[597] | 1 | |
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| 2 | %'civ_input': function associated with the interface 'civ_input.fig' for PIV, spline interpolation and stereo PIV (patch) |
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| 3 | %------------------------------------------------------------------------ |
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| 4 | % provides an interface for the software menucivx |
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| 5 | % function varargout = civ_input(varargin) |
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| 6 | % provides an interface for the software menucivx |
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| 7 | % |
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| 8 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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| 9 | % Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr |
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| 10 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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| 11 | % This file is part of the toolbox UVMAT. |
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| 12 | % |
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| 13 | % UVMAT is free software; you can redistribute it and/or modify |
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| 14 | % it under the terms of the GNU General Public License as published by |
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| 15 | % the Free Software Foundation; either version 2 of the License, or |
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| 16 | % (at your option) any later version. |
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| 17 | % |
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| 18 | % UVMAT is distributed in the hope that it will be useful, |
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| 19 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 20 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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| 21 | % GNU General Public License (file UVMAT/COPYING.txt) for more details. |
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| 22 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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| 23 | function varargout = civ_input(varargin) |
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| 24 | %TODO: search range |
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| 25 | |
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| 26 | |
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[598] | 27 | % Last Modified by GUIDE v2.5 01-Apr-2013 10:00:57 |
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[597] | 28 | % Begin initialization code - DO NOT EDIT |
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| 29 | gui_Singleton = 1; |
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| 30 | gui_State = struct('gui_Name', mfilename, ... |
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| 31 | 'gui_Singleton', gui_Singleton, ... |
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| 32 | 'gui_OpeningFcn', @civ_input_OpeningFcn, ... |
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| 33 | 'gui_OutputFcn', @civ_input_OutputFcn, ... |
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| 34 | 'gui_LayoutFcn', [] , ... |
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| 35 | 'gui_Callback', []); |
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| 36 | |
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[598] | 37 | if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback$','once')) |
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[597] | 38 | gui_State.gui_Callback = str2func(varargin{1}); |
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| 39 | end |
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| 40 | |
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| 41 | if nargout |
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| 42 | [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); |
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| 43 | else |
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| 44 | gui_mainfcn(gui_State, varargin{:}); |
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| 45 | end |
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| 46 | |
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| 47 | % End initialization code - DO NOT EDIT |
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| 48 | |
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| 49 | %------------------------------------------------------------------------ |
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| 50 | % --- Executes just before civ_input is made visible. |
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| 51 | function civ_input_OpeningFcn(hObject, eventdata, handles, Param) |
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| 52 | %------------------------------------------------------------------------ |
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| 53 | % This function has no output args, see OutputFcn. |
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| 54 | |
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| 55 | %% General settings |
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| 56 | handles.output = Param; |
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| 57 | guidata(hObject, handles); % Update handles structure |
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| 58 | set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display) |
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| 59 | |
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[598] | 60 | %% set visibility options |
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| 61 | set(handles.num_MaxDiff,'Visible','on') |
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| 62 | set(handles.num_MaxVel,'Visible','on') |
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| 63 | set(handles.title_MaxVel,'Visible','on') |
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| 64 | set(handles.title_MaxDiff,'Visible','on') |
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| 65 | set(handles.num_Nx,'Visible','off') |
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| 66 | set(handles.num_Ny,'Visible','off') |
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| 67 | set(handles.title_Nx,'Visible','off') |
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| 68 | set(handles.title_Ny,'Visible','off') |
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| 69 | set(handles.num_CorrSmooth,'Style','popupmenu') |
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| 70 | set(handles.num_CorrSmooth,'Value',1) |
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| 71 | set(handles.num_CorrSmooth,'String',{'1';'2'}) |
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| 72 | set(handles.CheckThreshold,'Visible','on') |
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| 73 | set(handles.CheckDeformation,'Value',0)% desactivate (work in progress) |
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| 74 | set(handles.CheckDecimal,'Value',0)% desactivate (work in progress) |
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| 75 | |
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| 76 | %% prepare the GUI with input parameters |
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| 77 | % from the GUI series |
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| 78 | |
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| 79 | %from the input file |
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| 80 | filecell=get_file_series(Param); |
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| 81 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
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| 82 | errormsg=display_file_name(handles,filecell{1}); |
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| 83 | if ~isempty(errormsg) |
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| 84 | msgbox_uvmat('ERROR',errormsg) |
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[597] | 85 | end |
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[598] | 86 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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| 87 | if isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'Program')&& strcmp(Param.ActionInput.Program,'civ_series') |
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| 88 | fill_GUI(Param.ActionInput,handles.civ_input) |
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[597] | 89 | end |
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[598] | 90 | set(handles.civ_input,'WindowStyle','modal')% Make the GUI modal |
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[597] | 91 | drawnow |
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[598] | 92 | uiwait(handles.civ_input); |
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[597] | 93 | |
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| 94 | %Program_Callback([],[], handles) |
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| 95 | |
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| 96 | %------------------------------------------------------------------------ |
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| 97 | % --- Outputs from this function are returned to the command line. |
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| 98 | function varargout = civ_input_OutputFcn(hObject, eventdata, handles) |
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| 99 | %------------------------------------------------------------------------ |
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| 100 | % Get default command line output from handles structure |
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| 101 | varargout{1} = handles.output; |
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[598] | 102 | delete(handles.civ_input) |
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[597] | 103 | |
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| 104 | % --- Executes when user attempts to close get_field. |
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[598] | 105 | function civ_input_CloseRequestFcn(hObject, eventdata, handles) |
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[597] | 106 | if isequal(get(handles.get_field, 'waitstatus'), 'waiting') |
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| 107 | % The GUI is still in UIWAIT, us UIRESUME |
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[598] | 108 | uiresume(handles.civ_input); |
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[597] | 109 | else |
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| 110 | % The GUI is no longer waiting, just close it |
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[598] | 111 | delete(handles.civ_input); |
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[597] | 112 | end |
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| 113 | %------------------------------------------------------------------------ |
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| 114 | % --- Function activated by the Open/Browse... option in the upper menu bar. |
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| 115 | function MenuBrowse_Callback(hObject, eventdata, handles) |
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| 116 | %------------------------------------------------------------------------ |
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| 117 | %% get the current input root file name to initiate the browser |
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| 118 | filebase=get(handles.RootPath,'String'); |
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| 119 | oldfile=''; %default |
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| 120 | if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name |
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| 121 | dir_perso=prefdir; |
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| 122 | profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); |
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| 123 | if exist(profil_perso,'file') |
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| 124 | h=load (profil_perso); |
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| 125 | if isfield(h,'filebase')&& ischar(h.filebase) |
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| 126 | oldfile=h.filebase; |
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| 127 | end |
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| 128 | if isfield(h,'RootPath') && ischar(h.RootPath) |
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| 129 | oldfile=h.RootPath; |
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| 130 | end |
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| 131 | end |
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| 132 | else |
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| 133 | oldfile=filebase; |
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| 134 | end |
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| 135 | |
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| 136 | %% get the new input file with the browser |
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| 137 | menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)'; |
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| 138 | '*.xml', '.xml files '; ... |
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| 139 | '*.civ', '.civ files '; ... |
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| 140 | '*.png','.png image files'; ... |
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| 141 | '*.jpg',' jpeg image files'; ... |
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| 142 | '*.tif','.tif image files'; ... |
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| 143 | '*.avi;*.AVI','.avi movie files'; ... |
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| 144 | '*.nc','.netcdf files'; ... |
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| 145 | '*.*', 'All Files (*.*)'}; |
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| 146 | [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile); |
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| 147 | fileinput=[PathName FileName];%complete file name |
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| 148 | sizf=size(fileinput); |
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| 149 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
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| 150 | |
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| 151 | %% case of the xml file opened as input (TODO: check and see whether it is useful) |
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| 152 | [path,name,ext]=fileparts(fileinput); |
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| 153 | testeditxml=0; |
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| 154 | % if isequal(ext,'.xml') |
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| 155 | % testeditxml=1; |
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| 156 | % t_browse=xmltree(fileinput); |
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| 157 | % head_element=get(t_browse,1); |
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| 158 | % if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc') |
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| 159 | % testeditxml=0; |
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| 160 | % end |
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| 161 | % end |
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| 162 | % if testeditxml==1 || isequal(ext,'.xls') |
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| 163 | % heditxml=editxml({fileinput}); |
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| 164 | % set(heditxml,'Tag','browser') |
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| 165 | % waitfor(heditxml,'Tag','idle') |
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| 166 | % if ~ishandle(heditxml) |
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| 167 | % return |
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| 168 | % end |
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| 169 | % attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes'); |
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| 170 | % set(handles.browse,'UserData',fileinput)% store for future opening with browser |
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| 171 | % fileinput=get(attr,'UserData'); |
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| 172 | % if ~exist(fileinput,'file') |
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| 173 | % return |
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| 174 | % end |
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| 175 | % end |
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| 176 | [tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput); |
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| 177 | |
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| 178 | %% prepare the GUI with parameters from the input file |
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| 179 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
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| 180 | errormsg=display_file_name(handles,fileinput); |
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| 181 | if ~isempty(errormsg) |
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| 182 | msgbox_uvmat('ERROR',erromsg) |
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| 183 | end |
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| 184 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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| 185 | |
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| 186 | %------------------------------------------------------------------------ |
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| 187 | % --- Open again the file whose name has been recorded in MenuFile_1 |
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| 188 | function MenuFile_1_Callback(hObject, eventdata, handles) |
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| 189 | %------------------------------------------------------------------------ |
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| 190 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
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| 191 | fileinput=get(handles.MenuFile_1,'Label'); |
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| 192 | errormsg=display_file_name(handles,fileinput); |
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| 193 | if ~isempty(errormsg) |
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| 194 | msgbox_uvmat('ERROR',errormsg) |
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| 195 | end |
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| 196 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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| 197 | |
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| 198 | % ----------------------------------------------------------------------- |
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| 199 | % --- Open again the file whose name has been recorded in MenuFile_2 |
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| 200 | function MenuFile_2_Callback(hObject, eventdata, handles) |
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| 201 | %------------------------------------------------------------------------ |
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| 202 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
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| 203 | fileinput=get(handles.MenuFile_2,'Label'); |
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| 204 | errormsg=display_file_name(handles,fileinput); |
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| 205 | if ~isempty(errormsg) |
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| 206 | msgbox_uvmat('ERROR',errormsg) |
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| 207 | end |
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| 208 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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| 209 | |
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| 210 | % ----------------------------------------------------------------------- |
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| 211 | % --- Open again the file whose name has been recorded in MenuFile_3 |
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| 212 | function MenuFile_3_Callback(hObject, eventdata, handles) |
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| 213 | %------------------------------------------------------------------------ |
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| 214 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
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| 215 | fileinput=get(handles.MenuFile_3,'Label'); |
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| 216 | errormsg=display_file_name(handles,fileinput); |
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| 217 | if ~isempty(errormsg) |
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| 218 | msgbox_uvmat('ERROR',errormsg) |
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| 219 | end |
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| 220 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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| 221 | |
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| 222 | % ----------------------------------------------------------------------- |
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| 223 | % --- Open again the file whose name has been recorded in MenuFile_4 |
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| 224 | function MenuFile_4_Callback(hObject, eventdata, handles) |
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| 225 | %------------------------------------------------------------------------ |
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| 226 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
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| 227 | fileinput=get(handles.MenuFile_4,'Label'); |
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| 228 | errormsg=display_file_name(handles,fileinput); |
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| 229 | if ~isempty(errormsg) |
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| 230 | msgbox_uvmat('ERROR',errormsg) |
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| 231 | end |
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| 232 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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| 233 | |
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| 234 | % ----------------------------------------------------------------------- |
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| 235 | % --- Open again the file whose name has been recorded in MenuFile_5 |
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| 236 | function MenuFile_5_Callback(hObject, eventdata, handles) |
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| 237 | %------------------------------------------------------------------------ |
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| 238 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
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| 239 | fileinput=get(handles.MenuFile_5,'Label'); |
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| 240 | errormsg=display_file_name(handles,fileinput); |
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| 241 | if ~isempty(errormsg) |
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| 242 | msgbox_uvmat('ERROR',errormsg) |
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| 243 | end |
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| 244 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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| 245 | |
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| 246 | % ----------------------------------------------------------------------- |
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| 247 | % ----------------------------------------------------------------------- |
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| 248 | % --- Open the help html file |
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| 249 | function MenuHelp_Callback(hObject, eventdata, handles) |
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| 250 | % ----------------------------------------------------------------------- |
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| 251 | path_civ=fileparts(which ('civ')); |
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| 252 | helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html'); |
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| 253 | if isempty(dir(helpfile)) |
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| 254 | 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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| 255 | else |
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| 256 | addpath (fullfile(path_civ,'uvmat_doc')) |
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| 257 | web([helpfile '#civ']) |
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| 258 | end |
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| 259 | |
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| 260 | %------------------------------------------------------------------------ |
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| 261 | % --- Function activated when a new filebase (image series) is introduced |
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| 262 | function RootPath_Callback(hObject, eventdata, handles) |
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| 263 | %------------------------------------------------------------------------ |
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| 264 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
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| 265 | RootPath=get(handles.RootPath,'String'); |
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| 266 | SubDirImages=get(handles.SubDirImages,'String'); |
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| 267 | RootFile=get(handles.RootFile,'String'); |
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| 268 | ref_i=str2num(get(handles.ref_i,'String')); |
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| 269 | ref_j=str2num(get(handles.ref_j,'String')); |
