1 | %'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch) |
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2 | %------------------------------------------------------------------------ |
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3 | % provides an interface for the software menucivx |
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4 | % function varargout = civ(varargin) |
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5 | % provides an interface for the software menucivx |
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6 | % |
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7 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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8 | % Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr |
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9 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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10 | % This file is part of the toolbox UVMAT. |
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11 | % |
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12 | % UVMAT is free software; you can redistribute it and/or modify |
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13 | % it under the terms of the GNU General Public License as published by |
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14 | % the Free Software Foundation; either version 2 of the License, or |
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15 | % (at your option) any later version. |
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16 | % |
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17 | % UVMAT is distributed in the hope that it will be useful, |
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18 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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19 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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20 | % GNU General Public License (file UVMAT/COPYING.txt) for more details. |
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21 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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22 | function varargout = civ(varargin) |
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23 | %TODO: search range |
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24 | |
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25 | % Last Modified by GUIDE v2.5 08-May-2012 22:14:39 |
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26 | % Begin initialization code - DO NOT EDIT |
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27 | gui_Singleton = 1; |
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28 | gui_State = struct('gui_Name', mfilename, ... |
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29 | 'gui_Singleton', gui_Singleton, ... |
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30 | 'gui_OpeningFcn', @civ_OpeningFcn, ... |
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31 | 'gui_OutputFcn', @civ_OutputFcn, ... |
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32 | 'gui_LayoutFcn', [] , ... |
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33 | 'gui_Callback', []); |
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34 | if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback$','once')) |
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35 | gui_State.gui_Callback = str2func(varargin{1}); |
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36 | end |
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37 | |
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38 | if nargout |
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39 | [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); |
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40 | else |
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41 | gui_mainfcn(gui_State, varargin{:}); |
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42 | end |
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43 | % End initialization code - DO NOT EDIT |
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44 | |
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45 | %------------------------------------------------------------------------ |
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46 | % --- Executes just before civ is made visible. |
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47 | function civ_OpeningFcn(hObject, eventdata, handles, fileinput) |
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48 | %------------------------------------------------------------------------ |
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49 | % This function has no output args, see OutputFcn. |
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50 | |
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51 | %% General settings |
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52 | handles.output = hObject; |
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53 | guidata(hObject, handles); % Update handles structure |
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54 | set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display) |
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55 | |
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56 | %% Adjust the GUI according to the binaries available in PARAM.xml |
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57 | path_civ=fileparts(which('civ')); %path to civ |
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58 | addpath (path_civ) ; %add the path to civ, (useful in case of change of working directory after civ has been s opened in the working directory) |
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59 | errormsg=[];%default error message |
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60 | xmlfile='PARAM.xml'; |
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61 | if exist(xmlfile,'file') |
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62 | try |
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63 | t=xmltree(xmlfile); |
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64 | sparam=convert(t); |
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65 | catch |
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66 | errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr}; |
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67 | end |
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68 | else |
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69 | errormsg=[xmlfile ' not found: path to civx binaries undefined']; |
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70 | end |
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71 | if ~isempty(errormsg) |
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72 | msgbox_uvmat('WARNING',errormsg); |
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73 | end |
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74 | test_batch=0;%default: ,no batch mode available |
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75 | if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode') |
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76 | test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod |
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77 | end |
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78 | if test_batch==0 |
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79 | set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated) |
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80 | set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated) |
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81 | end |
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82 | if isfield(sparam.RunParam,'CivBin') |
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83 | if ~exist(sparam.RunParam.CivBin,'file') |
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84 | sparam.RunParam.CivBin=fullfile(path_civ,sparam.RunParam.CivBin); |
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85 | end |
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86 | else |
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87 | sparam.RunParam.CivBin=''; |
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88 | end |
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89 | |
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90 | %% load the list of previously browsed files in the upper bar menu Open/ |
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91 | dir_perso=prefdir; % path to the directory .matlab for personal data |
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92 | profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab |
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93 | if exist(profil_perso,'file') |
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94 | h=load (profil_perso); |
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95 | if isfield(h,'MenuFile') |
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96 | for ifile=1:min(length(h.MenuFile),5) |
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97 | eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});']) |
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98 | end |
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99 | end |
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100 | end |
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101 | |
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102 | %% prepare the GUI with parameters from the input file if opened from uvmat |
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103 | if exist('fileinput','var')% && isfield(param,'RootName') && ~isempty(param.RootName) |
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104 | 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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105 | errormsg=display_file_name(handles,fileinput); |
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106 | if ~isempty(errormsg) |
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107 | msgbox_uvmat('ERROR',errormsg) |
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108 | end |
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109 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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110 | end |
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111 | |
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112 | %------------------------------------------------------------------------ |
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113 | % --- Outputs from this function are returned to the command line. |
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114 | function varargout = civ_OutputFcn(hObject, eventdata, handles) |
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115 | %------------------------------------------------------------------------ |
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116 | % Get default command line output from handles structure |
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117 | varargout{1} = handles.output; |
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118 | |
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119 | %------------------------------------------------------------------------ |
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120 | % --- Function activated by the Open/Browse... option in the upper menu bar. |
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121 | function MenuBrowse_Callback(hObject, eventdata, handles) |
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122 | %------------------------------------------------------------------------ |
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123 | %% get the current input root file name to initiate the browser |
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124 | filebase=get(handles.RootPath,'String'); |
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125 | oldfile=''; %default |
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126 | if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name |
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127 | dir_perso=prefdir; |
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128 | profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); |
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129 | if exist(profil_perso,'file') |
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130 | h=load (profil_perso); |
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131 | if isfield(h,'filebase')&& ischar(h.filebase) |
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132 | oldfile=h.filebase; |
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133 | end |
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134 | if isfield(h,'RootPath') && ischar(h.RootPath) |
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135 | oldfile=h.RootPath; |
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136 | end |
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137 | end |
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138 | else |
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139 | oldfile=filebase; |
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140 | end |
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141 | |
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142 | %% get the new input file with the browser |
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143 | menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)'; |
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144 | '*.xml', '.xml files '; ... |
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145 | '*.civ', '.civ files '; ... |
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146 | '*.png','.png image files'; ... |
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147 | '*.jpg',' jpeg image files'; ... |
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148 | '*.tif','.tif image files'; ... |
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149 | '*.avi;*.AVI','.avi movie files'; ... |
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150 | '*.nc','.netcdf files'; ... |
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151 | '*.*', 'All Files (*.*)'}; |
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152 | [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile); |
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153 | fileinput=[PathName FileName];%complete file name |
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154 | sizf=size(fileinput); |
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155 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
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156 | |
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157 | %% case of the xml file opened as input (TODO: check and see whether it is useful) |
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158 | [path,name,ext]=fileparts(fileinput); |
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159 | testeditxml=0; |
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160 | % if isequal(ext,'.xml') |
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161 | % testeditxml=1; |
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162 | % t_browse=xmltree(fileinput); |
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163 | % head_element=get(t_browse,1); |
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164 | % if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc') |
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165 | % testeditxml=0; |
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166 | % end |
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167 | % end |
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168 | % if testeditxml==1 || isequal(ext,'.xls') |
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169 | % heditxml=editxml({fileinput}); |
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170 | % set(heditxml,'Tag','browser') |
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171 | % waitfor(heditxml,'Tag','idle') |
