---|
| 4045 | Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png',''); |
---|
[284] | 4046 | fid=fopen([filename '.civ1.cmx'],'w'); |
---|
| 4047 | fprintf(fid,['############## CMX file' '\n' ]); |
---|
[315] | 4048 | fprintf(fid, ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
| 4049 | fprintf(fid, ['LastImage ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
[284] | 4050 | fprintf(fid, ['XX' '\n' ]); |
---|
[315] | 4051 | if isfield(Param.Civ1,'Mask') |
---|
| 4052 | fprintf(fid, ['Mask ' 'y' '\n' ]); |
---|
| 4053 | fprintf(fid, ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]); |
---|
| 4054 | else |
---|
| 4055 | fprintf(fid, ['Mask ' 'n' '\n' ]); |
---|
| 4056 | fprintf(fid, ['MaskName ' 'noFile use default' '\n' ]); |
---|
| 4057 | end |
---|
| 4058 | fprintf(fid, ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]); %VERIFIER CAS GENERAL ? |
---|
[284] | 4059 | fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ1.Bx) ' ' num2str(Param.Civ1.By) '\n' ]); |
---|
[287] | 4060 | fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ1.Searchx) ' ' num2str(Param.Civ1.Searchy) '\n' ]); |
---|
[284] | 4061 | fprintf(fid, ['RO ' num2str(Param.Civ1.Rho) '\n' ]); |
---|
[315] | 4062 | if isfield(Param.Civ1,'Grid') |
---|
[313] | 4063 | fprintf(fid, ['GridSpacing ' '25' ' ' '25' '\n' ]); |
---|
| 4064 | else |
---|
| 4065 | fprintf(fid, ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]); |
---|
| 4066 | end |
---|
[284] | 4067 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
[315] | 4068 | fprintf(fid, ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]); |
---|
| 4069 | fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]); |
---|
[284] | 4070 | fprintf(fid, ['XX 1' '\n' ]); |
---|
| 4071 | fprintf(fid, ['ShiftXY ' num2str(Param.Civ1.Shiftx) ' ' num2str(Param.Civ1.Shifty) '\n' ]); |
---|
[315] | 4072 | if isfield(Param.Civ1,'Grid') |
---|
[313] | 4073 | fprintf(fid, ['Grid ' 'y' '\n' ]); |
---|
[315] | 4074 | fprintf(fid, ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]); |
---|
[313] | 4075 | else |
---|
| 4076 | fprintf(fid, ['Grid ' 'n' '\n' ]); |
---|
| 4077 | fprintf(fid, ['GridName ' 'noFile use default' '\n' ]); |
---|
| 4078 | end |
---|
[284] | 4079 | fprintf(fid, ['XX 85' '\n' ]); |
---|
| 4080 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
| 4081 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
| 4082 | fprintf(fid, ['Hart 1' '\n' ]); |
---|
| 4083 | fprintf(fid, [ 'DecimalShift 0' '\n' ]); |
---|
| 4084 | fprintf(fid, ['Deformation 0' '\n' ]); |
---|
| 4085 | fprintf(fid, ['CorrelationMin 0' '\n' ]); |
---|
| 4086 | fprintf(fid, ['IntensityMin 0' '\n' ]); |
---|
[309] | 4087 | if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated |
---|
| 4088 | fprintf(fid, ['SeuilImage n' '\n' ]); |
---|
| 4089 | fprintf(fid, ['SeuilImageValues 0 4096' '\n' ]);%not used in principle |
---|
| 4090 | else% Image threshold activated |
---|
| 4091 | if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma) |
---|
[315] | 4092 | Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default |
---|
[309] | 4093 | end |
---|
| 4094 | fprintf(fid, ['SeuilImage y' '\n' ]); |
---|
| 4095 | fprintf(fid, ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]); |
---|
| 4096 | end |
---|
[284] | 4097 | fprintf(fid, ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ? |
---|
| 4098 | fprintf(fid, ['ImageUsedBefore null null' '\n' ]); |
---|
| 4099 | fclose(fid); |
---|
| 4100 | |
---|
[309] | 4101 | if(isunix) %unix (or Mac) system |
---|