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| 270 | NomType=get(handles.NomType,'String'); |
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| 271 | ImaExt=get(handles.ImaExt,'String'); |
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| 272 | fileinput=fullfile_uvmat(RootPath,SubDirImages,RootFile,ImaExt,NomType,ref_i,[],ref_j); |
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| 273 | errormsg=display_file_name(handles,fileinput); |
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| 274 | if ~isempty(errormsg) |
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| 275 | msgbox_uvmat('ERROR',errormsg) |
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| 276 | end |
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| 277 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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| 278 | |
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| 279 | %------------------------------------------------------------------------ |
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| 280 | % --- general function activated for an input file series |
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| 281 | function errormsg=display_file_name(handles,fileinput) |
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| 282 | %------------------------------------------------------------------------ |
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| 283 | set(handles.ListCompareMode,'Visible','on') |
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| 284 | errormsg='';%default empty error message |
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| 285 | drawnow |
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| 286 | |
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| 287 | %% enable OK, BATCH button and 'status' display |
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[598] | 288 | % set(handles.OK, 'Enable','On') |
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| 289 | % set(handles.OK,'BackgroundColor',[1 0 0])%set RUN button to red color |
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| 290 | % if isfield(handles,'status') |
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| 291 | % set(handles.status,'Value',0); %suppress the 'status' display |
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| 292 | % status_Callback([], [], handles) |
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| 293 | % end |
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[597] | 294 | |
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| 295 | %% determine nomenclature types and extension of the input files |
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| 296 | [RootPath,SubDir,RootFile,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput); |
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| 297 | NomTypeNc='';%default |
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| 298 | |
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| 299 | %% case of xml file as input, read the civ_input parameters |
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| 300 | ind_opening=0;%default |
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| 301 | if strcmp(ExtInput,'.xml') |
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| 302 | %reinitialise menus |
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| 303 | set(handles.ListPairMode,'Value',1) |
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| 304 | set(handles.ListPairMode,'String',{''}) |
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| 305 | set(handles.ListPairCiv1,'Value',1) |
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| 306 | set(handles.ListPairCiv1,'String',{''}) |
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| 307 | set(handles.ListPairCiv2,'Value',1) |
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| 308 | set(handles.ListPairCiv2,'String',{''}) |
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| 309 | Param=xml2struct(fileinput); %read parameters from the xml input file |
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| 310 | fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file |
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| 311 | return |
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| 312 | end |
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| 313 | |
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| 314 | %% case of netcdf file as input, get the civ_input processing stage and look for a coresponding image |
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| 315 | imageinput=fileinput;%default |
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| 316 | if strcmp(ExtInput,'.nc') |
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| 317 | NomTypeNc=NomTypeInput; |
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| 318 | if isempty(regexp(NomTypeInput,'[ab|AB|-]', 'once')) |
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| 319 | set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs |
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| 320 | set(handles.RootFile_1,'Visible','On'); |
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| 321 | else |
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| 322 | set(handles.ListCompareMode,'Value',1) |
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| 323 | set(handles.RootFile_1,'Visible','Off'); |
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| 324 | end |
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| 325 | imageinput=''; |
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| 326 | Data=nc2struct(fileinput,'ListGlobalAttribute','Conventions','absolut_time_T0','CivStage','Civ2_ImageA','Civ1_ImageA','Civ2_ImageB','Civ1_ImageB','fix','patch','civ2','fix2'); |
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| 327 | if isfield(Data,'Txt') |
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| 328 | errormsg=Data.Txt; |
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| 329 | return |
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| 330 | end |
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| 331 | % settings for new civ_input data, |
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| 332 | if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data, |
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| 333 | set(handles.Program,'Value',1) %select civ/Matlab by default |
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| 334 | Program_Callback([],[], handles) |
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| 335 | if ~isempty(Data.CivStage)%test for civ files |
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| 336 | ind_opening=Data.CivStage; |
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| 337 | end |
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| 338 | if ~isempty(Data.Civ2_ImageB)%get the corresponding input image in the netcdf file |
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| 339 | imageinput=Data.Civ2_ImageB; |
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| 340 | [tild,ImaName,ImaExt]=fileparts(Data.Civ2_ImageA); |
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| 341 | set(handles.RootFile_1,'String',[ImaName ImaExt]) |
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| 342 | elseif ~isempty(Data.Civ1_ImageB) |
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| 343 | imageinput=Data.Civ1_ImageB; |
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| 344 | [tild,ImaName,ImaExt]=fileparts(Data.Civ1_ImageA); |
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| 345 | set(handles.RootFile_1,'String',[ImaName ImaExt]) |
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| 346 | end |
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| 347 | % settings for civx data, |
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| 348 | elseif ~isempty(Data.absolut_time_T0')% case of civx data, |
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| 349 | set(handles.Program,'Value',3) %select Cix by default |
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| 350 | Program_Callback([],[], handles) |
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| 351 | if ~isempty(Data.fix2) |
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| 352 | ind_opening=5; |
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| 353 | elseif ~isempty(Data.civ2) |
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| 354 | ind_opening=4; |
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| 355 | elseif ~isempty(Data.patch) |
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| 356 | ind_opening=3; |
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| 357 | elseif ~isempty(Data.fix) |
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| 358 | ind_opening=2; |
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| 359 | end |
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| 360 | else |
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| 361 | errormsg='the input netcdf file is not civ data'; |
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| 362 | return |
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| 363 | end |
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| 364 | % look for the corresponding input images |
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| 365 | check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$','once'));%detect pair label by letter |
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| 366 | NomTypeIma=NomTypeInput; |
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| 367 | if check_letter |
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| 368 | NomTypeIma=NomTypeInput(1:end-1); |
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| 369 | else |
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| 370 | r=regexp(NomTypeIma,'.-(?<num2>\d+)$','names'); |
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| 371 | if ~isempty(r) |
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| 372 | NomTypeIma=regexprep(NomTypeIma,['-' r.num2],''); |
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| 373 | end |
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| 374 | r=regexp(NomTypeIma,'.-(?<num2>\d+)','names'); |
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| 375 | if ~isempty(r) |
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| 376 | NomTypeIma=regexprep(NomTypeIma,['-' r.num2],''); |
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| 377 | end |
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| 378 | end |
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| 379 | if ~exist(imageinput,'file') |
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| 380 | imageinput=fullfile_uvmat(RootPath,regexprep(SubDir,'.civ(_?)(\d*)$',''),RootFile,'.png',NomTypeIma,i1,[],j1); |
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| 381 | end |
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| 382 | end |
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| 383 | |
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| 384 | %% no corresponding image found, select manually with the browser |
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| 385 | ImaExt=ExtInput; |
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| 386 | if ~isempty(NomTypeNc) |
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| 387 | %no corresponding image found, select manually with the browser |
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| 388 | if ~exist(imageinput,'file') |
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| 389 | menu={'*.png;*.jpg;*.tif;*.avi;*.AVI', '(*.png,*.jpg ,*.tif, *.avi,*.AVI)'; |
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| 390 | '*.png','.png image files'; ... |
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| 391 | '*.jpg',' jpeg image files'; ... |
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| 392 | '*.tif','.tif image files'; ... |
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| 393 | '*.avi;*.AVI','.avi movie files'; ... |
---|
| 394 | '*.*', 'All Files (*.*)'}; |
---|
| 395 | [FileName, PathName] = uigetfile( menu, 'Pick an input image file',fileparts(fileparts(fileinput))); |
---|
| 396 | imageinput=[PathName FileName];%complete file name |
---|
| 397 | if ~exist(imageinput,'file') |
---|
| 398 | return %abandon of the browser is cancelled |
---|
| 399 | end |
---|
| 400 | end |
---|
| 401 | %fileinput=imageinput; |
---|
| 402 | end |
---|
| 403 | |
---|
| 404 | %% scan the image file series |
---|
| 405 | [FilePath,FileName,ImaExt]=fileparts(imageinput); |
---|
| 406 | % detect the file type, get the movie object if relevant, and look for the corresponding file series: |
---|
| 407 | % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists |
---|
| 408 | [RootPath,SubDirImages,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,MovieObject]=find_file_series(FilePath,[FileName ImaExt]); |
---|
| 409 | switch FileType |
---|
| 410 | case {'image','multimage','video','mmreader'} |
---|
| 411 | otherwise |
---|
| 412 | errormsg='invalid input file: enter an image, a movie or civ .nc file'; |
---|
| 413 | return |
---|
| 414 | end |
---|
| 415 | set(handles.RootPath,'String',RootPath) |
---|
| 416 | set(handles.SubDirImages,'String',SubDirImages) |
---|
| 417 | set(handles.RootFile,'String',RootFile) |
---|
| 418 | if strcmp(ExtInput,'.nc') |
---|
| 419 | SubDirCiv=regexprep(SubDir,['^' SubDirImages],'');%suppress the root SuddirImages; |
---|
| 420 | else |
---|
| 421 | SubDirCiv= '.civ'; |
---|
| 422 | end |
---|
| 423 | set(handles.SubdirCiv1,'String',SubDirCiv) |
---|
| 424 | set(handles.SubdirCiv2,'String',SubDirCiv) |
---|
| 425 | browse=get(handles.RootPath,'UserData'); |
---|
| 426 | browse.incr_pair=[0 0];%default |
---|
| 427 | |
---|
| 428 | %% scan the images if a civ_input file has been opened |
---|
| 429 | MinIndex_i=min(i1_series(i1_series>0)); |
---|
| 430 | MinIndex_j=min(j1_series(j1_series>0)); |
---|
| 431 | MaxIndex_i=max(i1_series(i1_series>0)); |
---|
| 432 | MaxIndex_j=max(j1_series(j1_series>0)); |
---|
| 433 | |
---|
| 434 | %% look for an image documentation file |
---|
| 435 | XmlFileName=find_imadoc(RootPath,SubDir,RootFile,ImaExt); |
---|
| 436 | if isempty(XmlFileName) |
---|
| 437 | if (strcmp(FileType,'video') || strcmp(FileType,'mmreader')) |
---|
| 438 | ext_imadoc=ImaExt;% the timing from the video movie is used |
---|
| 439 | else |
---|
| 440 | ext_imadoc=''; |
---|
| 441 | end |
---|
| 442 | else |
---|
| 443 | [tild,tild,ext_imadoc]=fileparts(XmlFileName); |
---|
| 444 | end |
---|
| 445 | set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used |
---|
| 446 | |
---|
| 447 | %% read the time in the image documentation file |
---|
| 448 | time=[]; |
---|
| 449 | TimeUnit=''; %default |
---|
| 450 | CoordUnit='';%default |
---|
| 451 | pxcm_search=1; |
---|
| 452 | if ~isempty(XmlFileName) |
---|
| 453 | set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning |
---|
| 454 | drawnow |
---|
| 455 | [XmlData,warntext]=imadoc2struct(XmlFileName); |
---|
| 456 | nom_type_read=[]; |
---|
| 457 | if isfield(XmlData,'Time') && ~isempty(XmlData.Time) |
---|
| 458 | time=XmlData.Time; |
---|
| 459 | %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml |
---|
| 460 | if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector |
---|
| 461 | if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once')) |
---|
| 462 | time=time'; |
---|
| 463 | MaxIndex_i=MaxIndex_j; |
---|
| 464 | MaxIndex_j=1; |
---|
| 465 | end |
---|
| 466 | end |
---|
| 467 | end |
---|
| 468 | if isfield(XmlData,'Camera') && isfield(XmlData.Camera,'TimeUnit') |
---|
| 469 | TimeUnit=XmlData.Camera.TimeUnit; |
---|
| 470 | end |
---|
| 471 | if isfield(XmlData,'GeometryCalib') |
---|
| 472 | tsai=XmlData.GeometryCalib; |
---|
| 473 | if isfield(tsai,'fx_fy') |
---|
| 474 | pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range |
---|
| 475 | end |
---|
| 476 | if isfield(tsai,'CoordUnit') |
---|
| 477 | CoordUnit=tsai.CoordUnit; |
---|
| 478 | end |
---|
| 479 | end |
---|
| 480 | end |
---|
| 481 | if isempty(time) && (strcmp(FileType,'video') || strcmp(FileType,'mmreader')) |
---|
| 482 | set(handles.ListPairMode,'Value',1); |
---|
| 483 | dt=1/get(MovieObject,'FrameRate');%time interval between successive frames |
---|
| 484 | if strcmp(NomTypeIma,'*') |
---|
| 485 | set(handles.ListPairMode,'String',{'series(Di)'}) |
---|
| 486 | MaxIndex_i=get(MovieObject,'NumberOfFrames'); |
---|
| 487 | time=(dt*(0:MaxIndex_i-1))';%list of image times |
---|
| 488 | else |
---|
| 489 | set(handles.ListPairMode,'String',[{'series(Dj)'};{'series(Di)'}]) |
---|
| 490 | MaxIndex_i=max(i1_series(i1_series>0)); |
---|
| 491 | MaxIndex_j=get(MovieObject,'NumberOfFrames'); |
---|
| 492 | time=ones(MaxIndex_i,1)*(dt*(0:MaxIndex_j-1));%list of image times |
---|
| 493 | enable_j(handles,'on') |
---|
| 494 | end |
---|
| 495 | TimeUnit='s'; |
---|
| 496 | set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter |
---|
| 497 | end |
---|
| 498 | |
---|
| 499 | %% timing display |
---|
| 500 | %show the reference image edit box if relevant (not needed for movies or in the absence of time information |
---|
| 501 | if numel(time)>=2 % if there are at least two time values to define dt |
---|
| 502 | if size(time,1)<MaxIndex_i; |
---|
| 503 | msgbox_uvmat('WARNING','maximum i index restricted by the timing of the xml file'); |
---|
| 504 | elseif size(time,2)<MaxIndex_j |
---|
| 505 | msgbox_uvmat('WARNING','maximum j index restricted by the timing of the xml file'); |
---|
| 506 | end |
---|
| 507 | MaxIndex_i=min(size(time,1),MaxIndex_i);%possibly adjust the max index according to time data |
---|
| 508 | MaxIndex_j=min(size(time,2),MaxIndex_j); |
---|
| 509 | time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices) |
---|
| 510 | time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros |
---|
| 511 | else |
---|
| 512 | set(handles.ImaDoc,'String',''); %xml file not used for timing |
---|
| 513 | time=(i1_series(:,1)+0:size(i1_series,3)-1);% time=index i |
---|
| 514 | time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices |
---|
| 515 | TimeUnit='frame'; |
---|
| 516 | end |
---|
| 517 | set(handles.ImaDoc,'UserData',time); %store the matrix of times |
---|
| 518 | set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms) |
---|
| 519 | set(handles.TimeUnit,'String',TimeUnit); |
---|
| 520 | set(handles.nb_field,'String',num2str(MaxIndex_i)); |
---|
| 521 | set(handles.nb_field2,'String',num2str(MaxIndex_j)); |
---|
| 522 | set(handles.CoordUnit,'String',CoordUnit) |
---|
| 523 | set(handles.SearchRange,'UserData', pxcm_search); |
---|
| 524 | set(handles.ImaExt,'String',ImaExt) |
---|
| 525 | set(handles.NomType,'String',NomTypeIma) |
---|
| 526 | |
---|
| 527 | %% set the reference indices from the input file indices |
---|
| 528 | num_ref_i=str2num(get(handles.ref_i,'String')); |
---|
| 529 | num_ref_j=str2num(get(handles.ref_j,'String')); |
---|
| 530 | % for movies don't modify except if the current ref is outside index bounds |
---|
| 531 | %if strcmp(ExtInput,'.nc')|| ~(strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader') && num_ref_i<=MaxIndex_i && num_ref_j<=MaxIndex_j) |
---|
| 532 | if ~isempty(i1)% if i1 has been selected by the input |
---|
| 533 | num_ref_i=i1;%default ref index |
---|
| 534 | if ~isempty(i2) |
---|
| 535 | num_ref_i=floor((num_ref_i+i2)/2); |
---|
| 536 | end |
---|
| 537 | if ~isempty(j1) |
---|
| 538 | num_ref_j=j1; |
---|
| 539 | if ~isempty(j2) |
---|
| 540 | num_ref_j=floor((num_ref_j+j2)/2); |
---|
| 541 | end |
---|
| 542 | end |
---|
| 543 | end |
---|
| 544 | if num_ref_i>MaxIndex_i||num_ref_i<MinIndex_i |
---|
| 545 | num_ref_i=round((MinIndex_i+MaxIndex_i)/2); |
---|
| 546 | end |
---|
| 547 | if ~isempty(num_ref_j)&&~isempty(MaxIndex_j)&& ~isempty(MinIndex_j) |
---|
| 548 | if (num_ref_j>MaxIndex_j||num_ref_j<MinIndex_j) |
---|
| 549 | num_ref_j=round((MinIndex_j+MaxIndex_j)/2); |
---|
| 550 | end |
---|
| 551 | end |
---|
| 552 | if isempty(num_ref_j) |
---|
| 553 | num_ref_j=1; |
---|
| 554 | end |
---|
| 555 | |
---|
| 556 | %% update i and j index range if a nc file has been opened or pb withmin max image indices: |
---|
| 557 | % then set first and last to the inputfile index by default |
---|
| 558 | first_i=str2num(get(handles.first_i,'String')); |
---|
| 559 | last_i=str2num(get(handles.last_i,'String')); |
---|
| 560 | if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i)||ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i |
---|
| 561 | first_i=num_ref_i; |
---|
| 562 | last_i=num_ref_i; |
---|
| 563 | set(handles.first_i,'String',num2str(first_i)); |
---|
| 564 | set(handles.last_i,'String',num2str(last_i));% |
---|
| 565 | end |
---|
| 566 | |
---|
| 567 | %j index range |
---|
| 568 | first_j=str2num(get(handles.first_j,'String')); |
---|
| 569 | last_j=str2num(get(handles.last_j,'String')); |
---|
| 570 | if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j)||ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j |
---|
| 571 | first_j=num_ref_j; |
---|
| 572 | last_j=num_ref_j; |
---|
| 573 | set(handles.first_j,'String',num2str(first_j)); |
---|
| 574 | set(handles.last_j,'String',num2str(last_j));% |
---|
| 575 | end |
---|
| 576 | if num_ref_i>last_i || num_ref_i<first_i |
---|
| 577 | num_ref_i=round((first_i+last_i)/2); |
---|
| 578 | end |
---|
| 579 | if num_ref_j>last_j || num_ref_j<first_j |
---|
| 580 | num_ref_j=round((first_j+last_j)/2); |
---|
| 581 | end |
---|
| 582 | set(handles.ref_i,'String',num2str(num_ref_i)) |
---|
| 583 | set(handles.ref_j,'String',num2str(num_ref_j)) |
---|
| 584 | |
---|
| 585 | %% set the civ_input options depending on the input file content when a nc file has been opened |
---|
| 586 | ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'}; |
---|
| 587 | checkbox=zeros(size(ListOptions));%default |
---|
| 588 | if ind_opening==0%case of image opening, start with Civ1 |
---|
| 589 | for index=1:numel(ListOptions) |
---|
| 590 | checkbox(index)=get(handles.(ListOptions{index}),'Value'); |
---|
| 591 | end |
---|
| 592 | index_max=find(checkbox, 1, 'last' ); |
---|
| 593 | if isempty(index_max),index_max=1;end |
---|
| 594 | for index=1:index_max |
---|
| 595 | set(handles.(ListOptions{index}),'Value',1)% select all operations starting from CIV1 |
---|
| 596 | end |
---|
| 597 | else |
---|
| 598 | for index = 1:min(ind_opening,5) |
---|
| 599 | set(handles.(ListOptions{index}),'value',0) |
---|
| 600 | end |
---|
| 601 | set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1) |
---|
| 602 | for index = ind_opening+2:6 |
---|
| 603 | set(handles.(ListOptions{index}),'value',0) |
---|
| 604 | end |
---|
| 605 | end |
---|
| 606 | %list_operation={'CheckCiv1','CheckFix1','CheckPatch1','CheckCiv2','CheckFix2','CheckPatch2'}; |
---|
| 607 | |
---|
| 608 | %set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1) |
---|
| 609 | update_CivOptions(handles,ind_opening) |
---|
| 610 | |
---|
| 611 | %% set the menus of image pairs and default selection for civ_input %%%%%%%%%%%%%%%%%%% |
---|
| 612 | %check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter |
---|
| 613 | if isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1) |
---|
| 614 | set(handles.ListPairMode,'Value',1) |
---|
| 615 | set(handles.ListPairMode,'String',{'series(Di)'}) |
---|
| 616 | elseif MaxIndex_i==1 && MaxIndex_j>1% simple series in j |
---|
| 617 | set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'}) |
---|
| 618 | if MaxIndex_j <= 10 |
---|
| 619 | set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large |
---|
| 620 | end |
---|
| 621 | elseif ~(strcmp(FileType,'video') || strcmp(FileType,'mmreader')) |
---|
| 622 | set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice |
---|
| 623 | if strcmp(NomTypeNc,'_1-2_1') |
---|
| 624 | set(handles.ListPairMode,'Value',3)% advise 'series(Di)' |
---|
| 625 | elseif MaxIndex_j <= 10 |
---|
| 626 | set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large |
---|
| 627 | end |
---|
| 628 | end |
---|
| 629 | |
---|
| 630 | %% scan files to update the subdirectory list display |
---|
| 631 | listot=dir(RootPath);%directory of RootPath |
---|
| 632 | idir=0; |
---|
| 633 | listdir={''};%default |
---|
| 634 | % get the list of existing civ_input subdirectories in the path of theinput root file |
---|
| 635 | for ilist=1:length(listot) |
---|
| 636 | if listot(ilist).isdir |
---|
| 637 | name=listot(ilist).name; |
---|
| 638 | if ~isequal(name,'.') && ~isequal(name,'..') |
---|
| 639 | idir=idir+1; |
---|
| 640 | listdir{idir,1}=listot(ilist).name; |
---|
| 641 | end |
---|
| 642 | end |
---|
| 643 | end |
---|
| 644 | |
---|
| 645 | %% store info |
---|
| 646 | set(handles.RootPath,'UserData',browse)% store the nomenclature type |
---|
| 647 | |
---|
| 648 | %% list the possible index pairs, depending on the option set in ListPairMode |
---|
| 649 | ListPairMode_Callback([], [], handles) |
---|
| 650 | |
---|
| 651 | %% store the root input filename for future opening |
---|
| 652 | profil_perso=fullfile(prefdir,'uvmat_perso.mat'); |
---|
| 653 | if exist(profil_perso,'file') |
---|
| 654 | save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat |
---|
| 655 | else |
---|
| 656 | txt=ver('MATLAB'); |
---|
| 657 | Release=txt.Release; |
---|
| 658 | relnumb=str2double(Release(3:4)); |
---|
| 659 | if relnumb >= 14 |
---|
| 660 | save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat |
---|
| 661 | else |
---|
| 662 | save (profil_perso,'RootPath'); %store the root name for future opening of uvmat |
---|
| 663 | end |
---|
| 664 | end |
---|
| 665 | set(handles.RootPath,'BackgroundColor',[1 1 1]) |
---|
| 666 | |
---|
| 667 | %------------------------------------------------------------------------ |
---|
| 668 | % --- Executes on carriage return on the subdir checkciv1 edit window |
---|
| 669 | function SubdirCiv1_Callback(hObject, eventdata, handles) |
---|
| 670 | %------------------------------------------------------------------------ |
---|
| 671 | SubDir=get(handles.SubdirCiv1,'String'); |
---|
| 672 | menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update |
---|
| 673 | ichoice=find(strcmp(SubDir,menu_str),1); |
---|
| 674 | if isempty(ichoice) |
---|
| 675 | ilist=numel(menu_str); %select 'new...' in the menu |
---|
| 676 | else |
---|
| 677 | ilist=ichoice; |
---|
| 678 | end |
---|
| 679 | set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu |
---|
| 680 | if get(handles.CheckCiv1,'Value')% if Civ1 is performed |
---|
| 681 | set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1 |
---|
| 682 | % set(handles.ListSubdirCiv2,'Value',ilist) |
---|
| 683 | else % if Civ1 data already exist |
---|
| 684 | errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory |
---|