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172 | % if ~ishandle(heditxml) |
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173 | % return |
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174 | % end |
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175 | % attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes'); |
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176 | % set(handles.browse,'UserData',fileinput)% store for future opening with browser |
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177 | % fileinput=get(attr,'UserData'); |
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178 | % if ~exist(fileinput,'file') |
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179 | % return |
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180 | % end |
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181 | % end |
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182 | [tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput); |
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183 | |
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184 | %% prepare the GUI with parameters from the input file |
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185 | 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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186 | errormsg=display_file_name(handles,fileinput); |
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187 | if ~isempty(errormsg) |
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188 | msgbox_uvmat('ERROR',erromsg) |
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189 | end |
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190 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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191 | |
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192 | %------------------------------------------------------------------------ |
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193 | % --- Open again the file whose name has been recorded in MenuFile_1 |
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194 | function MenuFile_1_Callback(hObject, eventdata, handles) |
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195 | %------------------------------------------------------------------------ |
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196 | 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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197 | fileinput=get(handles.MenuFile_1,'Label'); |
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198 | errormsg=display_file_name(handles,fileinput); |
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199 | if ~isempty(errormsg) |
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200 | msgbox_uvmat('ERROR',errormsg) |
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201 | end |
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202 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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203 | |
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204 | % ----------------------------------------------------------------------- |
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205 | % --- Open again the file whose name has been recorded in MenuFile_2 |
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206 | function MenuFile_2_Callback(hObject, eventdata, handles) |
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207 | %------------------------------------------------------------------------ |
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208 | 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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209 | fileinput=get(handles.MenuFile_2,'Label'); |
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210 | errormsg=display_file_name(handles,fileinput); |
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211 | if ~isempty(errormsg) |
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212 | msgbox_uvmat('ERROR',errormsg) |
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213 | end |
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214 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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215 | |
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216 | % ----------------------------------------------------------------------- |
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217 | % --- Open again the file whose name has been recorded in MenuFile_3 |
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218 | function MenuFile_3_Callback(hObject, eventdata, handles) |
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219 | %------------------------------------------------------------------------ |
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220 | 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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221 | fileinput=get(handles.MenuFile_3,'Label'); |
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222 | errormsg=display_file_name(handles,fileinput); |
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223 | if ~isempty(errormsg) |
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224 | msgbox_uvmat('ERROR',errormsg) |
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225 | end |
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226 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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227 | |
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228 | % ----------------------------------------------------------------------- |
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229 | % --- Open again the file whose name has been recorded in MenuFile_4 |
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230 | function MenuFile_4_Callback(hObject, eventdata, handles) |
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231 | %------------------------------------------------------------------------ |
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232 | 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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233 | fileinput=get(handles.MenuFile_4,'Label'); |
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234 | errormsg=display_file_name(handles,fileinput); |
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235 | if ~isempty(errormsg) |
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236 | msgbox_uvmat('ERROR',errormsg) |
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237 | end |
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238 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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239 | |
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240 | % ----------------------------------------------------------------------- |
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241 | % --- Open again the file whose name has been recorded in MenuFile_5 |
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242 | function MenuFile_5_Callback(hObject, eventdata, handles) |
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243 | %------------------------------------------------------------------------ |
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244 | 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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245 | fileinput=get(handles.MenuFile_5,'Label'); |
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246 | errormsg=display_file_name(handles,fileinput); |
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247 | if ~isempty(errormsg) |
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248 | msgbox_uvmat('ERROR',errormsg) |
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249 | end |
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250 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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251 | |
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252 | % ----------------------------------------------------------------------- |
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253 | % ----------------------------------------------------------------------- |
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254 | % --- Open the help html file |
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255 | function MenuHelp_Callback(hObject, eventdata, handles) |
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256 | % ----------------------------------------------------------------------- |
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257 | path_civ=fileparts(which ('civ')); |
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258 | helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html'); |
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259 | if isempty(dir(helpfile)) |
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260 | 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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261 | else |
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262 | addpath (fullfile(path_civ,'uvmat_doc')) |
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263 | web([helpfile '#civ']) |
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264 | end |
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265 | |
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266 | %------------------------------------------------------------------------ |
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267 | % --- Function activated when a new filebase (image series) is introduced |
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268 | function RootPath_Callback(hObject, eventdata, handles) |
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269 | %------------------------------------------------------------------------ |
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270 | 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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271 | RootPath=get(handles.RootPath,'String'); |
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272 | RootFile=get(handles.RootFile,'String'); |
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273 | ref_i=str2num(get(handles.ref_i,'String')); |
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274 | ref_j=str2num(get(handles.ref_j,'String')); |
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275 | NomType=get(handles.NomType,'String'); |
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276 | ImaExt=get(handles.ImaExt,'String'); |
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277 | fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j); |
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278 | errormsg=display_file_name(handles,fileinput); |
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279 | if ~isempty(errormsg) |
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280 | msgbox_uvmat('ERROR',errormsg) |
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281 | end |
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282 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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283 | |
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284 | %------------------------------------------------------------------------ |
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285 | % --- general function activated for an input file series |
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286 | function errormsg=display_file_name(handles,fileinput) |
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287 | %------------------------------------------------------------------------ |
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288 | set(handles.ListCompareMode,'Visible','on') |
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289 | errormsg='';%default empty error message |
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290 | drawnow |
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291 | |
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292 | %% enable RUN, BATCH button and 'status' display |
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293 | set(handles.RUN, 'Enable','On') |
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294 | set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color |
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295 | set(handles.BATCH,'Enable','On') |
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296 | set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color |
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297 | if isfield(handles,'status') |
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298 | set(handles.status,'Value',0); %suppress the 'status' display |
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299 | status_Callback([], [], handles) |
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300 | end |
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301 | |
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302 | %% determine nomenclature types and extension of the input files |
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303 | [RootPath,SubDir,RootFile,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput); |
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304 | NomTypeNc='';%default |
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305 | |
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306 | %% case of netcdf file as input, look for a coresponding image |
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307 | ind_opening=0;%default |
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308 | if strcmp(ExtInput,'.xml') |
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309 | Param=xml2struct(fileinput); |
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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 | if strcmp(ExtInput,'.nc') |
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314 | NomTypeNc=NomTypeInput; |
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315 | if isempty(regexp(NomTypeInput,'[ab|AB|-]')) |
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316 | set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs |
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317 | [RootPath,SubDir]=fileparts(RootPath); |
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318 | set(handles.RootFile_1,'Visible','On'); |
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319 | else |
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320 | set(handles.ListCompareMode,'Value',1) |
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321 | set(handles.RootFile_1,'Visible','Off'); |
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322 | end |
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323 | 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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324 | if isfield(Data,'Txt') |
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325 | errormsg=Data.Txt; |
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326 | return |
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327 | end |
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328 | if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data, |
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329 | set(handles.ListProgram,'Value',2) %select civ/Matlab by default |
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330 | ListProgram_Callback([],[], handles) |
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331 | if ~isempty(Data.CivStage)%test for civ files |
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332 | ind_opening=Data.CivStage; |
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333 | end |
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334 | if ~isempty(Data.Civ2_ImageB)%get the corresponding input image in the netcdf file |
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335 | imageinput=Data.Civ2_ImageB; |
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336 | [tild,ImaName,ImaExt]=fileparts(Data.Civ2_ImageA); |
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337 | set(handles.RootFile_1,'String',[ImaName ImaExt]) |