[284] | 4102 | cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file |
---|
| 4103 | cmd=[cmd Param.xml.Civ1Bin ' -f ' filename '.cmx >' filename '.civ1.log \n ' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx |
---|
| 4104 | cmd=[cmd 'rm ' filename '.cmx']; |
---|
| 4105 | else %Windows system |
---|
| 4106 | filename=regexprep(filename,'\\','\\\\'); |
---|
| 4107 | cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n ']; |
---|
| 4108 | cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')... |
---|
| 4109 | '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file |
---|
[290] | 4110 | cmd=[cmd 'del "' filename '.cmx"']; |
---|
[284] | 4111 | end |
---|
[285] | 4112 | |
---|
| 4113 | |
---|
| 4114 | function cmd=cmd_fix(filename,Param,fixname) |
---|
| 4115 | %% |
---|
[291] | 4116 | switch fixname |
---|
| 4117 | case 'Fix1' |
---|
| 4118 | fi2_value=num2str(Param.(fixname).CheckF2); |
---|
| 4119 | case 'Fix2' |
---|
| 4120 | fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why... |
---|
| 4121 | end |
---|
[285] | 4122 | filename=regexprep(filename,'.nc',''); |
---|
[287] | 4123 | MaskName_string='';%default |
---|
[316] | 4124 | % if Param.(fixname).CheckMask |
---|
| 4125 | % MaskName_string=[' -maskName "' Param.(fixname).Mask '"']; |
---|
| 4126 | % end |
---|
[287] | 4127 | MaxVel_string='';%default |
---|
| 4128 | if ~isempty(Param.(fixname).MaxVel) |
---|
[289] | 4129 | MaxVel_string=[' -threshV ' num2str(Param.(fixname).MaxVel)]; |
---|
[287] | 4130 | end |
---|
[285] | 4131 | if isunix |
---|
[287] | 4132 | cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ... |
---|
[291] | 4133 | ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ... |
---|
[287] | 4134 | ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string... |
---|
| 4135 | ' >' filename '.' lower(fixname) '.log 2>&1']; |
---|
[285] | 4136 | else |
---|
| 4137 | cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)... |
---|
[291] | 4138 | ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ... |
---|
[288] | 4139 | ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string... |
---|
| 4140 | ' > "' filename '.' lower(fixname) '.log"']; |
---|
[285] | 4141 | cmd=regexprep(cmd,'\\','\\\\'); |
---|
| 4142 | end |
---|
[286] | 4143 | |
---|
| 4144 | |
---|
| 4145 | function cmd=cmd_patch(filename,Param,patchname) |
---|
| 4146 | %% ------------------------------------------------------------------------ |
---|
| 4147 | filename=regexprep(filename,'.nc',''); |
---|
| 4148 | if isunix |
---|
| 4149 | cmd=[Param.xml.PatchBin... |
---|
| 4150 | ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)... |
---|
[292] | 4151 | ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)... |
---|
[286] | 4152 | ' -nopt ' num2str(Param.(patchname).SubdomainSize) ... |
---|
| 4153 | ' > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file |
---|
| 4154 | else |
---|
| 4155 | cmd=['"' Param.xml.PatchBin... |
---|
| 4156 | '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)... |
---|
[292] | 4157 | ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)... |
---|
[286] | 4158 | ' -nopt ' num2str(Param.(patchname).SubdomainSize)... |
---|
| 4159 | ' > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file |
---|
| 4160 | cmd=regexprep(cmd,'\\','\\\\'); |
---|
| 4161 | end |
---|
[290] | 4162 | |
---|
| 4163 | %------------------------------------------------------------------------ |
---|
| 4164 | % --- CheckCiv2 CheckCiv2 CheckCiv2 CheckCiv2 |
---|
| 4165 | function cmd=cmd_civ2(filename,Param) |