| 685 | if ~isempty(errormsg) |
---|
| 686 | msgbox_uvmat('ERROR',errormsg) |
---|
| 687 | end |
---|
| 688 | end |
---|
| 689 | |
---|
| 690 | %------------------------------------------------------------------------ |
---|
| 691 | % --- Executes on carriage return on the SubDir checkciv1 edit window |
---|
| 692 | function SubdirCiv2_Callback(hObject, eventdata, handles) |
---|
| 693 | %------------------------------------------------------------------------ |
---|
| 694 | SubDir=get(handles.SubdirCiv1,'String'); |
---|
| 695 | menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update |
---|
| 696 | ichoice=find(strcmp(SubDir,menu_str),1); |
---|
| 697 | if isempty(ichoice) |
---|
| 698 | ilist=numel(menu_str); %select 'new...' in the menu |
---|
| 699 | else |
---|
| 700 | ilist=ichoice; |
---|
| 701 | end |
---|
| 702 | set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu |
---|
| 703 | %update the list of available pairs from netcdf files in the new directory |
---|
| 704 | if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value') |
---|
| 705 | errormsg=find_netcpair_civ(handles,2); |
---|
| 706 | if ~isempty(errormsg) |
---|
| 707 | msgbox_uvmat('ERROR',errormsg) |
---|
| 708 | end |
---|
| 709 | end |
---|
| 710 | |
---|
| 711 | %------------------------------------------------------------------------ |
---|
| 712 | % --- Executes on button press in CheckCiv1. |
---|
| 713 | function CheckCiv1_Callback(hObject, eventdata, handles) |
---|
| 714 | %------------------------------------------------------------------------ |
---|
| 715 | update_CivOptions(handles,0) |
---|
| 716 | |
---|
| 717 | %------------------------------------------------------------------------ |
---|
| 718 | % --- Executes on button press in CheckFix1. |
---|
| 719 | function CheckFix1_Callback(hObject, eventdata, handles) |
---|
| 720 | %------------------------------------------------------------------------ |
---|
| 721 | update_CivOptions(handles,0) |
---|
| 722 | |
---|
| 723 | %------------------------------------------------------------------------ |
---|
| 724 | % --- Executes on button press in CheckPatch1. |
---|
| 725 | function CheckPatch1_Callback(hObject, eventdata, handles) |
---|
| 726 | %------------------------------------------------------------------------ |
---|
| 727 | update_CivOptions(handles,0) |
---|
| 728 | |
---|
| 729 | %------------------------------------------------------------------------ |
---|
| 730 | % --- Executes on button press in CheckCiv2. |
---|
| 731 | function CheckCiv2_Callback(hObject, eventdata, handles) |
---|
| 732 | %------------------------------------------------------------------------ |
---|
| 733 | update_CivOptions(handles,0) |
---|
| 734 | |
---|
| 735 | %------------------------------------------------------------------------ |
---|
| 736 | % --- Executes on button press in CheckFix2. |
---|
| 737 | function CheckFix2_Callback(hObject, eventdata, handles) |
---|
| 738 | %------------------------------------------------------------------------ |
---|
| 739 | update_CivOptions(handles,0) |
---|
| 740 | |
---|
| 741 | %------------------------------------------------------------------------ |
---|
| 742 | % --- Executes on button press in CheckPatch2. |
---|
| 743 | function CheckPatch2_Callback(hObject, eventdata, handles) |
---|
| 744 | %------------------------------------------------------------------------ |
---|
| 745 | update_CivOptions(handles,0) |
---|
| 746 | |
---|
| 747 | %------------------------------------------------------------------------ |
---|
| 748 | % --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2 |
---|
| 749 | function update_CivOptions(handles,opening) |
---|
| 750 | %------------------------------------------------------------------------ |
---|
| 751 | checkbox=zeros(1,6); |
---|
| 752 | checkbox(1)=get(handles.CheckCiv1,'Value'); |
---|
| 753 | checkbox(2)=get(handles.CheckFix1,'Value'); |
---|
| 754 | checkbox(3)=get(handles.CheckPatch1,'Value'); |
---|
| 755 | checkbox(4)=get(handles.CheckCiv2,'Value'); |
---|
| 756 | checkbox(5)=get(handles.CheckFix2,'Value'); |
---|
| 757 | checkbox(6)=get(handles.CheckPatch2,'Value'); |
---|
| 758 | ind_selected=find(checkbox,1); |
---|
| 759 | if ~isempty(ind_selected) |
---|
| 760 | RootPath=get(handles.RootPath,'String'); |
---|
| 761 | if isempty(RootPath) |
---|
| 762 | msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...') |
---|
| 763 | return |
---|
| 764 | end |
---|
| 765 | end |
---|
| 766 | set(handles.PairIndices,'Visible','on') |
---|
| 767 | set(handles.SubdirCiv1,'Visible','on') |
---|
| 768 | set(handles.TitleSubdirCiv1,'Visible','on') |
---|
| 769 | if opening==0 |
---|
| 770 | errormsg=find_netcpair_civ(handles,1); % select the available netcdf files |
---|
| 771 | if ~isempty(errormsg) |
---|
| 772 | msgbox_uvmat('ERROR',errormsg) |
---|
| 773 | end |
---|
| 774 | end |
---|
| 775 | if max(checkbox(4:6))% case of civ2 pair choice needed |
---|
| 776 | set(handles.TitlePairCiv2,'Visible','on') |
---|
| 777 | set(handles.TitleSubdirCiv2,'Visible','on') |
---|
| 778 | set(handles.SubdirCiv2,'Visible','on') |
---|
| 779 | %set(handles.ListSubdirCiv2,'Visible','on') |
---|
| 780 | set(handles.ListPairCiv2,'Visible','on') |
---|
| 781 | if ~opening |
---|
| 782 | errormsg=find_netcpair_civ(handles,2); % select the available netcdf files |
---|
| 783 | if ~isempty(errormsg) |
---|
| 784 | msgbox_uvmat('ERROR',errormsg) |
---|
| 785 | end |
---|
| 786 | end |
---|
| 787 | else |
---|
| 788 | set(handles.TitleSubdirCiv2,'Visible','off') |
---|
| 789 | set(handles.SubdirCiv2,'Visible','off') |
---|
| 790 | set(handles.ListPairCiv2,'Visible','off') |
---|
| 791 | end |
---|
| 792 | options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'}; |
---|
| 793 | for ilist=1:length(options) |
---|
| 794 | if checkbox(ilist) |
---|
| 795 | set(handles.(options{ilist}),'Visible','on') |
---|
| 796 | else |
---|
| 797 | set(handles.(options{ilist}),'Visible','off') |
---|
| 798 | end |
---|
| 799 | end |
---|
| 800 | |
---|
| 801 | %------------------------------------------------------------------------ |
---|
| 802 | % --- Executes on button press in OK: processing on local computer |
---|
| 803 | function OK_Callback(hObject, eventdata, handles) |
---|
| 804 | %------------------------------------------------------------------------ |
---|
| 805 | |
---|
[598] | 806 | handles.output.ActionInput=read_GUI(handles.civ_input); |
---|
[597] | 807 | guidata(hObject, handles);% Update handles structure |
---|
[598] | 808 | uiresume(handles.civ_input); |
---|
[597] | 809 | drawnow |
---|
| 810 | |
---|
| 811 | return |
---|
| 812 | |
---|
| 813 | |
---|
| 814 | set(handles.OK, 'Enable','Off') |
---|
| 815 | set(handles.OK,'BackgroundColor',[0.831 0.816 0.784]) |
---|
| 816 | set(handles.OK,'UserData',now)% record the time of launch |
---|
| 817 | |
---|
| 818 | errormsg=launch_jobs(hObject, eventdata, handles); |
---|
| 819 | set(handles.OK, 'Enable','On') |
---|
| 820 | set(handles.OK,'BackgroundColor',[1 0 0]) |
---|
| 821 | |
---|
| 822 | % display errors or start status callback to visualise results |
---|
| 823 | if ~isempty(errormsg) |
---|
| 824 | display(errormsg) |
---|
| 825 | msgbox_uvmat('ERROR',errormsg) |
---|
| 826 | elseif isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3) |
---|
| 827 | set(handles.status,'Value',1);%suppress status display |
---|
| 828 | status_Callback(hObject, eventdata, handles) |
---|
| 829 | end |
---|
| 830 | |
---|
[598] | 831 | % %------------------------------------------------------------------- |
---|
| 832 | % % --- Executes on button press in status. |
---|
| 833 | % function status_Callback(hObject, eventdata, handles) |
---|
| 834 | % %------------------------------------------------------------------- |
---|
| 835 | % val=get(handles.status,'Value'); |
---|
| 836 | % if val==0 |
---|
| 837 | % set(handles.status,'BackgroundColor',[0 1 0]) |
---|
| 838 | % hfig=findobj(allchild(0),'name','civ_status'); |
---|
| 839 | % if ~isempty(hfig) |
---|
| 840 | % delete(hfig) |
---|
| 841 | % end |
---|
| 842 | % return |
---|
| 843 | % end |
---|
| 844 | % set(handles.status,'BackgroundColor',[1 1 0]) |
---|
| 845 | % drawnow |
---|
| 846 | % listtype={'civ1','fix1','patch1','civ2','fix2','patch2'}; |
---|
| 847 | % Param.CheckCiv1=get(handles.CheckCiv1,'Value'); |
---|
| 848 | % Param.CheckFix1=get(handles.CheckFix1,'Value'); |
---|
| 849 | % Param.CheckPatch1=get(handles.CheckPatch1,'Value'); |
---|
| 850 | % Param.CheckCiv2=get(handles.CheckCiv2,'Value'); |
---|
| 851 | % Param.CheckFix2=get(handles.CheckFix2,'Value'); |
---|
| 852 | % Param.CheckPatch2=get(handles.CheckPatch2,'Value'); |
---|
| 853 | % box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2]; |
---|
| 854 | % |
---|
| 855 | % option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test) |
---|
| 856 | % filecell=get(handles.civ_input,'UserData');%retrieve the list of output files expected for PIV |
---|
| 857 | % test_new=0; |
---|
| 858 | % if ~isfield(filecell,'nc') |
---|
| 859 | % test_new=1; |
---|
| 860 | % [ref_i,ref_j,errormsg]=find_ref_indices(handles); |
---|
| 861 | % if ~isempty(errormsg) |
---|
| 862 | % msgbox_uvmat('ERROR',errormsg) |
---|
| 863 | % return |
---|
| 864 | % end |
---|
| 865 | % filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status |
---|
| 866 | % end |
---|
| 867 | % if ~isequal(box_test(4:6),[0 0 0]) |
---|
| 868 | % civ_files=filecell.nc.civ2;%case of civ2 operations |
---|
| 869 | % else |
---|
| 870 | % civ_files=filecell.nc.civ1; |
---|
| 871 | % end |
---|
| 872 | % [root,filename,ext]=fileparts(civ_files{1}); |
---|
| 873 | % [rootroot,SubDir,extdir]=fileparts(root); |
---|
| 874 | % hfig=findobj(allchild(0),'name','civ_status'); |
---|
| 875 | % if isempty(hfig) |
---|
| 876 | % hfig=figure('DeleteFcn',@stop_status); |
---|
| 877 | % set(hfig,'MenuBar','none')% suppress the menu bar |
---|
| 878 | % set(hfig,'NumberTitle','off')%suppress the fig number in the title |
---|
| 879 | % set(hfig,'name','civ_status') |
---|
| 880 | % set(hfig,'tag','civ_status') |
---|
| 881 | % set(hfig,'UserData',civ_files) |
---|
| 882 | % hlist= uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list'); |
---|
| 883 | % uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...'); |
---|
| 884 | % uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]); |
---|
| 885 | % %uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI); |
---|
| 886 | % uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@stop_status); |
---|
| 887 | % hrefresh=uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.1 0.01 0.2 0.07],'String','Refresh','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@refresh_GUI); |
---|
| 888 | % BarPosition=[0.05 0.81 0.01 0.05]; |
---|
| 889 | % uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar'); |
---|
| 890 | % drawnow |
---|
| 891 | % end |
---|
| 892 | % StatusData.time_ref=get(handles.OK,'UserData');% get the time of launch |
---|
| 893 | % StatusData.option_civ=option_civ; |
---|
| 894 | % set(hrefresh,'UserData',StatusData) |
---|
| 895 | % filepath=fileparts(civ_files{1}); |
---|
| 896 | % set(hlist,'UserData',fileparts(filepath)) |
---|
| 897 | % refresh_GUI(hrefresh,[]) |
---|
[597] | 898 | |
---|
| 899 | % %------------------------------------------------------------------------ |
---|
[598] | 900 | % % launched by refreshing the status figure |
---|
| 901 | % function refresh_GUI(hObject, eventdata) |
---|
[597] | 902 | % %------------------------------------------------------------------------ |
---|
[598] | 903 | % Tabchar={}; |
---|
| 904 | % BarPosition=[0.05 0.81 0.01 0.05]; |
---|
| 905 | % hfig=get(hObject,'parent'); |
---|
| 906 | % StatusData=get(hObject,'UserData'); |
---|
| 907 | % civ_files=get(hfig,'UserData'); |
---|
| 908 | % [filepath,filename,ext]=fileparts(civ_files{1}); |
---|
| 909 | % [tild,SubDir,extdir]=fileparts(filepath); |
---|
| 910 | % SubDir=[SubDir extdir]; |
---|
| 911 | % option_civ=StatusData.option_civ; |
---|
| 912 | % nbfiles=numel(civ_files); |
---|
| 913 | % testrecent=0; |
---|
| 914 | % count=0; |
---|
| 915 | % datnum=zeros(1,nbfiles); |
---|
| 916 | % filefound=cell(1,nbfiles); |
---|
| 917 | % for ifile=1:nbfiles |
---|
| 918 | % detect=exist(civ_files{ifile},'file'); % check the existence of the file |
---|
| 919 | % option=0; |
---|
| 920 | % if detect==0 |
---|
| 921 | % option_str='not created'; |
---|
| 922 | % else |
---|
| 923 | % datfile=dir(civ_files{ifile}); |
---|
| 924 | % if isfield(datfile,'datenum') |
---|
| 925 | % datnum(ifile)=datfile.datenum;%only available in recent matlab versions |
---|
| 926 | % testrecent=1; |
---|
| 927 | % end |
---|
| 928 | % filefound(ifile)={datfile.name}; |
---|
| 929 | % |
---|
| 930 | % % check the content netcdf file |
---|
| 931 | % Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix'); |
---|
| 932 | % option_list={'civ1','fix1','patch1','civ2','fix2','patch2'}; |
---|
| 933 | % if ~isempty(Data.CivStage) |
---|
| 934 | % option=Data.CivStage;%case of Matlab civ |
---|
| 935 | % else |
---|
| 936 | % if ~isempty(Data.patch2) && isequal(Data.patch2,1) |
---|
| 937 | % option=6; |
---|
| 938 | % elseif ~isempty(Data.fix2) && isequal(Data.fix2,1) |
---|
| 939 | % option=5; |
---|
| 940 | % elseif ~isempty(Data.civ2) && isequal(Data.civ2,1); |
---|
| 941 | % option=4; |
---|
| 942 | % elseif ~isempty(Data.patch) && isequal(Data.patch,1); |
---|
| 943 | % option=3; |
---|
| 944 | % elseif ~isempty(Data.fix) && isequal(Data.fix,1); |
---|
| 945 | % option=2; |
---|
| 946 | % else |
---|
| 947 | % option=1; |
---|
| 948 | % end |
---|
| 949 | % end |
---|
| 950 | % option_str=option_list{option}; |
---|
| 951 | % if datnum(ifile)<StatusData.time_ref |
---|
| 952 | % option_str=[option_str ' --OLD--']; |
---|
| 953 | % end |
---|
| 954 | % end |
---|
| 955 | % if option >= option_civ |
---|
| 956 | % count=count+1; |
---|
| 957 | % end |
---|
| 958 | % [filepath,filename,ext]=fileparts(civ_files{ifile}); |
---|
| 959 | % Tabchar{ifile,1}=[fullfile(SubDir,filename) ext '...' option_str]; |
---|
| 960 | % end |
---|
| 961 | % datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files |
---|
| 962 | % if isempty(datnum) |
---|
| 963 | % if testrecent |
---|
| 964 | % message='no civ result created yet'; |
---|
| 965 | % else |
---|
| 966 | % message=''; |
---|
| 967 | % end |
---|
| 968 | % else |
---|
| 969 | % datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files |
---|
| 970 | % [first,ind]=min(datnum); |
---|
| 971 | % [last,indlast]=max(datnum); |
---|
| 972 | % message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification: ' cell2mat(filefound(ind)) ' : ' datestr(first)];... |
---|
| 973 | % ['latest modification: ' cell2mat(filefound(indlast)) ' : ' datestr(last)]}; |
---|
| 974 | % end |
---|
| 975 | % hlist=findobj(hfig,'tag','list'); |
---|
| 976 | % hmsgbox=findobj(hfig,'tag','msgbox'); |
---|
| 977 | % hwaitbar=findobj(hfig,'tag','waitbar'); |
---|
| 978 | % set(hlist,'String',Tabchar) |
---|
| 979 | % set(hmsgbox,'String', message) |
---|
| 980 | % if count>0 %&& ~test_new |
---|
| 981 | % BarPosition(3)=0.9*count/nbfiles; |
---|
| 982 | % set(hwaitbar,'Position',BarPosition) |
---|
| 983 | % end |
---|
| 984 | % |
---|
| 985 | % |
---|
| 986 | % %------------------------------------------------------------------------ |
---|
| 987 | % % launched by deleting the status figure |
---|
| 988 | % function stop_status(hObject, eventdata) |
---|
| 989 | % %------------------------------------------------------------------------ |
---|
| 990 | % hciv=findobj(allchild(0),'tag','civ'); |
---|
| 991 | % hhciv=guidata(hciv); |
---|
| 992 | % set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ |
---|
| 993 | % set(hhciv.status,'BackgroundColor',[0 1 0]) |
---|
| 994 | % |
---|
| 995 | % % %------------------------------------------------------------------------ |
---|
| 996 | % % % launched by pressing OK on the status figure |
---|
| 997 | % % function close_GUI(hObject, eventdata) |
---|
| 998 | % % %------------------------------------------------------------------------ |
---|
| 999 | % % delete(gcbf) |
---|
| 1000 | % |
---|
[597] | 1001 | |
---|
[598] | 1002 | % %------------------------------------------------------------------------ |
---|
| 1003 | % % --- Main lauch command, called by OK and BATCH |
---|
| 1004 | % function errormsg=launch_jobs(hObject, eventdata, handles) |
---|
| 1005 | % %------------------------------------------------------------------------ |
---|
| 1006 | % errormsg='';%default |
---|
| 1007 | % |
---|
| 1008 | % %% read the input parameters from the GUI civ_input |
---|
| 1009 | % Param=read_GUI(handles.civ_input); |
---|
| 1010 | % |
---|
| 1011 | % %% check the selected list of operations: |
---|
| 1012 | % operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'}; |
---|
| 1013 | % box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2]; |
---|
| 1014 | % index_first=find(box_test==1,1); |
---|
| 1015 | % if isempty(index_first) |
---|
| 1016 | % errormsg='no selected operation'; |
---|
| 1017 | % return |
---|
[597] | 1018 | % end |
---|
[598] | 1019 | % index_last=find(box_test==1,1,'last'); |
---|
| 1020 | % box_used=box_test(index_first : index_last); |
---|
| 1021 | % [box_missing,ind_missing]=min(box_used); |
---|
| 1022 | % if isequal(box_missing,0); %there is a missing step in the sequence of operations |
---|
| 1023 | % errormsg=['missing' cell2mat(operations(ind_missing))]; |
---|
| 1024 | % return |
---|
| 1025 | % end |
---|
| 1026 | % |
---|
| 1027 | % %% check mask if selecetd |
---|
| 1028 | % %could be included in get_mask callback ? |
---|
| 1029 | % if isequal(get(handles.CheckMask,'Value'),1) |
---|
| 1030 | % maskname=get(handles.Mask,'String'); |
---|
| 1031 | % if ~exist(maskname,'file') |
---|
| 1032 | % get_mask_civ1_Callback(hObject, eventdata, handles); |
---|
| 1033 | % end |
---|
| 1034 | % end |
---|
| 1035 | % if isequal(get(handles.CheckMask,'Value'),1) |
---|
| 1036 | % maskname=get(handles.Mask,'String'); |
---|
| 1037 | % if ~exist(maskname,'file') |
---|
| 1038 | % get_mask_fix1_Callback(hObject, eventdata, handles); |
---|
| 1039 | % end |
---|
| 1040 | % end |
---|
| 1041 | % if isequal(get(handles.CheckMask,'Value'),1) |
---|
| 1042 | % maskname=get(handles.Mask,'String'); |
---|
| 1043 | % if ~exist(maskname,'file') |
---|
| 1044 | % get_mask_civ2_Callback(hObject, eventdata, handles); |
---|
| 1045 | % end |
---|
| 1046 | % end |
---|
| 1047 | % if isequal(get(handles.CheckMask,'Value'),1) |
---|
| 1048 | % maskname=get(handles.Mask,'String'); |
---|
| 1049 | % if ~exist(maskname,'file') |
---|
| 1050 | % get_mask_fix2_Callback(hObject, eventdata, handles); |
---|
| 1051 | % end |
---|
| 1052 | % end |
---|
| 1053 | % |
---|
| 1054 | % %% reinitialise status callback |
---|
| 1055 | % if isfield(handles,'status') |
---|
| 1056 | % set(handles.status,'Value',0);%suppress status display |
---|
| 1057 | % status_Callback([], [], handles) |
---|
| 1058 | % end |
---|
| 1059 | % |
---|
| 1060 | % %% read the PARAM.xml file to get the binaries (and batch_mode if batch) |
---|
| 1061 | % % path_civ=fileparts(which('civ')); %path to the source directory of uvmat |
---|
| 1062 | % % xmlfile=fullfile(path_civ,'PARAM.xml'); |
---|
| 1063 | % % s=[]; |
---|
| 1064 | % % if exist(xmlfile,'file')% search parameter xml file in the whole matlab path |
---|
| 1065 | % % t=xmltree(xmlfile); |
---|
| 1066 | % % s=convert(t); |
---|
| 1067 | % % end% default configuration |
---|
| 1068 | % % if ~isfield(s,'RunParam') |
---|
| 1069 | % % Param.xml.Civ1Bin=fullfile('bin','civ1'); |
---|
| 1070 | % % Param.xml.Civ2Bin=fullfile('bin','civ2'); |
---|
| 1071 | % % Param.xml.FixBin=fullfile('bin','fix_flag'); |
---|
| 1072 | % % Param.xml.PatchBin=fullfile('bin','patch_up'); |
---|
| 1073 | % % end |
---|
| 1074 | % % if strcmp(Param.RunMode,'cluster') %computation dispatched on a cluster |
---|
| 1075 | % % if isfield(s,'BatchParam') |
---|
| 1076 | % % Param.xml=s.BatchParam; |
---|
| 1077 | % % if isfield(Param.xml,'BatchMode') |
---|
| 1078 | % % batch_mode=Param.xml.BatchMode; |
---|
| 1079 | % % if ~ismember(batch_mode,{'sge','oar'}) |
---|
| 1080 | % % errormsg=['batch mode ' batch_mode ' not supported by UVMAT']; |
---|
| 1081 | % % return |
---|
| 1082 | % % end |
---|
| 1083 | % % end |
---|
| 1084 | % % else |
---|
| 1085 | % % %default configuration |
---|
| 1086 | % % Param.xml.Civ1Bin=fullfile('bin','civ1'); |
---|
| 1087 | % % Param.xml.Civ2Bin=fullfile('bin','civ2'); |
---|
| 1088 | % % Param.xml.FixBin=fullfile('bin','fix_flag'); |
---|
| 1089 | % % Param.xml.PatchBin=fullfile('bin','patch_up'); |
---|
| 1090 | % % % Param.xml.CivmBin=fullfile('bin','civ_matlab'); |
---|
| 1091 | % % Param.xml.BatchMode='oar';% TODO : allow choice for sge |
---|
| 1092 | % % end |
---|
| 1093 | % % else % run |
---|
| 1094 | % % if isfield(s,'RunParam') |
---|
| 1095 | % % Param.xml=s.RunParam; |
---|
| 1096 | % % else %default configuration |
---|
| 1097 | % % Param.xml.Civ1Bin=fullfile('bin','civ1'); |
---|
| 1098 | % % Param.xml.Civ2Bin=fullfile('bin','civ2'); |
---|
| 1099 | % % Param.xml.FixBin=fullfile('bin','fix_flag'); |
---|
| 1100 | % % Param.xml.PatchBin=fullfile('bin','patch_up'); |
---|
| 1101 | % % end |
---|
| 1102 | % % end |
---|
| 1103 | % % %Param.xml.CivmBin=fullfile('bin','civ_matlab'); |
---|
| 1104 | % % |
---|
| 1105 | % % %% check if the binaries exist : to move in civ_opening |
---|
| 1106 | % % binary_list={}; |
---|
| 1107 | % % switch Param.Program |
---|
| 1108 | % % case 'CivX' |
---|
| 1109 | % % binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'}; |
---|
| 1110 | % % case 'CivAll'% desactivated option |
---|
| 1111 | % % binary_list={'Civ'}; |
---|
| 1112 | % % % case 'civ_matlab.sh'% compiled version of civ_matlab |
---|
| 1113 | % % % binary_list={'CivmBin'}; |
---|
| 1114 | % % end |
---|
| 1115 | % % for bin_name=binary_list %loop on the list of binaries |
---|
| 1116 | % % if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list |
---|
| 1117 | % % if ~isunix |
---|
| 1118 | % % Param.xml.(bin_name{1})=[regexprep(Param.xml.(bin_name{1}),'/','\') '.exe']; |
---|
| 1119 | % % end |
---|
| 1120 | % % if exist(Param.xml.(bin_name{1}),'file') |
---|
| 1121 | % % [path,name,ext]=fileparts(Param.xml.(bin_name{1})); |
---|
| 1122 | % % currentdir=pwd; |
---|
| 1123 | % % if isempty(path) |
---|
| 1124 | % % path=fileparts(which('civ.m')); |
---|
| 1125 | % % end |
---|
| 1126 | % % if exist(path,'dir') |
---|
| 1127 | % % cd(path); |
---|
| 1128 | % % binpath=pwd;%path of the binary |
---|
| 1129 | % % Param.xml.(bin_name{1})=fullfile(binpath,[name ext]); |
---|
| 1130 | % % cd(currentdir); |
---|
| 1131 | % % else |
---|
| 1132 | % % errormsg=['path ' path ' for binaries specified in PARAM.xml does not exist']; |
---|
| 1133 | % % return |
---|
| 1134 | % % end |
---|
| 1135 | % % else %look for the full path if the file name has been defined with a relative path in PARAM.xm |
---|
| 1136 | % % fullname=fullfile(path_civ,Param.xml.(bin_name{1})); |
---|
| 1137 | % % if exist(fullname,'file') |
---|
| 1138 | % % Param.xml.(bin_name{1})=fullname; |
---|
| 1139 | % % else |
---|
| 1140 | % % errormsg=['Binary ' Param.xml.(bin_name{1}) ' specified in PARAM.xml does not exist']; |
---|
| 1141 | % % return |
---|
| 1142 | % % end |
---|
| 1143 | % % end |
---|
| 1144 | % % end |
---|
| 1145 | % % end |
---|
| 1146 | % % if strcmp(Param.Program,'civ_matlab.sh') |
---|
| 1147 | % % if ~exist(fullfile(path_civ,'civ_matlab.sh'),'file') |
---|
| 1148 | % % errormsg=[{'no file civ_matlab.sh found'}; {'run compile_functions.m to create it by compiling civ_matlab.m'}]; |
---|
| 1149 | % % return |
---|
| 1150 | % % end |
---|
| 1151 | % % end |
---|
| 1152 | % % |
---|
| 1153 | % % %% set the list of files and check them |
---|
| 1154 | % % display('checking the files...') |
---|
| 1155 | % % [ref_i,ref_j,errormsg]=find_ref_indices(handles); |
---|
| 1156 | % % if ~isempty(errormsg) |
---|
| 1157 | % % return |
---|
| 1158 | % % end |
---|
| 1159 | % % [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,tild,tild,compare,errormsg]=... |
---|
| 1160 | % % set_civ_filenames(handles,ref_i,ref_j,box_test); |
---|
| 1161 | % % if ~isempty(errormsg) |
---|
| 1162 | % % return |
---|
| 1163 | % % end |
---|
| 1164 | % % set(handles.civ_input,'UserData',filecell);%store for futur use of status callback |
---|
| 1165 | % % display('files OK, processing...') |
---|
| 1166 | % % |
---|
| 1167 | % % %% create subfolders for log, cmx, nml, xml, bat |
---|
| 1168 | % % RootBat=fileparts(filecell.nc.civ1{1,1}); |
---|
| 1169 | % % switch(Param.Program) |
---|
| 1170 | % % case {'CivX','CivAll'} |
---|
| 1171 | % % dir_list={'0_BAT','0_CMX','0_LOG'}; |
---|
| 1172 | % % case {'civ_matlab','civ_matlab.sh'} |
---|
| 1173 | % % dir_list={'0_BAT','0_XML'}; |
---|
| 1174 | % % end |
---|
| 1175 | % % for k=1:length(dir_list) |
---|
| 1176 | % % if ~exist(fullfile(RootBat,dir_list{k}),'dir') |
---|
| 1177 | % % mkdir(fullfile(RootBat,dir_list{k})); |
---|
| 1178 | % % end |
---|
| 1179 | % % end |
---|
| 1180 | % |
---|
| 1181 | % %% get information on input images or movies |
---|
| 1182 | % nbfield=numel(i1_civ1); |
---|
| 1183 | % nbslice=numel(j1_civ1); |
---|
| 1184 | % % if strcmp(Param.Program,'civ_matlab') |
---|
| 1185 | % if Param.CheckCiv1 |
---|
| 1186 | % [Param.Civ1.FileTypeA,ImageInfoA_civ1,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1}); |
---|
| 1187 | % [Param.Civ1.FileTypeB,ImageInfoB_civ1,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1}); |
---|
| 1188 | % end |
---|
| 1189 | % if Param.CheckCiv2 |
---|
| 1190 | % [Param.Civ2.FileTypeA,ImageInfoA_civ2,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1}); |
---|
| 1191 | % [Param.Civ2.FileTypeB,ImageInfoB_civ2,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1}); |
---|
| 1192 | % end |
---|
| 1193 | % % end |
---|
| 1194 | % |
---|
| 1195 | % %% MAIN LOOP |
---|
| 1196 | % time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
| 1197 | % TimeUnit=get(handles.TimeUnit,'String'); |
---|
| 1198 | % checkframe=strcmp(TimeUnit,'frame'); |
---|
| 1199 | % batch_file_list=[];%should be renamed file_list, can be used for xml or bash files |
---|
| 1200 | % NomTypeIma=get(handles.NomType,'String'); |
---|
| 1201 | % for ifile=1:nbfield |
---|
| 1202 | % for j=1:nbslice |
---|
| 1203 | % |
---|
| 1204 | % % define output file name |
---|
| 1205 | % if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1 |
---|
| 1206 | % Param.OutputFile=filecell.nc.civ2{ifile,j}; |
---|
| 1207 | % else |
---|
| 1208 | % Param.OutputFile=filecell.nc.civ1{ifile,j}; |
---|
| 1209 | % end |
---|
| 1210 | % Param.OutputFile=regexprep(Param.OutputFile,'.nc',''); |
---|
| 1211 | % |
---|
| 1212 | % if Param.CheckCiv1 |
---|
| 1213 | % % read image-dependent parameters |
---|
| 1214 | % if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j) |