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338 | elseif ~isempty(Data.Civ1_ImageB) |
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339 | imageinput=Data.Civ1_ImageB; |
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340 | [tild,ImaName,ImaExt]=fileparts(Data.Civ1_ImageA); |
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341 | set(handles.RootFile_1,'String',[ImaName ImaExt]) |
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342 | end |
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343 | |
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344 | elseif ~isempty(Data.absolut_time_T0')% case of civx data, |
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345 | set(handles.ListProgram,'Value',1) %select Cix by default |
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346 | ListProgram_Callback([],[], handles) |
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347 | if ~isempty(Data.fix2) |
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348 | ind_opening=5; |
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349 | elseif ~isempty(Data.civ2) |
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350 | ind_opening=4; |
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351 | elseif ~isempty(Data.patch) |
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352 | ind_opening=3; |
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353 | elseif ~isempty(Data.fix) |
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354 | ind_opening=2; |
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355 | end |
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356 | % look for the corresponding input images |
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357 | check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$'));%detect pair label by letter |
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358 | NomTypeIma=NomTypeInput; |
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359 | if check_letter |
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360 | NomTypeIma=NomTypeInput(1:end-1); |
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361 | else |
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362 | r=regexp(NomTypeIma,'.-(?<num2>\d+)$','names'); |
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363 | if ~isempty(r) |
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364 | NomTypeIma=regexprep(NomTypeIma,['-' r.num2],''); |
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365 | end |
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366 | r=regexp(NomTypeIma,'.-(?<num2>\d+)','names'); |
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367 | if ~isempty(r) |
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368 | NomTypeIma=regexprep(NomTypeIma,['-' r.num2],''); |
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369 | end |
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370 | end |
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371 | imageinput=fullfile_uvmat(RootPath,'',RootFile,'.png',NomTypeIma,i1,[],j1); |
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372 | else |
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373 | errormsg='the input netcdf file is not civ data'; |
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374 | return |
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375 | end |
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376 | end |
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377 | |
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378 | %no corresponding image found, select manually with the browser |
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379 | ImaExt=ExtInput; |
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380 | if ~isempty(NomTypeNc) |
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381 | %no corresponding image found, select manually with the browser |
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382 | if ~exist(imageinput,'file') |
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383 | menu={'*.png;*.jpg;*.tif;*.avi;*.AVI', '(*.png,*.jpg ,*.tif, *.avi,*.AVI)'; |
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384 | '*.png','.png image files'; ... |
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385 | '*.jpg',' jpeg image files'; ... |
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386 | '*.tif','.tif image files'; ... |
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387 | '*.avi;*.AVI','.avi movie files'; ... |
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388 | '*.*', 'All Files (*.*)'}; |
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389 | [FileName, PathName] = uigetfile( menu, 'Pick an input image file',fileparts(fileparts(fileinput))); |
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390 | imageinput=[PathName FileName];%complete file name |
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391 | |
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392 | end |
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393 | fileinput=imageinput; |
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394 | end |
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395 | |
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396 | %% scan the image file series |
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397 | [FilePath,FileName,ImaExt]=fileparts(fileinput); |
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398 | % detect the file type, get the movie object if relevant, and look for the corresponding file series: |
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399 | % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists |
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400 | [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomTypeIma,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName ImaExt]); |
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401 | |
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402 | % [RootPath,FileName,ImaExt]=fileparts(fileinput); |
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403 | % [RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,Object]=find_file_series(RootPath,[FileName ImaExt]); |
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404 | % if strcmp(NomTypeInput,'*')% movies will be opened at the first frame |
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405 | % i1=1; |
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406 | % i2=[]; |
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407 | % j1=[]; |
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408 | % j2=[]; |
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409 | % end |
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410 | switch FileType |
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411 | case {'image','multimage','video'} |
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412 | otherwise |
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413 | errormsg='invalid input file: enter an image, a movie or civ .nc file'; |
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414 | return |
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415 | end |
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416 | % RootName=fullfile(RootPath,RootFile); |
---|
417 | set(handles.RootPath,'String',RootPath) |
---|
418 | set(handles.RootFile,'String',RootFile) |
---|
419 | browse=get(handles.RootPath,'UserData'); |
---|
420 | % browse.nom_type_nc=NomTypeNc; |
---|
421 | browse.incr_pair=[0 0];%default |
---|
422 | |
---|
423 | %% fill reference indices from the input file indices |
---|
424 | num_ref_i=i1;%efaulmt ref index |
---|
425 | if ~isempty(i2) |
---|
426 | num_ref_i=floor((num_ref_i+i2)/2); |
---|
427 | end |
---|
428 | num_ref_j=j1; |
---|
429 | if ~isempty(j2) |
---|
430 | num_ref_j=floor((num_ref_j+j2)/2); |
---|
431 | end |
---|
432 | |
---|
433 | %% scan the images if a civ file has been opened |
---|
434 | MinIndex_i=min(i1_series(i1_series>0)); |
---|
435 | MinIndex_j=min(j1_series(j1_series>0)); |
---|
436 | MaxIndex_i=max(i1_series(i1_series>0)); |
---|
437 | MaxIndex_j=max(j1_series(j1_series>0)); |
---|
438 | |
---|
439 | %% look for an image documentation file |
---|
440 | ext_imadoc='';%default |
---|
441 | RootName=fullfile(RootPath,RootFile); |
---|
442 | if exist([RootName '.xml'],'file') |
---|
443 | ext_imadoc='.xml'; |
---|
444 | elseif exist([RootName '.civxml'],'file') |
---|
445 | ext_imadoc='.civxml'; |
---|
446 | elseif exist([RootName '.civ'],'file') |
---|
447 | ext_imadoc='.civ'; |
---|
448 | elseif exist([RootName '.avi'],'file') |
---|
449 | ext_imadoc='.avi'; |
---|
450 | elseif exist([RootName '.AVI'],'file') |
---|
451 | ext_imadoc='.AVI'; |
---|
452 | end |
---|
453 | set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used |
---|
454 | |
---|
455 | %% read the time in the image documentation file |
---|
456 | time=[]; |
---|
457 | TimeUnit=''; %default |
---|
458 | CoordUnit='';%default |
---|
459 | pxcm_search=1; |
---|
460 | if ~isempty(ext_imadoc) |
---|
461 | set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning |
---|
462 | drawnow |
---|
463 | switch ext_imadoc |
---|
464 | case '.civxml'%OBSOLETE |
---|
465 | [tild,tild,time]=read_civxml([RootName '.civxml']); |
---|
466 | mode='pair j1-j2'; |
---|
467 | if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat |
---|
468 | nom_type_ima='_i_j'; |
---|
469 | end |
---|
470 | case '.xml' |
---|
471 | [XmlData,warntext]=imadoc2struct([RootName '.xml']); |
---|
472 | ext_ima_read=[]; |
---|
473 | nom_type_read=[]; |
---|
474 | if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file |
---|
475 | %[PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName); |
---|
476 | [tild,tild,tild,tild,tild,tild,tild,tild,nom_type_read]=fileparts_uvmat(XmlData.Heading.ImageName); |
---|
477 | fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file, |
---|
478 | if ~exist(fullname,'file') |
---|
479 | msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist']) |
---|
480 | end |
---|
481 | end |
---|
482 | if isfield(XmlData,'Time') |
---|
483 | time=XmlData.Time; |
---|
484 | %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml |
---|
485 | if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector |
---|
486 | if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once')) |
---|
487 | time=time'; |
---|
488 | MaxIndex_i=MaxIndex_j; |
---|
489 | MaxIndex_j=1; |
---|
490 | end |
---|
491 | end |
---|
492 | end |
---|
493 | if isfield(XmlData,'TimeUnit') |
---|
494 | TimeUnit=XmlData.TimeUnit; |
---|
495 | end |
---|
496 | |
---|
497 | if isfield(XmlData,'GeometryCalib') |
---|
498 | tsai=XmlData.GeometryCalib; |
---|
499 | if isfield(tsai,'fx_fy') |
---|
500 | pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range |
---|
501 | end |
---|
502 | if isfield(tsai,'CoordUnit') |
---|
503 | CoordUnit=tsai.CoordUnit; |
---|
504 | end |
---|
505 | end |
---|
506 | case '.civ'% OBSOLETE: case of .civ image documentation file |
---|
507 | [error,time,TimeUnit,mode,npx,npy]=read_imatext([RootName '.civ']); |
---|
508 | if error==2, msgbox_uvmat('WARNING',['no file ' RootName '.civ']); |
---|
509 | elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
---|
510 | end |
---|
511 | nom_type_ima='001a'; |
---|
512 | case {'.avi','.AVI'} |
---|
513 | nom_type_ima='*'; |
---|
514 | ImaExt=ext_imadoc; |
---|
515 | set(handles.ListPairMode,'Value',1); |
---|
516 | set(handles.ListPairMode,'String',{'series(Di)'}) |
---|
517 | dt=0.04;%default |
---|
518 | if exist([RootName ext_imadoc],'file')==2 |
---|
519 | hhh=which('videoreader'); |
---|
520 | if isempty(hhh)%use old video function of matlab |
---|
521 | imainfo=aviinfo([RootName ext_imadoc]);%read infos on the avi movie |
---|
522 | dt=1/imainfo.FramesPerSecond;%time interval between successive frames |
---|
523 | MaxIndex_i=imainfo.NumFrames;%number of frames |
---|
524 | % XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)'; |
---|
525 | % nbfield=imainfo.NumFrames; |
---|
526 | % set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec |
---|
527 | % ColorType=imainfo.ImageType;%='truecolor' for color images |
---|
528 | else %use video function videoreader of matlab |
---|
529 | imainfo=get(videoreader([RootName ext_imadoc]));%read infos on the avi movie |
---|
530 | dt=1/imainfo.FrameRate;%time interval between successive frames |
---|
531 | MaxIndex_i=imainfo.NumberOfFrames;%number of frames |
---|
532 | % XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)'; |
---|
533 | % nbfield=imainfo.NumberOfFrames; |
---|
534 | % set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec |
---|
535 | % ColorType='truecolor'; |
---|
536 | end |
---|
537 | |
---|
538 | time=(dt*(0:MaxIndex_i-1))';%list of image times |
---|
539 | TimeUnit='s'; |
---|
540 | end |
---|
541 | set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter |
---|
542 | end |
---|
543 | end |
---|
544 | %% timing display |
---|
545 | %show the reference image edit box if relevant (not needed for movies or in the absence of time information |
---|
546 | if numel(time)>=2 % if there are at least two time values to define dt |
---|
547 | MaxIndex_i=min(size(time,1),MaxIndex_i); |
---|
548 | MaxIndex_j=min(size(time,2),MaxIndex_j); |
---|
549 | time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices) |
---|
550 | time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros |
---|
551 | set(handles.ImaDoc,'UserData',time); %store the matrix of times |
---|
552 | set(handles.dt_unit,'String',['dt in m' TimeUnit]); |
---|
553 | set(handles.TimeUnit,'String',TimeUnit); |
---|
554 | else |
---|
555 | set(handles.ImaDoc,'String',''); %xml file not used for timing |
---|
556 | time=(i1_series(:,1)+0:size(i1_series,1)-1);% time=index i |
---|
557 | time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices |
---|
558 | TimeUnit='frame'; |
---|
559 | end |
---|
560 | set(handles.ImaDoc,'UserData',time); %store the matrix of times |
---|
561 | set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms) |
---|
562 | set(handles.TimeUnit,'String',TimeUnit); |
---|
563 | set(handles.nb_field,'String',num2str(MaxIndex_i)); |
---|
564 | set(handles.nb_field2,'String',num2str(MaxIndex_j)); |
---|
565 | set(handles.CoordUnit,'String',CoordUnit) |
---|
566 | set(handles.SearchRange,'UserData', pxcm_search); |
---|
567 | set(handles.ImaExt,'String',ImaExt) |
---|
568 | set(handles.NomType,'String',NomTypeIma) |
---|
569 | set(handles.ref_i,'String',num2str(num_ref_i)) |
---|
570 | set(handles.ref_j,'String',num2str(num_ref_j)) |
---|
571 | |
---|
572 | %% update i and j index range if a nc file has been opened or pb withmin max image indices: |
---|
573 | % then set first and last to the inputfile index by default |
---|
574 | first_i=str2num(get(handles.first_i,'String')); |
---|
575 | last_i=str2num(get(handles.last_i,'String')); |
---|
576 | if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i) |
---|
577 | set(handles.first_i,'String',num2str(num_ref_i)); |
---|
578 | set(handles.last_i,'String',num2str(num_ref_i));% |
---|
579 | end |
---|
580 | if ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i |
---|
581 | set(handles.first_i,'String',num2str(num_ref_i)); |
---|
582 | set(handles.last_i,'String',num2str(num_ref_i));% |
---|
583 | end |
---|
584 | |
---|
585 | %j index range |
---|
586 | first_j=str2num(get(handles.first_j,'String')); |
---|
587 | last_j=str2num(get(handles.last_i,'String')); |
---|
588 | if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j) |
---|
589 | set(handles.first_j,'String',num2str(num_ref_j)); |
---|
590 | set(handles.last_j,'String',num2str(num_ref_j));% |
---|
591 | elseif ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j |
---|
592 | set(handles.first_j,'String',num2str(num_ref_j)); |
---|
593 | set(handles.last_j,'String',num2str(num_ref_j));% |
---|
594 | end |
---|
595 | |
---|
596 | %% set the civ options depending on the input file content when a nc file has been opened |
---|
597 | ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'}; |
---|
598 | if ind_opening~=0 |
---|
599 | for index = 1:ind_opening |
---|
600 | set(handles.(ListOptions{index}),'value',0) |
---|
601 | end |
---|
602 | end |
---|
603 | for index = ind_opening+2:6 |
---|