---|
| 4166 | %------------------------------------------------------------------------ |
---|
| 4167 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
| 4168 | % global civ2Bin sge%name of the executable for checkciv1 calculation |
---|
| 4169 | filename=regexprep(filename,'.nc',''); |
---|
| 4170 | if isequal(Param.Civ2.Dt,'0') |
---|
| 4171 | Param.Civ2.Dt='1' ;%case of 'displacement' mode |
---|
| 4172 | end |
---|
[315] | 4173 | Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png',''); |
---|
| 4174 | Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ? |
---|
[290] | 4175 | [fid,errormsg]=fopen([filename '.civ2.cmx'],'w'); |
---|
| 4176 | if isequal(fid,-1) |
---|
| 4177 | msgbox_uvmat('ERROR',errormsg) |
---|
| 4178 | cmd=''; |
---|
| 4179 | return |
---|
| 4180 | end |
---|
| 4181 | fprintf(fid,['############## CMX file' '\n' ]); |
---|
[315] | 4182 | fprintf(fid, ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
| 4183 | fprintf(fid, ['LastImage ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
[290] | 4184 | fprintf(fid, ['XX' '\n' ]); |
---|
[315] | 4185 | if isfield(Param.Civ2,'Mask') |
---|
| 4186 | fprintf(fid, ['Mask ' 'y' '\n' ]); |
---|
| 4187 | fprintf(fid, ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]); |
---|
| 4188 | else |
---|
| 4189 | fprintf(fid, ['Mask ' 'n' '\n' ]); |
---|
| 4190 | fprintf(fid, ['MaskName ' 'noFile use default' '\n' ]); |
---|
| 4191 | end |
---|
| 4192 | % fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]); |
---|
| 4193 | % fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
| 4194 | fprintf(fid, ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); |
---|
[309] | 4195 | % fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]); %VERIFIER CAS GENERAL ? |
---|
[290] | 4196 | fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n' ]); |
---|
| 4197 | fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n']); |
---|
| 4198 | fprintf(fid, ['RO ' num2str(Param.Civ2.Rho) '\n']); |
---|
[315] | 4199 | if isfield(Param.Civ2,'Grid') |
---|
[313] | 4200 | fprintf(fid, ['GridSpacing ' '25' ' ' '25' '\n' ]); |
---|
| 4201 | else |
---|
| 4202 | fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]); |
---|
| 4203 | end |
---|
| 4204 | % fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']); |
---|
[290] | 4205 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
[315] | 4206 | fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]); |
---|
| 4207 | fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]); |
---|
[290] | 4208 | fprintf(fid, ['XX 1' '\n' ]); |
---|
| 4209 | fprintf(fid, 'ShiftXY 0 0\n'); |
---|
[315] | 4210 | if isfield(Param.Civ2,'Grid') |
---|
[313] | 4211 | fprintf(fid, ['Grid ' 'y' '\n' ]); |
---|
[315] | 4212 | fprintf(fid, ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]); |
---|
[313] | 4213 | else |
---|
| 4214 | fprintf(fid, ['Grid ' 'n' '\n' ]); |
---|
| 4215 | fprintf(fid, ['GridName ' 'noFile use default' '\n' ]); |
---|
| 4216 | end |
---|
| 4217 | % fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]); |
---|
| 4218 | % fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']); |
---|
[290] | 4219 | fprintf(fid, ['XX 85' '\n' ]); |
---|
| 4220 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
| 4221 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
| 4222 | fprintf(fid, ['Hart 1' '\n' ]); |
---|
| 4223 | fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']); |
---|
| 4224 | fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']); |
---|