---|
| 1215 | % Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1)); |
---|
| 1216 | % else |
---|
| 1217 | % Param.Civ1.Dt=1; |
---|
[597] | 1218 | % end |
---|
[598] | 1219 | % Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2); |
---|
| 1220 | % if strcmp(Param.Program,'CivX') |
---|
| 1221 | % Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE? |
---|
| 1222 | % Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);% |
---|
| 1223 | % end |
---|
| 1224 | % Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j}; |
---|
| 1225 | % Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j}; |
---|
| 1226 | % Param.Civ1.ImageBitDepth=ImageInfoA_civ1.BitDepth; |
---|
| 1227 | % Param.Civ1.ImageWidth=ImageInfoA_civ1.Width; |
---|
| 1228 | % Param.Civ1.ImageHeight=ImageInfoA_civ1.Height; |
---|
| 1229 | % if strcmp(NomTypeIma,'*') |
---|
| 1230 | % Param.Civ1.FrameIndexA=i1_civ1(ifile); |
---|
| 1231 | % Param.Civ1.FrameIndexB=i2_civ1(ifile); |
---|
| 1232 | % else% case of movies indexed with i, the frame index is then in j |
---|
| 1233 | % Param.Civ1.FrameIndexA=j1_civ1(j); |
---|
| 1234 | % Param.Civ1.FrameIndexB=j2_civ1(j); |
---|
| 1235 | % end |
---|
| 1236 | % % read mask )parameters |
---|
| 1237 | % if Param.Civ1.CheckMask % the lines below should be changed with the new gui |
---|
| 1238 | % if ~exist(Param.Civ1.Mask,'file') |
---|
| 1239 | % maskbase=[filecell.filebase '_' Param.Civ1.Mask]; % |
---|
| 1240 | % nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); % |
---|
| 1241 | % i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1; |
---|
| 1242 | % [RootPathMask,RootFileMask]=fileparts(maskbase); |
---|
| 1243 | % Param.Civ1.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask); |
---|
| 1244 | % end |
---|
| 1245 | % end |
---|
| 1246 | % % read grid parameters |
---|
| 1247 | % if Param.Civ1.CheckGrid |
---|
| 1248 | % if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid') |
---|
| 1249 | % nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); % |
---|
| 1250 | % if ~isnan(nbslice_grid) |
---|
| 1251 | % i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1; |
---|
| 1252 | % Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)]; |
---|
| 1253 | % if ~exist(Param.Civ1.GridName,'file') |
---|
| 1254 | % errormsg='grid file absent for civ1'; |
---|
| 1255 | % return |
---|
| 1256 | % end |
---|
| 1257 | % elseif ~exist(Param.Civ1.Grid,'file') |
---|
| 1258 | % errormsg='grid file absent for civ1'; |
---|
| 1259 | % return |
---|
| 1260 | % end |
---|
| 1261 | % end |
---|
| 1262 | % end |
---|
| 1263 | % |
---|
| 1264 | % end |
---|
| 1265 | % |
---|
| 1266 | % if Param.CheckCiv2==1 |
---|
| 1267 | % Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j}; |
---|
| 1268 | % Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j}; |
---|
| 1269 | % if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j) |
---|
| 1270 | % Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1); |
---|
| 1271 | % else |
---|
| 1272 | % Param.Civ2.Dt=1; |
---|
| 1273 | % end |
---|
| 1274 | % Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2; |
---|
| 1275 | % if strcmp(Param.Program,'CivX') |
---|
| 1276 | % Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc); |
---|
| 1277 | % Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc); |
---|
| 1278 | % end |
---|
| 1279 | % Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j}; |
---|
| 1280 | % Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc' |
---|
| 1281 | % |
---|
| 1282 | % % mask |
---|
| 1283 | % if Param.Civ2.CheckMask |
---|
| 1284 | % if ~exist(Param.Civ2.Mask,'file') |
---|
| 1285 | % maskbase=[filecell.filebase '_' Param.Civ2.Mask]; % |
---|
| 1286 | % nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); % |
---|
| 1287 | % i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1; |
---|
| 1288 | % [RootPathMask,RootFileMask]=fileparts(maskbase); |
---|
| 1289 | % Param.Civ2.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask); |
---|
| 1290 | % % Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i'); |
---|
| 1291 | % end |
---|
| 1292 | % end |
---|
| 1293 | % %grid |
---|
| 1294 | % if Param.Civ2.CheckGrid |
---|
| 1295 | % if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid') |
---|
| 1296 | % nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); % |
---|
| 1297 | % if ~isnan(nbslice_grid) |
---|
| 1298 | % i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1; |
---|
| 1299 | % Param.Civ2.Grid=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)]; |
---|
| 1300 | % % Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; |
---|
| 1301 | % end |
---|
| 1302 | % end |
---|
| 1303 | % end |
---|
| 1304 | % |
---|
| 1305 | % Param.Civ2.ImageBitDepth=ImageInfoA_civ2.BitDepth; |
---|
| 1306 | % Param.Civ2.ImageWidth=ImageInfoA_civ2.Width; |
---|
| 1307 | % Param.Civ2.ImageHeight=ImageInfoA_civ2.Height; |
---|
| 1308 | % if strcmp(NomTypeIma,'*') |
---|
| 1309 | % Param.Civ2.FrameIndexA=i1_civ2(ifile); |
---|
| 1310 | % Param.Civ2.FrameIndexB=i2_civ2(ifile); |
---|
| 1311 | % else% case of movies indexed with i, the frame index is then in j |
---|
| 1312 | % Param.Civ2.FrameIndexA=j1_civ2(j); |
---|
| 1313 | % Param.Civ2.FrameIndexB=j2_civ2(j); |
---|
| 1314 | % end |
---|
| 1315 | % end |
---|
| 1316 | % |
---|
| 1317 | % % write the command and eventually the cmx, xml or nml files |
---|
| 1318 | % cmd=write_cmd(Param); |
---|
| 1319 | % write_param(Param); |
---|
| 1320 | % |
---|
| 1321 | % % create the command file name .m, .bat or .sh depending on the ok option |
---|
| 1322 | % switch Param.Program |
---|
| 1323 | % case {'civ_matlab'} |
---|
| 1324 | % filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.m'); |
---|
| 1325 | % [BatRoot,BatFile]=fileparts(filename_bat); |
---|
| 1326 | % BatFile=regexprep(BatFile,'-','__');%transform name to suppress'-' (not valid for .m files) |
---|
| 1327 | % filename_bat=[fullfile(BatRoot,BatFile) '.m']; |
---|
| 1328 | % case {'CivX','CivAll','civ_matlab.sh'} |
---|
| 1329 | % switch computer |
---|
| 1330 | % case {'PCWIN','PCWIN64'} |
---|
| 1331 | % filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.bat'); |
---|
| 1332 | % case {'GLNX86','GLNXA64','MACI64'} |
---|
| 1333 | % filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.sh'); |
---|
| 1334 | % end |
---|
| 1335 | % end |
---|
| 1336 | % |
---|
| 1337 | % % print the command in the bat file |
---|
| 1338 | % [fid,message]=fopen(filename_bat,'w'); |
---|
| 1339 | % if isequal(fid,-1) |
---|
| 1340 | % errormsg=['creation of .bat file: ' message]; |
---|
| 1341 | % return |
---|
| 1342 | % end |
---|
| 1343 | % fprintf(fid,cmd); |
---|
| 1344 | % fclose(fid); |
---|
| 1345 | % |
---|
| 1346 | % % special case for civ_matlab on cluster |
---|
| 1347 | % if strcmp(Param.Program,'civ_matlab') && strcmp(Param.RunMode,'cluster') |
---|
| 1348 | % filename_bat2=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.sh'); |
---|
| 1349 | % [fid,message]=fopen(filename_bat2,'w'); |
---|
| 1350 | % if isequal(fid,-1) |
---|
| 1351 | % errormsg=['creation of .bat file: ' message]; |
---|
| 1352 | % return |
---|
| 1353 | % end |
---|
| 1354 | % fprintf(fid,['#!/bin/bash \n' ... |
---|
| 1355 | % '/etc/sysprofile \n'... |
---|
| 1356 | % 'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'... |
---|
| 1357 | % 'addpath(''' path_civ ''');\n']); |
---|
| 1358 | % % for p=1:length(batch_file_list) |
---|
| 1359 | % fprintf(fid,['run ' filename_bat '\n']); |
---|
| 1360 | % % end |
---|
| 1361 | % fprintf(fid, 'exit\nEND_MATLAB\n'); |
---|
| 1362 | % fclose(fid); |
---|
| 1363 | % filename_bat=filename_bat2; |
---|
| 1364 | % end |
---|
| 1365 | % |
---|
| 1366 | % switch computer |
---|
| 1367 | % case {'GLNX86','GLNXA64','MACI64'} |
---|
| 1368 | % system(['chmod +x ' filename_bat]); |
---|
| 1369 | % end |
---|
| 1370 | % batch_file_list{length(batch_file_list)+1}=filename_bat; |
---|
| 1371 | % end |
---|
| 1372 | % end |
---|
| 1373 | % |
---|
| 1374 | % %% start calculation |
---|
| 1375 | % %computation on cluster |
---|
| 1376 | % %if batch ==3 |
---|
| 1377 | % switch Param.RunMode, |
---|
| 1378 | % case 'cluster' |
---|
| 1379 | % switch batch_mode |
---|
| 1380 | % case 'sge' %at the moment only psmn ENS Lyon uses it |
---|
| 1381 | % for p=1:length(batch_file_list) |
---|
| 1382 | % %cmd=['!qsub -p ' pvalue ' -q civ_input.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}]; |
---|
| 1383 | % cmd=['!qsub -q piv1,piv2,piv3 '... |
---|
| 1384 | % '-e ' regexprep(batch_file_list{p},'.bat','.errors') ' -o ' regexprep(batch_file_list{p},'.bat','.log ')... |
---|
| 1385 | % ' -v ' 'LD_LIBRARY_PATH=/home/sjoubaud/matlab_sylvain/civx/lib ' batch_file_list{p}]; |
---|
| 1386 | % display(cmd);eval(cmd); |
---|
| 1387 | % end |
---|
| 1388 | % case 'oar_old' % to remove |
---|
| 1389 | % for p=1:length(batch_file_list) |
---|
| 1390 | % oar_command=['!oarsub -n CIVX -q nicejob '... |
---|
| 1391 | % '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')... |
---|
| 1392 | % '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00" ' batch_file_list{p}]; |
---|
| 1393 | % display(oar_command);eval(oar_command); |
---|
| 1394 | % end |
---|
| 1395 | % case 'oar' |
---|
| 1396 | % max_walltime=3600*12; % 12h max |
---|
| 1397 | % oar_modes={'oar-parexec','oar-dispatch','mpilauncher'}; |
---|
| 1398 | % text={'Batch processing on servcalcul3 LEGI';... |
---|
| 1399 | % 'Please choose one of the followint modes';... |
---|
| 1400 | % '* oar-parexec : default and best choice';... |
---|
| 1401 | % '* oar-dispatch : jobs in a container of several cores';... |
---|
| 1402 | % '* mpilauncher : one single parallel mpi job using several cores';... |
---|
| 1403 | % '**********************************'... |
---|
| 1404 | % }; |
---|
| 1405 | % [S,v]=listdlg('PromptString',text,'ListString',oar_modes,... |
---|
| 1406 | % 'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode'); |
---|
| 1407 | % switch oar_modes{S} |
---|
| 1408 | % case 'oar-parexec' %oar-dispatch.pl |
---|
| 1409 | % if strcmp(Param.Program,'civ_matlab') |
---|
| 1410 | % ncores=1; |
---|
| 1411 | % msgbox_uvmat('WARNING','Number of cores =1: select the compiled version civ_matlab.sh for multi-core processing'); |
---|
| 1412 | % else |
---|
| 1413 | % answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''}); |
---|
| 1414 | % ncores=str2double(answer{1}); |
---|
| 1415 | % end |
---|
| 1416 | % |
---|
| 1417 | % extra_oar=answer{2}; |
---|
| 1418 | % walltime_onejob=600;%seconds |
---|
| 1419 | % filename_joblist=fullfile(RootBat,'job_list.txt'); |
---|
| 1420 | % fid=fopen(filename_joblist,'w'); |
---|
| 1421 | % for p=1:length(batch_file_list) |
---|
| 1422 | % fprintf(fid,[batch_file_list{p} '\n']); |
---|
| 1423 | % end |
---|
| 1424 | % fclose(fid); |
---|
| 1425 | % oar_command=['oarsub -n CIVX '... |
---|
| 1426 | % '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '... |
---|
| 1427 | % '-l /core=' num2str(ncores) ','... |
---|
| 1428 | % 'walltime=' datestr(min(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,max_walltime/86400),13) ' '... |
---|
| 1429 | % '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '... |
---|
| 1430 | % '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '... |
---|
| 1431 | % extra_oar ' '... |
---|
| 1432 | % '"oar-parexec -s -f ' filename_joblist ' '... |
---|
| 1433 | % '-l ' filename_joblist '.log"\n']; |
---|
| 1434 | % filename_oarcommand=fullfile(RootBat,'oar_command'); |
---|
| 1435 | % fid=fopen(filename_oarcommand,'w'); |
---|
| 1436 | % fprintf(fid,oar_command); |
---|
| 1437 | % fclose(fid); |
---|
| 1438 | % fprintf(oar_command);% display in command line |
---|
| 1439 | % system(oar_command); |
---|
| 1440 | % % eval(['! . ' filename |
---|
| 1441 | % % _oarcommand]) |
---|
| 1442 | % case 'oar-dispatch' %oar-dispatch.pl |
---|
| 1443 | % ncores=str2double(... |
---|
| 1444 | % inputdlg('Number of cores (max 36)','oarsub parameter',1,{'6'})... |
---|
| 1445 | % ); |
---|
| 1446 | % walltime_onejob=600;%seconds |
---|
| 1447 | % filename_joblist=fullfile(RootBat,'job_list.txt'); |
---|
| 1448 | % fid=fopen(filename_joblist,'w'); |
---|
| 1449 | % for p=1:length(batch_file_list) |
---|
| 1450 | % oar_command=['oarsub -n CIVX '... |
---|
| 1451 | % '-E ' regexprep(batch_file_list{p},'\.bat\>','.stderr') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.stdout ')... |
---|
| 1452 | % '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '" ' batch_file_list{p}]; |
---|
| 1453 | % fprintf(fid,[oar_command '\n']); |
---|
| 1454 | % end |
---|
| 1455 | % fclose(fid); |
---|
| 1456 | % oar_command=['oarsub -t container -n civx-container '... |
---|
| 1457 | % '-l /core=' num2str(ncores)... |
---|
| 1458 | % ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '... |
---|
| 1459 | % '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '... |
---|
| 1460 | % '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '... |
---|
| 1461 | % '"oar-dispatch -f ' filename_joblist '"']; |
---|
| 1462 | % filename_oarcommand=fullfile(RootBat,'oar_command'); |
---|
| 1463 | % fid=fopen(filename_oarcommand,'w'); |
---|
| 1464 | % fprintf(fid,[oar_command '\n']); |
---|
| 1465 | % fclose(fid); |
---|
| 1466 | % display(oar_command); |
---|
| 1467 | % eval(['! . ' filename_oarcommand]) |
---|
| 1468 | % case 'mpilauncher' |
---|
| 1469 | % filename_joblist=fullfile(RootBat,'job_list.txt'); |
---|
| 1470 | % fid=fopen(filename_joblist,'w'); |
---|
| 1471 | % |
---|
| 1472 | % for p=1:length(batch_file_list) |
---|
| 1473 | % fprintf(fid,[batch_file_list{p} '\n']); |
---|
| 1474 | % end |
---|
| 1475 | % fclose(fid) |
---|
| 1476 | % text_oarscript=[... |
---|
| 1477 | % '#!/bin/bash \n'... |
---|
| 1478 | % '#OAR -n Mylauncher \n'... |
---|
| 1479 | % '#OAR -l node=4/core=5,walltime=0:15:00 \n'... |
---|
| 1480 | % '#OAR -E ' fullfile(RootBat,'stderrfile.log') ' \n'... |
---|
| 1481 | % '#OAR -O ' fullfile(RootBat,'stdoutfile.log') ' \n'... |
---|
| 1482 | % '# ========================================================= \n'... |
---|
| 1483 | % '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'... |
---|
| 1484 | % '# application for coriolis PIV post-processing. \n'... |
---|
| 1485 | % '# OAR uses oarshmost wrapper to propagate the user environement. \n'... |
---|
| 1486 | % '# This wrapper assert that the user has the same environment on all the \n'... |
---|
| 1487 | % '# allocated nodes (basic behavior needed by most MPI applications). \n'... |
---|
| 1488 | % '# \n'... |
---|
| 1489 | % '# REQUIREMENT: \n'... |
---|
| 1490 | % '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'... |
---|
| 1491 | % '# If a different location is used, change the line following the comment "Bidouille" \n'... |
---|
| 1492 | % '# ========================================================= \n'... |
---|
| 1493 | % '# USER should only modify these 2 lines \n'... |
---|
| 1494 | % 'WORKDIR=' pwd ' \n'... |
---|
| 1495 | % 'COMMANDE="mpilauncher -f ' filename_joblist '" \n'... |
---|
| 1496 | % '# ========================================================= \n'... |
---|
| 1497 | % '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'... |
---|
| 1498 | % 'echo "job starting on: "`hostname` \n'... |
---|
| 1499 | % 'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'... |
---|
| 1500 | % 'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'... |
---|
| 1501 | % '#========== Bidouille ============== \n'... |
---|
| 1502 | % 'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...% 'cd $WORKDIR \n'... |
---|
| 1503 | % 'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'... |
---|
| 1504 | % 'echo "I run: $CMD" \n'... |
---|
| 1505 | % '$CMD \n'... |
---|
| 1506 | % 'echo "job ending" \n'... |
---|
| 1507 | % ]; |
---|
| 1508 | % % oarsub -S ./oar.sub |
---|
| 1509 | % filename_oarscript=fullfile(RootBat,'oar_command'); |
---|
| 1510 | % fid=fopen(filename_oarscript,'w'); |
---|
| 1511 | % fprintf(fid,[text_oarscript]); |
---|
| 1512 | % fclose(fid); |
---|
| 1513 | % eval(['!chmod +x ' filename_oarscript]); |
---|
| 1514 | % eval(['!oarsub -S ' filename_oarscript]); |
---|
| 1515 | % end |
---|
| 1516 | % end |
---|
| 1517 | % case {'background','local'} |
---|
| 1518 | % switch Param.Program |
---|
| 1519 | % case {'civ_matlab'} |
---|
| 1520 | % switch Param.RunMode |
---|
| 1521 | % case 'background' |
---|
| 1522 | % switch computer |
---|
| 1523 | % case {'PCWIN','PCWIN64'} |
---|
| 1524 | % filename_superbat=fullfile(RootBat,'job_list.bat'); |
---|
| 1525 | % fid=fopen(filename_superbat,'w'); |
---|
| 1526 | % if fid==-1 |
---|
| 1527 | % msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat]) |
---|
| 1528 | % return |
---|
| 1529 | % end |
---|
| 1530 | % fprintf(fid,['matlab -automation '... |
---|
| 1531 | % '-r "addpath(''' regexprep(path_civ,'\\','\\\\') ''');']); |
---|
| 1532 | % for p=1:length(batch_file_list) |
---|
| 1533 | % fprintf(fid,['run ' regexprep(batch_file_list{p},'\\','\\\\') ';']); |
---|
| 1534 | % end |
---|
| 1535 | % fprintf(fid, 'exit"'); |
---|
| 1536 | % fclose(fid); |
---|
| 1537 | % dos([filename_superbat ' &']); |
---|
| 1538 | % case {'GLNX86','GLNXA64','MACI64'} |
---|
| 1539 | % filename_superbat=fullfile(RootBat,'job_list.sh'); |
---|
| 1540 | % fid=fopen(filename_superbat,'w'); |
---|
| 1541 | % if fid==-1 |
---|
| 1542 | % msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat]) |
---|
| 1543 | % return |
---|
| 1544 | % end |
---|
| 1545 | % fprintf(fid,['#!/bin/bash \n' ... |
---|
| 1546 | % '/etc/sysprofile \n'... |
---|
| 1547 | % 'matlab -nodisplay -nosplash -nojvm -logfile <<END_MATLAB \n'... |
---|
| 1548 | % 'addpath(''' path_civ ''');\n']); |
---|
| 1549 | % for p=1:length(batch_file_list) |
---|
| 1550 | % fprintf(fid,['run ' batch_file_list{p} '\n']); |
---|
| 1551 | % end |
---|
| 1552 | % fprintf(fid, 'exit\nEND_MATLAB\n'); |
---|
| 1553 | % fclose(fid); |
---|
| 1554 | % system(['chmod +x ' filename_superbat]); |
---|
| 1555 | % system([filename_superbat ' &']); |
---|
| 1556 | % end |
---|
| 1557 | % case 'local' |
---|
| 1558 | % for p=1:length(batch_file_list) |
---|
| 1559 | % fid=fopen(batch_file_list{p}); |
---|
| 1560 | % eval(fscanf(fid,'%s')); |
---|
| 1561 | % fclose(fid); |
---|
| 1562 | % end |
---|
| 1563 | % end |
---|
| 1564 | % case {'CivX','CivAll','civ_matlab.sh'} |
---|
| 1565 | % switch computer |
---|
| 1566 | % case {'PCWIN','PCWIN64'} |
---|
| 1567 | % filename_superbat=fullfile(RootBat,'job_list.bat'); |
---|
| 1568 | % fid=fopen(filename_superbat,'w'); |
---|
| 1569 | % if fid==-1 |
---|
| 1570 | % msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat]) |
---|
| 1571 | % return |
---|
| 1572 | % end |
---|
| 1573 | % for p=1:length(batch_file_list) |
---|
| 1574 | % fprintf(fid,['@call "' regexprep(batch_file_list{p},'\\','\\\\') '"' '\n']); |
---|
| 1575 | % end |
---|
| 1576 | % fclose(fid); |
---|
| 1577 | % system(['chmod +x ' filename_superbat]); |
---|
| 1578 | % case {'GLNX86','GLNXA64','MACI64'} |
---|
| 1579 | % filename_superbat=fullfile(RootBat,'job_list.bat'); |
---|
| 1580 | % fid=fopen(filename_superbat,'w'); |
---|
| 1581 | % if fid==-1 |
---|
| 1582 | % msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat]) |
---|
| 1583 | % return |
---|
| 1584 | % end |
---|
| 1585 | % for p=1:length(batch_file_list) |
---|
| 1586 | % fprintf(fid,['sh ' batch_file_list{p} '\n']); |
---|
| 1587 | % end |
---|
| 1588 | % fclose(fid); |
---|
| 1589 | % system(['chmod +x ' filename_superbat]); |
---|
| 1590 | % end |
---|
| 1591 | % switch Param.RunMode |
---|
| 1592 | % case 'background' |
---|
| 1593 | % system([filename_superbat ' &']);% execute main commmand see what it does in dos ? |
---|
| 1594 | % case 'local' |
---|
| 1595 | % system(filename_superbat); |
---|
| 1596 | % end |
---|
| 1597 | % end |
---|
| 1598 | % end |
---|
| 1599 | % |
---|
| 1600 | % |
---|
| 1601 | % %% save interface state |
---|
| 1602 | % if isfield(filecell,'nc') |
---|
| 1603 | % if isfield(filecell.nc,'civ2') |
---|
| 1604 | % fileresu=filecell.nc.civ2{1,1}; |
---|
| 1605 | % else |
---|
| 1606 | % fileresu=filecell.nc.civ1{1,1}; |
---|
| 1607 | % end |
---|
| 1608 | % end |
---|
| 1609 | % [RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu); |
---|
| 1610 | % namedoc=fullfile(RootPath,SubDir,RootFile); |
---|
| 1611 | % detect=1; |
---|
| 1612 | % while detect==1 |
---|
| 1613 | % namefigfull=[namedoc '.fig']; |
---|
| 1614 | % hh=dir(namefigfull); |
---|
| 1615 | % if ~isempty(hh) |
---|
| 1616 | % detect=1; |
---|
| 1617 | % namedoc=[namedoc '.0']; |
---|
| 1618 | % else |
---|
| 1619 | % detect=0; |
---|
| 1620 | % end |
---|
| 1621 | % end |
---|
| 1622 | % Param=rmfield(Param,'status'); |
---|
| 1623 | % Param=rmfield(Param,'xml'); |
---|
| 1624 | % t=struct2xml(Param); |
---|
| 1625 | % t=set(t,1,'name','Civ');% set the head label |
---|
| 1626 | % save(t,[namedoc '.civ.xml']); %save GUI parameters as xml file |
---|
| 1627 | % % saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml) |
---|
| 1628 | % |
---|
| 1629 | % %Save info in personal profile (initiate browser next time) TODO |
---|
| 1630 | % MenuFile={}; |
---|
| 1631 | % dir_perso=prefdir; |
---|
| 1632 | % profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); |
---|
| 1633 | % if exist(profil_perso,'file') |
---|
| 1634 | % hh=load (profil_perso); |
---|
| 1635 | % if isfield(hh,'MenuFile') |
---|
| 1636 | % MenuFile=hh.MenuFile; |
---|
| 1637 | % end |
---|
| 1638 | % if isfield(filecell.nc,'civ2') |
---|
| 1639 | % MenuFile=[filecell.nc.civ2{1,1}; MenuFile]; |
---|
| 1640 | % else |
---|
| 1641 | % MenuFile=[filecell.nc.civ1{1,1}; MenuFile]; |
---|
| 1642 | % end |
---|
| 1643 | % save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat |
---|
| 1644 | % else |
---|
| 1645 | % MenuFile=filecell.ima1.civ1(1,1); |
---|
| 1646 | % save (profil_perso,'MenuFile') |
---|
| 1647 | % end |
---|
[597] | 1648 | |
---|
[598] | 1649 | % %------------------------------------------------------------------------ |
---|
| 1650 | % % --- determine the list of reference indices of processing file |
---|
| 1651 | % function [ref_i,ref_j,errormsg]=find_ref_indices(handles) |
---|
| 1652 | % %------------------------------------------------------------------------ |
---|
| 1653 | % errormsg=''; %default error message |
---|
| 1654 | % first_i=str2double(get(handles.first_i,'String'));%first index i |
---|
| 1655 | % last_i=str2double(get(handles.last_i,'String'));%last index i |
---|
| 1656 | % incr_i=str2double(get(handles.incr_i,'String'));% increment |
---|
| 1657 | % if isequal(get(handles.first_j,'Visible'),'on') |
---|
| 1658 | % first_j=str2double(get(handles.first_j,'String'));%first index j |
---|
| 1659 | % last_j=str2double(get(handles.last_j,'String'));%last index j |
---|
| 1660 | % incr_j=str2double(get(handles.incr_j,'String'));% increment |
---|
| 1661 | % else |
---|
| 1662 | % first_j=1; |
---|
| 1663 | % last_j=1; |
---|
| 1664 | % incr_j=1; |
---|
| 1665 | % end |
---|
| 1666 | % ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair) |
---|
| 1667 | % ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair) |
---|
| 1668 | % if isnan(first_i)||isnan(first_j) |
---|
| 1669 | % errormsg='first field number not defined'; |
---|
| 1670 | % elseif isnan(last_i)||isnan(last_j) |
---|
| 1671 | % errormsg='last field number not defined'; |
---|
| 1672 | % elseif isnan(incr_i)||isnan(incr_j) |
---|
| 1673 | % errormsg='increment in field number not defined'; |
---|
| 1674 | % elseif last_i < first_i || last_j < first_j |
---|
| 1675 | % errormsg='last field number must be larger than the first one'; |
---|
| 1676 | % end |
---|
[597] | 1677 | |
---|
| 1678 | %------------------------------------------------------------------------ |
---|
| 1679 | % --- determine the list of filenames and indices needed for launch_job |
---|
| 1680 | %------------------------------------------------------------------------ |
---|
| 1681 | % OUTPUT: |
---|
| 1682 | % filecell: structure of cell arrays {ref_i,ref_j} containing all the filenames involved in the civ_input process |
---|
| 1683 | % the indices ref_i and ref_j correspond to the list of reference indices |
---|
| 1684 | % .filebase=fullfile(RootPath,RootFile) used to construct mask names, grid names, CivDoc xml file |
---|
| 1685 | % .ima1.civ1,.ima1.civ2: first image for civ1 and civ2 respectively (possibly different) |
---|
| 1686 | % .ima2.civ1,.ima2.civ2: second image for civ1 and civ2 respectively (possibly different) |
---|
| 1687 | % .nc.civ1,.nc.civ2: netcdf files containing civ1 and civ2 data respectively (possibly different) |
---|
| 1688 | % i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2: arrays of files indices, needed for timing records |
---|
| 1689 | function [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,NomType_nc,file_ref_fix1,file_ref_fix2,compare,errormsg]=... |
---|
| 1690 | set_civ_filenames(handles,ref_i,ref_j,checkbox) |
---|
| 1691 | %------------------------------------------------------------------------ |
---|
| 1692 | filecell=[];%default |
---|
| 1693 | errormsg=''; |
---|
| 1694 | ListProgram=get(handles.Program,'String'); |
---|
| 1695 | CivMode=ListProgram{get(handles.Program,'Value')};%Program to use , CivX or Matlab |
---|
| 1696 | |
---|
| 1697 | %% get the root name and check dir |
---|
| 1698 | RootPath=get(handles.RootPath,'String'); |
---|
| 1699 | SubDirImages=get(handles.SubDirImages,'String'); |
---|
| 1700 | RootFile=get(handles.RootFile,'String'); |
---|
| 1701 | filecell.filebase=fullfile(RootPath,SubDirImages,RootFile); |
---|
| 1702 | if isempty(filecell.filebase) |
---|
| 1703 | errormsg='please open an image with the upper menu option Open/Browse...'; |
---|
| 1704 | return |
---|
| 1705 | end |
---|
| 1706 | if ~exist(RootPath,'dir') |
---|
| 1707 | errormsg=['path to images ' RootPath ' not found']; |
---|
| 1708 | return |
---|
| 1709 | end |
---|
| 1710 | [tild,message]=fileattrib(RootPath); |
---|
| 1711 | if ~isempty(message) && ~isequal(message.UserWrite,1) |
---|
| 1712 | errormsg=['No writting access to ' RootPath]; |
---|
| 1713 | return |
---|
| 1714 | end |
---|
| 1715 | %check result directory |
---|
| 1716 | subdir_civ1=regexprep(get(handles.SubdirCiv1,'String'),'^.','');%subdirectory subdir_civ1 for the netcdf output data |
---|
| 1717 | subdir_civ2=regexprep(get(handles.SubdirCiv2,'String'),'^.',''); |
---|
| 1718 | if isequal(subdir_civ1,''),subdir_civ1='civ'; end% put default subdir |
---|
| 1719 | % subdir_civ1=[ '.' subdir_civ1]; |
---|
| 1720 | % subdir_civ2=[ '.' subdir_civ2]; |
---|
| 1721 | if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir |
---|
| 1722 | subdir_civ1=[SubDirImages '.' subdir_civ1]; |
---|
| 1723 | subdir_civ2=[SubDirImages '.' subdir_civ2]; |
---|
| 1724 | |
---|
| 1725 | %% choose root names depending on ListCompareMode =displacement, shift, PIV or stereo PIV |
---|