604 | set(handles.(ListOptions{index}),'value',0) |
---|
605 | end |
---|
606 | set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1) |
---|
607 | update_CivOptions(handles,1) |
---|
608 | |
---|
609 | %% set the menus of image pairs and default selection for civ %%%%%%%%%%%%%%%%%%% |
---|
610 | %check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter |
---|
611 | if isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1) |
---|
612 | set(handles.ListPairMode,'Value',1) |
---|
613 | set(handles.ListPairMode,'String',{'series(Di)'}) |
---|
614 | elseif MaxIndex_i==1 && MaxIndex_j>1% simple series in j |
---|
615 | set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'}) |
---|
616 | if MaxIndex_j <= 10 |
---|
617 | set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large |
---|
618 | end |
---|
619 | else |
---|
620 | set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice |
---|
621 | if strcmp(NomTypeNc,'_1-2_1') |
---|
622 | set(handles.ListPairMode,'Value',3)% advise 'series(Di)' |
---|
623 | elseif MaxIndex_j <= 10 |
---|
624 | set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large |
---|
625 | end |
---|
626 | end |
---|
627 | |
---|
628 | %% scan files to update the subdirectory list display |
---|
629 | listot=dir(RootPath);%directory of RootPath |
---|
630 | idir=0; |
---|
631 | listdir={''};%default |
---|
632 | % get the list of existing civ subdirectories in the path of theinput root file |
---|
633 | for ilist=1:length(listot) |
---|
634 | if listot(ilist).isdir |
---|
635 | name=listot(ilist).name; |
---|
636 | if ~isequal(name,'.') && ~isequal(name,'..') |
---|
637 | idir=idir+1; |
---|
638 | listdir{idir,1}=listot(ilist).name; |
---|
639 | end |
---|
640 | end |
---|
641 | end |
---|
642 | |
---|
643 | %% update the selection for civ1 and civ2 |
---|
644 | if ~isempty(SubDir)% subdir for civ1 and civ2 initiated by the input |
---|
645 | SubdirCiv1=SubDir; |
---|
646 | SubdirCiv2=SubDir; |
---|
647 | set(handles.SubdirCiv1,'String',SubDir) |
---|
648 | set(handles.SubdirCiv2,'String',SubDir) |
---|
649 | else% currently selected subdir preserved |
---|
650 | SubdirCiv1=get(handles.SubdirCiv1,'String'); |
---|
651 | SubdirCiv2=get(handles.SubdirCiv2,'String'); |
---|
652 | if isempty(SubdirCiv1)% default subdir name='CIV' |
---|
653 | set(handles.SubdirCiv1,'String','CIV'); |
---|
654 | SubdirCiv1='CIV'; |
---|
655 | end |
---|
656 | if isempty(SubdirCiv2)% default subdir name='CIV' |
---|
657 | set(handles.SubdirCiv2,'String','CIV'); |
---|
658 | SubdirCiv2='CIV'; |
---|
659 | end |
---|
660 | end |
---|
661 | |
---|
662 | %% update the subdirectory menus |
---|
663 | ValueCiv1=find(strcmp(SubdirCiv1,listdir));%search the index of subdir in the cell listdir |
---|
664 | if isempty(ValueCiv1)% if the input subdir is not found |
---|
665 | ValueCiv1=numel(listdir)+1;%new subdirectory requested for civ1 |
---|
666 | end |
---|
667 | ValueCiv2=find(strcmp(SubdirCiv2,listdir));%search the index of subdir in the cell listdir |
---|
668 | if isempty(ValueCiv2)% if the input subdir is not found |
---|
669 | ValueCiv2=numel(listdir)+1;%new subdirectory requested for civ2 |
---|
670 | end |
---|
671 | set(handles.ListSubdirCiv1,'String',[listdir;'new...']) |
---|
672 | set(handles.ListSubdirCiv2,'String',[listdir;'new...']) |
---|
673 | set(handles.ListSubdirCiv1,'Value',ValueCiv1) |
---|
674 | set(handles.ListSubdirCiv2,'Value',ValueCiv2) |
---|
675 | if isempty(listdir) |
---|
676 | set(handles.SubdirCiv1,'String','CIV') |
---|
677 | set(handles.SubdirCiv2,'String','CIV') |
---|
678 | end |
---|
679 | |
---|
680 | %% store info |
---|
681 | set(handles.RootPath,'UserData',browse)% store the nomenclature type |
---|
682 | |
---|
683 | %% list the possible index pairs, depending on the option set in ListPairMode |
---|
684 | ListPairMode_Callback([], [], handles) |
---|
685 | |
---|
686 | %% store the root input filename for future opening |
---|
687 | profil_perso=fullfile(prefdir,'uvmat_perso.mat'); |
---|
688 | if exist(profil_perso,'file') |
---|
689 | save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat |
---|
690 | else |
---|
691 | txt=ver('MATLAB'); |
---|
692 | Release=txt.Release; |
---|
693 | relnumb=str2double(Release(3:4)); |
---|
694 | if relnumb >= 14 |
---|
695 | save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat |
---|
696 | else |
---|
697 | save (profil_perso,'RootPath'); %store the root name for future opening of uvmat |
---|
698 | end |
---|
699 | end |
---|
700 | set(handles.RootPath,'BackgroundColor',[1 1 1]) |
---|
701 | |
---|
702 | %------------------------------------------------------------------------ |
---|
703 | % --- Executes on carriage return on the subdir checkciv1 edit window |
---|
704 | function SubdirCiv1_Callback(hObject, eventdata, handles) |
---|
705 | %------------------------------------------------------------------------ |
---|
706 | SubDir=get(handles.SubdirCiv1,'String'); |
---|
707 | menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update |
---|
708 | ichoice=find(strcmp(SubDir,menu_str),1); |
---|
709 | if isempty(ichoice) |
---|
710 | ilist=numel(menu_str); %select 'new...' in the menu |
---|
711 | else |
---|
712 | ilist=ichoice; |
---|
713 | end |
---|
714 | set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu |
---|
715 | if get(handles.CheckCiv1,'Value')% if Civ1 is performed |
---|
716 | set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1 |
---|
717 | set(handles.ListSubdirCiv2,'Value',ilist) |
---|
718 | else % if Civ1 data already exist |
---|
719 | errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory |
---|
720 | if ~isempty(errormsg) |
---|
721 | msgbox_uvmat('ERROR',errormsg) |
---|
722 | end |
---|
723 | end |
---|
724 | |
---|
725 | %------------------------------------------------------------------------ |
---|
726 | % --- Executes on carriage return on the SubDir checkciv1 edit window |
---|
727 | function SubdirCiv2_Callback(hObject, eventdata, handles) |
---|
728 | %------------------------------------------------------------------------ |
---|
729 | SubDir=get(handles.SubdirCiv1,'String'); |
---|
730 | menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update |
---|
731 | ichoice=find(strcmp(SubDir,menu_str),1); |
---|
732 | if isempty(ichoice) |
---|
733 | ilist=numel(menu_str); %select 'new...' in the menu |
---|
734 | else |
---|
735 | ilist=ichoice; |
---|
736 | end |
---|
737 | set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu |
---|
738 | %update the list of available pairs from netcdf files in the new directory |
---|
739 | if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value') |
---|
740 | errormsg=find_netcpair_civ(handles,2); |
---|
741 | if ~isempty(errormsg) |
---|
742 | msgbox_uvmat('ERROR',errormsg) |
---|
743 | end |
---|
744 | end |
---|
745 | |
---|
746 | %------------------------------------------------------------------------ |
---|
747 | % --- Executes on button press in CheckCiv1. |
---|
748 | function CheckCiv1_Callback(hObject, eventdata, handles) |
---|
749 | %------------------------------------------------------------------------ |
---|
750 | update_CivOptions(handles,0) |
---|
751 | |
---|
752 | %------------------------------------------------------------------------ |
---|
753 | % --- Executes on button press in CheckFix1. |
---|
754 | function CheckFix1_Callback(hObject, eventdata, handles) |
---|
755 | %------------------------------------------------------------------------ |
---|
756 | update_CivOptions(handles,0) |
---|
757 | |
---|
758 | %------------------------------------------------------------------------ |
---|
759 | % --- Executes on button press in CheckPatch1. |
---|
760 | function CheckPatch1_Callback(hObject, eventdata, handles) |
---|
761 | %------------------------------------------------------------------------ |
---|
762 | update_CivOptions(handles,0) |
---|
763 | |
---|
764 | %------------------------------------------------------------------------ |
---|
765 | % --- Executes on button press in CheckCiv2. |
---|
766 | function CheckCiv2_Callback(hObject, eventdata, handles) |
---|
767 | %------------------------------------------------------------------------ |
---|
768 | update_CivOptions(handles,0) |
---|
769 | |
---|
770 | %------------------------------------------------------------------------ |
---|
771 | % --- Executes on button press in CheckFix2. |
---|
772 | function CheckFix2_Callback(hObject, eventdata, handles) |
---|
773 | %------------------------------------------------------------------------ |
---|
774 | update_CivOptions(handles,0) |
---|
775 | |
---|
776 | %------------------------------------------------------------------------ |
---|
777 | % --- Executes on button press in CheckPatch2. |
---|
778 | function CheckPatch2_Callback(hObject, eventdata, handles) |
---|
779 | %------------------------------------------------------------------------ |
---|
780 | update_CivOptions(handles,0) |
---|
781 | |
---|
782 | %------------------------------------------------------------------------ |
---|
783 | % --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2 |
---|
784 | function update_CivOptions(handles,opening) |
---|
785 | %------------------------------------------------------------------------ |
---|
786 | checkbox=zeros(1,6); |
---|
787 | checkbox(1)=get(handles.CheckCiv1,'Value'); |
---|
788 | checkbox(2)=get(handles.CheckFix1,'Value'); |
---|
789 | checkbox(3)=get(handles.CheckPatch1,'Value'); |
---|
790 | checkbox(4)=get(handles.CheckCiv2,'Value'); |
---|
791 | checkbox(5)=get(handles.CheckFix2,'Value'); |
---|
792 | checkbox(6)=get(handles.CheckPatch2,'Value'); |
---|
793 | ind_selected=find(checkbox,1); |
---|
794 | if ~isempty(ind_selected) |
---|
795 | RootPath=get(handles.RootPath,'String'); |
---|
796 | if isempty(RootPath) |
---|
797 | msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...') |
---|
798 | return |
---|
799 | end |
---|
800 | end |
---|
801 | set(handles.PairIndices,'Visible','on') |
---|
802 | set(handles.SubdirCiv1,'Visible','on') |
---|
803 | set(handles.ListSubdirCiv1,'Visible','on') |
---|
804 | set(handles.TitleSubdirCiv1,'Visible','on') |
---|
805 | if ~opening |
---|
806 | errormsg=find_netcpair_civ(handles,1); % select the available netcdf files |
---|
807 | if ~isempty(errormsg) |
---|
808 | msgbox_uvmat('ERROR',errormsg) |
---|
809 | end |
---|
810 | end |
---|
811 | if max(checkbox(4:6))% case of civ2 pair choice needed |
---|
812 | set(handles.TitlePairCiv2,'Visible','on') |
---|
813 | set(handles.TitleSubdirCiv2,'Visible','on') |
---|
814 | set(handles.SubdirCiv2,'Visible','on') |
---|
815 | set(handles.ListSubdirCiv2,'Visible','on') |
---|
816 | set(handles.ListPairCiv2,'Visible','on') |
---|
817 | if ~opening |
---|
818 | errormsg=find_netcpair_civ(handles,2); % select the available netcdf files |
---|
819 | if ~isempty(errormsg) |
---|
820 | msgbox_uvmat('ERROR',errormsg) |
---|
821 | end |
---|
822 | end |
---|
823 | else |
---|
824 | set(handles.TitleSubdirCiv2,'Visible','off') |
---|
825 | set(handles.SubdirCiv2,'Visible','off') |
---|
826 | set(handles.ListSubdirCiv2,'Visible','off') |
---|
827 | set(handles.ListPairCiv2,'Visible','off') |
---|
828 | end |
---|
829 | options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'}; |
---|
830 | for ilist=1:length(options) |
---|
831 | if checkbox(ilist) |
---|
832 | set(handles.(options{ilist}),'Visible','on') |
---|
833 | else |
---|
834 | set(handles.(options{ilist}),'Visible','off') |
---|
835 | end |
---|
836 | end |
---|
837 | |
---|
838 | %------------------------------------------------------------------------ |
---|
839 | % --- Executes on button press in RUN: processing on local computer |
---|
840 | function RUN_Callback(hObject, eventdata, handles) |
---|
841 | %------------------------------------------------------------------------ |
---|
842 | set(handles.RUN, 'Enable','Off') |
---|
843 | set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784]) |
---|
844 | batch=0; |
---|
845 | errormsg=launch_jobs(hObject, eventdata, handles,batch); |
---|
846 | set(handles.RUN, 'Enable','On') |
---|
847 | set(handles.RUN,'BackgroundColor',[1 0 0]) |
---|
848 | |
---|
849 | % display errors or start status callback to visualise results |
---|
850 | if ~isempty(errormsg) |
---|
851 | display(errormsg) |
---|
852 | msgbox_uvmat('ERROR',errormsg) |
---|
853 | elseif isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3) |
---|
854 | set(handles.status,'Value',1);%suppress status display |
---|
855 | status_Callback(hObject, eventdata, handles) |
---|
856 | end |
---|
857 | |
---|
858 | %------------------------------------------------------------------------ |
---|
859 | % --- Executes on button press in BATCH: remote processing |
---|
860 | function BATCH_Callback(hObject, eventdata, handles) |
---|
861 | % ----------------------------------------------------------------------- |
---|
862 | set(handles.BATCH, 'Enable','Off') |
---|
863 | set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784]) |
---|
864 | batch=1; |
---|
865 | errormsg=launch_jobs(hObject, eventdata, handles, batch); |
---|
866 | set(handles.BATCH, 'Enable','On') |
---|
867 | set(handles.BATCH,'BackgroundColor',[1 0 0]) |
---|
868 | |
---|
869 | % display errors or start status callback to visualise results |
---|
870 | if ~isempty(errormsg) |
---|
871 | display(errormsg) |
---|
872 | msgbox_uvmat('ERROR',errormsg) |
---|
873 | elseif isfield(handles,'status') |
---|
874 | set(handles.status,'Value',1);%suppress status display |
---|
875 | status_Callback(hObject, eventdata, handles) |
---|
876 | end |
---|
877 | |
---|
878 | %------------------------------------------------------------------- |
---|
879 | % --- Executes on button press in status. |
---|
880 | function status_Callback(hObject, eventdata, handles) |
---|
881 | %------------------------------------------------------------------- |
---|
882 | val=get(handles.status,'Value'); |
---|
883 | if val==0 |
---|
884 | set(handles.status,'BackgroundColor',[0 1 0]) |
---|
885 | hfig=findobj(allchild(0),'name','civ_status'); |
---|
886 | if ~isempty(hfig) |
---|
887 | delete(hfig) |
---|
888 | end |
---|
889 | return |
---|
890 | end |
---|
891 | set(handles.status,'BackgroundColor',[1 1 0]) |
---|
892 | drawnow |
---|
893 | listtype={'civ1','fix1','patch1','civ2','fix2','patch2'}; |
---|
894 | Param.CheckCiv1=get(handles.CheckCiv1,'Value'); |
---|
895 | Param.CheckFix1=get(handles.CheckFix1,'Value'); |
---|
896 | Param.CheckPatch1=get(handles.CheckPatch1,'Value'); |
---|
897 | Param.CheckCiv2=get(handles.CheckCiv2,'Value'); |
---|
898 | Param.CheckFix2=get(handles.CheckFix2,'Value'); |
---|
899 | Param.CheckPatch2=get(handles.CheckPatch2,'Value'); |
---|
900 | box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2]; |
---|
901 | |
---|
902 | option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test) |
---|
903 | filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV |
---|
904 | test_new=0; |
---|
905 | if ~isfield(filecell,'nc') |
---|
906 | test_new=1; |
---|
907 | [ref_i,ref_j,errormsg]=find_ref_indices(handles); |
---|
908 | if ~isempty(errormsg) |
---|
909 | msgbox_uvmat('ERROR',errormsg) |
---|
910 | return |
---|
911 | end |
---|
912 | filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status |
---|
913 | end |
---|
914 | if ~isequal(box_test(4:6),[0 0 0]) |
---|
915 | civ_files=filecell.nc.civ2;%case of civ2 operations |
---|
916 | else |
---|
917 | civ_files=filecell.nc.civ1; |
---|
918 | end |
---|
919 | [root,filename,ext]=fileparts(civ_files{1}); |
---|
920 | [rootroot,SubDir,extdir]=fileparts(root); |
---|
921 | hfig=findobj(allchild(0),'name','civ_status'); |
---|
922 | if isempty(hfig) |
---|
923 | hfig=figure('DeleteFcn',@stop_status); |
---|
924 | set(hfig,'MenuBar','none')% suppress the menu bar |
---|
925 | set(hfig,'NumberTitle','off')%suppress the fig number in the title |
---|
926 | set(hfig,'name','civ_status') |
---|
927 | set(hfig,'tag','civ_status') |
---|
928 | set(hfig,'UserData',civ_files) |
---|
929 | hlist= uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list'); |
---|
930 | uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...'); |
---|
931 | uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]); |
---|
932 | 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); |
---|