| 4225 | fprintf(fid, ['CorrelationMin 0' '\n' ]); |
---|
| 4226 | fprintf(fid, ['IntensityMin 0' '\n' ]); |
---|
[309] | 4227 | |
---|
| 4228 | if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated |
---|
| 4229 | fprintf(fid, ['SeuilImage n' '\n' ]); |
---|
| 4230 | fprintf(fid, ['SeuilImageValues 0 4096' '\n' ]);%not used in principle |
---|
| 4231 | else% Image threshold activated |
---|
| 4232 | if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma) |
---|
[315] | 4233 | Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default |
---|
[309] | 4234 | end |
---|
| 4235 | fprintf(fid, ['SeuilImage y' '\n' ]); |
---|
| 4236 | fprintf(fid, ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]); |
---|
| 4237 | end |
---|
[290] | 4238 | fprintf(fid, ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ? |
---|
| 4239 | fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']); |
---|
| 4240 | fclose(fid); |
---|
| 4241 | |
---|
| 4242 | if(isunix) |
---|
| 4243 | cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'... |
---|
| 4244 | Param.xml.Civ2Bin ' -f ' filename '.cmx >' filename '.civ2.log \n '... % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx |
---|
| 4245 | 'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx |
---|
| 4246 | else |
---|
| 4247 | filename=regexprep(filename,'\\','\\\\'); |
---|
| 4248 | cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'... |
---|
| 4249 | '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename '.cmx" >"' filename '.civ2.log" \n'... |
---|
| 4250 | 'del "' filename '.cmx" \n']; |
---|
| 4251 | end |
---|
[309] | 4252 | |
---|
| 4253 | %------------------------------------------------------------------------ |
---|
| 4254 | % --- CheckCiv1 Unified: TO ABADON |
---|
| 4255 | function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par) |
---|
| 4256 | %------------------------------------------------------------------------ |
---|
| 4257 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
| 4258 | %global CivBin%name of the executable for checkciv1 calculation |
---|
| 4259 | |
---|
[315] | 4260 | civ1.image1=par.ImageA; |
---|
| 4261 | civ1.image2=par.ImageB; |
---|
[309] | 4262 | civ1.imageSize_X=par.npx; |
---|
| 4263 | civ1.imageSize_Y=par.npy; |
---|
| 4264 | civ1.outputFileName=[filename '.nc']; |
---|
| 4265 | civ1.correlationBoxesSize_X=par.ibx; |
---|
| 4266 | civ1.correlationBoxesSize_Y=par.iby; |
---|
| 4267 | civ1.searchBoxesSize_X=par.isx; |
---|
| 4268 | civ1.searchBoxesSize_Y=par.isy; |
---|
| 4269 | civ1.globalShift_X=par.shiftx; |
---|
| 4270 | civ1.globalShift_Y=par.shifty; |
---|
| 4271 | civ1.ro=par.rho; |
---|
| 4272 | civ1.hart='y'; |
---|
| 4273 | if isequal(par.gridflag,'y') |
---|
| 4274 | civ1.grid=par.gridname; |
---|
| 4275 | else |
---|
| 4276 | civ1.grid='n'; |
---|
| 4277 | civ1.gridSpacing_X=par.dx; |
---|
| 4278 | civ1.gridSpacing_Y=par.dy; |
---|
| 4279 | end |
---|
| 4280 | if isequal(par.maskflag,'y') |
---|
| 4281 | civ1.mask=par.maskname; |
---|
| 4282 | end |
---|
| 4283 | civ1.dt=par.Dt; |
---|
| 4284 | civ1.unit='pixel'; |
---|
[315] | 4285 | civ1.absolut_time_T0=par.Time; |
---|
| 4286 | civ1.pixcmx='1'; |
---|
| 4287 | civ1.pixcmy='1'; |
---|
[309] | 4288 | civ1.convectFlow='n'; |
---|
| 4289 | |
---|
| 4290 | xml_civ1_parameters=civ1; |
---|
| 4291 | |
---|
| 4292 | %------------------------------------------------------------------------ |
---|
| 4293 | % --- CheckCiv2 Unified: TO ABADON |
---|
| 4294 | function civ2=CIV2_CMD_Unified(filename,namelog,par) |
---|