| 1726 | ListCompareMode=get(handles.ListCompareMode,'String'); |
---|
| 1727 | compare=ListCompareMode{get(handles.ListCompareMode,'Value')}; |
---|
| 1728 | |
---|
| 1729 | % set the nomenclature type of the nc files depending on the pair mode |
---|
| 1730 | if strcmp(compare,'displacement')||strcmp(compare,'shift') |
---|
| 1731 | mode='displacement'; |
---|
| 1732 | else |
---|
| 1733 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 1734 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 1735 | mode=mode_list{mode_value}; |
---|
| 1736 | end |
---|
| 1737 | NomType_ima2=get(handles.NomType,'String'); |
---|
| 1738 | NomType_nc=nomtype2pair(NomType_ima2,mode); |
---|
| 1739 | |
---|
| 1740 | % set the rootfile and image indexing |
---|
| 1741 | RootFile_ima2=get(handles.RootFile,'String');%root file for the second image series |
---|
| 1742 | ext_ima=get(handles.ImaExt,'String'); % image extension (the same for all images) |
---|
| 1743 | switch compare |
---|
| 1744 | case {'PIV','PIV volume'} |
---|
| 1745 | RootFile_ima1=RootFile_ima2;% root name of the two image series is the same |
---|
| 1746 | NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one |
---|
| 1747 | RootFile_nc=RootFile_ima2; |
---|
| 1748 | case 'displacement' |
---|
| 1749 | RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1 |
---|
| 1750 | NomType_ima1='';% no indexing of the first image, a fixed reference for the whole series |
---|
| 1751 | RootFile_nc=RootFile_ima2; |
---|
| 1752 | case 'shift' |
---|
| 1753 | RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1 |
---|
| 1754 | NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one |
---|
| 1755 | RootFile_nc=[RootFile_ima1 '-' RootFile_ima2]; |
---|
| 1756 | end |
---|
| 1757 | |
---|
| 1758 | %determine the list of file indices involved |
---|
| 1759 | [i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=... |
---|
| 1760 | find_pair_indices(handles,ref_i,ref_j,mode); |
---|
| 1761 | |
---|
| 1762 | %determine the new filebase for 'displacement' ListPairMode (comparison of two series) |
---|
| 1763 | %filebase_B=filebase;% root name of the second field series for stereo |
---|
| 1764 | % filebase_A=filebase;%default |
---|
| 1765 | % if strcmp(compare,'PIV') |
---|
| 1766 | % filebase_AB=filebase; |
---|
| 1767 | % else |
---|
| 1768 | % [Path2,Name2]=fileparts(filebase_B); |
---|
| 1769 | % Name1=RootFile_ima1; |
---|
| 1770 | % filebase_AB=fullfile(Path2,[Name2 '-' Name1]); |
---|
| 1771 | % end |
---|
| 1772 | % [RootPath_AB,RootFile_AB]=fileparts(filebase_AB); |
---|
| 1773 | % % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B); |
---|
| 1774 | % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B); |
---|
| 1775 | % [RootPath_nc,RootFile_nc]=fileparts(filebase_B);%default |
---|
| 1776 | % if strcmp(compare,'displacement') |
---|
| 1777 | % % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B); |
---|
| 1778 | % % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B); |
---|
| 1779 | % [RootPath_nc,RootFile_nc]=fileparts(filebase_B); |
---|
| 1780 | % elseif strcmp(compare,'shift') |
---|
| 1781 | % RootPath_nc=RootPath_AB; |
---|
| 1782 | % RootFile_nc=RootFile_AB; |
---|
| 1783 | % end |
---|
| 1784 | % else |
---|
| 1785 | % filebase_ima1=filebase_B; |
---|
| 1786 | % filebase_ima2=filebase_B; |
---|
| 1787 | % filebase_nc=filebase_B; |
---|
| 1788 | % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1); |
---|
| 1789 | % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2); |
---|
| 1790 | % [RootPath_nc,RootFile_nc]=fileparts(filebase_nc); |
---|
| 1791 | % [RootPath_A,RootFile_A]=fileparts(filebase_A); |
---|
| 1792 | |
---|
| 1793 | |
---|
| 1794 | %% determine reference files for fix: |
---|
| 1795 | file_ref_fix1={};%default |
---|
| 1796 | file_ref_fix2={}; |
---|
| 1797 | nbfield=length(i1_civ1); |
---|
| 1798 | nbslice=length(j1_civ1); |
---|
| 1799 | if checkbox(2)==1% fix1 performed |
---|
| 1800 | ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback |
---|
| 1801 | if ~isempty(ref) |
---|
| 1802 | first_i=str2double(get(handles.first_i,'String')); |
---|
| 1803 | last_i=str2double(get(handles.last_i,'String')); |
---|
| 1804 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
| 1805 | first_j=str2double(get(handles.first_j,'String')); |
---|
| 1806 | last_j=str2double(get(handles.last_j,'String')); |
---|
| 1807 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
| 1808 | num_i_ref=first_i:incr_i:last_i; |
---|
| 1809 | num_j_ref=first_j:incr_j:last_j; |
---|
| 1810 | if isequal(mode,'displacement') |
---|
| 1811 | num_i1=num_i_ref; |
---|
| 1812 | num_i2=num_i_ref; |
---|
| 1813 | num_j1=num_j_ref; |
---|
| 1814 | num_j2=num_j_ref; |
---|
| 1815 | elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2') |
---|
| 1816 | num_i1=num_i_ref; |
---|
| 1817 | num_i2=num_i1; |
---|
| 1818 | num_j1=ref.num_a*ones(size(num_i_ref)); |
---|
| 1819 | num_j2=ref.num_b*ones(size(num_i_ref)); |
---|
| 1820 | elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)') |
---|
| 1821 | delta1=floor((ref.num2-ref.num1)/2); |
---|
| 1822 | delta2=ceil((ref.num2-ref.num1)/2); |
---|
| 1823 | num_i1=num_i_ref-delta1*ones(size(num_i_ref)); |
---|
| 1824 | num_i2=num_i_ref+delta2*ones(size(num_i_ref)); |
---|
| 1825 | if isempty(ref.num_a) |
---|
| 1826 | ref.num_a=1; |
---|
| 1827 | end |
---|
| 1828 | num_j1=ref.num_a*ones(size(num_i1)); |
---|
| 1829 | num_j2=num_j1; |
---|
| 1830 | elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)') |
---|
| 1831 | delta1=floor((ref.num_b-ref.num_a)/2); |
---|
| 1832 | delta2=ceil((ref.num_b-ref.num_a)/2); |
---|
| 1833 | num_i1=ref.num1*ones(size(num_i_ref)); |
---|
| 1834 | num_i2=num_i1; |
---|
| 1835 | num_j1=num_j_ref-delta1*ones(size(num_j_ref)); |
---|
| 1836 | num_j2=num_j_ref+delta2*ones(size(num_j_ref)); |
---|
| 1837 | end |
---|
| 1838 | for ifile=1:nbfield |
---|
| 1839 | for j=1:nbslice |
---|
| 1840 | [RootPathRef,RootFile]=fileparts(ref.filebase); |
---|
| 1841 | file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j)); |
---|
| 1842 | file_ref_fix1(ifile,j)={file_ref}; |
---|
| 1843 | if ~exist(file_ref,'file') |
---|
| 1844 | errormsg=['reference file ' file_ref ' not found for fix1']; |
---|
| 1845 | return |
---|
| 1846 | end |
---|
| 1847 | end |
---|
| 1848 | end |
---|
| 1849 | end |
---|
| 1850 | end |
---|
| 1851 | |
---|
| 1852 | %% determine reference files for fix2: |
---|
| 1853 | if checkbox(5)==1% fix2 performed |
---|
| 1854 | ref=get(handles.ref_fix2,'UserData'); |
---|
| 1855 | if ~isempty(ref) |
---|
| 1856 | first_i=str2double(get(handles.first_i,'String')); |
---|
| 1857 | last_i=str2double(get(handles.last_i,'String')); |
---|
| 1858 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
| 1859 | first_j=str2double(get(handles.first_j,'String')); |
---|
| 1860 | last_j=str2double(get(handles.last_j,'String')); |
---|
| 1861 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
| 1862 | num_i_ref=first_i:incr_i:last_i; |
---|
| 1863 | num_j_ref=first_j:incr_j:last_j; |
---|
| 1864 | if isequal(mode,'displacement') |
---|
| 1865 | num_i1=num_i_ref; |
---|
| 1866 | num_i2=num_i_ref; |
---|
| 1867 | num_j1=num_j_ref; |
---|
| 1868 | num_j2=num_j_ref; |
---|
| 1869 | elseif isequal(mode,'pair j1-j2') |
---|
| 1870 | num_i1=num_i_ref; |
---|
| 1871 | num_i2=num_i1; |
---|
| 1872 | num_j1=ref.num_a; |
---|
| 1873 | num_j2=ref.num_b; |
---|
| 1874 | elseif isequal(mode,'series(Di)') |
---|
| 1875 | delta1=floor((ref.num2-ref.num1)/2); |
---|
| 1876 | delta2=ceil((ref.num2-ref.num1)/2); |
---|
| 1877 | num_i1=num_i_ref-delta1*ones(size(num_i_ref)); |
---|
| 1878 | num_i2=num_i_ref+delta2*ones(size(num_i_ref)); |
---|
| 1879 | num_j1=ref.num_a*ones(size(num_i1)); |
---|
| 1880 | num_j2=num_j1; |
---|
| 1881 | elseif isequal(mode,'series(Dj)') |
---|
| 1882 | delta1=floor((ref.num_b-ref.num_a)/2); |
---|
| 1883 | delta2=ceil((ref.num_b-ref.num_a)/2); |
---|
| 1884 | num_i1=ref.num1*ones(size(num_i_ref)); |
---|
| 1885 | num_i2=num_i1; |
---|
| 1886 | num_j1=num_j_ref-delta1*ones(size(num_j_ref)); |
---|
| 1887 | num_j2=num_j_ref+delta2*ones(size(num_j_ref)); |
---|
| 1888 | end |
---|
| 1889 | for ifile=1:nbfield |
---|
| 1890 | for j=1:nbslice |
---|
| 1891 | [RootPathRef,RootFile]=fileparts(ref.filebase); |
---|
| 1892 | file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j)); |
---|
| 1893 | file_ref_fix2(ifile,j)={file_ref}; |
---|
| 1894 | if ~exist(file_ref,'file') |
---|
| 1895 | errormsg=['reference file ' file_ref ' not found for fix2']; |
---|
| 1896 | return |
---|
| 1897 | end |
---|
| 1898 | end |
---|
| 1899 | end |
---|
| 1900 | end |
---|
| 1901 | end |
---|
| 1902 | |
---|
| 1903 | %% check the existence of the netcdf and image files involved |
---|
| 1904 | % %%%%%%%%%%%% case CheckCiv1 activated %%%%%%%%%%%%% |
---|
| 1905 | if checkbox(1)==1; |
---|
| 1906 | detect=1; |
---|
| 1907 | vers=0; |
---|
| 1908 | subdir_civ1_new=subdir_civ1; |
---|
| 1909 | answer='No'; |
---|
| 1910 | while detect==1 %create a new subdir if the netcdf files already exist |
---|
| 1911 | for ifile=1:nbfield |
---|
| 1912 | for j=1:nbslice |
---|
| 1913 | filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
| 1914 | detect=exist(filename,'file')==2; |
---|
| 1915 | if detect% if a netcdf file already exists |
---|
| 1916 | if strcmp(answer,'No') |
---|
| 1917 | answer=msgbox_uvmat('INPUT_Y-N',['overwrite existing civ files in ' subdir_civ1_new]); |
---|
| 1918 | end |
---|
| 1919 | if strcmp(answer,'Yes') |
---|
| 1920 | detect=0; |
---|
| 1921 | filecell.nc.civ1(ifile,j)={filename}; |
---|
| 1922 | else |
---|
| 1923 | r=regexp(subdir_civ1_new,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number |
---|
| 1924 | if isempty(r) |
---|
| 1925 | r(1).root=[subdir_civ1_new '_']; |
---|
| 1926 | r(1).num1='0'; |
---|
| 1927 | end |
---|
| 1928 | subdir_civ1_new=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1 |
---|
| 1929 | subdir_civ2=subdir_civ1_new; |
---|
| 1930 | end |
---|
| 1931 | break |
---|
| 1932 | end |
---|
| 1933 | filecell.nc.civ1(ifile,j)={filename}; |
---|
| 1934 | end |
---|
| 1935 | if detect% if a netcdf file already exists |
---|
| 1936 | break |
---|
| 1937 | end |
---|
| 1938 | end |
---|
| 1939 | |
---|
| 1940 | %create the new SubdirCiv1 |
---|
| 1941 | if ~exist(fullfile(RootPath,subdir_civ1_new),'dir') |
---|
| 1942 | [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new)); |
---|
| 1943 | if ~strcmp(msg1,'') |
---|
| 1944 | errormsg=['cannot create ' subdir_civ1_new ': ' msg1];%error message for directory creation |
---|
| 1945 | return |
---|
| 1946 | elseif isunix |
---|
| 1947 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
| 1948 | if ~strcmp(msg2,'') |
---|
| 1949 | errormsg=['pb of permission for ' fullfile(RootPath,subdir_civ1_new) ': ' msg2];%error message for directory creation |
---|
| 1950 | return |
---|
| 1951 | end |
---|
| 1952 | end |
---|
| 1953 | end |
---|
| 1954 | if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series |
---|
| 1955 | for ifile=1:nbfield |
---|
| 1956 | for j=1:nbslice |
---|
| 1957 | filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
| 1958 | detect=exist(filename,'file')==2; |
---|
| 1959 | if detect% if a netcdf file already exists |
---|
| 1960 | indstr=regexp(subdir_civ1_new,'\D'); |
---|
| 1961 | if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number |
---|
| 1962 | vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1; |
---|
| 1963 | subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)]; |
---|
| 1964 | else |
---|
| 1965 | vers=vers+1; |
---|
| 1966 | subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)]; |
---|
| 1967 | end |
---|
| 1968 | subdir_civ2=subdir_civ1; |
---|
| 1969 | break |
---|
| 1970 | end |
---|
| 1971 | filecell.ncA.civ1(ifile,j)={filename}; |
---|
| 1972 | end |
---|
| 1973 | if detect% if a netcdf file already exists |
---|
| 1974 | break |
---|
| 1975 | end |
---|
| 1976 | end |
---|
| 1977 | %create the new SubdirCiv1 |
---|
| 1978 | if ~exist(fullfile(RootPath,subdir_civ1_new),'dir') |
---|
| 1979 | [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new)); |
---|
| 1980 | if ~strcmp(msg1,'') |
---|
| 1981 | errormsg=['cannot create ' subdir_civ1_new ': ' msg1]; |
---|
| 1982 | return |
---|
| 1983 | else |
---|
| 1984 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
| 1985 | if ~strcmp(msg2,'') |
---|
| 1986 | errormsg=['pb of permission for ' subdir_civ1_new ': ' msg2];%error message for directory creation |
---|
| 1987 | return |
---|
| 1988 | end |
---|
| 1989 | end |
---|
| 1990 | end |
---|
| 1991 | end |
---|
| 1992 | end |
---|
| 1993 | subdir_civ1=subdir_civ1_new; |
---|
| 1994 | % get image names |
---|
| 1995 | for ifile=1:nbfield |
---|
| 1996 | for j=1:nbslice |
---|
| 1997 | filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j)); |
---|
| 1998 | idetect(j)=exist(filename,'file')==2; |
---|
| 1999 | filecell.ima1.civ1(ifile,j)={filename}; %first image |
---|
| 2000 | filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j)); |
---|
| 2001 | idetect_1(j)=exist(filename,'file')==2; |
---|
| 2002 | filecell.ima2.civ1(ifile,j)={filename};%second image |
---|
| 2003 | end |
---|
| 2004 | [idetectmin,indexj]=min(idetect); |
---|
| 2005 | if idetectmin==0, |
---|
| 2006 | errormsg=[filecell.ima1.civ1{ifile,indexj} ' not found']; |
---|
| 2007 | return |
---|
| 2008 | end |
---|
| 2009 | [idetectmin,indexj]=min(idetect_1); |
---|
| 2010 | if idetectmin==0, |
---|
| 2011 | errormsg=[filecell.ima2.civ1{ifile,indexj} ' not found']; |
---|
| 2012 | return |
---|
| 2013 | end |
---|
| 2014 | end |
---|
| 2015 | if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)')) |
---|
| 2016 | for ifile=1:nbfield |
---|
| 2017 | for j=1:nbslice |
---|
| 2018 | filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j)); |
---|
| 2019 | idetect(j)=exist(filename,'file')==2; |
---|
| 2020 | filecell.imaA1.civ1(ifile,j)={filename} ;%first image |
---|
| 2021 | filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j)); |
---|
| 2022 | idetect_1(j)=exist(filename,'file')==2; |
---|
| 2023 | filecell.imaA2.civ1(ifile,j)={filename};%second image |
---|
| 2024 | end |
---|
| 2025 | [idetectmin,indexj]=min(idetect); |
---|
| 2026 | if idetectmin==0, |
---|
| 2027 | errormsg=[filecell.imaA1.civ1{ifile,indexj} ' not found']; |
---|
| 2028 | return |
---|
| 2029 | end |
---|
| 2030 | [idetectmin,indexj]=min(idetect_1); |
---|
| 2031 | if idetectmin==0, |
---|
| 2032 | errormsg=[filecell.imaA2.civ1{ifile,indexj} ' not found']; |
---|
| 2033 | return |
---|
| 2034 | end |
---|
| 2035 | end |
---|
| 2036 | end |
---|
| 2037 | |
---|
| 2038 | %%%%%%%%%%%%% checkfix1 or checkpatch1 activated but no checkciv1 %%%%%%%%%%%%% |
---|
| 2039 | elseif (checkbox(2)==1 || checkbox(3)==1); |
---|
| 2040 | for ifile=1:nbfield |
---|
| 2041 | for j=1:nbslice |
---|
| 2042 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
| 2043 | detect=exist(filename,'file')==2; |
---|
| 2044 | if detect==0 |
---|
| 2045 | errormsg=[filename ' not found']; |
---|
| 2046 | return |
---|
| 2047 | end |
---|
| 2048 | filecell.nc.civ1(ifile,j)={filename}; |
---|
| 2049 | end |
---|
| 2050 | end |
---|
| 2051 | if strcmp(compare,'stereo PIV') |
---|
| 2052 | for ifile=1:nbfield |
---|
| 2053 | for j=1:nbslice |
---|
| 2054 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
| 2055 | filecell.ncA.civ1(ifile,j)={filename}; |
---|
| 2056 | if ~exist(filename,'file') |
---|
| 2057 | errormsg=['input file ' filename ' not found']; |
---|
| 2058 | return |
---|
| 2059 | end |
---|
| 2060 | end |
---|
| 2061 | end |
---|
| 2062 | end |
---|
| 2063 | end |
---|
| 2064 | |
---|
| 2065 | %%%%%%%%%%%%% if checkciv2 performed with pairs different than checkciv1 %%%%%%%%%%%%% |
---|
| 2066 | testdiff=0; |
---|
| 2067 | if (checkbox(4)==1)&&... |
---|
| 2068 | ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1)) |
---|
| 2069 | testdiff=1; |
---|
| 2070 | detect=1; |
---|
| 2071 | vers=0; |
---|
| 2072 | subdir_civ2_new=subdir_civ2; |
---|
| 2073 | while detect==1 %create a new subdir if the netcdf files already exist |
---|
| 2074 | for ifile=1:nbfield |
---|
| 2075 | for j=1:nbslice |
---|
| 2076 | filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
| 2077 | detect=exist(filename,'file')==2; |
---|
| 2078 | if detect% if a netcdf file already exists |
---|
| 2079 | indstr=regexp(subdir_civ2,'\D'); |
---|
| 2080 | if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number |
---|
| 2081 | vers=str2double(subdir_civ2(indstr(end)+1:end))+1; |
---|
| 2082 | subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)]; |
---|
| 2083 | else |
---|
| 2084 | vers=vers+1; |
---|
| 2085 | subdir_civ2_new=[subdir_civ1 '_' num2str(vers)]; |
---|
| 2086 | end |
---|
| 2087 | break |
---|
| 2088 | end |
---|
| 2089 | filecell.nc.civ2(ifile,j)={filename}; |
---|
| 2090 | end |
---|
| 2091 | if detect% if a netcdf file already exists |
---|
| 2092 | break |
---|
| 2093 | end |
---|
| 2094 | end |
---|
| 2095 | %create the new subdir_civ2_new |
---|
| 2096 | if ~exist(fullfile(RootPath,subdir_civ2_new),'dir') |
---|
| 2097 | [xx,m2]=mkdir(fullfile(RootPath,subdir_civ2_new)); |
---|
| 2098 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
| 2099 | if ~isequal(m2,'') |
---|
| 2100 | errormsg=['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2]; |
---|
| 2101 | return |
---|
| 2102 | end |
---|
| 2103 | end |
---|
| 2104 | if strcmp(compare,'stereo PIV')%check second nc series |
---|
| 2105 | for ifile=1:nbfield |
---|
| 2106 | for j=1:nbslice |
---|
| 2107 | filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
| 2108 | detect=exist(filename,'file')==2; |
---|
| 2109 | if detect% if a netcdf file already exists |
---|
| 2110 | indstr=regexp(subdir_civ2,'\D'); |
---|
| 2111 | if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number |
---|
| 2112 | vers=str2double(subdir_civ2(indstr(end)+1:end))+1; |
---|
| 2113 | subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)]; |
---|
| 2114 | else |
---|
| 2115 | vers=vers+1; |
---|
| 2116 | subdir_civ2_new=[subdir_civ1 '_' num2str(vers)]; |
---|
| 2117 | end |
---|
| 2118 | break |
---|
| 2119 | end |
---|
| 2120 | filecell.ncA.civ2(ifile,j)={filename}; |
---|
| 2121 | end |
---|
| 2122 | if detect% if a netcdf file already exists |
---|
| 2123 | break |
---|
| 2124 | end |
---|
| 2125 | end |
---|
| 2126 | subdir_civ2=subdir_civ2_new; |
---|
| 2127 | %create the new SubdirCiv1 |
---|
| 2128 | if ~exist(fullfile(RootPath,subdir_civ2_new),'dir') |
---|
| 2129 | [xx,m2]=mkdir(subdir_civ2_new); |
---|
| 2130 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
| 2131 | if ~isequal(m2,'') |
---|
| 2132 | errormsg= ['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2];%error message for directory creation |
---|
| 2133 | return |
---|
| 2134 | end |
---|
| 2135 | end |
---|
| 2136 | end |
---|
| 2137 | end |
---|
| 2138 | subdir_civ2=subdir_civ2_new; |
---|
| 2139 | end |
---|
| 2140 | |
---|
| 2141 | %%%%%%%%%%%%% if checkciv2 results are obtained or used %%%%%%%%%%%%% |
---|
| 2142 | if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2 |
---|
| 2143 | %check source netcdf file of checkciv1 estimates |
---|
| 2144 | if checkbox(1)==0; %no civ1 performed |
---|
| 2145 | for ifile=1:nbfield |
---|
| 2146 | for j=1:nbslice |
---|
| 2147 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));% |
---|
| 2148 | filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file |
---|
| 2149 | if ~exist(filename,'file') |
---|
| 2150 | errormsg=['input file ' filename ' not found']; |
---|
| 2151 | return |
---|
| 2152 | end |
---|
| 2153 | if ~testdiff % civ2 or patch2 are written in the same file as civ1 |
---|
| 2154 | if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated |
---|
| 2155 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2'); |
---|
| 2156 | if isfield(Data,'Txt') |
---|
| 2157 | errormsg=Data.Txt; |
---|
| 2158 | return |
---|
| 2159 | elseif ~isempty(Data.CivStage)% case of new civ files |
---|
| 2160 | if Data.CivStage<4 %test for civ files |
---|
| 2161 | errormsg=['no civ2 data in ' filename]; |
---|
| 2162 | return |
---|
| 2163 | end |
---|
| 2164 | elseif isempty(Data.civ2)||isequal(Data.civ2,0) |
---|
| 2165 | errormsg=['no civ2 data in ' filename]; |
---|
| 2166 | return |
---|
| 2167 | end |
---|
| 2168 | elseif checkbox(3)==0; %check the existence of patch if it is not calculated |
---|
| 2169 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch'); |
---|
| 2170 | if isfield(Data,'Txt') |
---|
| 2171 | errormsg=Data.Txt; |
---|
| 2172 | return |
---|
| 2173 | elseif ~isempty(Data.CivStage) |
---|
| 2174 | if Data.CivStage<3 %test for civ files |
---|
| 2175 | errormsg=['no patch data in ' filename]; |
---|
| 2176 | return |
---|
| 2177 | end |
---|
| 2178 | elseif isempty(Data.patch)||isequal(Data.patch,0) |
---|
| 2179 | errormsg=['no patch data in ' filename]; |
---|
| 2180 | return |
---|
| 2181 | end |
---|
| 2182 | end |
---|
| 2183 | end |
---|
| 2184 | end |
---|
| 2185 | end |
---|
| 2186 | if strcmp(compare,'stereo PIV') |
---|
| 2187 | for ifile=1:nbfield |
---|
| 2188 | for j=1:nbslice |
---|
| 2189 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
| 2190 | filecell.ncA.civ2(ifile,j)={filename}; |
---|
| 2191 | if ~exist(filename,'file') |
---|
| 2192 | errormsg=['input file ' filename ' not found']; |
---|
| 2193 | return |
---|
| 2194 | end |
---|
| 2195 | end |
---|
| 2196 | end |
---|
| 2197 | end |
---|
| 2198 | end |
---|
| 2199 | |
---|
| 2200 | detect=1; |
---|
| 2201 | % while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data |
---|
| 2202 | for ifile=1:nbfield |
---|
| 2203 | for j=1:nbslice |
---|
| 2204 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
| 2205 | detect=exist(filename,'file')==2; |
---|
| 2206 | filecell.nc.civ2(ifile,j)={filename}; |
---|
| 2207 | end |
---|
| 2208 | end |
---|
| 2209 | %get first image names for checkciv2 |
---|
| 2210 | if checkbox(1)==1 && isequal(i1_civ1,i1_civ2) && isequal(j1_civ1,j1_civ2) |
---|
| 2211 | filecell.ima1.civ2=filecell.ima1.civ1; |
---|
| 2212 | elseif checkbox(4)==1 |
---|
| 2213 | for ifile=1:nbfield |
---|
| 2214 | for j=1:nbslice |
---|
| 2215 | filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,ext_ima,NomType_ima1,i1_civ2(ifile),[],j1_civ2(j)); |
---|
| 2216 | idetect_2(j)=exist(filename,'file')==2; |
---|
| 2217 | filecell.ima1.civ2(ifile,j)={filename};%first image |
---|
| 2218 | end |
---|
| 2219 | [idetectmin,indexj]=min(idetect_2); |
---|
| 2220 | if idetectmin==0, |
---|
| 2221 | errormsg=['input image ' filecell.ima1.civ2{ifile,indexj} ' not found']; |
---|
| 2222 | return |
---|
| 2223 | end |
---|
| 2224 | end |
---|
| 2225 | end |
---|
| 2226 | |
---|
| 2227 | %get second image names for checkciv2 |
---|
| 2228 | if checkbox(1)==1 && isequal(i2_civ1,i2_civ2) && isequal(j2_civ1,j2_civ2) |
---|
| 2229 | filecell.ima2.civ2=filecell.ima2.civ1; |
---|
| 2230 | elseif checkbox(4)==1 |
---|
| 2231 | for ifile=1:nbfield |
---|
| 2232 | for j=1:nbslice |
---|
| 2233 | filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,ext_ima,NomType_ima2,i2_civ2(ifile),[],j2_civ2(j)); |
---|
| 2234 | idetect_3(j)=exist(filename,'file')==2; |
---|
| 2235 | filecell.ima2.civ2(ifile,j)={filename};%first image |
---|
| 2236 | end |
---|
| 2237 | [idetectmin,indexj]=min(idetect_3); |
---|
| 2238 | if idetectmin==0, |
---|
| 2239 | errormsg=['input image ' filecell.ima2.civ2{ifile,indexj} ' not found']; |
---|
| 2240 | return |
---|
| 2241 | end |
---|
| 2242 | end |
---|
| 2243 | end |
---|
| 2244 | end |
---|
| 2245 | if (checkbox(5) || checkbox(6)) && ~checkbox(4) % need to read an existing netcdf civ2 file |
---|
| 2246 | if ~testdiff |
---|
| 2247 | filecell.nc.civ2=filecell.nc.civ1;% file already checked |
---|
| 2248 | else % check the civ2 files |
---|
| 2249 | for ifile=1:nbfield |
---|
| 2250 | for j=1:nbslice |
---|
| 2251 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
| 2252 | filecell.nc.civ2(ifile,j)={filename}; |
---|
| 2253 | if ~exist(filename,'file') |
---|
| 2254 | errormsg=['input file ' filename ' not found']; |
---|
| 2255 | return |
---|
| 2256 | else |
---|
| 2257 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2'); |
---|
| 2258 | if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files |
---|
| 2259 | errormsg=['no civ2 data in ' filename]; |
---|
| 2260 | return |
---|
| 2261 | elseif isempty(Data.civ2)||isequal(Data.civ2,0) |
---|
| 2262 | errormsg=['no civ2 data in ' filename]; |
---|
| 2263 | return |
---|
| 2264 | end |
---|
| 2265 | end |
---|
| 2266 | end |
---|
| 2267 | end |
---|
| 2268 | end |
---|
| 2269 | end |
---|
| 2270 | |
---|
| 2271 | %%%%%%%%%%%%% if stereo fields are calculated by PATCH %%%%%%%%%%%%% |
---|
| 2272 | if strcmp(compare,'stereo PIV') |
---|
| 2273 | if checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1) |
---|
| 2274 | for ifile=1:nbfield |
---|
| 2275 | for j=1:nbslice |
---|
| 2276 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_AB,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
| 2277 | filecell.st(ifile,j)={filename}; |
---|
| 2278 | end |
---|
| 2279 | end |
---|
| 2280 | end |
---|
| 2281 | if checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1) |
---|
| 2282 | for ifile=1:nbfield |
---|
| 2283 | for j=1:nbslice |
---|
| 2284 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_AB,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
| 2285 | filecell.st(ifile,j)={filename}; |
---|
| 2286 | end |
---|
| 2287 | end |
---|
| 2288 | end |
---|
| 2289 | end |
---|
| 2290 | set(handles.SubdirCiv1,'String',regexprep(subdir_civ1,['^' SubDirImages],''));%suppress the root SuddirImages;);%update the edit box |
---|
| 2291 | set(handles.SubdirCiv2,'String',regexprep(subdir_civ2,['^' SubDirImages],''));%update the edit box |
---|
| 2292 | |
---|
| 2293 | % For CivX COPY IMAGES TO THE FORMAT .png IF NEEDED |
---|
| 2294 | if strcmp(CivMode,'CivX') |
---|
| 2295 | NomType_imanew1=NomType_ima1; |
---|
| 2296 | NomType_imanew2=NomType_ima2; |
---|
| 2297 | if ~isequal(ext_ima,'.png') |
---|
| 2298 | if checkbox(1) %if civ1 is performed |
---|
| 2299 | [FileType,FileInfo,MovieObject]=get_file_type(filecell.ima1.civ1{1}); |
---|
| 2300 | check_j=0; |
---|
| 2301 | if strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader')||strcmp(FileType,'multimage') |
---|
| 2302 | if max(j1_civ1)>1 |
---|
| 2303 | check_j=1; |
---|
| 2304 | NomType_imanew1='_1_1'; |
---|
| 2305 | else |
---|
| 2306 | NomType_imanew1='_1'; |
---|
| 2307 | end |
---|
| 2308 | end |
---|
| 2309 | h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar |
---|
| 2310 | for ifile=1:nbfield |
---|
| 2311 | waitbar(ifile/nbfield); |
---|
| 2312 | for j=1:nbslice |
---|
| 2313 | filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,'.png',NomType_imanew1,i1_civ1(ifile),[],j1_civ1(j)); |
---|
| 2314 | if ~exist(filename,'file') |
---|
| 2315 | if check_j |
---|
| 2316 | A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ1(j)); |