933 | 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); |
---|
934 | BarPosition=[0.05 0.81 0.01 0.05]; |
---|
935 | uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar'); |
---|
936 | drawnow |
---|
937 | end |
---|
938 | set(hrefresh,'UserData',option_civ) |
---|
939 | filepath=fileparts(civ_files{1}); |
---|
940 | set(hlist,'UserData',fileparts(filepath)) |
---|
941 | refresh_GUI(hrefresh,[]) |
---|
942 | |
---|
943 | %------------------------------------------------------------------------ |
---|
944 | % launched by refreshing the status figure |
---|
945 | function refresh_GUI(hObject, eventdata) |
---|
946 | %------------------------------------------------------------------------ |
---|
947 | Tabchar={}; |
---|
948 | BarPosition=[0.05 0.81 0.01 0.05]; |
---|
949 | hfig=get(hObject,'parent'); |
---|
950 | civ_files=get(hfig,'UserData'); |
---|
951 | [filepath,filename,ext]=fileparts(civ_files{1}); |
---|
952 | [tild,SubDir,extdir]=fileparts(filepath); |
---|
953 | SubDir=[SubDir extdir]; |
---|
954 | option_civ=get(hObject,'UserData'); |
---|
955 | nbfiles=numel(civ_files); |
---|
956 | count=0; |
---|
957 | testrecent=0; |
---|
958 | % while count<nbfiles |
---|
959 | count=0; |
---|
960 | datnum=zeros(1,nbfiles); |
---|
961 | for ifile=1:nbfiles |
---|
962 | detect=exist(civ_files{ifile},'file'); % check the existence of the file |
---|
963 | option=0; |
---|
964 | if detect==0 |
---|
965 | option_str='not created'; |
---|
966 | else |
---|
967 | datfile=dir(civ_files{ifile}); |
---|
968 | if isfield(datfile,'datenum') |
---|
969 | datnum(ifile)=datfile.datenum;%only available in recent matlab versions |
---|
970 | testrecent=1; |
---|
971 | end |
---|
972 | filefound(ifile)={datfile.name}; |
---|
973 | lastfield=''; |
---|
974 | % check the content netcdf file |
---|
975 | Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix'); |
---|
976 | option_list={'civ1','fix1','patch1','civ2','fix2','patch2'}; |
---|
977 | if ~isempty(Data.CivStage) |
---|
978 | option=Data.CivStage;%case of Matlab civ |
---|
979 | else |
---|
980 | if ~isempty(Data.patch2) && isequal(Data.patch2,1) |
---|
981 | option=6; |
---|
982 | elseif ~isempty(Data.fix2) && isequal(Data.fix2,1) |
---|
983 | option=5; |
---|
984 | elseif ~isempty(Data.civ2) && isequal(Data.civ2,1); |
---|
985 | option=4; |
---|
986 | elseif ~isempty(Data.patch) && isequal(Data.patch,1); |
---|
987 | option=3; |
---|
988 | elseif ~isempty(Data.fix) && isequal(Data.fix,1); |
---|
989 | option=2; |
---|
990 | else |
---|
991 | option=1; |
---|
992 | end |
---|
993 | end |
---|
994 | option_str=option_list{option}; |
---|
995 | end |
---|
996 | if option >= option_civ |
---|
997 | count=count+1; |
---|
998 | end |
---|
999 | [filepath,filename,ext]=fileparts(civ_files{ifile}); |
---|
1000 | Tabchar{ifile,1}=[fullfile(SubDir,filename) ext '...' option_str]; |
---|
1001 | end |
---|
1002 | datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files |
---|
1003 | if isempty(datnum) |
---|
1004 | if testrecent |
---|
1005 | message='no civ result created yet'; |
---|
1006 | else |
---|
1007 | message=''; |
---|
1008 | end |
---|
1009 | else |
---|
1010 | datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files |
---|
1011 | [first,ind]=min(datnum); |
---|
1012 | [last,indlast]=max(datnum); |
---|
1013 | % if test_new |
---|
1014 | % message='existing file status, no processing launched yet'; |
---|
1015 | % else |
---|
1016 | message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification: ' cell2mat(filefound(ind)) ' : ' datestr(first)];... |
---|
1017 | ['latest modification: ' cell2mat(filefound(indlast)) ' : ' datestr(last)]}; |
---|
1018 | % end |
---|
1019 | end |
---|
1020 | %hfig=findobj(allchild(0),'name','civ_status'); |
---|
1021 | % if isempty(hfig)% the status list has been deleted |
---|
1022 | % return |
---|
1023 | % else |
---|
1024 | hlist=findobj(hfig,'tag','list'); |
---|
1025 | hmsgbox=findobj(hfig,'tag','msgbox'); |
---|
1026 | hwaitbar=findobj(hfig,'tag','waitbar'); |
---|
1027 | set(hlist,'String',Tabchar) |
---|
1028 | set(hmsgbox,'String', message) |
---|
1029 | if count>0 %&& ~test_new |
---|
1030 | BarPosition(3)=0.9*count/nbfiles; |
---|
1031 | set(hwaitbar,'Position',BarPosition) |
---|
1032 | end |
---|
1033 | % end |
---|
1034 | % [root,filename,ext]=fileparts(civ_files{1}); |
---|
1035 | % [rootroot,SubDir,extdir]=fileparts(root); |
---|
1036 | % |
---|
1037 | % set(hlist,'UserData',rootroot) |
---|
1038 | % if count<10||(nbfiles-count)<10 |
---|
1039 | % pause(.5)% wait 0.5 seconds for next check |
---|
1040 | % else |
---|
1041 | % pause(10)% wait 10 seconds for next check |
---|
1042 | % end |
---|
1043 | % end |
---|
1044 | |
---|
1045 | %------------------------------------------------------------------------ |
---|
1046 | % launched by deleting the status figure |
---|
1047 | function stop_status(hObject, eventdata) |
---|
1048 | %------------------------------------------------------------------------ |
---|
1049 | hciv=findobj(allchild(0),'tag','civ'); |
---|
1050 | hhciv=guidata(hciv); |
---|
1051 | set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ |
---|
1052 | set(hhciv.status,'BackgroundColor',[0 1 0]) |
---|
1053 | |
---|
1054 | %------------------------------------------------------------------------ |
---|
1055 | % launched by pressing OK on the status figure |
---|
1056 | function close_GUI(hObject, eventdata) |
---|
1057 | %------------------------------------------------------------------------ |
---|
1058 | delete(gcbf) |
---|
1059 | |
---|
1060 | |
---|
1061 | %------------------------------------------------------------------------ |
---|
1062 | % --- Main lauch command, called by RUN and BATCH |
---|
1063 | function errormsg=launch_jobs(hObject, eventdata, handles, batch) |
---|
1064 | %----------------------------------------------------------------------- |
---|
1065 | errormsg='';%default |
---|
1066 | |
---|
1067 | %% read the input parameters from the GUI civ |
---|
1068 | Param=read_GUI(handles.civ); |
---|
1069 | |
---|
1070 | %% check the selected list of operations: |
---|
1071 | operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'}; |
---|
1072 | box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2]; |
---|
1073 | index_first=find(box_test==1,1); |
---|
1074 | if isempty(index_first) |
---|
1075 | errormsg='no selected operation'; |
---|
1076 | return |
---|
1077 | end |
---|
1078 | index_last=find(box_test==1,1,'last'); |
---|
1079 | box_used=box_test(index_first : index_last); |
---|
1080 | [box_missing,ind_missing]=min(box_used); |
---|
1081 | if isequal(box_missing,0); %there is a missing step in the sequence of operations |
---|
1082 | errormsg=['missing' cell2mat(operations(ind_missing))]; |
---|
1083 | return |
---|
1084 | end |
---|
1085 | |
---|
1086 | %% check mask if selecetd |
---|
1087 | %could be included in get_mask callback ? |
---|
1088 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
1089 | maskname=get(handles.Mask,'String'); |
---|
1090 | if ~exist(maskname,'file') |
---|
1091 | get_mask_civ1_Callback(hObject, eventdata, handles); |
---|
1092 | end |
---|
1093 | end |
---|
1094 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
1095 | maskname=get(handles.Mask,'String'); |
---|
1096 | if ~exist(maskname,'file') |
---|
1097 | get_mask_fix1_Callback(hObject, eventdata, handles); |
---|
1098 | end |
---|
1099 | end |
---|
1100 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
1101 | maskname=get(handles.Mask,'String'); |
---|
1102 | if ~exist(maskname,'file') |
---|
1103 | get_mask_civ2_Callback(hObject, eventdata, handles); |
---|
1104 | end |
---|
1105 | end |
---|
1106 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
1107 | maskname=get(handles.Mask,'String'); |
---|
1108 | if ~exist(maskname,'file') |
---|
1109 | get_mask_fix2_Callback(hObject, eventdata, handles); |
---|
1110 | end |
---|
1111 | end |
---|
1112 | |
---|
1113 | %% reinitialise status callback |
---|
1114 | if isfield(handles,'status') |
---|
1115 | set(handles.status,'Value',0);%suppress status display |
---|
1116 | status_Callback(hObject, eventdata, handles) |
---|
1117 | end |
---|
1118 | |
---|
1119 | %% read the PARAM.xml file to get the binaries (and batch_mode if batch) |
---|
1120 | path_civ=fileparts(which('civ')); %path to the source directory of uvmat |
---|
1121 | xmlfile='PARAM.xml'; |
---|
1122 | if exist(xmlfile,'file')% search parameter xml file in the whole matlab path |
---|
1123 | t=xmltree(xmlfile); |
---|
1124 | s=convert(t); |
---|
1125 | else |
---|
1126 | errormsg=['no file ' xmlfile]; |
---|
1127 | return |
---|
1128 | end |
---|
1129 | test_interp=0; %eviter les variables test_ (LG) |
---|
1130 | if batch |
---|
1131 | if isfield(s,'BatchParam') |
---|
1132 | Param.xml=s.BatchParam; |
---|
1133 | if isfield(Param.xml,'BatchMode') |
---|
1134 | batch_mode=Param.xml.BatchMode; |
---|
1135 | if ~ismember(batch_mode,{'sge','oar'}) |
---|
1136 | errormsg=['batch mode ' batch_mode ' not supported by UVMAT']; |
---|
1137 | return |
---|
1138 | end |
---|
1139 | end |
---|
1140 | else |
---|
1141 | errormsg='no batch civ binaries defined in PARAM.xml'; |
---|
1142 | return |
---|
1143 | end |
---|
1144 | else % run |
---|
1145 | if isfield(s,'RunParam') |
---|
1146 | Param.xml=s.RunParam; |
---|
1147 | else |
---|
1148 | errormsg='no run civ binaries defined in PARAM.xml'; |
---|
1149 | return |
---|
1150 | end |
---|
1151 | end |
---|
1152 | |
---|
1153 | %% check batch mode supported |
---|
1154 | if batch |
---|
1155 | switch batch_mode |
---|
1156 | case 'sge' |
---|
1157 | test_command='qstat'; |
---|
1158 | case 'oar' |
---|
1159 | test_command='oarstat'; |
---|
1160 | end |
---|
1161 | [s,w]=system(test_command); |
---|
1162 | if ~isequal(s,0) |
---|
1163 | errormsg=[batch_mode ' batch system not available']; |
---|
1164 | return |
---|
1165 | end |
---|
1166 | end |
---|
1167 | |
---|
1168 | %% check if the binaries exist |
---|
1169 | ListProgram=get(handles.ListProgram,'String'); |
---|
1170 | CivMode=ListProgram{get(handles.ListProgram,'Value')}; |
---|
1171 | binary_list={}; |
---|
1172 | switch CivMode |
---|
1173 | case 'CivX' |
---|
1174 | binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'}; |
---|
1175 | case 'CivAll'% desactivated option |
---|
1176 | binary_list={'Civ'}; |
---|
1177 | case 'Matlab' |
---|
1178 | if batch |
---|
1179 | % verifier MenuMatlab installe sur le cluster |
---|
1180 | % difficile a faire a priori |
---|
1181 | end |
---|
1182 | end |
---|
1183 | for bin_name=binary_list %loop on the list of binaries |
---|
1184 | if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list |
---|
1185 | if exist(Param.xml.(bin_name{1}),'file') |
---|
1186 | [path,name,ext]=fileparts(Param.xml.(bin_name{1})); |
---|
1187 | currentdir=pwd; |
---|
1188 | if exist(path,'dir') |
---|
1189 | cd(path); |
---|
1190 | binpath=pwd;%path of the binary |
---|
1191 | Param.xml.(bin_name{1})=fullfile(binpath,[name ext]); |
---|
1192 | cd(currentdir) |
---|
1193 | else |
---|
1194 | errormsg=['path ' path ' for binaries defined in PARAM.xml does not exist']; |
---|
1195 | return |
---|
1196 | end |
---|
1197 | else %look for the full path if the file name has been defined with a relative path in PARAM.xm |
---|
1198 | fullname=fullfile(path_civ,Param.xml.(bin_name{1})); |
---|
1199 | if exist(fullname,'file') |
---|
1200 | Param.xml.(bin_name{1})=fullname; |
---|
1201 | else |
---|
1202 | errormsg=['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist']; |
---|
1203 | return |
---|
1204 | end |
---|
1205 | end |
---|
1206 | end |
---|
1207 | end |
---|
1208 | display('files OK, processing...') |
---|
1209 | |
---|
1210 | %% set the list of files and check them |
---|
1211 | display('checking the files...') |
---|
1212 | [ref_i,ref_j,errormsg]=find_ref_indices(handles); |
---|
1213 | if ~isempty(errormsg) |
---|
1214 | return |
---|
1215 | end |
---|
1216 | [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,xx,yy,compare]=... |
---|
1217 | set_civ_filenames(handles,ref_i,ref_j,box_test); |
---|
1218 | |
---|
1219 | Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention) |
---|
1220 | set(handles.civ,'UserData',filecell);%store for futur use of status callback |
---|
1221 | if isempty(filecell)% (error message displayed in fct set_civ_filenames) |
---|
1222 | return |
---|
1223 | end |
---|
1224 | nbfield=numel(i1_civ1); |
---|
1225 | nbslice=numel(j1_civ1); |
---|
1226 | if ~strcmp(CivMode,'CivX') |
---|
1227 | if Param.CheckCiv1 |
---|
1228 | [Param.Civ1.FileTypeA,FileInfo,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1}); |
---|
1229 | [Param.Civ1.FileTypeB,FileInfo,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1}); |
---|
1230 | end |
---|
1231 | if Param.CheckCiv2 |
---|
1232 | [Param.Civ2.FileTypeA,FileInfo,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1}); |
---|
1233 | [Param.Civ2.FileTypeB,FileInfo,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1}); |
---|
1234 | end |
---|
1235 | end |
---|
1236 | |
---|
1237 | %% MAIN LOOP |
---|
1238 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
1239 | TimeUnit=get(handles.TimeUnit,'String'); |
---|
1240 | checkframe=strcmp(TimeUnit,'frame'); |
---|
1241 | batch_file_list=[];%should be renamed file_list, can be used for xml or bash files |
---|
1242 | |
---|
1243 | for ifile=1:nbfield |
---|
1244 | for j=1:nbslice |
---|
1245 | % initiate system command |
---|
1246 | switch CivMode |
---|
1247 | case 'CivX' |
---|
1248 | if isunix % check: necessaire aussi en RUN? |
---|
1249 | cmd=['#!/bin/bash \n '... |
---|
1250 | '#$ -cwd \n '... |
---|
1251 | 'hostname && date \n '... |
---|
1252 | 'umask 002 \n'];%allow writting access to created files for user group |
---|
1253 | else |
---|
1254 | cmd=[]; |
---|
1255 | end |
---|
1256 | case 'CivAll' |
---|
1257 | CivAllxml=xmltree;% xml contents, all parameters |
---|
1258 | CivAllCmd=''; |
---|
1259 | CivAllxml=set(CivAllxml,1,'name','CivDoc'); |
---|
1260 | end |
---|
1261 | |
---|
1262 | % define output file name |
---|
1263 | if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1 |
---|
1264 | OutputFile=filecell.nc.civ2{ifile,j}; |
---|
1265 | else |
---|
1266 | OutputFile=filecell.nc.civ1{ifile,j}; |
---|
1267 | end |
---|
1268 | OutputFile=regexprep(OutputFile,'.nc',''); |
---|
1269 | |
---|
1270 | if Param.CheckCiv1 |
---|
1271 | % read image-dependent parameters |
---|
1272 | Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j}; |
---|
1273 | Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j}; |
---|
1274 | if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j) |
---|
1275 | Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1)); |
---|
1276 | else |
---|
1277 | Param.Civ1.Dt=1; |
---|
1278 | end |
---|
1279 | Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2); |
---|
1280 | if strcmp(CivMode,'CivX') |
---|
1281 | Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE? |
---|
1282 | Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);% |
---|
1283 | end |
---|
1284 | form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats |
---|
1285 | if isempty(form) |
---|
1286 | ImageInfo=get(VideoReader(filecell.ima1.civ1{1,1})); |
---|
1287 | Param.Civ1.ImageBitDepth=ImageInfo.BitsPerPixel/3; |
---|
1288 | else |
---|
1289 | ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size |
---|
1290 | Param.Civ1.ImageBitDepth=ImageInfo.BitDepth; |
---|
1291 | end |
---|
1292 | Param.Civ1.ImageWidth=ImageInfo.Width; |
---|
1293 | Param.Civ1.ImageHeight=ImageInfo.Height; |
---|
1294 | Param.Civ1.i1=i1_civ1(ifile); |
---|
1295 | Param.Civ1.i2=i2_civ1(ifile); |
---|
1296 | % read mask parameters |
---|
1297 | if Param.Civ1.CheckMask % the lines below should be changed with the new gui |
---|
1298 | if ~exist(Param.Civ1.Mask,'file') |
---|
1299 | maskbase=[filecell.filebase '_' Param.Civ1.Mask]; % |
---|
1300 | nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); % |
---|
1301 | i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1; |
---|
1302 | [RootPathMask,RootFileMask]=fileparts(maskbase); |
---|
1303 | Param.Civ1.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask); |
---|
1304 | end |
---|
1305 | end |
---|
1306 | % read grid parameters |
---|
1307 | if Param.Civ1.CheckGrid |
---|
1308 | if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid') |
---|