| 4295 | %------------------------------------------------------------------------ |
---|
| 4296 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
| 4297 | %global CivBin%name of the executable for checkciv1 calculation |
---|
| 4298 | |
---|
| 4299 | filename=regexprep(filename,'.nc',''); |
---|
| 4300 | |
---|
[315] | 4301 | civ2.image1=par.ImageA; |
---|
| 4302 | civ2.image2=par.ImageB; |
---|
[309] | 4303 | civ2.imageSize_X=par.npx; |
---|
| 4304 | civ2.imageSize_Y=par.npy; |
---|
| 4305 | civ2.inputFileName=[par.filename_nc1 '.nc']; |
---|
| 4306 | civ2.outputFileName=[filename '.nc']; |
---|
| 4307 | civ2.correlationBoxesSize_X=par.ibx; |
---|
| 4308 | civ2.correlationBoxesSize_Y=par.iby; |
---|
| 4309 | civ2.ro=par.rho; |
---|
| 4310 | %checkciv2.decimalShift=par.CheckDecimal; |
---|
| 4311 | %checkciv2.CheckDeformation=par.CheckDeformation; |
---|
| 4312 | if isequal(par.decimal,'1') |
---|
| 4313 | civ2.decimalShift='y'; |
---|
| 4314 | else |
---|
| 4315 | civ2.decimalShift='n'; |
---|
| 4316 | end |
---|
| 4317 | if isequal(par.deformation,'1') |
---|
| 4318 | civ2.deformation='y'; |
---|
| 4319 | else |
---|
| 4320 | civ2.deformation='n'; |
---|
| 4321 | end |
---|
| 4322 | if isequal(par.gridflag,'y') |
---|
| 4323 | civ2.grid=par.gridname; |
---|
| 4324 | else |
---|
| 4325 | civ2.grid='n'; |
---|
| 4326 | civ2.gridSpacing_X=par.dx; |
---|
| 4327 | civ2.gridSpacing_Y=par.dy; |
---|
| 4328 | end |
---|
| 4329 | civ2.gridSpacing_X='10'; |
---|
| 4330 | civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee |
---|
| 4331 | if isequal(par.maskflag,'y') |
---|
| 4332 | civ2.mask=par.maskname; |
---|
| 4333 | else |
---|
| 4334 | civ2.mask='n'; |
---|
| 4335 | end |
---|
| 4336 | civ2.dt=par.Dt; |
---|
| 4337 | civ2.unit='pixel'; |
---|
[315] | 4338 | civ2.absolut_time_T0=par.Time; |
---|
| 4339 | civ2.pixcmx='1'; |
---|
| 4340 | civ2.pixcmy='1'; |
---|
[309] | 4341 | civ2.convectFlow='n'; |
---|
[317] | 4342 | |
---|
| 4343 | |
---|
| 4344 | % --- Executes on button press in TestPatch1. |
---|
| 4345 | function TestPatch1_Callback(hObject, eventdata, handles) |
---|
| 4346 | set(handles.TestPatch1,'BackgroundColor',[1 1 0]) |
---|
| 4347 | drawnow |
---|
| 4348 | if get(handles.TestPatch1,'Value') |
---|
| 4349 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 4350 | if strcmp(get(handles.ref_j,'Visible'),'on') |
---|
| 4351 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
| 4352 | else |
---|
| 4353 | ref_j=1;%default |
---|
| 4354 | end |
---|
| 4355 | [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=... |
---|
| 4356 | set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]); |
---|
| 4357 | |
---|
| 4358 | Data.ListVarName={'ny','nx','A'}; |
---|
| 4359 | Data.VarDimName= {'ny','nx',{'ny','nx'}}; |
---|
| 4360 | |
---|
| 4361 | Param=read_GUI(handles.civ) |
---|
| 4362 | Param.CheckOutputFile=0; |
---|
| 4363 | [Data,errormsg]=civ_matlab(Param,filecell.nc.civ1{1})% get the grid of x, y positions set for PIV |
---|
| 4364 | if ~isempty(errormsg) |
---|
| 4365 | msgbox_uvmat('ERROR',Data.Txt) |
---|
| 4366 | return |
---|
| 4367 | end |
---|
| 4368 | set(handles.TestCiv1,'BackgroundColor',[1 0 0]) |
---|
| 4369 | else |
---|
| 4370 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
| 4371 | if ~isempty(corrfig) |
---|
| 4372 | delete(corrfig) |
---|
| 4373 | end |
---|
| 4374 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
| 4375 | if ~isempty(hview_field) |
---|
| 4376 | delete(hview_field) |
---|
| 4377 | end |
---|
| 4378 | end |
---|
| 4379 | |
---|