---|
| 2317 | else |
---|
| 2318 | A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ1(ifile)); |
---|
| 2319 | end |
---|
| 2320 | imwrite(uint16(sum(A,3)),filename,'BitDepth',16); |
---|
| 2321 | end |
---|
| 2322 | filecell.ima1.civ1(ifile,j)={filename}; |
---|
| 2323 | filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,'.png',NomType_imanew1,i2_civ1(ifile),[],j2_civ1(j)); |
---|
| 2324 | if ~exist(filename,'file') |
---|
| 2325 | if check_j |
---|
| 2326 | A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j2_civ1(j)); |
---|
| 2327 | else |
---|
| 2328 | A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i2_civ1(ifile)); |
---|
| 2329 | end |
---|
| 2330 | imwrite(uint16(sum(A,3)),filename,'BitDepth',16); |
---|
| 2331 | end |
---|
| 2332 | filecell.ima2.civ1(ifile,j)={filename}; |
---|
| 2333 | end |
---|
| 2334 | end |
---|
| 2335 | close(h) |
---|
| 2336 | end |
---|
| 2337 | if checkbox(4) %if civ2 is performed |
---|
| 2338 | [FileType,FileInfo,MovieObject]=get_file_type(filecell.ima1.civ2{1}); |
---|
| 2339 | check_j=0; |
---|
| 2340 | if strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader')||strcmp(FileType,'multimage') |
---|
| 2341 | if max(j1_civ2)>1 |
---|
| 2342 | check_j=1; |
---|
| 2343 | NomType_imanew1='_1_1'; |
---|
| 2344 | else |
---|
| 2345 | NomType_imanew1='_1'; |
---|
| 2346 | end |
---|
| 2347 | end |
---|
| 2348 | h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar |
---|
| 2349 | for ifile=1:nbfield |
---|
| 2350 | waitbar(ifile/nbfield); |
---|
| 2351 | for j=1:nbslice |
---|
| 2352 | filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,'.png',NomType_imanew1,i1_civ2(ifile),[],j1_civ2(j)); |
---|
| 2353 | if ~exist(filename,'file') |
---|
| 2354 | if check_j |
---|
| 2355 | A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ2(j)); |
---|
| 2356 | else |
---|
| 2357 | A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ2(ifile)); |
---|
| 2358 | end |
---|
| 2359 | imwrite(uint16(sum(A,3)),filename,'BitDepth',16); |
---|
| 2360 | end |
---|
| 2361 | filecell.ima1.civ2(ifile,j)={filename}; |
---|
| 2362 | filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,'.png',NomType_imanew2,i2_civ2(ifile),[],j2_civ2(j)); |
---|
| 2363 | if ~exist(filename,'file') |
---|
| 2364 | if check_j |
---|
| 2365 | A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ2(j)); |
---|
| 2366 | else |
---|
| 2367 | A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ2(ifile)); |
---|
| 2368 | end |
---|
| 2369 | imwrite(uint16(sum(A,3)),filename,'BitDepth',16); |
---|
| 2370 | end |
---|
| 2371 | filecell.ima2.civ2(ifile,j)={filename}; |
---|
| 2372 | end |
---|
| 2373 | end |
---|
| 2374 | close(h); |
---|
| 2375 | end |
---|
| 2376 | end |
---|
| 2377 | end |
---|
| 2378 | |
---|
| 2379 | %------------------------------------------------------------------------ |
---|
| 2380 | % --- determine the list of index pairs of processing file |
---|
| 2381 | function [i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=... |
---|
| 2382 | find_pair_indices(handles,ref_i,ref_j,mode) |
---|
| 2383 | %------------------------------------------------------------------------ |
---|
| 2384 | |
---|
| 2385 | list_civ1=get(handles.ListPairCiv1,'String'); |
---|
| 2386 | index_civ1=get(handles.ListPairCiv1,'Value'); |
---|
| 2387 | str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1 |
---|
| 2388 | if isempty(str_civ1)||isequal(str_civ1,'') |
---|
| 2389 | msgbox_uvmat('ERROR','no image pair selected for civ1') |
---|
| 2390 | return |
---|
| 2391 | end |
---|
| 2392 | list_civ2=get(handles.ListPairCiv2,'String'); |
---|
| 2393 | index_civ2=get(handles.ListPairCiv2,'Value'); |
---|
| 2394 | if index_civ2>length(list_civ2) |
---|
| 2395 | list_civ2=list_civ1; |
---|
| 2396 | index_civ2=index_civ1; |
---|
| 2397 | end |
---|
| 2398 | str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2 |
---|
| 2399 | |
---|
| 2400 | if isequal (mode,'series(Di)') |
---|
| 2401 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
| 2402 | i1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers |
---|
| 2403 | i2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i)); |
---|
| 2404 | j1_civ1=ref_j; |
---|
| 2405 | j2_civ1=ref_j; |
---|
| 2406 | i1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i)); |
---|
| 2407 | i2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i)); |
---|
| 2408 | j1_civ2=ref_j; |
---|
| 2409 | j2_civ2=ref_j; |
---|
| 2410 | |
---|
| 2411 | % adjust the first and last field number |
---|
| 2412 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
| 2413 | if isnan(lastfield) |
---|
| 2414 | indsel=find((i1_civ1 >= 1)&(i1_civ2 >= 1)); |
---|
| 2415 | else |
---|
| 2416 | indsel=find((i2_civ1 <= lastfield)&(i2_civ2 <= lastfield)&(i1_civ1 >= 1)&(i1_civ2 >= 1)); |
---|
| 2417 | end |
---|
| 2418 | if length(indsel)>=1 |
---|
| 2419 | firstind=indsel(1); |
---|
| 2420 | lastind=indsel(end); |
---|
| 2421 | set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields |
---|
| 2422 | set(handles.last_i,'String',num2str(ref_i(lastind))) |
---|
| 2423 | ref_i=ref_i(indsel); |
---|
| 2424 | i1_civ1=i1_civ1(indsel); |
---|
| 2425 | i1_civ2=i1_civ2(indsel); |
---|
| 2426 | i2_civ1=i2_civ1(indsel); |
---|
| 2427 | i2_civ2=i2_civ2(indsel); |
---|
| 2428 | end |
---|
| 2429 | elseif isequal (mode,'series(Dj)') |
---|
| 2430 | lastfield_j=str2double(get(handles.nb_field2,'String')); |
---|
| 2431 | i1_civ1=ref_i;% set of first image numbers |
---|
| 2432 | i2_civ1=ref_i; |
---|
| 2433 | j1_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j)); |
---|
| 2434 | j2_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j)); |
---|
| 2435 | i1_civ2=ref_i; |
---|
| 2436 | i2_civ2=ref_i; |
---|
| 2437 | j1_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j)); |
---|
| 2438 | j2_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j)); |
---|
| 2439 | % adjust the first and last field number |
---|
| 2440 | if isnan(lastfield_j) |
---|
| 2441 | indsel=find((j1_civ1 >= 1)&(j1_civ2 >= 1)); |
---|
| 2442 | else |
---|
| 2443 | indsel=find((j2_civ1 <= lastfield_j)&(j2_civ2 <= lastfield_j)&(j1_civ1 >= 1)&(j1_civ2 >= 1)); |
---|
| 2444 | end |
---|
| 2445 | if length(indsel)>=1 |
---|
| 2446 | firstind=indsel(1); |
---|
| 2447 | lastind=indsel(end); |
---|
| 2448 | set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields |
---|
| 2449 | set(handles.last_j,'String',num2str(ref_j(lastind))) |
---|
| 2450 | ref_j=ref_j(indsel); |
---|
| 2451 | j1_civ1=j1_civ1(indsel); |
---|
| 2452 | j2_civ1=j2_civ1(indsel); |
---|
| 2453 | j1_civ2=j1_civ2(indsel); |
---|
| 2454 | j2_civ2=j2_civ2(indsel); |
---|
| 2455 | end |
---|
| 2456 | elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) |
---|
| 2457 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
| 2458 | i1_civ1=ref_i; |
---|
| 2459 | i2_civ1=ref_i; |
---|
| 2460 | j1_civ1=displ_num(1,index_civ1); |
---|
| 2461 | j2_civ1=displ_num(2,index_civ1); |
---|
| 2462 | i1_civ2=ref_i; |
---|
| 2463 | i2_civ2=ref_i; |
---|
| 2464 | j1_civ2=displ_num(1,index_civ2); |
---|
| 2465 | j2_civ2=displ_num(2,index_civ2); |
---|
| 2466 | elseif isequal(mode,'displacement') |
---|
| 2467 | i1_civ1=ref_i; |
---|
| 2468 | i2_civ1=ref_i; |
---|
| 2469 | j1_civ1=ref_j; |
---|
| 2470 | j2_civ1=ref_j; |
---|
| 2471 | i1_civ2=ref_i; |
---|
| 2472 | i2_civ2=ref_i; |
---|
| 2473 | j1_civ2=ref_j; |
---|
| 2474 | j2_civ2=ref_j; |
---|
| 2475 | end |
---|
| 2476 | |
---|
| 2477 | %------------------------------------------------------------------------ |
---|
| 2478 | % --- Executes on button press in ListCompareMode. |
---|
| 2479 | function ListCompareMode_Callback(hObject, eventdata, handles) |
---|
| 2480 | %------------------------------------------------------------------------ |
---|
| 2481 | ListCompareMode=get(handles.ListCompareMode,'String'); |
---|
| 2482 | option=ListCompareMode{get(handles.ListCompareMode,'Value')}; |
---|
| 2483 | switch option |
---|
| 2484 | case 'PIV' |
---|
| 2485 | set(handles.RootFile_1,'Visible','Off'); |
---|
| 2486 | set(handles.sub_txt,'Visible','off') |
---|
| 2487 | set(handles.RootFile_1,'String',[]); |
---|
| 2488 | mode_store=get(handles.ListCompareMode,'UserData'); |
---|
| 2489 | set(handles.ListPairMode,'Visible','on') |
---|
| 2490 | set(handles.ListPairMode,'Value',1) |
---|
| 2491 | set(handles.ListPairMode,'String',mode_store) |
---|
| 2492 | set(handles.CheckStereo,'Value',0) |
---|
| 2493 | case 'PIV volume' |
---|
| 2494 | set(handles.RootFile_1,'Visible','Off'); |
---|
| 2495 | set(handles.sub_txt,'Visible','off') |
---|
| 2496 | set(handles.RootFile_1,'String',[]); |
---|
| 2497 | mode_store=get(handles.ListCompareMode,'UserData'); |
---|
| 2498 | set(handles.ListPairMode,'Visible','on') |
---|
| 2499 | set(handles.ListPairMode,'Value',1) |
---|
| 2500 | set(handles.ListPairMode,'String',{'series(Di)'}) |
---|
| 2501 | set(handles.CheckStereo,'Value',0) |
---|
| 2502 | set(handles.last_j,'String',get(handles.nb_field2,'String'))% select the whole volume scan by default |
---|
| 2503 | set(handles.incr_i,'String',num2str(2))% |
---|
| 2504 | otherwise |
---|
| 2505 | filebase=get(handles.RootPath,'String'); |
---|
| 2506 | set(handles.sub_txt,'Visible','on') |
---|
| 2507 | set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible |
---|
| 2508 | mode_store=get(handles.ListPairMode,'String');%get the present 'mode' |
---|
| 2509 | set(handles.ListCompareMode,'UserData',mode_store);%store the mode display |
---|
| 2510 | set(handles.ListPairMode,'Visible','off') |
---|
| 2511 | |
---|
| 2512 | %% open an image file with the browser |
---|
| 2513 | ind_opening=1;%default |
---|
| 2514 | browse.incr_pair=[0 0]; %default |
---|
| 2515 | oldfile=get(handles.RootPath,'String'); |
---|
| 2516 | menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)'; |
---|
| 2517 | '*.png','.png image files'; ... |
---|
| 2518 | '*.jpg',' jpeg image files'; ... |
---|
| 2519 | '*.tif','.tif image files'; ... |
---|
| 2520 | '*.avi;*.AVI','.avi movie files'; ... |
---|
| 2521 | '*.*', 'All Files (*.*)'}; |
---|
| 2522 | if strcmp(option,'displacement') |
---|
| 2523 | comment='Pick the reference file for displacements'; |
---|
| 2524 | else |
---|
| 2525 | comment='Pick a file of the second series'; |
---|
| 2526 | end |
---|
| 2527 | [FileName, PathName] = uigetfile( menu, comment,oldfile); |
---|
| 2528 | fileinput=[PathName FileName];%complete file name |
---|
| 2529 | sizf=size(fileinput); |
---|
| 2530 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
| 2531 | [path,name,ext]=fileparts(fileinput); |
---|
| 2532 | [path1]=fileparts(filebase); |
---|
| 2533 | if isunix |
---|
| 2534 | [status,path]=system(['readlink ' path]); |
---|
| 2535 | [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths |
---|
| 2536 | end |
---|
| 2537 | if ~strcmp(path1,path) |
---|
| 2538 | msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one') |
---|
| 2539 | return |
---|
| 2540 | end |
---|
| 2541 | if strcmp(option,'displacement') |
---|
| 2542 | [tild,RootFile_1]=fileparts(name); |
---|
| 2543 | else |
---|
| 2544 | [FilePath,FileName,Ext]=fileparts(fileinput); |
---|
| 2545 | % detect the file type, get the movie object if relevant, and look for the corresponding file series: |
---|
| 2546 | % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists |
---|
| 2547 | [RootPath,SubDir,RootFile_1,i1_series,i2_series,j1_series,j2_series,nom_type_1,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName Ext]); |
---|
| 2548 | |
---|
| 2549 | %check image nom type |
---|
| 2550 | if ~strcmp(nom_type_1,get(handles.NomType,'String')) |
---|
| 2551 | msgbox_uvmat('ERROR','The second image series must have the same indexing type as the first one, or use the option displacement for a fixed image') |
---|
| 2552 | return |
---|
| 2553 | end |
---|
| 2554 | end |
---|
| 2555 | %check image extension |
---|
| 2556 | if ~strcmp(ext,get(handles.ImaExt,'String')) |
---|
| 2557 | msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one') |
---|
| 2558 | return |
---|
| 2559 | end |
---|
| 2560 | set(handles.RootFile_1,'String',RootFile_1); |
---|
| 2561 | |
---|
| 2562 | end |
---|
| 2563 | ListPairMode_Callback(hObject, eventdata, handles) |
---|
| 2564 | |
---|
| 2565 | |
---|
| 2566 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 2567 | % Callbacks in the uipanel Pair Indices |
---|
| 2568 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 2569 | %------------------------------------------------------------------------ |
---|
| 2570 | % --- Executes on button press in ListPairMode. |
---|
| 2571 | function ListPairMode_Callback(hObject, eventdata, handles) |
---|
| 2572 | %------------------------------------------------------------------------ |
---|
| 2573 | compare_list=get(handles.ListCompareMode,'String'); |
---|
| 2574 | val=get(handles.ListCompareMode,'Value'); |
---|
| 2575 | compare=compare_list{val}; |
---|
| 2576 | if strcmp(compare,'displacement')||strcmp(compare,'shift') |
---|
| 2577 | mode='displacement'; |
---|
| 2578 | else |
---|
| 2579 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2580 | if ischar(mode_list) |
---|
| 2581 | mode_list={mode_list}; |
---|
| 2582 | end |
---|
| 2583 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2584 | mode=mode_list{mode_value}; |
---|
| 2585 | end |
---|
| 2586 | displ_num=[];%default |
---|
| 2587 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 2588 | % last_i=str2num(get(handles.last_i,'String')); |
---|
| 2589 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
| 2590 | TimeUnit=get(handles.TimeUnit,'String'); |
---|
| 2591 | checkframe=strcmp(TimeUnit,'frame'); |
---|
| 2592 | siztime=size(time); |
---|
| 2593 | nbfield=siztime(1)-1; |
---|
| 2594 | nbfield2=siztime(2)-1; |
---|
| 2595 | indchosen=1; %%first pair selected by default |
---|
| 2596 | %displ_num used to define the indices of the civ_input 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 size(time,2)>1 && ~checkframe |
---|
| 2614 | dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%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 | enable_j(handles, 'off') |
---|
| 2629 | elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') |
---|
| 2630 | index=1:200; |
---|
| 2631 | displ_num(1,index)=-floor(index/2); |
---|
| 2632 | displ_num(2,index)=ceil(index/2); |
---|
| 2633 | displ_num(3:4,index)=zeros(2,200); |
---|
| 2634 | enable_j(handles, 'on') |
---|
| 2635 | elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') |
---|
| 2636 | index=1:200; |
---|
| 2637 | displ_num(1:2,index)=zeros(2,200); |
---|
| 2638 | displ_num(3,index)=-floor(index/2); |
---|
| 2639 | displ_num(4,index)=ceil(index/2); |
---|
| 2640 | enable_i(handles, 'on') |
---|
| 2641 | if nbfield2 > 1 |
---|
| 2642 | enable_j(handles, 'on') |
---|
| 2643 | else |
---|
| 2644 | enable_j(handles, 'off') |
---|
| 2645 | end |
---|
| 2646 | elseif isequal(mode,'displacement')%the pairs have the same indices |
---|
| 2647 | displ_num(1,1)=0; |
---|
| 2648 | displ_num(2,1)=0; |
---|
| 2649 | displ_num(3,1)=0; |
---|
| 2650 | displ_num(4,1)=0; |
---|
| 2651 | if nbfield > 1 || nbfield==0 |
---|
| 2652 | enable_i(handles, 'on') |
---|
| 2653 | else |
---|
| 2654 | enable_j(handles, 'off') |
---|
| 2655 | end |
---|
| 2656 | if nbfield2 > 1 |
---|
| 2657 | enable_j(handles, 'on') |
---|
| 2658 | else |
---|
| 2659 | enable_j(handles, 'off') |
---|
| 2660 | end |
---|
| 2661 | end |
---|
| 2662 | set(handles.ListPairCiv1,'UserData',displ_num); |
---|
| 2663 | errormsg=find_netcpair_civ( handles,1); |
---|
| 2664 | if ~isempty(errormsg) |
---|
| 2665 | msgbox_uvmat('ERROR',errormsg) |
---|
| 2666 | end |
---|
| 2667 | % find_netcpair_civ2(handles) |
---|
| 2668 | |
---|
| 2669 | function enable_i(handles, state) |
---|
| 2670 | set(handles.itext,'Visible',state) |
---|
| 2671 | set(handles.first_i,'Visible',state) |
---|
| 2672 | set(handles.last_i,'Visible',state) |
---|
| 2673 | set(handles.incr_i,'Visible',state) |
---|
| 2674 | set(handles.nb_field,'Visible',state) |
---|
| 2675 | set(handles.ref_i,'Visible',state) |
---|
| 2676 | |
---|
| 2677 | function enable_j(handles, state) |
---|
| 2678 | set(handles.jtext,'Visible',state) |
---|
| 2679 | set(handles.first_j,'Visible',state) |
---|
| 2680 | set(handles.last_j,'Visible',state) |
---|
| 2681 | set(handles.incr_j,'Visible',state) |
---|
| 2682 | set(handles.nb_field2,'Visible',state) |
---|
| 2683 | set(handles.ref_j,'Visible',state) |
---|
| 2684 | |
---|
| 2685 | |
---|
| 2686 | %------------------------------------------------------------------------ |
---|
| 2687 | % --- Executes on selection change in ListPairCiv1. |
---|
| 2688 | function ListPairCiv1_Callback(hObject, eventdata, handles) |
---|
| 2689 | %------------------------------------------------------------------------ |
---|
| 2690 | %reproduce by default the chosen pair in the checkciv2 menu |
---|
| 2691 | list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs |
---|
| 2692 | index_pair=get(handles.ListPairCiv1,'Value'); |
---|
| 2693 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
| 2694 | list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs |
---|
| 2695 | if index_pair<=length(list_pair2) |
---|
| 2696 | set(handles.ListPairCiv2,'Value',index_pair); |
---|
| 2697 | end |
---|
| 2698 | |
---|
| 2699 | %update first_i and last_i according to the chosen image pairs |
---|
| 2700 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2701 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2702 | mode=mode_list{mode_value}; |
---|
| 2703 | if isequal(mode,'series(Di)') |
---|
| 2704 | first_i=str2double(get(handles.first_i,'String')); |
---|
| 2705 | last_i=str2double(get(handles.last_i,'String')); |
---|
| 2706 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
| 2707 | num_i=first_i:incr_i:last_i; |
---|
| 2708 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
| 2709 | if ~isnan(lastfield) |
---|
| 2710 | test_find=(num_i-floor(index_pair/2)*ones(size(num_i))>0)& ... |
---|
| 2711 | (num_i+ceil(index_pair/2)*ones(size(num_i))<=lastfield); |
---|
| 2712 | num_i=num_i(test_find); |
---|
| 2713 | end |
---|
| 2714 | set(handles.first_i,'String',num2str(num_i(1))); |
---|
| 2715 | set(handles.last_i,'String',num2str(num_i(end))); |
---|
| 2716 | elseif isequal(mode,'series(Dj)') |
---|
| 2717 | first_j=str2double(get(handles.first_j,'String')); |
---|
| 2718 | last_j=str2double(get(handles.last_j,'String')); |
---|
| 2719 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
| 2720 | num_j=first_j:incr_j:last_j; |
---|
| 2721 | lastfield2=str2double(get(handles.nb_field2,'String')); |
---|
| 2722 | if ~isnan(lastfield2) |
---|
| 2723 | test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... |
---|
| 2724 | (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); |
---|
| 2725 | num_j=num_j(test_find); |
---|
| 2726 | end |
---|
| 2727 | set(handles.first_j,'String',num2str(num_j(1))); |
---|
| 2728 | set(handles.last_j,'String',num2str(num_j(end))); |
---|
| 2729 | end |
---|
| 2730 | |
---|
| 2731 | %------------------------------------------------------------------------ |
---|
| 2732 | % --- Executes on selection change in ListPairCiv2. |
---|
| 2733 | function ListPairCiv2_Callback(hObject, eventdata, handles) |
---|
| 2734 | %------------------------------------------------------------------------ |
---|
| 2735 | index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu |
---|
| 2736 | |
---|
| 2737 | %update first_i and last_i according to the chosen image pairs |
---|
| 2738 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2739 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2740 | mode=mode_list{mode_value}; |
---|
| 2741 | if isequal(mode,'series(Di)') |
---|
| 2742 | first_i=str2double(get(handles.first_i,'String')); |
---|
| 2743 | last_i=str2double(get(handles.last_i,'String')); |
---|
| 2744 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
| 2745 | num_i=first_i:incr_i:last_i; |
---|
| 2746 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
| 2747 | if ~isnan(lastfield) |
---|
| 2748 | test_find=(num_i-floor(index_pair/2)*ones(size(num_i))>0)& ... |
---|
| 2749 | (num_i+ceil(index_pair/2)*ones(size(num_i))<=lastfield); |
---|
| 2750 | num_i=num_i(test_find); |
---|
| 2751 | end |
---|
| 2752 | set(handles.first_i,'String',num2str(num_i(1))); |
---|
| 2753 | set(handles.last_i,'String',num2str(num_i(end))); |
---|
| 2754 | elseif isequal(mode,'series(Dj)') |
---|
| 2755 | first_j=str2double(get(handles.first_j,'String')); |
---|
| 2756 | last_j=str2double(get(handles.last_j,'String')); |
---|
| 2757 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
| 2758 | num_j=first_j:incr_j:last_j; |
---|
| 2759 | lastfield2=str2double(get(handles.nb_field2,'String')); |
---|
| 2760 | if ~isnan(lastfield2) |
---|
| 2761 | test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... |
---|
| 2762 | (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); |
---|
| 2763 | num_j=num_j(test_find); |
---|
| 2764 | end |
---|
| 2765 | set(handles.first_j,'String',num2str(num_j(1))); |
---|
| 2766 | set(handles.last_j,'String',num2str(num_j(end))); |
---|
| 2767 | end |
---|
| 2768 | |
---|
| 2769 | %------------------------------------------------------------------------ |
---|
| 2770 | function ref_i_Callback(hObject, eventdata, handles) |
---|
| 2771 | %------------------------------------------------------------------------ |
---|
| 2772 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2773 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2774 | mode=mode_list{mode_value}; |
---|
| 2775 | errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files |
---|
| 2776 | if isequal(mode,'series(Di)') || ...% we do patch2 only |
---|
| 2777 | (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) |
---|
| 2778 | errormsg=find_netcpair_civ( handles,2); |
---|
| 2779 | end |
---|
| 2780 | if ~isempty(errormsg) |
---|
| 2781 | msgbox_uvmat('ERROR',errormsg) |
---|
| 2782 | end |
---|
| 2783 | |
---|
| 2784 | %------------------------------------------------------------------------ |
---|
| 2785 | function ref_j_Callback(hObject, eventdata, handles) |
---|
| 2786 | %------------------------------------------------------------------------ |
---|
| 2787 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2788 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2789 | mode=mode_list{mode_value}; |
---|
| 2790 | if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)') |
---|
| 2791 | errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files |
---|
| 2792 | end |
---|
| 2793 | if isequal(mode,'series(Dj)') || ... |
---|
| 2794 | (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) |
---|
| 2795 | errormsg=find_netcpair_civ(handles,2); |
---|
| 2796 | end |
---|
| 2797 | if ~isempty(errormsg) |
---|
| 2798 | msgbox_uvmat('ERROR',errormsg) |
---|
| 2799 | end |
---|
| 2800 | |
---|
| 2801 | %------------------------------------------------------------------------ |
---|
| 2802 | % determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of |
---|
| 2803 | % the field series set by first_i, incr, last_i |
---|
| 2804 | % index=1: look for pairs for civ1 |
---|
| 2805 | % index=2: look for pairs for civ2 |
---|
| 2806 | function errormsg=find_netcpair_civ(handles,index) |
---|
| 2807 | %------------------------------------------------------------------------ |
---|
| 2808 | set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock) |
---|
| 2809 | |
---|
| 2810 | %% initialisation |
---|
| 2811 | errormsg=''; |
---|
| 2812 | browse=get(handles.RootPath,'UserData'); |
---|
| 2813 | compare_list=get(handles.ListCompareMode,'String'); |
---|
| 2814 | val=get(handles.ListCompareMode,'Value'); |
---|
| 2815 | compare=compare_list{val}; |
---|
| 2816 | if strcmp(compare,'displacement')||strcmp(compare,'shift') |
---|
| 2817 | mode='displacement'; |
---|
| 2818 | else |
---|
| 2819 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 2820 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 2821 | if isempty(mode_list) |
---|
| 2822 | return |
---|
| 2823 | end |
---|
| 2824 | mode=mode_list{mode_value}; |
---|
| 2825 | end |
---|
| 2826 | nom_type_ima=get(handles.NomType,'String'); |
---|
| 2827 | |
---|
| 2828 | %% determine nom_type_nc, nomenclature type of the .nc files: |
---|
| 2829 | [nom_type_nc]=nomtype2pair(nom_type_ima,mode); |
---|
| 2830 | |
---|
| 2831 | %% reads .nc subdirectoy and image numbers from the interface |
---|
| 2832 | SubDirImages=get(handles.SubDirImages,'String'); |
---|
| 2833 | subdir_civ1=[SubDirImages get(handles.SubdirCiv1,'String')];%subdirectory subdir_civ1 for the netcdf data |
---|
| 2834 | subdir_civ2=[SubDirImages get(handles.SubdirCiv2,'String')];%subdirectory subdir_civ2 for the netcdf data |
---|
| 2835 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 2836 | ref_j=[]; |
---|
| 2837 | if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') |
---|
| 2838 | ref_j=0; |
---|
| 2839 | elseif strcmp(get(handles.ref_j,'Visible'),'on') |
---|
| 2840 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
| 2841 | end |
---|
| 2842 | if isempty(ref_j) |
---|
| 2843 | ref_j=1; |
---|
| 2844 | end |
---|
| 2845 | time=get(handles.ImaDoc,'UserData');%get the set of times |
---|
| 2846 | TimeUnit=get(handles.TimeUnit,'String'); |
---|
| 2847 | checkframe=strcmp(TimeUnit,'frame'); |
---|
| 2848 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
| 2849 | |
---|
| 2850 | %% eliminate the first pairs inconsistent with the position |
---|
| 2851 | if isempty(displ_num) |
---|
| 2852 | nbpair=0; |
---|
| 2853 | else |
---|
| 2854 | nbpair=length(displ_num(1,:));%nbre of displayed pairs |
---|
| 2855 | if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') |
---|
| 2856 | nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index |
---|
| 2857 | elseif isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
| 2858 | nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index |
---|
| 2859 | end |
---|
| 2860 | end |
---|
| 2861 | nbpair=min(200,nbpair);%limit the number of displayed pairs to 200 |
---|
| 2862 | |
---|
| 2863 | %% case with no Civ1 operation, netcdf files need to exist for reading |
---|
| 2864 | displ_pair={''}; |
---|
| 2865 | select=ones(size(1:nbpair));%flag for displayed pairs =1 for display |
---|
| 2866 | testpair=0; |
---|
| 2867 | RootPath=get(handles.RootPath,'String'); |
---|
| 2868 | RootFile=get(handles.RootFile,'String'); |
---|
| 2869 | if index==1 % case civ1 |
---|
| 2870 | if ~get(handles.CheckCiv1,'Value') % |
---|
| 2871 | if ~exist(fullfile(RootPath,subdir_civ1),'dir') |
---|
| 2872 | errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']; |
---|
| 2873 | set(handles.ListPairCiv1,'String',{}); |
---|
| 2874 | return |
---|
| 2875 | end |
---|
| 2876 | for ipair=1:nbpair |
---|
| 2877 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,... |
---|
| 2878 | ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair)); |