1309 | nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); % |
---|
1310 | if ~isnan(nbslice_grid) |
---|
1311 | i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1; |
---|
1312 | Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)]; |
---|
1313 | % Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')]; |
---|
1314 | if ~exist(Param.Civ1.GridName,'file') |
---|
1315 | errormsg='grid file absent for civ1'; |
---|
1316 | return |
---|
1317 | end |
---|
1318 | elseif ~exist(Param.Civ1.Grid,'file') |
---|
1319 | errormsg='grid file absent for civ1'; |
---|
1320 | return |
---|
1321 | end |
---|
1322 | end |
---|
1323 | end |
---|
1324 | |
---|
1325 | % send command |
---|
1326 | switch CivMode |
---|
1327 | case 'CivX' |
---|
1328 | [cmd_civ,errormsg]=cmd_civ1(filecell.nc.civ1{ifile,j},Param); |
---|
1329 | cmd=[cmd cmd_civ '\n']; |
---|
1330 | if ~isempty(errormsg) |
---|
1331 | return |
---|
1332 | end |
---|
1333 | case 'CivAll' |
---|
1334 | CivAllCmd=[CivAllCmd ' civ1 ']; |
---|
1335 | str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1); |
---|
1336 | fieldnames=fields(str); |
---|
1337 | [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1'); |
---|
1338 | for ilist=1:length(fieldnames) |
---|
1339 | val=eval(['str.' fieldnames{ilist}]); |
---|
1340 | if ischar(val) |
---|
1341 | [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist}); |
---|
1342 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1343 | end |
---|
1344 | end |
---|
1345 | end |
---|
1346 | end |
---|
1347 | |
---|
1348 | if Param.CheckFix1 |
---|
1349 | switch CivMode |
---|
1350 | case 'CivX' |
---|
1351 | cmd=[cmd... |
---|
1352 | cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n']; |
---|
1353 | case 'CivAll'%to abandon |
---|
1354 | fix1.inputFileName=filecell.nc.civ1{ifile,j} ; |
---|
1355 | fix1.fi1=num2str(param.fix1.flagindex1(1)); |
---|
1356 | fix1.fi2=num2str(param.fix1.flagindex1(2)); |
---|
1357 | fix1.fi3=num2str(param.fix1.flagindex1(3)); |
---|
1358 | fix1.threshC=num2str(param.fix1.thresh_vecC1); |
---|
1359 | fix1.threshV=num2str(param.fix1.thresh_vel1); |
---|
1360 | fieldnames=fields(fix1); |
---|
1361 | [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1'); |
---|
1362 | for ilist=1:length(fieldnames) |
---|
1363 | val=eval(['fix1.' fieldnames{ilist}]); |
---|
1364 | if ischar(val) |
---|
1365 | [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist}); |
---|
1366 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1367 | end |
---|
1368 | end |
---|
1369 | CivAllCmd=[CivAllCmd ' fix1 ']; |
---|
1370 | end |
---|
1371 | end |
---|
1372 | |
---|
1373 | %CheckPatch1 |
---|
1374 | if Param.CheckPatch1==1 |
---|
1375 | switch CivMode |
---|
1376 | case 'CivX' |
---|
1377 | cmd=[cmd... |
---|
1378 | cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n']; |
---|
1379 | case 'CivAll' |
---|
1380 | patch1.inputFileName=filecell.nc.civ1{ifile,j} ; |
---|
1381 | patch1.nopt=subdomain_patch1; |
---|
1382 | patch1.maxdiff=thresh_patch1; |
---|
1383 | patch1.ro=rho_patch1; |
---|
1384 | test_grid=get(handles.get_gridpatch1,'Value'); |
---|
1385 | if test_grid |
---|
1386 | patch1.gridflag='y'; |
---|
1387 | gridname=get(handles.grid_patch1,'String'); |
---|
1388 | if isequal(gridname(end-3:end),'grid') |
---|
1389 | nbslice_grid=str2double(gridname(1:end-4)); % |
---|
1390 | if ~isnan(nbslice_grid) |
---|
1391 | i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1; |
---|
1392 | patch1.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)]; |
---|
1393 | % patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; |
---|
1394 | if ~exist(patch1.gridPatch,'file') |
---|
1395 | errormsg='grid file absent for patch1'; |
---|
1396 | return |
---|
1397 | end |
---|
1398 | elseif exist(gridname,'file') |
---|
1399 | patch1.gridPatch=gridname; |
---|
1400 | else |
---|
1401 | errormsg='grid file absent for patch1'; |
---|
1402 | return |
---|
1403 | end |
---|
1404 | end |
---|
1405 | else |
---|
1406 | patch1.gridPatch='none'; |
---|
1407 | patch1.gridflag='n'; |
---|
1408 | patch1.m=nx_patch1; |
---|
1409 | patch1.n=ny_patch1; |
---|
1410 | end |
---|
1411 | patch1.convectFlow='n'; |
---|
1412 | fieldnames=fields(patch1); |
---|
1413 | [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1'); |
---|
1414 | for ilist=1:length(fieldnames) |
---|
1415 | val=eval(['patch1.' fieldnames{ilist}]); |
---|
1416 | if ischar(val) |
---|
1417 | [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist}); |
---|
1418 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1419 | end |
---|
1420 | end |
---|
1421 | CivAllCmd=[CivAllCmd ' patch1 ']; |
---|
1422 | end |
---|
1423 | end |
---|
1424 | if Param.CheckCiv2==1 |
---|
1425 | Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j}; |
---|
1426 | Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j}; |
---|
1427 | if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j) |
---|
1428 | Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1); |
---|
1429 | else |
---|
1430 | Param.Civ2.Dt=1; |
---|
1431 | end |
---|
1432 | Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2; |
---|
1433 | if strcmp(CivMode,'CivX') |
---|
1434 | Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc); |
---|
1435 | Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc); |
---|
1436 | end |
---|
1437 | Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j}; |
---|
1438 | Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc' |
---|
1439 | |
---|
1440 | % mask |
---|
1441 | if Param.Civ2.CheckMask |
---|
1442 | if ~exist(Param.Civ2.Mask,'file') |
---|
1443 | maskbase=[filecell.filebase '_' Param.Civ2.Mask]; % |
---|
1444 | nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); % |
---|
1445 | i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1; |
---|
1446 | [RootPathMask,RootFileMask]=fileparts(maskbase); |
---|
1447 | Param.Civ2.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask); |
---|
1448 | % Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i'); |
---|
1449 | end |
---|
1450 | end |
---|
1451 | %grid |
---|
1452 | if Param.Civ2.CheckGrid |
---|
1453 | if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid') |
---|
1454 | nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); % |
---|
1455 | if ~isnan(nbslice_grid) |
---|
1456 | i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1; |
---|
1457 | Param.Civ2.Grid=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)]; |
---|
1458 | % Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; |
---|
1459 | end |
---|
1460 | end |
---|
1461 | end |
---|
1462 | form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats |
---|
1463 | if isempty(form) |
---|
1464 | ImageInfo=get(VideoReader(filecell.ima1.civ2{1,1})); |
---|
1465 | Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3; |
---|
1466 | else |
---|
1467 | ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size |
---|
1468 | Param.Civ2.ImageBitDepth=ImageInfo.BitDepth; |
---|
1469 | end |
---|
1470 | Param.Civ2.ImageWidth=ImageInfo.Width; |
---|
1471 | Param.Civ2.ImageHeight=ImageInfo.Height; |
---|
1472 | Param.Civ2.i1=i1_civ2(ifile); |
---|
1473 | Param.Civ2.i2=i2_civ2(ifile); |
---|
1474 | switch CivMode |
---|
1475 | case 'CivX' |
---|
1476 | cmd=[cmd... |
---|
1477 | cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n']; |
---|
1478 | case 'CivAll' |
---|
1479 | CivAllCmd=[CivAllCmd ' civ2 ']; |
---|
1480 | str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2); |
---|
1481 | fieldnames=fields(str); |
---|
1482 | [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2'); |
---|
1483 | for ilist=1:length(fieldnames) |
---|
1484 | val=eval(['str.' fieldnames{ilist}]); |
---|
1485 | if ischar(val) |
---|
1486 | [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist}); |
---|
1487 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1488 | end |
---|
1489 | end |
---|
1490 | end |
---|
1491 | end |
---|
1492 | |
---|
1493 | % CheckFix2 |
---|
1494 | if Param.CheckFix2==1 |
---|
1495 | switch CivMode |
---|
1496 | case 'CivX' |
---|
1497 | cmd=[cmd... |
---|
1498 | cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n']; |
---|
1499 | case 'CivAll' |
---|
1500 | fix2.inputFileName=filecell.nc.civ2{ifile,j} ; |
---|
1501 | fix2.fi1=num2str(flagindex2(1)); |
---|
1502 | fix2.fi2=num2str(flagindex2(2)); |
---|
1503 | fix2.fi3=num2str(flagindex2(3)); |
---|
1504 | fix2.threshC=num2str(thresh_vec2C); |
---|
1505 | fix2.threshV=num2str(thresh_vel2); |
---|
1506 | fieldnames=fields(fix2); |
---|
1507 | [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2'); |
---|
1508 | for ilist=1:length(fieldnames) |
---|
1509 | val=eval(['fix2.' fieldnames{ilist}]); |
---|
1510 | if ischar(val) |
---|
1511 | [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist}); |
---|
1512 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1513 | end |
---|
1514 | end |
---|
1515 | CivAllCmd=[CivAllCmd ' fix2 ']; |
---|
1516 | end |
---|
1517 | end |
---|
1518 | |
---|
1519 | %CheckPatch2 |
---|
1520 | if Param.CheckPatch2==1 |
---|
1521 | |
---|
1522 | switch CivMode |
---|
1523 | |
---|
1524 | case 'CivX' |
---|
1525 | cmd=[cmd... |
---|
1526 | cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n']; |
---|
1527 | |
---|
1528 | case 'CivAll' |
---|
1529 | patch2.inputFileName=filecell.nc.civ1{ifile,j} ; |
---|
1530 | patch2.nopt=subdomain_patch2; |
---|
1531 | patch2.maxdiff=thresh_patch2; |
---|
1532 | patch2.ro=rho_patch2; |
---|
1533 | test_grid=get(handles.get_gridpatch2,'Value'); |
---|
1534 | if test_grid |
---|
1535 | patch2.gridflag='y'; |
---|
1536 | gridname=get(handles.grid_patch2,'String'); |
---|
1537 | if isequal(gridname(end-3:end),'grid') |
---|
1538 | nbslice_grid=str2double(gridname(1:end-4)); % |
---|
1539 | if ~isnan(nbslice_grid) |
---|
1540 | i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1; |
---|
1541 | patch2.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)]; |
---|
1542 | % patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; |
---|
1543 | if ~exist(patch2.gridPatch,'file') |
---|
1544 | errormsg='grid file absent for patch2'; |
---|
1545 | return |
---|
1546 | end |
---|
1547 | elseif exist(gridname,'file') |
---|
1548 | patch2.gridPatch=gridname; |
---|
1549 | else |
---|
1550 | errormsg='grid file absent for patch2'; |
---|
1551 | return |
---|
1552 | end |
---|
1553 | end |
---|
1554 | else |
---|
1555 | patch2.gridPatch='none'; |
---|
1556 | patch2.gridflag='n'; |
---|
1557 | patch2.m=nx_patch2; |
---|
1558 | patch2.n=ny_patch2; |
---|
1559 | end |
---|
1560 | patch2.convectFlow='n'; |
---|
1561 | fieldnames=fields(patch2); |
---|
1562 | [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2'); |
---|
1563 | for ilist=1:length(fieldnames) |
---|
1564 | val=eval(['patch2.' fieldnames{ilist}]); |
---|
1565 | if ischar(val) |
---|
1566 | [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist}); |
---|
1567 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1568 | end |
---|
1569 | end |
---|
1570 | CivAllCmd=[CivAllCmd ' patch2 ']; |
---|
1571 | end |
---|
1572 | end |
---|
1573 | |
---|
1574 | switch CivMode |
---|
1575 | |
---|
1576 | case {'CivX','CivAll'} |
---|
1577 | if isequal(CivMode,'CivAll') |
---|
1578 | save(CivAllxml,[OutputFile '.xml']); |
---|
1579 | cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml ' CivAllCmd ' >' OutputFile '.log' '\n']; |
---|
1580 | end |
---|
1581 | % create the .bat file used in run or batch |
---|
1582 | filename_bat=[OutputFile '.bat']; |
---|
1583 | [fid,message]=fopen(filename_bat,'w'); |
---|
1584 | if isequal(fid,-1) |
---|
1585 | errormsg=['creation of .bat file: ' message]; |
---|
1586 | return |
---|
1587 | end |
---|
1588 | fprintf(fid,cmd); |
---|
1589 | fclose(fid); |
---|
1590 | if isunix |
---|
1591 | system(['chmod +x ' filename_bat]); |
---|
1592 | end |
---|
1593 | batch_file_list{length(batch_file_list)+1}=filename_bat; |
---|
1594 | |
---|
1595 | case 'Matlab' |
---|
1596 | drawnow |
---|
1597 | if ~strcmp(compare,'stereo PIV') |
---|
1598 | filename_xml=[OutputFile '.civ.xml']; |
---|
1599 | t=struct2xml(Param); |
---|
1600 | save(t,filename_xml) |
---|
1601 | if batch |
---|
1602 | path_civ=fileparts(which('civ')); |
---|
1603 | filename_bat=[OutputFile '.bat']; |
---|
1604 | [fid,message]=fopen(filename_bat,'w'); |
---|
1605 | if isequal(fid,-1) |
---|
1606 | errormsg= ['creation of .bat file: ' message]; |
---|
1607 | return |
---|
1608 | end |
---|
1609 | text_matlabscript=[... |
---|
1610 | '#!/bin/bash \n'... |
---|
1611 | '. /etc/sysprofile \n'... |
---|
1612 | 'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'... |
---|
1613 | 'cd(''' path_civ '''); \n'... |
---|
1614 | 'civ_matlab(''' filename_xml ''',''' OutputFile '.nc''); \n'... |
---|
1615 | 'exit \n'... |
---|
1616 | 'END_MATLAB \n']; |
---|
1617 | fprintf(fid,text_matlabscript); |
---|
1618 | fclose(fid); |
---|
1619 | if isunix |
---|
1620 | system(['chmod +x ' filename_bat]); |
---|
1621 | end |
---|
1622 | batch_file_list{length(batch_file_list)+1}=filename_bat; |
---|
1623 | else |
---|
1624 | [tild,errormsg]=civ_matlab(Param,filecell.nc.civ1{ifile,j}); |
---|
1625 | if isempty(errormsg) |
---|
1626 | display([filecell.nc.civ1{ifile,j} ' written']) |
---|
1627 | end |
---|
1628 | end |
---|
1629 | end |
---|
1630 | end |
---|
1631 | end |
---|
1632 | end |
---|
1633 | |
---|
1634 | if batch |
---|
1635 | switch batch_mode |
---|
1636 | |
---|
1637 | case 'sge' %at the moment only psmn ENS Lyon uses it |
---|
1638 | for p=1:length(batch_file_list) |
---|
1639 | %cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}]; |
---|
1640 | cmd=['!qsub -q piv1,piv2,piv3 '... |
---|
1641 | '-e ' regexprep(batch_file_list{p},'.bat','.errors') ' -o ' regexprep(batch_file_list{p},'.bat','.log ')... |
---|
1642 | ' -v ' 'LD_LIBRARY_PATH=/home/sjoubaud/matlab_sylvain/civx/lib ' batch_file_list{p}]; |
---|
1643 | display(cmd);eval(cmd); |
---|
1644 | end |
---|
1645 | case 'oar_old' |
---|
1646 | for p=1:length(batch_file_list) |
---|
1647 | oar_command=['!oarsub -n CIVX -q nicejob '... |
---|
1648 | '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')... |
---|
1649 | '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00" ' batch_file_list{p}]; |
---|
1650 | display(oar_command);eval(oar_command); |
---|
1651 | end |
---|
1652 | case 'oar' |
---|
1653 | |
---|
1654 | max_walltime=3600*12; % 12h max |
---|
1655 | oar_modes={'oar-parexec','oar-dispatch','mpilauncher'}; |
---|
1656 | text={'Batch processing on servcalcul3 LEGI';... |
---|
1657 | 'Please choose one of the followint modes';... |
---|
1658 | '* oar-parexec : default and best choice';... |
---|
1659 | '* oar-dispatch : jobs in a container of several cores';... |
---|
1660 | '* mpilauncher : one single parallel mpi job using several cores';... |
---|
1661 | '**********************************'... |
---|
1662 | }; |
---|
1663 | [S,v]=listdlg('PromptString',text,'ListString',oar_modes,... |
---|
1664 | 'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode'); |
---|
1665 | switch oar_modes{S} |
---|
1666 | case 'oar-parexec' %oar-dispatch.pl |
---|
1667 | answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''}); |
---|
1668 | ncores=str2double(answer{1}); |
---|
1669 | extra_oar=answer{2}; |
---|
1670 | walltime_onejob=600;%seconds |
---|
1671 | filename_joblist=fullfile(Rootbat,'job_list.txt'); |
---|
1672 | fid=fopen(filename_joblist,'w'); |
---|
1673 | for p=1:length(batch_file_list) |
---|
1674 | fprintf(fid,[batch_file_list{p} '\n']); |
---|
1675 | end |
---|
1676 | fclose(fid) |
---|
1677 | oar_command=['oarsub -n CIVX '... |
---|
1678 | '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '... |
---|
1679 | '-l /core=' num2str(ncores) ','... |
---|
1680 | 'walltime=' datestr(min(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,max_walltime/86400),13) ' '... |
---|
1681 | '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '... |
---|
1682 | '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '... |
---|
1683 | extra_oar ' '... |
---|
1684 | '"oar-parexec -s -f ' filename_joblist ' '... |
---|
1685 | '-l ' filename_joblist '.log"']; |
---|
1686 | filename_oarcommand=fullfile(Rootbat,'oar_command'); |
---|
1687 | fid=fopen(filename_oarcommand,'w'); |
---|
1688 | fprintf(fid,[oar_command '\n']); |
---|
1689 | fclose(fid); |
---|
1690 | display(oar_command); |
---|
1691 | eval(['! . ' filename_oarcommand]) |
---|
1692 | case 'oar-dispatch' %oar-dispatch.pl |
---|
1693 | ncores=str2double(... |
---|
1694 | inputdlg('Number of cores (max 36)','oarsub parameter',1,{'6'})... |
---|
1695 | ); |
---|
1696 | walltime_onejob=600;%seconds |
---|
1697 | filename_joblist=fullfile(Rootbat,'job_list.txt'); |
---|
1698 | fid=fopen(filename_joblist,'w'); |
---|
1699 | for p=1:length(batch_file_list) |
---|
1700 | oar_command=['oarsub -n CIVX '... |
---|
1701 | '-E ' regexprep(batch_file_list{p},'\.bat\>','.stderr') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.stdout ')... |
---|
1702 | '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '" ' batch_file_list{p}]; |
---|
1703 | fprintf(fid,[oar_command '\n']); |
---|
1704 | end |
---|
1705 | fclose(fid); |
---|
1706 | oar_command=['oarsub -t container -n civx-container '... |
---|
1707 | '-l /core=' num2str(ncores)... |
---|
1708 | ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '... |
---|
1709 | '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '... |
---|
1710 | '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '... |
---|
1711 | '"oar-dispatch -f ' filename_joblist '"']; |
---|
1712 | filename_oarcommand=fullfile(Rootbat,'oar_command'); |
---|
1713 | fid=fopen(filename_oarcommand,'w'); |
---|
1714 | fprintf(fid,[oar_command '\n']); |
---|
1715 | fclose(fid); |
---|
1716 | display(oar_command); |
---|
1717 | eval(['! . ' filename_oarcommand]) |
---|
1718 | case 'mpilauncher' |
---|
1719 | filename_joblist=fullfile(Rootbat,'job_list.txt'); |
---|
1720 | fid=fopen(filename_joblist,'w'); |
---|
1721 | |
---|
1722 | for p=1:length(batch_file_list) |
---|
1723 | fprintf(fid,[batch_file_list{p} '\n']); |
---|
1724 | end |
---|
1725 | fclose(fid) |
---|
1726 | text_oarscript=[... |
---|
1727 | '#!/bin/bash \n'... |
---|
1728 | '#OAR -n Mylauncher \n'... |
---|
1729 | '#OAR -l node=4/core=5,walltime=0:15:00 \n'... |
---|
1730 | '#OAR -E ' fullfile(Rootbat,'stderrfile.log') ' \n'... |
---|
1731 | '#OAR -O ' fullfile(Rootbat,'stdoutfile.log') ' \n'... |
---|
1732 | '# ========================================================= \n'... |
---|
1733 | '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'... |
---|
1734 | '# application for coriolis PIV post-processing. \n'... |
---|
1735 | '# OAR uses oarshmost wrapper to propagate the user environement. \n'... |
---|
1736 | '# This wrapper assert that the user has the same environment on all the \n'... |
---|
1737 | '# allocated nodes (basic behavior needed by most MPI applications). \n'... |
---|
1738 | '# \n'... |
---|
1739 | '# REQUIREMENT: \n'... |
---|
1740 | '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'... |
---|
1741 | '# If a different location is used, change the line following the comment "Bidouille" \n'... |
---|
1742 | '# ========================================================= \n'... |
---|
1743 | '# USER should only modify these 2 lines \n'... |
---|
1744 | 'WORKDIR=' pwd ' \n'... |
---|
1745 | 'COMMANDE="mpilauncher -f ' filename_joblist '" \n'... |
---|
1746 | '# ========================================================= \n'... |
---|
1747 | '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'... |
---|
1748 | 'echo "job starting on: "`hostname` \n'... |
---|
1749 | 'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'... |
---|
1750 | 'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'... |
---|
1751 | '#========== Bidouille ============== \n'... |
---|
1752 | 'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...% 'cd $WORKDIR \n'... |
---|
1753 | 'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'... |
---|
1754 | 'echo "I run: $CMD" \n'... |
---|
1755 | '$CMD \n'... |
---|
1756 | 'echo "job ending" \n'... |
---|
1757 | ]; |
---|
1758 | % oarsub -S ./oar.sub |
---|
1759 | filename_oarscript=fullfile(Rootbat,'oar_command'); |
---|
1760 | fid=fopen(filename_oarscript,'w'); |
---|
1761 | fprintf(fid,[text_oarscript]); |
---|
1762 | fclose(fid); |
---|
1763 | eval(['!chmod +x ' filename_oarscript]); |
---|
1764 | eval(['!oarsub -S ' filename_oarscript]); |
---|
1765 | end |
---|
1766 | end |
---|
1767 | else |
---|
1768 | if ~isequal(CivMode,'Matlab') |
---|
1769 | filename_superbat=fullfile(Rootbat,'job_list.bat'); |
---|
1770 | fid=fopen(filename_superbat,'w'); |
---|
1771 | if fid==-1 |
---|
1772 | msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat]) |
---|
1773 | return |
---|
1774 | end |
---|
1775 | for p=1:length(batch_file_list) |
---|
1776 | if isunix |
---|
1777 | fprintf(fid,['sh ' batch_file_list{p} '\n']); |
---|
1778 | else |
---|
1779 | fprintf(fid,['@call "' regexprep(batch_file_list{p},'\\','\\\\') '"' '\n']); |
---|
1780 | end |
---|
1781 | end |
---|
1782 | fclose(fid); |
---|
1783 | if(isunix) |
---|
1784 | system(['chmod +x ' filename_superbat]); |
---|
1785 | end |
---|
1786 | system([filename_superbat ' &']);% execute main commmand |
---|
1787 | end |
---|
1788 | end |
---|
1789 | |
---|
1790 | |
---|
1791 | %% save interface state |
---|
1792 | if isfield(filecell,'nc') |
---|
1793 | if isfield(filecell.nc,'civ2') |
---|
1794 | fileresu=filecell.nc.civ2{1,1}; |
---|
1795 | else |
---|
1796 | fileresu=filecell.nc.civ1{1,1}; |
---|
1797 | end |
---|
1798 | end |
---|
1799 | [RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu); |
---|
1800 | namedoc=fullfile(RootPath,SubDir,RootFile); |
---|
1801 | detect=1; |
---|
1802 | while detect==1 |
---|
1803 | namefigfull=[namedoc '.fig']; |
---|
1804 | hh=dir(namefigfull); |
---|
1805 | if ~isempty(hh) |
---|
1806 | detect=1; |
---|
1807 | namedoc=[namedoc '.0']; |
---|
1808 | else |
---|
1809 | detect=0; |
---|
1810 | end |
---|
1811 | end |
---|
1812 | Param=rmfield(Param,'status'); |
---|
1813 | Param=rmfield(Param,'xml'); |
---|
1814 | t=struct2xml(Param); |
---|
1815 | t=set(t,1,'Name','CivDoc');% set the head label |
---|
1816 | save(t,[namedoc '.CivDoc.xml']); %save GUI parameters as xml file |
---|
1817 | saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml) |
---|
1818 | |
---|
1819 | %Save info in personal profile (initiate browser next time) TODO |
---|
1820 | MenuFile={}; |
---|
1821 | dir_perso=prefdir; |
---|
1822 | profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); |
---|
1823 | if exist(profil_perso,'file') |
---|
1824 | hh=load (profil_perso); |
---|
1825 | if isfield(hh,'MenuFile') |
---|
1826 | MenuFile=hh.MenuFile; |
---|
1827 | end |
---|
1828 | if isfield(filecell.nc,'civ2') |
---|
1829 | MenuFile=[filecell.nc.civ2{1,1}; MenuFile]; |
---|
1830 | else |
---|
1831 | MenuFile=[filecell.nc.civ1{1,1}; MenuFile]; |
---|
1832 | end |
---|
1833 | save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat |
---|
1834 | else |
---|
1835 | MenuFile=filecell.ima1.civ1(1,1); |
---|
1836 | save (profil_perso,'MenuFile') |
---|
1837 | end |
---|
1838 | |
---|
1839 | %------------------------------------------------------------------------ |
---|
1840 | % --- determine the list of reference indices of processing file |
---|
1841 | function [ref_i,ref_j,errormsg]=find_ref_indices(handles) |
---|
1842 | %------------------------------------------------------------------------ |
---|
1843 | errormsg=''; %default error message |
---|
1844 | first_i=str2double(get(handles.first_i,'String'));%first index i |
---|
1845 | last_i=str2double(get(handles.last_i,'String'));%last index i |
---|
1846 | incr_i=str2double(get(handles.incr_i,'String'));% increment |
---|
1847 | if isequal(get(handles.first_j,'Visible'),'on') |
---|
1848 | first_j=str2double(get(handles.first_j,'String'));%first index j |
---|
1849 | last_j=str2double(get(handles.last_j,'String'));%last index j |
---|
1850 | incr_j=str2double(get(handles.incr_j,'String'));% increment |
---|
1851 | else |
---|
1852 | first_j=1; |
---|
1853 | last_j=1; |
---|
1854 | incr_j=1; |
---|
1855 | end |
---|
1856 | ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair) |
---|
1857 | ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair) |
---|
1858 | if isnan(first_i)||isnan(first_j) |
---|
1859 | errormsg='first field number not defined'; |
---|
1860 | elseif isnan(last_i)||isnan(last_j) |
---|
1861 | errormsg='last field number not defined'; |
---|
1862 | elseif isnan(incr_i)||isnan(incr_j) |
---|
1863 | errormsg='increment in field number not defined'; |
---|
1864 | elseif last_i < first_i || last_j < first_j |
---|
1865 | errormsg='last field number must be larger than the first one'; |
---|
1866 | end |
---|
1867 | |
---|
1868 | %------------------------------------------------------------------------ |
---|
1869 | % --- determine the list of filenames and indices needed for launch_job |
---|
1870 | %------------------------------------------------------------------------ |
---|
1871 | % OUTPUT: |
---|
1872 | % filecell: structure of cell arrays {ref_i,ref_j} containing all the filenames involved in the civ process |
---|
1873 | % the indices ref_i and ref_j correspond to the list of reference indices |
---|
1874 | % .filebase=fullfile(RootPath,RootFile) used to construct mask names, grid names, CivDoc xml file |
---|
1875 | % .ima1.civ1,.ima1.civ2: first image for civ1 and civ2 respectively (possibly different) |
---|
1876 | % .ima2.civ1,.ima2.civ2: second image for civ1 and civ2 respectively (possibly different) |
---|
1877 | % .nc.civ1,.nc.civ2: netcdf files containing civ1 and civ2 data respectively (possibly different) |
---|
1878 | % i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2: arrays of files indices, needed for timing records |
---|
1879 | 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]=... |
---|
1880 | set_civ_filenames(handles,ref_i,ref_j,checkbox) |
---|
1881 | %------------------------------------------------------------------------ |
---|
1882 | filecell=[];%default |
---|
1883 | ListProgram=get(handles.ListProgram,'String'); |
---|
1884 | CivMode=ListProgram{get(handles.ListProgram,'Value')};%Program to use , CivX or Matlab |
---|
1885 | |
---|
1886 | %% get the root name and check dir |
---|
1887 | RootPath=get(handles.RootPath,'String'); |
---|
1888 | RootFile=get(handles.RootFile,'String'); |
---|
1889 | filecell.filebase=fullfile(RootPath,RootFile); |
---|
1890 | if isempty(filecell.filebase) |
---|
1891 | msgbox_uvmat('ERROR','please open an image with the upper menu option Open/Browse...') |
---|
1892 | return |
---|
1893 | end |
---|
1894 | if ~exist(RootPath,'dir') |
---|
1895 | msgbox_uvmat('ERROR',['path to images ' RootPath ' not found']) |
---|
1896 | return |
---|
1897 | end |
---|
1898 | [tild,message]=fileattrib(RootPath); |
---|
1899 | if ~isempty(message) && ~isequal(message.UserWrite,1) |
---|
1900 | msgbox_uvmat('ERROR',['No writting access to ' RootPath]) |
---|
1901 | return |
---|
1902 | end |
---|
1903 | %check result directory |
---|
1904 | subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data |
---|
1905 | subdir_civ2=get(handles.SubdirCiv2,'String'); |
---|
1906 | if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir |
---|
1907 | if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir |
---|
1908 | |
---|
1909 | %% choose root names depending on ListCompareMode =displacement, shift, PIV or stereo PIV |
---|
1910 | ListCompareMode=get(handles.ListCompareMode,'String'); |
---|
1911 | compare=ListCompareMode{get(handles.ListCompareMode,'Value')}; |
---|
1912 | |
---|
1913 | % set the nomenclature type of the nc files depending on the pair mode |
---|
1914 | if strcmp(compare,'displacement')||strcmp(compare,'shift') |
---|
1915 | mode='displacement'; |
---|
1916 | else |
---|
1917 | mode_list=get(handles.ListPairMode,'String'); |
---|
1918 | mode_value=get(handles.ListPairMode,'Value'); |
---|
1919 | mode=mode_list{mode_value}; |
---|
1920 | end |
---|
1921 | NomType_ima2=get(handles.NomType,'String'); |
---|
1922 | NomType_nc=nomtype2pair(NomType_ima2,mode); |
---|
1923 | |
---|
1924 | % set the rootfile and image indexing |
---|
1925 | RootFile_ima2=get(handles.RootFile,'String');%root file for the second image series |
---|
1926 | ext_ima=get(handles.ImaExt,'String'); % image extension (the same for all images) |
---|
1927 | switch compare |
---|
1928 | case 'PIV' |
---|
1929 | RootFile_ima1=RootFile_ima2;% root name of the two image series is the same |
---|
1930 | NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one |
---|
1931 | RootFile_nc=RootFile_ima2; |
---|
1932 | case 'displacement' |
---|
1933 | RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1 |
---|
1934 | NomType_ima1='';% no indexing of the first image, a fixed reference for the whole series |
---|
1935 | RootFile_nc=RootFile_ima2; |
---|
1936 | case 'shift' |
---|
1937 | RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1 |
---|
1938 | NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one |
---|
1939 | RootFile_nc=[RootFile_ima1 '-' RootFile_ima2]; |
---|
1940 | end |
---|
1941 | |
---|
1942 | %determine the list of file indices involved |
---|
1943 | [i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=... |
---|
1944 | find_pair_indices(handles,ref_i,ref_j,mode); |
---|
1945 | |
---|
1946 | %determine the new filebase for 'displacement' ListPairMode (comparison of two series) |
---|
1947 | %filebase_B=filebase;% root name of the second field series for stereo |
---|
1948 | % filebase_A=filebase;%default |
---|
1949 | % if strcmp(compare,'PIV') |
---|
1950 | % filebase_AB=filebase; |
---|
1951 | % else |
---|
1952 | % [Path2,Name2]=fileparts(filebase_B); |
---|
1953 | % Name1=RootFile_ima1; |
---|
1954 | % filebase_AB=fullfile(Path2,[Name2 '-' Name1]); |
---|
1955 | % end |
---|
1956 | % [RootPath_AB,RootFile_AB]=fileparts(filebase_AB); |
---|
1957 | % % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B); |
---|
1958 | % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B); |
---|
1959 | % [RootPath_nc,RootFile_nc]=fileparts(filebase_B);%default |
---|
1960 | % if strcmp(compare,'displacement') |
---|
1961 | % % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B); |
---|
1962 | % % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B); |
---|
1963 | % [RootPath_nc,RootFile_nc]=fileparts(filebase_B); |
---|
1964 | % elseif strcmp(compare,'shift') |
---|
1965 | % RootPath_nc=RootPath_AB; |
---|
1966 | % RootFile_nc=RootFile_AB; |
---|
1967 | % end |
---|
1968 | % else |
---|
1969 | % filebase_ima1=filebase_B; |
---|
1970 | % filebase_ima2=filebase_B; |
---|
1971 | % filebase_nc=filebase_B; |
---|
1972 | % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1); |
---|
1973 | % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2); |
---|
1974 | % [RootPath_nc,RootFile_nc]=fileparts(filebase_nc); |
---|
1975 | % [RootPath_A,RootFile_A]=fileparts(filebase_A); |
---|
1976 | |
---|
1977 | |
---|
1978 | %% determine reference files for fix: |
---|
1979 | file_ref_fix1={};%default |
---|
1980 | file_ref_fix2={}; |
---|
1981 | nbfield=length(i1_civ1); |
---|
1982 | nbslice=length(j1_civ1); |
---|
1983 | if checkbox(2)==1% fix1 performed |
---|
1984 | ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback |
---|
1985 | if ~isempty(ref) |
---|
1986 | first_i=str2double(get(handles.first_i,'String')); |
---|
1987 | last_i=str2double(get(handles.last_i,'String')); |
---|
1988 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
1989 | first_j=str2double(get(handles.first_j,'String')); |
---|
1990 | last_j=str2double(get(handles.last_j,'String')); |
---|
1991 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
1992 | num_i_ref=first_i:incr_i:last_i; |
---|
1993 | num_j_ref=first_j:incr_j:last_j; |
---|
1994 | if isequal(mode,'displacement') |
---|
1995 | num_i1=num_i_ref; |
---|
1996 | num_i2=num_i_ref; |
---|
1997 | num_j1=num_j_ref; |
---|
1998 | num_j2=num_j_ref; |
---|
1999 | elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2') |
---|
2000 | num_i1=num_i_ref; |
---|
2001 | num_i2=num_i1; |
---|
2002 | num_j1=ref.num_a*ones(size(num_i_ref)); |
---|
2003 | num_j2=ref.num_b*ones(size(num_i_ref)); |
---|
2004 | elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)') |
---|
2005 | delta1=floor((ref.num2-ref.num1)/2); |
---|
2006 | delta2=ceil((ref.num2-ref.num1)/2); |
---|
2007 | num_i1=num_i_ref-delta1*ones(size(num_i_ref)); |
---|
2008 | num_i2=num_i_ref+delta2*ones(size(num_i_ref)); |
---|
2009 | if isempty(ref.num_a) |
---|
2010 | ref.num_a=1; |
---|
2011 | end |
---|
2012 | num_j1=ref.num_a*ones(size(num_i1)); |