---|
| 2879 | select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist |
---|
| 2880 | end |
---|
| 2881 | % case of no displayed pair |
---|
| 2882 | if isequal(select,zeros(size(1:nbpair))) |
---|
| 2883 | if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0]) |
---|
| 2884 | num_i1=ref_i-floor(browse.incr_pair(1)/2); |
---|
| 2885 | num_i2=ref_i+ceil(browse.incr_pair(1)/2); |
---|
| 2886 | num_j1=ref_j-floor(browse.incr_pair(2)/2); |
---|
| 2887 | num_j2=ref_j+ceil(browse.incr_pair(2)/2); |
---|
| 2888 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2); |
---|
| 2889 | select(1)=exist(filename,'file')==2; |
---|
| 2890 | testpair=1; |
---|
| 2891 | else |
---|
| 2892 | % if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
| 2893 | % errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]; |
---|
| 2894 | % else |
---|
| 2895 | errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1]; |
---|
| 2896 | % end |
---|
| 2897 | set(handles.ListPairCiv1,'String',{''}); |
---|
| 2898 | %COMPLETER CAS STEREO |
---|
| 2899 | return |
---|
| 2900 | end |
---|
| 2901 | end |
---|
| 2902 | end |
---|
| 2903 | else %case civ2 alone |
---|
| 2904 | if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value') |
---|
| 2905 | if ~exist(fullfile(RootPath,subdir_civ2),'dir') |
---|
| 2906 | msgbox_uvmat('ERROR',['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist']) |
---|
| 2907 | set(handles.ListPairCiv2,'Value',1); |
---|
| 2908 | set(handles.ListPairCiv2,'String',{''}); |
---|
| 2909 | return |
---|
| 2910 | end |
---|
| 2911 | for ipair=1:nbpair |
---|
| 2912 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,... |
---|
| 2913 | ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair)); |
---|
| 2914 | select(ipair)=exist(filename,'file')==2; |
---|
| 2915 | end |
---|
| 2916 | if isequal(select,zeros(size(1:nbpair))) |
---|
| 2917 | if isfield(browse,'incr_pair') |
---|
| 2918 | num_i1=ref_i-floor(browse.incr_pair(1)/2); |
---|
| 2919 | num_i2=ref_i+floor((browse.incr_pair(1)+1)/2); |
---|
| 2920 | num_j1=ref_j-floor(browse.incr_pair(2)/2); |
---|
| 2921 | num_j2=ref_j+floor((browse.incr_pair(2)+1)/2); |
---|
| 2922 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2); |
---|
| 2923 | select(1)=exist(filename,'file')==2; |
---|
| 2924 | else |
---|
| 2925 | if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
| 2926 | errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2]; |
---|
| 2927 | else |
---|
| 2928 | errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2]; |
---|
| 2929 | end |
---|
| 2930 | set(handles.ListPairCiv2,'Value',1); |
---|
| 2931 | set(handles.ListPairCiv2,'String',{''}); |
---|
| 2932 | return |
---|
| 2933 | end |
---|
| 2934 | end |
---|
| 2935 | end |
---|
| 2936 | end |
---|
| 2937 | |
---|
| 2938 | %% determine the menu display in .ListPairCiv1 |
---|
| 2939 | % the menu depends on the mode defined in ListPairMode_callback through the array displ_num: |
---|
| 2940 | % displ_num(1,:)=indices j1 |
---|
| 2941 | % displ_num(2,:)=indices j2 |
---|
| 2942 | % displ_num(3,:)=indices i1 |
---|
| 2943 | % displ_num(4,:)=indices i2 |
---|
| 2944 | % in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices |
---|
| 2945 | % are relative to the reference indices ref_i and ref_j respectively. |
---|
| 2946 | if isequal(mode,'series(Di)') |
---|
| 2947 | if testpair |
---|
| 2948 | displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; |
---|
| 2949 | else |
---|
| 2950 | for ipair=1:nbpair |
---|
| 2951 | if select(ipair) |
---|
| 2952 | displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))]; |
---|
| 2953 | %if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)&&displ_num(2,ipair)>=1 &&displ_num(1,ipair)>=1 |
---|
| 2954 | % dt=time(ref_i+1+displ_num(4,ipair),ref_j+1+displ_num(2,ipair))-time(ref_i+1+displ_num(3,ipair),ref_j+1+displ_num(1,ipair));%time interval dt |
---|
| 2955 | if ~checkframe && size(time,1)>=ref_i+1+ceil(ipair/2) && size(time,2)>=ref_j+1&& ref_i-floor(ipair/2)>=0 && ref_j>=0 |
---|
| 2956 | dt=time(ref_i+1+ceil(ipair/2),ref_j+1)-time(ref_i+1-floor(ipair/2),ref_j+1);%time interval dtref_j+1 |
---|
| 2957 | else |
---|
| 2958 | dt=1; |
---|
| 2959 | end |
---|
| 2960 | displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; |
---|
| 2961 | else |
---|
| 2962 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
| 2963 | end |
---|
| 2964 | end |
---|
| 2965 | end |
---|
| 2966 | elseif isequal(mode,'series(Dj)') |
---|
| 2967 | if testpair |
---|
| 2968 | displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; |
---|
| 2969 | else |
---|
| 2970 | for ipair=1:nbpair |
---|
| 2971 | if select(ipair) |
---|
| 2972 | displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))]; |
---|
| 2973 | if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair) |
---|
| 2974 | dt=time(ref_i+1+displ_num(4,ipair),ref_j+1+displ_num(2,ipair))-time(ref_i+1+displ_num(3,ipair),ref_j+1+displ_num(1,ipair));%time interval dt |
---|
| 2975 | displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; |
---|
| 2976 | end |
---|
| 2977 | else |
---|
| 2978 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
| 2979 | end |
---|
| 2980 | end |
---|
| 2981 | end |
---|
| 2982 | elseif isequal(mode,'pair j1-j2')%case of pairs |
---|
| 2983 | for ipair=1:nbpair |
---|
| 2984 | if select(ipair) |
---|
| 2985 | if ~checkframe && size(time,2)>1 |
---|
| 2986 | dt=time(ref_i+1+displ_num(4,ipair),displ_num(2,ipair)+1)-time(ref_i+1+displ_num(3,ipair),displ_num(1,ipair)+1);%time interval dt |
---|
| 2987 | else % time set by default to i index |
---|
| 2988 | dt=1; |
---|
| 2989 | end |
---|
| 2990 | displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ... |
---|
| 2991 | ' :dt= ' num2str(dt*1000)]; |
---|
| 2992 | else |
---|
| 2993 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
| 2994 | end |
---|
| 2995 | end |
---|
| 2996 | elseif isequal(mode,'displacement') |
---|
| 2997 | displ_pair={'Di=Dj=0'}; |
---|
| 2998 | end |
---|
| 2999 | if index==1 |
---|
| 3000 | set(handles.ListPairCiv1,'String',displ_pair'); |
---|
| 3001 | end |
---|
| 3002 | |
---|
| 3003 | %% determine the default selection in the pair menu |
---|
| 3004 | ichoice=find(select,1);% index of selected pair |
---|
| 3005 | if (isempty(ichoice) || ichoice < 1); ichoice=1; end; |
---|
| 3006 | initial=get(handles.ListPairCiv1,'Value');%initial choice of pair |
---|
| 3007 | if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1)) |
---|
| 3008 | set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu |
---|
| 3009 | end |
---|
| 3010 | initial=get(handles.ListPairCiv2,'Value'); |
---|
| 3011 | if initial>length(displ_pair')%|~isequal(select(initial),1) |
---|
| 3012 | if ichoice <= length(displ_pair') |
---|
| 3013 | set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2 |
---|
| 3014 | else |
---|
| 3015 | set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2 |
---|
| 3016 | end |
---|
| 3017 | end |
---|
| 3018 | set(handles.ListPairCiv2,'String',displ_pair'); |
---|
| 3019 | set(gcf,'Pointer','arrow') |
---|
| 3020 | |
---|
| 3021 | |
---|
| 3022 | |
---|
| 3023 | % %------------------------------------------------------------------------ |
---|
| 3024 | % % call 'view_field.fig' to display the field selected in the list of 'status' |
---|
| 3025 | % function open_view_field(hObject, eventdata) |
---|
| 3026 | % %------------------------------------------------------------------------ |
---|
| 3027 | % list=get(hObject,'String'); |
---|
| 3028 | % index=get(hObject,'Value'); |
---|
| 3029 | % rootroot=get(hObject,'UserData'); |
---|
| 3030 | % filename=list{index}; |
---|
| 3031 | % ind_dot=strfind(filename,'...'); |
---|
| 3032 | % filename=filename(1:ind_dot-1); |
---|
| 3033 | % filename=fullfile(rootroot,filename); |
---|
| 3034 | % delete(get(hObject,'parent'))%delete the display figure to stop the check process |
---|
| 3035 | % if exist(filename,'file')%visualise the vel field if it exists |
---|
| 3036 | % uvmat(filename) |
---|
| 3037 | % set(gcbo,'Value',1) |
---|
| 3038 | % end |
---|
| 3039 | |
---|
| 3040 | |
---|
| 3041 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 3042 | % Callbacks in the uipanel Reference Indices |
---|
| 3043 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 3044 | %------------------------------------------------------------------------ |
---|
| 3045 | function first_i_Callback(hObject, eventdata, handles) |
---|
| 3046 | %------------------------------------------------------------------------ |
---|
| 3047 | first_i=str2double(get(handles.first_i,'String')); |
---|
| 3048 | set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index |
---|
| 3049 | ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt) |
---|
| 3050 | |
---|
| 3051 | %------------------------------------------------------------------------ |
---|
| 3052 | function first_j_Callback(hObject, eventdata, handles) |
---|
| 3053 | %------------------------------------------------------------------------ |
---|
| 3054 | first_j=str2num(get(handles.first_j,'String')); |
---|
| 3055 | set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index |
---|
| 3056 | ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt) |
---|
| 3057 | |
---|
| 3058 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 3059 | % Callbacks in the uipanel Civ1 |
---|
| 3060 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 3061 | %------------------------------------------------------------------------ |
---|
| 3062 | % --- Executes on button press in SearchRange: determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 |
---|
| 3063 | function SearchRange_Callback(hObject, eventdata, handles) |
---|
| 3064 | %------------------------------------------------------------------------ |
---|
| 3065 | %determine pair numbers |
---|
| 3066 | if strcmp(get(handles.num_UMin,'Visible'),'off') |
---|
| 3067 | set(handles.u_title,'Visible','on') |
---|
| 3068 | set(handles.v_title,'Visible','on') |
---|
| 3069 | set(handles.num_UMin,'Visible','on') |
---|
| 3070 | set(handles.num_UMax,'Visible','on') |
---|
| 3071 | set(handles.num_VMin,'Visible','on') |
---|
| 3072 | set(handles.num_VMax,'Visible','on') |
---|
| 3073 | set(handles.CoordUnit,'Visible','on') |
---|
| 3074 | set(handles.TimeUnit,'Visible','on') |
---|
| 3075 | set(handles.slash_title,'Visible','on') |
---|
| 3076 | set(handles.min_title,'Visible','on') |
---|
| 3077 | set(handles.max_title,'Visible','on') |
---|
| 3078 | set(handles.unit_title,'Visible','on') |
---|
| 3079 | else |
---|
| 3080 | get_search_range(hObject, eventdata, handles) |
---|
| 3081 | end |
---|
| 3082 | |
---|
| 3083 | %------------------------------------------------------------------------ |
---|
| 3084 | % --- determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 and shift |
---|
| 3085 | function get_search_range(hObject, eventdata, handles) |
---|
| 3086 | %------------------------------------------------------------------------ |
---|
| 3087 | param_civ1=read_GUI(handles.Civ1); |
---|
| 3088 | umin=param_civ1.UMin; |
---|
| 3089 | umax=param_civ1.UMax; |
---|
| 3090 | vmin=param_civ1.VMin; |
---|
| 3091 | vmax=param_civ1.VMax; |
---|
| 3092 | %switch min_title and max_title in case of error |
---|
| 3093 | if umax<=umin |
---|
| 3094 | umin_old=umin; |
---|
| 3095 | umin=umax; |
---|
| 3096 | umax=umin_old; |
---|
| 3097 | set(handles.num_UMin,'String', num2str(umin)) |
---|
| 3098 | set(handles.num_UMax,'String', num2str(umax)) |
---|
| 3099 | end |
---|
| 3100 | if vmax<=vmin |
---|
| 3101 | vmin_old=vmin; |
---|
| 3102 | vmin=vmax; |
---|
| 3103 | vmax=vmin_old; |
---|
| 3104 | set(handles.num_VMin,'String', num2str(vmin)) |
---|
| 3105 | set(handles.num_VMax,'String', num2str(vmax)) |
---|
| 3106 | end |
---|
| 3107 | if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax)) |
---|
| 3108 | list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs |
---|
| 3109 | index=get(handles.ListPairCiv1,'Value'); |
---|
| 3110 | pair_string=list_pair{index}; |
---|
| 3111 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
| 3112 | pxcm=get(handles.SearchRange,'UserData'); |
---|
| 3113 | mode_list=get(handles.ListPairMode,'String'); |
---|
| 3114 | mode_value=get(handles.ListPairMode,'Value'); |
---|
| 3115 | mode=mode_list{mode_value}; |
---|
| 3116 | if isequal (mode, 'series(Di)' ) |
---|
| 3117 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 3118 | num1=ref_i-floor(index/2);% first image numbers |
---|
| 3119 | num2=ref_i+ceil(index/2); |
---|
| 3120 | num_a=1; |
---|
| 3121 | num_b=1; |
---|
| 3122 | elseif isequal (mode, 'series(Dj)') |
---|
| 3123 | num1=1; |
---|
| 3124 | num2=1; |
---|
| 3125 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
| 3126 | num_a=ref_j-floor(index/2);% first image numbers |
---|
| 3127 | num_b=ref_j+ceil(index/2); |
---|
| 3128 | elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) |
---|
| 3129 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 3130 | num1=ref_i; |
---|
| 3131 | num2=ref_i; |
---|
| 3132 | r=regexp(pair_string,'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names'); |
---|
| 3133 | if isempty(r) |
---|
| 3134 | r=regexp(pair_string,'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names'); |
---|
| 3135 | end |
---|
| 3136 | num_a=str2num(r.num1); |
---|
| 3137 | num_b=str2num(r.num2); |
---|
| 3138 | end |
---|
| 3139 | dt=time(num2+1,num_b+1)-time(num1+1,num_a+1); |
---|
| 3140 | ibx=str2double(get(handles.num_CorrBoxSize_1,'String')); |
---|
| 3141 | iby=str2double(get(handles.num_CorrBoxSize_2,'String')); |
---|
| 3142 | umin=dt*pxcm*umin; |
---|
| 3143 | umax=dt*pxcm*umax; |
---|
| 3144 | vmin=dt*pxcm*vmin; |
---|
| 3145 | vmax=dt*pxcm*vmax; |
---|
| 3146 | shiftx=round((umin+umax)/2); |
---|
| 3147 | shifty=round((vmin+vmax)/2); |
---|
| 3148 | isx=(umax+2-shiftx)*2+param_civ1.Bx; |
---|
| 3149 | isx=2*ceil(isx/2)+1; |
---|
| 3150 | isy=(vmax+2-shifty)*2+param_civ1.Bx; |
---|
| 3151 | isy=2*ceil(isy/2)+1; |
---|
| 3152 | set(handles.num_SearchBoxShift_1,'String',num2str(shiftx)); |
---|
| 3153 | set(handles.num_SearchBoxShift_2,'String',num2str(shifty)); |
---|
| 3154 | set(handles.num_SearchBoxSize_1,'String',num2str(isx)); |
---|
| 3155 | set(handles.num_SearchBoxSize_2,'String',num2str(isy)); |
---|
| 3156 | end |
---|
| 3157 | |
---|
| 3158 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 3159 | % Callbacks in the uipanel Fix1 |
---|
| 3160 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 3161 | %------------------------------------------------------------------------ |
---|
| 3162 | % --- Executes on button press in CheckMask. |
---|
| 3163 | function get_mask_fix1_Callback(hObject, eventdata, handles) |
---|
| 3164 | %------------------------------------------------------------------------ |
---|
| 3165 | maskval=get(handles.CheckMask,'Value'); |
---|
| 3166 | if isequal(maskval,0) |
---|
| 3167 | set(handles.Mask,'String','') |
---|
| 3168 | else |
---|
| 3169 | mask_displ='no mask'; %default |
---|
| 3170 | filebase=get(handles.RootPath,'String'); |
---|
| 3171 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
| 3172 | if isequal(flag_mask,1) |
---|
| 3173 | mask_displ=[num2str(nbslice) 'mask']; |
---|
| 3174 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
| 3175 | filebase_a=get(handles.RootFile_1,'String'); |
---|
| 3176 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
| 3177 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
| 3178 | mask_displ='no mask'; |
---|
| 3179 | end |
---|
| 3180 | end |
---|
| 3181 | if isequal(mask_displ,'no mask') |
---|
| 3182 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
| 3183 | {'*.png', ' (*.png)'; |
---|
| 3184 | '*.png', '.png files '; ... |
---|
| 3185 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3186 | 'Pick a mask file *.png',filebase); |
---|
| 3187 | mask_displ=fullfile(PathName,FileName); |
---|
| 3188 | if ~exist(mask_displ,'file') |
---|
| 3189 | mask_displ='no mask'; |
---|
| 3190 | end |
---|
| 3191 | end |
---|
| 3192 | if isequal(mask_displ,'no mask') |
---|
| 3193 | set(handles.CheckMask,'Value',0) |
---|
| 3194 | set(handles.CheckMask,'Value',0) |
---|
| 3195 | set(handles.CheckMask,'Value',0) |
---|
| 3196 | else |
---|
| 3197 | %set(handles.CheckMask,'Value',1) |
---|
| 3198 | set(handles.CheckMask,'Value',1) |
---|
| 3199 | end |
---|
| 3200 | set(handles.Mask,'String',mask_displ) |
---|
| 3201 | set(handles.Mask,'String',mask_displ) |
---|
| 3202 | set(handles.Mask,'String',mask_displ) |
---|
| 3203 | end |
---|
| 3204 | |
---|
| 3205 | %------------------------------------------------------------------------ |
---|
| 3206 | % --- Executes on button press in CheckMask: select box for mask option |
---|
| 3207 | function get_mask_civ2_Callback(hObject, eventdata, handles) |
---|
| 3208 | %------------------------------------------------------------------------ |
---|
| 3209 | maskval=get(handles.CheckMask,'Value'); |
---|
| 3210 | if isequal(maskval,0) |
---|
| 3211 | set(handles.Mask,'String','') |
---|
| 3212 | else |
---|
| 3213 | mask_displ='no mask'; %default |
---|
| 3214 | filebase=get(handles.RootPath,'String'); |
---|
| 3215 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
| 3216 | if isequal(flag_mask,1) |
---|
| 3217 | mask_displ=[num2str(nbslice) 'mask']; |
---|
| 3218 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
| 3219 | filebase_a=get(handles.RootFile_1,'String'); |
---|
| 3220 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
| 3221 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
| 3222 | mask_displ='no mask'; |
---|
| 3223 | end |
---|
| 3224 | end |
---|
| 3225 | if isequal(mask_displ,'no mask') |
---|
| 3226 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
| 3227 | {'*.png', ' (*.png)'; |
---|
| 3228 | '*.png', '.png files '; ... |
---|
| 3229 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3230 | 'Pick a mask file *.png',filebase); |
---|
| 3231 | mask_displ=fullfile(PathName,FileName); |
---|
| 3232 | if ~exist(mask_displ,'file') |
---|
| 3233 | mask_displ='no mask'; |
---|
| 3234 | end |
---|
| 3235 | end |
---|
| 3236 | if isequal(mask_displ,'no mask') |
---|
| 3237 | set(handles.CheckMask,'Value',0) |
---|
| 3238 | set(handles.CheckMask,'Value',0) |
---|
| 3239 | else |
---|
| 3240 | set(handles.CheckMask,'Value',1) |
---|
| 3241 | end |
---|
| 3242 | set(handles.Mask,'String',mask_displ) |
---|
| 3243 | set(handles.Mask,'String',mask_displ) |
---|
| 3244 | end |
---|
| 3245 | |
---|
| 3246 | %------------------------------------------------------------------------ |
---|
| 3247 | % --- Executes on button press in CheckMask. |
---|
| 3248 | function get_mask_fix2_Callback(hObject, eventdata, handles) |
---|
| 3249 | %------------------------------------------------------------------------ |
---|
| 3250 | maskval=get(handles.CheckMask,'Value'); |
---|
| 3251 | if isequal(maskval,0) |
---|
| 3252 | set(handles.Mask,'String','') |
---|
| 3253 | else |
---|
| 3254 | mask_displ='no mask'; %default |
---|
| 3255 | filebase=get(handles.RootPath,'String'); |
---|
| 3256 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
| 3257 | if isequal(flag_mask,1) |
---|
| 3258 | mask_displ=[num2str(nbslice) 'mask']; |
---|
| 3259 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
| 3260 | filebase_a=get(handles.RootFile_1,'String'); |
---|
| 3261 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
| 3262 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
| 3263 | mask_displ='no mask'; |
---|
| 3264 | end |
---|
| 3265 | end |
---|
| 3266 | if isequal(mask_displ,'no mask') |
---|
| 3267 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
| 3268 | {'*.png', ' (*.png)'; |
---|
| 3269 | '*.png', '.png files '; ... |
---|
| 3270 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3271 | 'Pick a mask file *.png',filebase); |
---|
| 3272 | mask_displ=fullfile(PathName,FileName); |
---|
| 3273 | if ~exist(mask_displ,'file') |
---|
| 3274 | mask_displ='no mask'; |
---|
| 3275 | end |
---|
| 3276 | end |
---|
| 3277 | if isequal(mask_displ,'no mask') |
---|
| 3278 | set(handles.CheckMask,'Value',0) |
---|
| 3279 | end |
---|
| 3280 | set(handles.Mask,'String',mask_displ) |
---|
| 3281 | end |
---|
| 3282 | |
---|
| 3283 | %------------------------------------------------------------------------ |
---|
| 3284 | % --- function called to look for mask files |
---|
| 3285 | function [nbslice, flag_mask]=get_mask(filebase,handles) |
---|
| 3286 | %------------------------------------------------------------------------ |
---|
| 3287 | %detect mask files, images with appropriate file base |
---|
| 3288 | %[filebase '_' xx 'mask'], xx=nbslice |
---|
| 3289 | %flag_mask=1 indicates detection |
---|
| 3290 | |
---|
| 3291 | flag_mask=0;%default |
---|
| 3292 | nbslice=1; |
---|
| 3293 | |
---|
| 3294 | % subdir=get(handles.SubdirCiv1,'String'); |
---|
| 3295 | [Path,Name]=fileparts(filebase); |
---|
| 3296 | if ~isdir(Path) |
---|
| 3297 | msgbox_uvmat('ERROR','no path for input files') |
---|
| 3298 | return |
---|
| 3299 | end |
---|
| 3300 | % currentdir=pwd; |
---|
| 3301 | % cd(Path);%move in the dir of the root name filebase |
---|
| 3302 | maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files |
---|
| 3303 | % cd(currentdir);%come back to the current working directory |
---|
| 3304 | if ~isempty(maskfiles) |
---|
| 3305 | % msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat') |
---|
| 3306 | % else |
---|
| 3307 | flag_mask=1; |
---|
| 3308 | maskname=maskfiles(1).name;% take the first mask file in the list |
---|
| 3309 | [Path2,Name,ext]=fileparts(maskname); |
---|
| 3310 | Namedouble=double(Name); |
---|
| 3311 | val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters |
---|
| 3312 | ind_mask=findstr('mask',Name); |
---|
| 3313 | i=ind_mask-1; |
---|
| 3314 | while val(i)==0 && i>0 |
---|
| 3315 | i=i-1; |
---|
| 3316 | end |
---|
| 3317 | nbslice=str2double(Name(i+1:ind_mask-1)); |
---|
| 3318 | if ~isnan(nbslice) && Name(i)=='_' |
---|
| 3319 | flag_mask=1; |
---|
| 3320 | else |
---|
| 3321 | msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2]) |
---|
| 3322 | return |
---|
| 3323 | nbslice=1; |
---|
| 3324 | end |
---|
| 3325 | end |
---|
| 3326 | |
---|
| 3327 | %------------------------------------------------------------------------ |
---|
| 3328 | % --- function called to look for grid files |
---|
| 3329 | function [nbslice, flag_grid]=get_grid(filebase,handles) |
---|
| 3330 | %------------------------------------------------------------------------ |
---|
| 3331 | flag_grid=0;%default |
---|
| 3332 | nbslice=1; |
---|
| 3333 | [Path,Name]=fileparts(filebase); |
---|
| 3334 | currentdir=pwd; |
---|
| 3335 | cd(Path);%move in the dir of the root name filebase |
---|
| 3336 | gridfiles=dir([Name '_*grid_*.grid']);%look for grid files |
---|
| 3337 | cd(currentdir);%come back to the current working directory |
---|
| 3338 | if ~isempty(gridfiles) |
---|
| 3339 | flag_grid=1; |
---|
| 3340 | gridname=gridfiles(1).name;% take the first grid file in the list |
---|
| 3341 | [Path2,Name,ext]=fileparts(gridname); |
---|
| 3342 | Namedouble=double(Name); |
---|
| 3343 | val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters |
---|
| 3344 | ind_grid=findstr('grid',Name); |
---|
| 3345 | i=ind_grid-1; |
---|
| 3346 | while val(i)==0 && i>0 |
---|
| 3347 | i=i-1; |
---|
| 3348 | end |
---|
| 3349 | nbslice=str2double(Name(i+1:ind_grid-1)); |
---|
| 3350 | if ~isnan(nbslice) && Name(i)=='_' |
---|
| 3351 | flag_grid=1; |
---|
| 3352 | else |
---|
| 3353 | msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2]) |
---|
| 3354 | return |
---|
| 3355 | nbslice=1; |
---|
| 3356 | end |
---|
| 3357 | end |
---|
| 3358 | |
---|
| 3359 | %------------------------------------------------------------------------ |
---|
| 3360 | % --- transform numbers to letters |
---|
| 3361 | function str=num2stra(num,nom_type) |
---|
| 3362 | %------------------------------------------------------------------------ |
---|
| 3363 | if isempty(nom_type) |
---|
| 3364 | str=''; |
---|
| 3365 | elseif strcmp(nom_type(end),'a') |
---|
| 3366 | str=char(96+num); |
---|
| 3367 | elseif strcmp(nom_type(end),'A') |
---|
| 3368 | str=char(96+num); |
---|
| 3369 | elseif isempty(nom_type(2:end))%a single index |
---|
| 3370 | str=''; |
---|
| 3371 | else |
---|
| 3372 | str=num2str(num); |
---|
| 3373 | end |
---|
| 3374 | |
---|
| 3375 | % %------------------------------------------------------------------------ |
---|
| 3376 | % % --- Executes on button press in ListSubdirCiv1. |
---|
| 3377 | % function ListSubdirCiv1_Callback(hObject, eventdata, handles) |
---|
| 3378 | % %------------------------------------------------------------------------ |
---|
| 3379 | % list_subdir_civ1=get(handles.ListSubdirCiv1,'String'); |
---|
| 3380 | % val=get(handles.ListSubdirCiv1,'Value'); |
---|
| 3381 | % SubDir=list_subdir_civ1{val}; |
---|
| 3382 | % if strcmp(SubDir,'new...') |
---|
| 3383 | % if get(handles.CheckCiv1,'Value') |
---|
| 3384 | % SubDir='CIV_INPUT'; %default subdirectory |
---|
| 3385 | % else |
---|
| 3386 | % msgbox_uvmat('ERROR','select CheckCiv1 to perform a new civ_input operation') |
---|
| 3387 | % return |
---|
| 3388 | % end |
---|
| 3389 | % end |
---|
| 3390 | % set(handles.SubdirCiv1,'String',SubDir); |
---|
| 3391 | % errormsg=find_netcpair_civ(handles,1); |
---|
| 3392 | % if ~isempty(errormsg) |
---|
| 3393 | % msgbox_uvmat('ERROR',errormsg) |
---|
| 3394 | % end |
---|
| 3395 | % |
---|
| 3396 | %------------------------------------------------------------------------ |
---|
| 3397 | % % --- Executes on button press in ListSubdirCiv2. |
---|
| 3398 | % function ListSubdirCiv2_Callback(hObject, eventdata, handles) |
---|
| 3399 | % %------------------------------------------------------------------------ |
---|
| 3400 | % list_subdir_civ2=get(handles.ListSubdirCiv2,'String'); |
---|
| 3401 | % val=get(handles.ListSubdirCiv2,'Value'); |
---|
| 3402 | % SubDir=list_subdir_civ2{val}; |
---|
| 3403 | % if strcmp(SubDir,'new...') |
---|
| 3404 | % if get(handles.CheckCiv2,'Value') |
---|
| 3405 | % SubDir='CIV_INPUT'; %default subdirectory |
---|
| 3406 | % else |
---|
| 3407 | % msgbox_uvmat('ERROR','select CheckCiv2 to perform a new civ_input operation') |
---|
| 3408 | % return |
---|
| 3409 | % end |
---|
| 3410 | % end |
---|
| 3411 | % set(handles.SubdirCiv2,'String',SubDir); |
---|
| 3412 | |
---|
| 3413 | %------------------------------------------------------------------------ |
---|
| 3414 | % --- Executes on button press in CheckGrid. |
---|
| 3415 | function CheckGrid_Callback(hObject, eventdata, handles) |
---|
| 3416 | %------------------------------------------------------------------------ |
---|
| 3417 | value=get(hObject,'Value'); |
---|
| 3418 | hparent=get(hObject,'parent');%handles of the parent panel |
---|
| 3419 | hchildren=get(hparent,'children'); |
---|
| 3420 | handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel |
---|
| 3421 | handle_dx=findobj(hchildren,'tag','num_Dx'); |
---|
| 3422 | handle_dy=findobj(hchildren,'tag','num_Dy'); |
---|
| 3423 | handle_title_dx=findobj(hchildren,'tag','title_Dx'); |
---|
| 3424 | handle_title_dy=findobj(hchildren,'tag','title_Dy'); |
---|
| 3425 | testgrid=0; |
---|
| 3426 | filegrid=''; |
---|
| 3427 | if value |
---|
| 3428 | filebase=get(handles.RootPath,'String'); |
---|
| 3429 | [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name |
---|
| 3430 | if isequal(flag_grid,1) |
---|
| 3431 | filegrid=[num2str(nbslice) 'grid']; |
---|
| 3432 | testgrid=1; |
---|
| 3433 | else % browse for a grid |
---|
| 3434 | filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData |
---|
| 3435 | if exist(filegrid,'file') |
---|
| 3436 | filebase=filegrid; |
---|
| 3437 | end |
---|
| 3438 | [FileName, PathName] = uigetfile( ... |
---|
| 3439 | {'*.grid', ' (*.grid)'; |
---|
| 3440 | '*.grid', '.grid files '; ... |
---|
| 3441 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3442 | 'Pick a file',filebase); |
---|
| 3443 | filegrid=fullfile(PathName,FileName); |
---|
| 3444 | set(hObject,'UserData',filegrid);%store for future use |
---|
| 3445 | if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file')) |
---|
| 3446 | testgrid=1; |
---|
| 3447 | end |
---|
| 3448 | end |
---|
| 3449 | end |
---|
| 3450 | if testgrid |
---|
| 3451 | set(handle_dx,'Visible','off'); |
---|
| 3452 | set(handle_dy,'Visible','off'); |
---|
| 3453 | set(handle_title_dy,'Visible','off'); |
---|
| 3454 | set(handle_title_dx,'Visible','off'); |
---|
| 3455 | set(handle_txtbox,'Visible','on') |
---|
| 3456 | set(handle_txtbox,'String',filegrid) |
---|
| 3457 | else |
---|
| 3458 | set(hObject,'Value',0); |
---|
| 3459 | set(handle_dx,'Visible','on'); |
---|
| 3460 | set(handle_dy,'Visible','on'); |
---|
| 3461 | set(handle_title_dy,'Visible','on'); |
---|
| 3462 | set(handle_title_dx,'Visible','on'); |
---|
| 3463 | set(handle_txtbox,'Visible','off') |
---|
| 3464 | end |
---|
| 3465 | |
---|
| 3466 | %% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame |
---|
| 3467 | PanelName=get(hparent,'tag'); |
---|
| 3468 | if strcmp(PanelName,'Civ1') |
---|
| 3469 | hchildren=get(handles.Civ2,'children'); |
---|
| 3470 | handle_checkbox=findobj(hchildren,'tag','CheckGrid'); |
---|
| 3471 | handle_txtbox=findobj(hchildren,'tag','Grid'); |
---|
| 3472 | handle_dx=findobj(hchildren,'tag','num_Dx'); |
---|
| 3473 | handle_dy=findobj(hchildren,'tag','num_Dy'); |
---|
| 3474 | handle_title_dx=findobj(hchildren,'tag','title_Dx'); |
---|
| 3475 | handle_title_dy=findobj(hchildren,'tag','title_Dy'); |
---|
| 3476 | set(handle_checkbox,'UserData',filegrid);%store for future use |
---|
| 3477 | if testgrid |
---|
| 3478 | set(handle_checkbox,'Value',1); |
---|
| 3479 | set(handle_dx,'Visible','off'); |
---|
| 3480 | set(handle_dy,'Visible','off'); |
---|
| 3481 | set(handle_title_dx,'Visible','off'); |
---|
| 3482 | set(handle_title_dy,'Visible','off'); |
---|
| 3483 | set(handle_txtbox,'Visible','on') |
---|
| 3484 | set(handle_txtbox,'String',filegrid) |
---|
| 3485 | end |
---|
| 3486 | end |
---|
| 3487 | |
---|
| 3488 | %------------------------------------------------------------------------ |
---|
| 3489 | % --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..) |
---|
| 3490 | function CheckMask_Callback(hObject, eventdata, handles) |
---|
| 3491 | %------------------------------------------------------------------------ |
---|
| 3492 | value=get(hObject,'Value'); |
---|
| 3493 | hparent=get(hObject,'parent'); |
---|
| 3494 | parent_tag=get(hparent,'Tag'); |
---|
| 3495 | hchildren=get(hparent,'children'); |
---|
| 3496 | handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel |
---|
| 3497 | testmask=0; |
---|
| 3498 | if value |
---|
| 3499 | filebase=get(handles.RootPath,'String'); |
---|
| 3500 | [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name |
---|
| 3501 | if isequal(flag_mask,1) |
---|
| 3502 | filemask=[num2str(nbslice) 'mask']; |
---|
| 3503 | testmask=1; |
---|
| 3504 | else % browse for a mask |
---|
| 3505 | filemask=get(hObject,'UserData');%look for previous mask name stored as UserData |
---|
| 3506 | if exist(filemask,'file') |
---|
| 3507 | filebase=filemask; |
---|
| 3508 | end |
---|
| 3509 | [FileName, PathName] = uigetfile( ... |
---|
| 3510 | {'*.png', ' (*.png)'; |
---|
| 3511 | '*.png', '.png files '; ... |
---|
| 3512 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3513 | 'Pick a mask file *.png',filebase); |
---|
| 3514 | filemask=fullfile(PathName,FileName); |
---|
| 3515 | set(hObject,'UserData',filemask);%store for future use |
---|
| 3516 | if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file')) |
---|
| 3517 | testmask=1; |
---|
| 3518 | end |
---|
| 3519 | end |
---|
| 3520 | end |
---|
| 3521 | if testmask |
---|
| 3522 | if strcmp(parent_tag,'Civ1') |
---|
| 3523 | set(handles.Mask,'Visible','on') |
---|
| 3524 | set(handles.Mask,'String',filemask) |
---|
| 3525 | set(handles.CheckMask,'Value',1) |
---|
| 3526 | end |
---|
| 3527 | else |
---|
| 3528 | set(hObject,'Value',0); |
---|
| 3529 | set(handle_txtbox,'Visible','off') |
---|
| 3530 | end |
---|
| 3531 | |
---|
| 3532 | %------------------------------------------------------------------------ |
---|
| 3533 | % --- Executes on button press in get_gridpatch1. |
---|
| 3534 | function get_gridpatch1_Callback(hObject, eventdata, handles) |
---|
| 3535 | %------------------------------------------------------------------------ |
---|
| 3536 | filebase=get(handles.RootPath,'String'); |
---|
| 3537 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
| 3538 | {'*.grid', ' (*.grid)'; |
---|
| 3539 | '*.grid', '.grid files '; ... |
---|
| 3540 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3541 | 'Pick a file',filebase); |
---|
| 3542 | filegrid=fullfile(PathName,FileName); |
---|
| 3543 | set(handles.grid_patch1,'string',filegrid); |
---|
| 3544 | |
---|
| 3545 | |
---|
| 3546 | %------------------------------------------------------------------------ |
---|
| 3547 | % --- Executes on button press in get_gridpatch2. |
---|
| 3548 | function get_gridpatch2_Callback(hObject, eventdata, handles) |
---|
| 3549 | %------------------------------------------------------------------------ |
---|
| 3550 | |
---|
| 3551 | |
---|
| 3552 | %------------------------------------------------------------------------ |
---|
| 3553 | % --- STEREO Interp |
---|
| 3554 | 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) |
---|
| 3555 | %------------------------------------------------------------------------ |
---|
| 3556 | namelog=[filename_nc(1:end-3) '_stinterp.log']; |
---|
| 3557 | cmd=[stinterpBin ' -f1 ' filename_A_nc ' -f2 ' filename_B_nc ' -f ' filename_nc ... |
---|
| 3558 | ' -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 |
---|
| 3559 | |
---|
| 3560 | % %------------------------------------------------------------------------ |
---|
| 3561 | % %--read images and convert them to the uint16 format used for PIV |
---|
| 3562 | % function A=read_image(filename,type_ima,num,movieobject) |
---|
| 3563 | % %------------------------------------------------------------------------ |
---|
| 3564 | % %num is the view number needed for an avi movie |
---|
| 3565 | % switch type_ima |
---|
| 3566 | % case 'movie' |
---|
| 3567 | % A=read(movieobject,num); |
---|
| 3568 | % case 'avi' |
---|
| 3569 | % mov=aviread(filename,num); |
---|
| 3570 | % A=frame2im(mov(1)); |
---|
| 3571 | % case 'multimage' |
---|
| 3572 | % A=imread(filename,num); |
---|
| 3573 | % case 'image' |
---|
| 3574 | % A=imread(filename); |
---|
| 3575 | % end |
---|
| 3576 | % siz=size(A); |
---|
| 3577 | % if length(siz)==3;%color images |
---|
| 3578 | % A=sum(double(A),3); |
---|
| 3579 | % A=uint16(A); |
---|
| 3580 | % end |
---|
| 3581 | |
---|
| 3582 | |
---|
| 3583 | %------------------------------------------------------------------------ |
---|
| 3584 | % --- Executes on button press in get_ref_fix1. |
---|
| 3585 | function get_ref_fix1_Callback(hObject, eventdata, handles) |
---|
| 3586 | %------------------------------------------------------------------------ |
---|
| 3587 | filebase=get(handles.RootPath,'String'); |
---|
| 3588 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
| 3589 | {'*.nc', ' (*.nc)'; |
---|
| 3590 | '*.nc', 'netcdf files '; ... |
---|
| 3591 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3592 | 'Pick a file',filebase); |
---|
| 3593 | |
---|
| 3594 | fileinput=[PathName FileName]; |
---|
| 3595 | sizf=size(fileinput); |
---|
| 3596 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
| 3597 | %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); |
---|
| 3598 | [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput); |
---|
| 3599 | ref.filebase=fullfile(Path,File); |
---|
| 3600 | % ref.num_a=stra2num(str_a); |
---|
| 3601 | % ref.num_b=stra2num(str_b); |
---|
| 3602 | % ref.num1=str2double(field_count); |
---|
| 3603 | % ref.num2=str2double(str2); |
---|
| 3604 | browse=[];%initialisation |
---|
| 3605 | if ~isequal(ref.ext,'.nc') |
---|
| 3606 | msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') |
---|
| 3607 | return |
---|
| 3608 | end |
---|
| 3609 | set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']); |
---|
| 3610 | set(handles.ref_fix1,'UserData',ref) |
---|
| 3611 | menu_field{1}='civ1'; |
---|
| 3612 | Data=nc2struct(fileinput,[]); |
---|
| 3613 | if isfield(Data,'patch') && isequal(Data.patch,1) |
---|
| 3614 | menu_field{2}='filter1'; |
---|
| 3615 | end |
---|
| 3616 | if isfield(Data,'civ2') && isequal(Data.civ2,1) |
---|
| 3617 | menu_field{3}='civ2'; |
---|
| 3618 | end |
---|
| 3619 | if isfield(Data,'patch2') && isequal(Data.patch2,1) |
---|
| 3620 | menu_field{4}='filter2'; |
---|
| 3621 | end |
---|
| 3622 | set(handles.field_ref1,'String',menu_field); |
---|
| 3623 | set(handles.field_ref1,'Value',length(menu_field)); |
---|
| 3624 | set(handles.num_MinVel,'Value',2); |
---|
| 3625 | set(handles.num_MinVel,'String','1');%default threshold |
---|
| 3626 | set(handles.ref_fix1,'Enable','on') |
---|
| 3627 | |
---|
| 3628 | %------------------------------------------------------------------------ |
---|
| 3629 | % --- Executes on button press in get_ref_fix2. |
---|
| 3630 | function get_ref_fix2_Callback(hObject, eventdata, handles) |
---|
| 3631 | %------------------------------------------------------------------------ |
---|
| 3632 | if isequal(get(handles.get_ref_fix2,'Value'),1) |
---|
| 3633 | filebase=get(handles.RootPath,'String'); |
---|
| 3634 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
| 3635 | {'*.nc', ' (*.nc)'; |
---|
| 3636 | '*.nc', 'netcdf files '; ... |
---|
| 3637 | '*.*', 'All Files (*.*)'}, ... |
---|
| 3638 | 'Pick a file',filebase); |
---|
| 3639 | fileinput=[PathName FileName]; |
---|
| 3640 | sizf=size(fileinput); |
---|
| 3641 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
| 3642 | %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); |
---|
| 3643 | [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput); |
---|
| 3644 | ref.filebase=fullfile(Path,File); |
---|
| 3645 | % ref.num_a=stra2num(str_a); |
---|
| 3646 | % ref.num_b=stra2num(str_b); |
---|
| 3647 | % ref.num1=str2num(field_count); |
---|
| 3648 | % ref.num2=str2num(str2); |
---|
| 3649 | browse=[];%initialisation |
---|
| 3650 | if ~isequal(ref.ext,'.nc') |
---|
| 3651 | msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') |
---|
| 3652 | return |
---|
| 3653 | end |
---|
| 3654 | set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']); |
---|
| 3655 | set(handles.ref_fix2,'UserData',ref) |
---|
| 3656 | menu_field{1}='civ1'; |
---|
| 3657 | Data=nc2struct(fileinput,[]); |
---|
| 3658 | if isfield(Data,'patch') && isequal(Data.patch,1) |
---|
| 3659 | menu_field{2}='filter1'; |
---|
| 3660 | end |
---|
| 3661 | if isfield(Data,'civ2') && isequal(Data.civ2,1) |
---|
| 3662 | menu_field{3}='civ2'; |
---|
| 3663 | end |
---|
| 3664 | if isfield(Data,'patch2') && isequal(Data.patch2,1) |
---|
| 3665 | menu_field{4}='filter2'; |
---|
| 3666 | end |
---|
| 3667 | set(handles.field_ref2,'String',menu_field); |
---|
| 3668 | set(handles.field_ref2,'Value',length(menu_field)); |
---|
| 3669 | set(handles.num_MinVel,'Value',2); |
---|
| 3670 | set(handles.num_MinVel,'String','1');%default threshold |
---|
| 3671 | set(handles.ref_fix2,'Enable','on') |
---|
| 3672 | set(handles.ref_fix2,'Visible','on') |
---|
| 3673 | set(handles.field_ref2,'Visible','on') |
---|
| 3674 | else |
---|
| 3675 | set(handles.ref_fix2,'Visible','off') |
---|
| 3676 | set(handles.field_ref2,'Visible','off') |
---|
| 3677 | end |
---|
| 3678 | |
---|
| 3679 | %------------------------------------------------------------------------ |
---|
| 3680 | function ref_fix1_Callback(hObject, eventdata, handles) |
---|
| 3681 | %------------------------------------------------------------------------ |
---|
| 3682 | set(handles.num_MinVel,'Value',1); |
---|
| 3683 | set(handles.field_ref1,'Value',1) |
---|
| 3684 | set(handles.field_ref1,'String',{' '}) |
---|
| 3685 | set(handles.ref_fix1,'UserData',[]); |
---|
| 3686 | set(handles.ref_fix1,'String',''); |
---|
| 3687 | set(handles.thresh_vel1,'String','0'); |
---|
| 3688 | |
---|
| 3689 | %------------------------------------------------------------------------ |
---|
| 3690 | function ref_fix2_Callback(hObject, eventdata, handles) |
---|
| 3691 | %------------------------------------------------------------------------ |
---|
| 3692 | set(handles.num_MinVel,'Value',1); |
---|
| 3693 | set(handles.field_ref2,'Value',1) |
---|
| 3694 | set(handles.field_ref2,'String',{' '}) |
---|
| 3695 | set(handles.ref_fix2,'UserData',[]); |
---|
| 3696 | set(handles.ref_fix2,'String',''); |
---|
| 3697 | set(handles.num_MinVel,'String','0'); |
---|
| 3698 | |
---|
| 3699 | %------------------------------------------------------------------------ |
---|
| 3700 | % --- TO ABANDON Executes on button press in test_stereo1. |
---|
| 3701 | function CheckStereo_Callback(hObject, eventdata, handles) |
---|
| 3702 | %------------------------------------------------------------------------ |
---|
| 3703 | hparent=get(hObject,'parent'); |
---|
| 3704 | parent_tag=get(hparent,'Tag'); |
---|
| 3705 | hchildren=get(hparent,'children'); |
---|
| 3706 | handle_txtbox=findobj(hchildren,'tag','txt_Mask'); |
---|
| 3707 | if isequal(get(hObject,'Value'),0) |
---|
| 3708 | set(handles.num_SubDomainSize,'Visible','on') |
---|
| 3709 | set(handles.num_FieldSmooth,'Visible','on') |
---|
| 3710 | else |
---|
| 3711 | set(handles.num_SubDomainSize,'Visible','off') |
---|
| 3712 | set(handles.num_FieldSmooth,'Visible','off') |
---|
| 3713 | end |
---|
| 3714 | |
---|
| 3715 | % %------------------------------------------------------------------------ |
---|
| 3716 | % % --- Executes on button press in CheckStereo. |
---|
| 3717 | % function StereoCheck_Callback(hObject, eventdata, handles) |
---|
| 3718 | % %------------------------------------------------------------------------ |
---|
| 3719 | % if isequal(get(handles.CheckStereo,'Value'),0) |
---|
| 3720 | % set(handles.num_subdomainsize,'Visible','on') |
---|
| 3721 | % set(handles.num_FieldSmooth,'Visible','on') |
---|
| 3722 | % else |
---|
| 3723 | % set(handles.num_subdomainsize,'Visible','off') |
---|
| 3724 | % set(handles.num_FieldSmooth,'Visible','off') |
---|
| 3725 | % end |
---|
| 3726 | |
---|
| 3727 | %------------------------------------------------------------------------ |
---|
| 3728 | % --- Executes on button press in TestCiv1: prepare the image correlation function |
---|
| 3729 | % activated by mouse motion |
---|
| 3730 | function TestCiv1_Callback(hObject, eventdata, handles) |
---|
| 3731 | %------------------------------------------------------------------------ |
---|
| 3732 | drawnow |
---|
| 3733 | if get(handles.TestCiv1,'Value') |
---|
| 3734 | set(handles.TestCiv1,'BackgroundColor',[0.7 0.7 0.7])% paint TestCiv1 button to grey to confirm civ launch |
---|
| 3735 | ref_i=str2double(get(handles.ref_i,'String'));% read reference i index |
---|
| 3736 | if strcmp(get(handles.ref_j,'Visible'),'on') |
---|
| 3737 | ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant |
---|
| 3738 | else |
---|
| 3739 | ref_j=1;%default j index |
---|
| 3740 | end |
---|
| 3741 | [filecell,i1,i2]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices |
---|
| 3742 | Data.ListVarName={'ny','nx','A'}; |
---|
| 3743 | Data.VarDimName= {'ny','nx',{'ny','nx'}}; |
---|
| 3744 | |
---|
| 3745 | Data.A=imread(filecell.ima1.civ1{1}); % read the first image |
---|
| 3746 | if ndims(Data.A)==3 %case of color image |
---|
| 3747 | Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}}; |
---|
| 3748 | end |
---|
| 3749 | Data.ny=[size(Data.A,1) 1]; |
---|
| 3750 | Data.nx=[1 size(Data.A,2)]; |
---|
| 3751 | Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly |
---|
| 3752 | par_civ1=read_GUI(handles.Civ1); |
---|
| 3753 | par_civ1.FileTypeA=get_file_type(filecell.ima1.civ1{1}); |
---|
| 3754 | par_civ1.ImageWidth=size(Data.A,2); |
---|
| 3755 | par_civ1.ImageHeight=size(Data.A,1); |
---|
| 3756 | par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation |
---|
| 3757 | par_civ1.FrameIndexA=num2str(i1); |
---|
| 3758 | par_civ1.FrameIndexB=num2str(i2); |
---|
| 3759 | Param.Civ1=par_civ1; |
---|
| 3760 | Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV |
---|
| 3761 | hview_field=view_field(Data); %view the image in the GUI view_field |
---|
| 3762 | set(0,'CurrentFigure',hview_field) |
---|
| 3763 | hhview_field=guihandles(hview_field); |
---|
| 3764 | set(hview_field,'CurrentAxes',hhview_field.PlotAxes) |
---|
| 3765 | ViewData=get(hview_field,'UserData'); |
---|
[598] | 3766 | ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field |
---|
[597] | 3767 | ViewData.PlotAxes.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field |
---|
| 3768 | ViewData.PlotAxes.X=Grid.Civ1_X; %keep the set of points in memeory |
---|
| 3769 | ViewData.PlotAxes.Y=Grid.Civ1_Y; |
---|
| 3770 | set(hview_field,'UserData',ViewData) |
---|
| 3771 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
| 3772 | if isempty(corrfig) |
---|
| 3773 | corrfig=figure; |
---|
| 3774 | set(corrfig,'tag','corrfig') |
---|
| 3775 | set(corrfig,'name','image correlation') |
---|
| 3776 | set(corrfig,'DeleteFcn',{@closeview_field})% |
---|
| 3777 | end |
---|
| 3778 | set(handles.TestCiv1,'BackgroundColor',[1 0 0]) |
---|
| 3779 | else |
---|
| 3780 | set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red |
---|
| 3781 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
| 3782 | if ~isempty(corrfig) |
---|
| 3783 | delete(corrfig) |
---|
| 3784 | end |
---|
| 3785 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
| 3786 | if ~isempty(hview_field) |
---|
| 3787 | delete(hview_field) |
---|
| 3788 | end |
---|
| 3789 | end |
---|
| 3790 | |
---|
| 3791 | %------------------------------------------------------------------------ |
---|
| 3792 | %----function introduced for the correlation window figure, activated by deleting this window |
---|
| 3793 | function closeview_field(gcbo,eventdata) |
---|
| 3794 | %------------------------------------------------------------------------ |
---|
| 3795 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
| 3796 | if ~isempty(hview_field) |
---|
| 3797 | delete(hview_field) |
---|
| 3798 | end |
---|
| 3799 | |
---|
| 3800 | %------------------------------------------------------------------------ |
---|
| 3801 | % --- Executes on button press in CheckThreshold. |
---|
| 3802 | function CheckThreshold_Callback(hObject, eventdata, handles) |
---|
| 3803 | %------------------------------------------------------------------------ |
---|
| 3804 | huipanel=get(hObject,'parent'); |
---|
| 3805 | obj(1)=findobj(huipanel,'Tag','num_MinIma'); |
---|
| 3806 | obj(2)=findobj(huipanel,'Tag','num_MaxIma'); |
---|
| 3807 | obj(3)=findobj(huipanel,'Tag','title_Threshold'); |
---|
| 3808 | if get(hObject,'Value') |
---|
| 3809 | set(obj,'Visible','on') |
---|
| 3810 | else |
---|
| 3811 | set(obj,'Visible','off') |
---|
| 3812 | end |
---|
| 3813 | |
---|
| 3814 | |
---|
| 3815 | |
---|
| 3816 | |
---|
| 3817 | %'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature |
---|
| 3818 | %--------------------------------------------------------------------- |
---|
| 3819 | function NomTypeNc=nomtype2pair(NomTypeIma,mode) |
---|
| 3820 | %--------------------------------------------------------------------- |
---|
| 3821 | % OUTPUT: |
---|
| 3822 | % NomTypeNc |
---|
| 3823 | %--------------------------------------------------------------------- |
---|
| 3824 | % INPUT: |
---|
| 3825 | % 'NomTypeIma': string defining the kind of nomenclature used for images |
---|
| 3826 | |
---|
| 3827 | NomTypeNc=NomTypeIma;%default |
---|
| 3828 | switch mode |
---|
| 3829 | case 'pair j1-j2' |
---|
| 3830 | if ~isempty(regexp(NomTypeIma,'a$')) |
---|
| 3831 | NomTypeNc=[NomTypeIma 'b']; |
---|
| 3832 | elseif ~isempty(regexp(NomTypeIma,'A$')) |
---|
| 3833 | NomTypeNc=[NomTypeIma 'B']; |
---|
| 3834 | else |
---|
| 3835 | r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); |
---|
| 3836 | if ~isempty(r) |
---|
| 3837 | NomTypeNc='_1_1-2'; |
---|
| 3838 | end |
---|
| 3839 | end |
---|
| 3840 | case 'series(Dj)' |
---|
| 3841 | % r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); |
---|
| 3842 | % if ~isempty(r) |
---|
| 3843 | NomTypeNc='_1_1-2'; |
---|
| 3844 | % end |
---|
| 3845 | case 'series(Di)' |
---|
| 3846 | r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); |
---|
| 3847 | if ~isempty(r) |
---|
| 3848 | NomTypeNc='_1-2_1'; |
---|
| 3849 | else |
---|
| 3850 | NomTypeNc='_1-2'; |
---|
| 3851 | end |
---|
| 3852 | end |
---|
| 3853 | |
---|
| 3854 | function NomType_Callback(hObject, eventdata, handles) |
---|
| 3855 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
---|
| 3856 | RootPath=get(handles.RootPath,'String'); |
---|
| 3857 | RootFile=get(handles.RootFile,'String'); |
---|
| 3858 | SubDirImages=get(handles.SubDirImages,'String'); |
---|
| 3859 | ref_i=str2num(get(handles.ref_i,'String')); |
---|
| 3860 | ref_j=str2num(get(handles.ref_j,'String')); |
---|
| 3861 | NomType=get(handles.NomType,'String'); |
---|
| 3862 | ImaExt=get(handles.ImaExt,'String'); |
---|
| 3863 | fileinput=fullfile_uvmat(RootPath,SubDirImages,RootFile,ImaExt,NomType,ref_i,[],ref_j); |
---|
| 3864 | errormsg=display_file_name(handles,fileinput); |
---|
| 3865 | if ~isempty(errormsg) |
---|
| 3866 | msgbox_uvmat('ERROR',errormsg) |
---|
| 3867 | end |
---|
| 3868 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
---|
| 3869 | |
---|
| 3870 | % --- Executes on selection change in Program. |
---|
| 3871 | function Program_Callback(hObject, eventdata, handles) |
---|
| 3872 | ListProgram=get(handles.Program,'String'); |
---|
| 3873 | Program=ListProgram{get(handles.Program,'value')}; |
---|
| 3874 | switch Program |
---|
| 3875 | case 'CivX' |
---|
| 3876 | set(handles.num_MaxDiff,'Visible','off') |
---|
| 3877 | set(handles.num_MaxVel,'Visible','off') |
---|
| 3878 | set(handles.title_MaxVel,'Visible','off') |
---|
| 3879 | set(handles.num_Nx,'Visible','on') |
---|
| 3880 | set(handles.num_Ny,'Visible','on') |
---|
| 3881 | set(handles.title_Nx,'Visible','on') |
---|
| 3882 | set(handles.title_Ny,'Visible','on') |
---|
| 3883 | set(handles.title_MaxDiff,'Visible','off') |
---|
| 3884 | set(handles.num_CorrSmooth,'Style','edit') |
---|
| 3885 | set(handles.num_CorrSmooth,'String','1') |
---|
| 3886 | set(handles.BATCH,'Enable','on') |
---|
| 3887 | set(handles.CheckThreshold,'Visible','off') |
---|
| 3888 | set(handles.CheckDeformation,'Value',1) |
---|
| 3889 | set(handles.CheckDecimal,'Value',1) |
---|
| 3890 | case {'civ_matlab','civ_matlab.sh'} |
---|
| 3891 | set(handles.num_MaxDiff,'Visible','on') |
---|
| 3892 | set(handles.num_MaxVel,'Visible','on') |
---|
| 3893 | set(handles.title_MaxVel,'Visible','on') |
---|
| 3894 | set(handles.title_MaxDiff,'Visible','on') |
---|
| 3895 | set(handles.num_Nx,'Visible','off') |
---|
| 3896 | set(handles.num_Ny,'Visible','off') |
---|
| 3897 | set(handles.title_Nx,'Visible','off') |
---|
| 3898 | set(handles.title_Ny,'Visible','off') |
---|
| 3899 | set(handles.num_CorrSmooth,'Style','popupmenu') |
---|
| 3900 | set(handles.num_CorrSmooth,'Value',1) |
---|
| 3901 | set(handles.num_CorrSmooth,'String',{'1';'2'}) |
---|
| 3902 | set(handles.CheckThreshold,'Visible','on') |
---|
| 3903 | set(handles.CheckDeformation,'Value',0)% desactivate (work in progress) |
---|
| 3904 | set(handles.CheckDecimal,'Value',0)% desactivate (work in progress) |
---|
| 3905 | end |
---|
| 3906 | |
---|
| 3907 | % --- Executes on button press in TestPatch1. |
---|
| 3908 | function TestPatch1_Callback(hObject, eventdata, handles) |
---|
| 3909 | set(handles.TestPatch1,'BackgroundColor',[1 1 0]) |
---|
| 3910 | drawnow |
---|
| 3911 | if get(handles.TestPatch1,'Value') |
---|
| 3912 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
| 3913 | if strcmp(get(handles.ref_j,'Visible'),'on') |
---|
| 3914 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
| 3915 | else |
---|
| 3916 | ref_j=1;%default |
---|
| 3917 | end |
---|
| 3918 | filecell=set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]); |
---|
| 3919 | Data.ListVarName={'ny','nx','A'}; |
---|
| 3920 | Data.VarDimName= {'ny','nx',{'ny','nx'}}; |
---|
| 3921 | param_patch1=read_GUI(handles.Patch1); |
---|
| 3922 | param_patch1.CivFile=filecell.nc.civ1{1}; |
---|
| 3923 | Param.Patch1=param_patch1; |
---|
| 3924 | for irho=1:7 |
---|
| 3925 | [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV |
---|
| 3926 | if ~isempty(errormsg) |
---|
| 3927 | msgbox_uvmat('ERROR',errormsg) |
---|
| 3928 | return |
---|
| 3929 | end |
---|
| 3930 | SmoothingParam(irho)=Param.Patch1.FieldSmooth; |
---|
| 3931 | Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0); |
---|
| 3932 | Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0); |
---|
| 3933 | DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff)) |
---|
| 3934 | NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff); |
---|
| 3935 | Param.Patch1.SmoothingParam=2*Param.Patch1.FieldSmooth; |
---|
| 3936 | end |
---|
| 3937 | figure |
---|
| 3938 | plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r') |
---|
| 3939 | set(handles.TestPatch1,'BackgroundColor',[1 0 0]) |
---|
| 3940 | else |
---|
| 3941 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
| 3942 | if ~isempty(corrfig) |
---|
| 3943 | delete(corrfig) |
---|
| 3944 | end |
---|
| 3945 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
| 3946 | if ~isempty(hview_field) |
---|
| 3947 | delete(hview_field) |
---|
| 3948 | end |
---|
| 3949 | end |
---|
| 3950 | |
---|
| 3951 | |
---|
| 3952 | % --- Executes on button press in TestCiv2. |
---|
| 3953 | function TestCiv2_Callback(hObject, eventdata, handles) |
---|