---|
2013 | num_j2=num_j1; |
---|
2014 | elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)') |
---|
2015 | delta1=floor((ref.num_b-ref.num_a)/2); |
---|
2016 | delta2=ceil((ref.num_b-ref.num_a)/2); |
---|
2017 | num_i1=ref.num1*ones(size(num_i_ref)); |
---|
2018 | num_i2=num_i1; |
---|
2019 | num_j1=num_j_ref-delta1*ones(size(num_j_ref)); |
---|
2020 | num_j2=num_j_ref+delta2*ones(size(num_j_ref)); |
---|
2021 | end |
---|
2022 | for ifile=1:nbfield |
---|
2023 | for j=1:nbslice |
---|
2024 | [RootPathRef,RootFile]=fileparts(ref.filebase); |
---|
2025 | file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j)); |
---|
2026 | file_ref_fix1(ifile,j)={file_ref}; |
---|
2027 | if ~exist(file_ref,'file') |
---|
2028 | msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1']) |
---|
2029 | filecell=[]; |
---|
2030 | return |
---|
2031 | end |
---|
2032 | end |
---|
2033 | end |
---|
2034 | end |
---|
2035 | end |
---|
2036 | |
---|
2037 | %% determine reference files for fix2: |
---|
2038 | if checkbox(5)==1% fix2 performed |
---|
2039 | ref=get(handles.ref_fix2,'UserData'); |
---|
2040 | if ~isempty(ref) |
---|
2041 | first_i=str2double(get(handles.first_i,'String')); |
---|
2042 | last_i=str2double(get(handles.last_i,'String')); |
---|
2043 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
2044 | first_j=str2double(get(handles.first_j,'String')); |
---|
2045 | last_j=str2double(get(handles.last_j,'String')); |
---|
2046 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
2047 | num_i_ref=first_i:incr_i:last_i; |
---|
2048 | num_j_ref=first_j:incr_j:last_j; |
---|
2049 | if isequal(mode,'displacement') |
---|
2050 | num_i1=num_i_ref; |
---|
2051 | num_i2=num_i_ref; |
---|
2052 | num_j1=num_j_ref; |
---|
2053 | num_j2=num_j_ref; |
---|
2054 | elseif isequal(mode,'pair j1-j2') |
---|
2055 | num_i1=num_i_ref; |
---|
2056 | num_i2=num_i1; |
---|
2057 | num_j1=ref.num_a; |
---|
2058 | num_j2=ref.num_b; |
---|
2059 | elseif isequal(mode,'series(Di)') |
---|
2060 | delta1=floor((ref.num2-ref.num1)/2); |
---|
2061 | delta2=ceil((ref.num2-ref.num1)/2); |
---|
2062 | num_i1=num_i_ref-delta1*ones(size(num_i_ref)); |
---|
2063 | num_i2=num_i_ref+delta2*ones(size(num_i_ref)); |
---|
2064 | num_j1=ref.num_a*ones(size(num_i1)); |
---|
2065 | num_j2=num_j1; |
---|
2066 | elseif isequal(mode,'series(Dj)') |
---|
2067 | delta1=floor((ref.num_b-ref.num_a)/2); |
---|
2068 | delta2=ceil((ref.num_b-ref.num_a)/2); |
---|
2069 | num_i1=ref.num1*ones(size(num_i_ref)); |
---|
2070 | num_i2=num_i1; |
---|
2071 | num_j1=num_j_ref-delta1*ones(size(num_j_ref)); |
---|
2072 | num_j2=num_j_ref+delta2*ones(size(num_j_ref)); |
---|
2073 | end |
---|
2074 | for ifile=1:nbfield |
---|
2075 | for j=1:nbslice |
---|
2076 | [RootPathRef,RootFile]=fileparts(ref.filebase); |
---|
2077 | file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j)); |
---|
2078 | file_ref_fix2(ifile,j)={file_ref}; |
---|
2079 | if ~exist(file_ref,'file') |
---|
2080 | msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2']) |
---|
2081 | filecell={}; |
---|
2082 | return |
---|
2083 | end |
---|
2084 | end |
---|
2085 | end |
---|
2086 | end |
---|
2087 | end |
---|
2088 | |
---|
2089 | %% check the existence of the netcdf and image files involved |
---|
2090 | % %%%%%%%%%%%% case CheckCiv1 activated %%%%%%%%%%%%% |
---|
2091 | if checkbox(1)==1; |
---|
2092 | detect=1; |
---|
2093 | vers=0; |
---|
2094 | subdir_civ1_new=subdir_civ1; |
---|
2095 | while detect==1 %create a new subdir if the netcdf files already exist |
---|
2096 | for ifile=1:nbfield |
---|
2097 | for j=1:nbslice |
---|
2098 | filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
2099 | detect=exist(filename,'file')==2; |
---|
2100 | if detect% if a netcdf file already exists |
---|
2101 | indstr=regexp(subdir_civ1_new,'\D'); |
---|
2102 | if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number |
---|
2103 | vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1; |
---|
2104 | subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)]; |
---|
2105 | else |
---|
2106 | vers=vers+1; |
---|
2107 | subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)]; |
---|
2108 | end |
---|
2109 | subdir_civ2=subdir_civ1_new; |
---|
2110 | break |
---|
2111 | end |
---|
2112 | filecell.nc.civ1(ifile,j)={filename}; |
---|
2113 | end |
---|
2114 | if detect% if a netcdf file already exists |
---|
2115 | break |
---|
2116 | end |
---|
2117 | end |
---|
2118 | |
---|
2119 | %create the new SubdirCiv1 |
---|
2120 | if ~exist(fullfile(RootPath,subdir_civ1_new),'dir') |
---|
2121 | [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new)); |
---|
2122 | |
---|
2123 | if ~strcmp(msg1,'') |
---|
2124 | msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation |
---|
2125 | filecell={}; |
---|
2126 | return |
---|
2127 | elseif isunix |
---|
2128 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
2129 | if ~strcmp(msg2,'') |
---|
2130 | msgbox_uvmat('ERROR',['pb of permission for ' fullfile(RootPath,subdir_civ1_new) ': ' msg2])%error message for directory creation |
---|
2131 | filecell={}; |
---|
2132 | return |
---|
2133 | end |
---|
2134 | end |
---|
2135 | end |
---|
2136 | if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series |
---|
2137 | for ifile=1:nbfield |
---|
2138 | for j=1:nbslice |
---|
2139 | filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
2140 | % filename=name_generator(filebase_A,i1_civ1(ifile),j1_civ1(j),'.nc',NomType_nc,1,i2_civ1(ifile),j2_civ1(j),subdir_civ1_new);% |
---|
2141 | detect=exist(filename,'file')==2; |
---|
2142 | if detect% if a netcdf file already exists |
---|
2143 | indstr=regexp(subdir_civ1_new,'\D'); |
---|
2144 | if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number |
---|
2145 | vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1; |
---|
2146 | subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)]; |
---|
2147 | else |
---|
2148 | vers=vers+1; |
---|
2149 | subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)]; |
---|
2150 | end |
---|
2151 | subdir_civ2=subdir_civ1; |
---|
2152 | break |
---|
2153 | end |
---|
2154 | filecell.ncA.civ1(ifile,j)={filename}; |
---|
2155 | end |
---|
2156 | if detect% if a netcdf file already exists |
---|
2157 | break |
---|
2158 | end |
---|
2159 | end |
---|
2160 | %create the new SubdirCiv1 |
---|
2161 | if ~exist(fullfile(RootPath,subdir_civ1_new),'dir') |
---|
2162 | [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new)); |
---|
2163 | if ~strcmp(msg1,'') |
---|
2164 | msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1]) |
---|
2165 | filecell={}; |
---|
2166 | return |
---|
2167 | else |
---|
2168 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
2169 | if ~strcmp(msg2,'') |
---|
2170 | msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation |
---|
2171 | filecell={}; |
---|
2172 | return |
---|
2173 | end |
---|
2174 | end |
---|
2175 | end |
---|
2176 | end |
---|
2177 | end |
---|
2178 | subdir_civ1=subdir_civ1_new; |
---|
2179 | % get image names |
---|
2180 | for ifile=1:nbfield |
---|
2181 | for j=1:nbslice |
---|
2182 | filename=fullfile_uvmat(RootPath,'',RootFile_ima1,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j)); |
---|
2183 | idetect(j)=exist(filename,'file')==2; |
---|
2184 | filecell.ima1.civ1(ifile,j)={filename}; %first image |
---|
2185 | filename=fullfile_uvmat(RootPath,'',RootFile_ima2,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j)); |
---|
2186 | idetect_1(j)=exist(filename,'file')==2; |
---|
2187 | filecell.ima2.civ1(ifile,j)={filename};%second image |
---|
2188 | end |
---|
2189 | [idetectmin,indexj]=min(idetect); |
---|
2190 | if idetectmin==0, |
---|
2191 | msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found']) |
---|
2192 | filecell={}; |
---|
2193 | return |
---|
2194 | end |
---|
2195 | [idetectmin,indexj]=min(idetect_1); |
---|
2196 | if idetectmin==0, |
---|
2197 | msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found']) |
---|
2198 | filecell={}; |
---|
2199 | return |
---|
2200 | end |
---|
2201 | end |
---|
2202 | if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)')) |
---|
2203 | for ifile=1:nbfield |
---|
2204 | for j=1:nbslice |
---|
2205 | filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j)); |
---|
2206 | idetect(j)=exist(filename,'file')==2; |
---|
2207 | filecell.imaA1.civ1(ifile,j)={filename} ;%first image |
---|
2208 | filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j)); |
---|
2209 | idetect_1(j)=exist(filename,'file')==2; |
---|
2210 | filecell.imaA2.civ1(ifile,j)={filename};%second image |
---|
2211 | end |
---|
2212 | [idetectmin,indexj]=min(idetect); |
---|
2213 | if idetectmin==0, |
---|
2214 | msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found']) |
---|
2215 | filecell={}; |
---|
2216 | % cd(currentdir) |
---|
2217 | return |
---|
2218 | end |
---|
2219 | [idetectmin,indexj]=min(idetect_1); |
---|
2220 | if idetectmin==0, |
---|
2221 | msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found']) |
---|
2222 | filecell={}; |
---|
2223 | % cd(currentdir) |
---|
2224 | return |
---|
2225 | end |
---|
2226 | end |
---|
2227 | end |
---|
2228 | |
---|
2229 | %%%%%%%%%%%%% checkfix1 or checkpatch1 activated but no checkciv1 %%%%%%%%%%%%% |
---|
2230 | elseif (checkbox(2)==1 || checkbox(3)==1); |
---|
2231 | for ifile=1:nbfield |
---|
2232 | for j=1:nbslice |
---|
2233 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
2234 | detect=exist(filename,'file')==2; |
---|
2235 | if detect==0 |
---|
2236 | msgbox_uvmat('ERROR',[filename ' not found']) |
---|
2237 | filecell={}; |
---|
2238 | % cd(currentdir) |
---|
2239 | return |
---|
2240 | end |
---|
2241 | filecell.nc.civ1(ifile,j)={filename}; |
---|
2242 | end |
---|
2243 | end |
---|
2244 | if strcmp(compare,'stereo PIV') |
---|
2245 | for ifile=1:nbfield |
---|
2246 | for j=1:nbslice |
---|
2247 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
2248 | filecell.ncA.civ1(ifile,j)={filename}; |
---|
2249 | if ~exist(filename,'file') |
---|
2250 | msgbox_uvmat('ERROR',['input file ' filename ' not found']) |
---|
2251 | set(handles.RUN, 'Enable','On') |
---|
2252 | set(handles.RUN,'BackgroundColor',[1 0 0]) |
---|
2253 | filecell={}; |
---|
2254 | %cd(currentdir) |
---|
2255 | return |
---|
2256 | end |
---|
2257 | end |
---|
2258 | end |
---|
2259 | end |
---|
2260 | end |
---|
2261 | |
---|
2262 | %%%%%%%%%%%%% if checkciv2 performed with pairs different than checkciv1 %%%%%%%%%%%%% |
---|
2263 | testdiff=0; |
---|
2264 | if (checkbox(4)==1)&&... |
---|
2265 | ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1)) |
---|
2266 | testdiff=1; |
---|
2267 | detect=1; |
---|
2268 | vers=0; |
---|
2269 | subdir_civ2_new=subdir_civ2; |
---|
2270 | while detect==1 %create a new subdir if the netcdf files already exist |
---|
2271 | for ifile=1:nbfield |
---|
2272 | for j=1:nbslice |
---|
2273 | filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2274 | detect=exist(filename,'file')==2; |
---|
2275 | if detect% if a netcdf file already exists |
---|
2276 | indstr=regexp(subdir_civ2,'\D'); |
---|
2277 | if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number |
---|
2278 | vers=str2double(subdir_civ2(indstr(end)+1:end))+1; |
---|
2279 | subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)]; |
---|
2280 | else |
---|
2281 | vers=vers+1; |
---|
2282 | subdir_civ2_new=[subdir_civ1 '_' num2str(vers)]; |
---|
2283 | end |
---|
2284 | break |
---|
2285 | end |
---|
2286 | filecell.nc.civ2(ifile,j)={filename}; |
---|
2287 | end |
---|
2288 | if detect% if a netcdf file already exists |
---|
2289 | break |
---|
2290 | end |
---|
2291 | end |
---|
2292 | %create the new subdir_civ2_new |
---|
2293 | if ~exist(fullfile(RootPath,subdir_civ2_new),'dir') |
---|
2294 | [xx,m2]=mkdir(fullfile(RootPath,subdir_civ2_new)); |
---|
2295 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
2296 | if ~isequal(m2,'') |
---|
2297 | msgbox_uvmat('ERROR',['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2]) |
---|
2298 | filecell={}; |
---|
2299 | return |
---|
2300 | end |
---|
2301 | end |
---|
2302 | if strcmp(compare,'stereo PIV')%check second nc series |
---|
2303 | for ifile=1:nbfield |
---|
2304 | for j=1:nbslice |
---|
2305 | filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2306 | detect=exist(filename,'file')==2; |
---|
2307 | if detect% if a netcdf file already exists |
---|
2308 | indstr=regexp(subdir_civ2,'\D'); |
---|
2309 | if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number |
---|
2310 | vers=str2double(subdir_civ2(indstr(end)+1:end))+1; |
---|
2311 | subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)]; |
---|
2312 | else |
---|
2313 | vers=vers+1; |
---|
2314 | subdir_civ2_new=[subdir_civ1 '_' num2str(vers)]; |
---|
2315 | end |
---|
2316 | break |
---|
2317 | end |
---|
2318 | filecell.ncA.civ2(ifile,j)={filename}; |
---|
2319 | end |
---|
2320 | if detect% if a netcdf file already exists |
---|
2321 | break |
---|
2322 | end |
---|
2323 | end |
---|
2324 | subdir_civ2=subdir_civ2_new; |
---|
2325 | %create the new SubdirCiv1 |
---|
2326 | if ~exist(fullfile(RootPath,subdir_civ2_new),'dir') |
---|
2327 | [xx,m2]=mkdir(subdir_civ2_new); |
---|
2328 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
2329 | if ~isequal(m2,'') |
---|
2330 | msgbox_uvmat('ERROR', ['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2])%error message for directory creation |
---|
2331 | % cd(currentdir) |
---|
2332 | filecell={}; |
---|
2333 | return |
---|
2334 | end |
---|
2335 | end |
---|
2336 | end |
---|
2337 | end |
---|
2338 | subdir_civ2=subdir_civ2_new; |
---|
2339 | end |
---|
2340 | %cd(currentdir);%come back to the current working directory |
---|
2341 | |
---|
2342 | %%%%%%%%%%%%% if checkciv2 results are obtained or used %%%%%%%%%%%%% |
---|
2343 | if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2 |
---|
2344 | %check source netcdf file of checkciv1 estimates |
---|
2345 | if checkbox(1)==0; %no civ1 performed |
---|
2346 | for ifile=1:nbfield |
---|
2347 | for j=1:nbslice |
---|
2348 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));% |
---|
2349 | filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file |
---|
2350 | if ~exist(filename,'file') |
---|
2351 | msgbox_uvmat('ERROR',['input file ' filename ' not found']) |
---|
2352 | filecell={}; |
---|
2353 | return |
---|
2354 | end |
---|
2355 | if ~testdiff % civ2 or patch2 are written in the same file as civ1 |
---|
2356 | if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated |
---|
2357 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2'); |
---|
2358 | if isfield(Data,'Txt') |
---|
2359 | msgbox_uvmat('ERROR',Data.Txt); |
---|
2360 | return |
---|
2361 | elseif ~isempty(Data.CivStage)% case of new civ files |
---|
2362 | if Data.CivStage<4 %test for civ files |
---|
2363 | msgbox_uvmat('ERROR',['no civ2 data in ' filename]) |
---|
2364 | filecell=[]; |
---|
2365 | return |
---|
2366 | end |
---|
2367 | elseif isempty(Data.civ2)||isequal(Data.civ2,0) |
---|
2368 | msgbox_uvmat('ERROR',['no civ2 data in ' filename]) |
---|
2369 | filecell=[]; |
---|
2370 | return |
---|
2371 | end |
---|
2372 | elseif checkbox(3)==0; %check the existence of patch if it is not calculated |
---|
2373 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch'); |
---|
2374 | if ~isempty(Data.CivStage) |
---|
2375 | if Data.CivStage<3 %test for civ files |
---|
2376 | msgbox_uvmat('ERROR',['no patch data in ' filename]) |
---|
2377 | filecell=[]; |
---|
2378 | return |
---|
2379 | end |
---|
2380 | elseif isempty(Data.patch)||isequal(Data.patch,0) |
---|
2381 | msgbox_uvmat('ERROR',['no patch data in ' filename]) |
---|
2382 | filecell=[]; |
---|
2383 | return |
---|
2384 | end |
---|
2385 | end |
---|
2386 | end |
---|
2387 | end |
---|
2388 | end |
---|
2389 | if strcmp(compare,'stereo PIV') |
---|
2390 | for ifile=1:nbfield |
---|
2391 | for j=1:nbslice |
---|
2392 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2393 | filecell.ncA.civ2(ifile,j)={filename}; |
---|
2394 | if ~exist(filename,'file') |
---|
2395 | msgbox_uvmat('ERROR',['input file ' filename ' not found']) |
---|
2396 | set(handles.RUN, 'Enable','On') |
---|
2397 | set(handles.RUN,'BackgroundColor',[1 0 0]) |
---|
2398 | return |
---|
2399 | end |
---|
2400 | end |
---|
2401 | end |
---|
2402 | end |
---|
2403 | end |
---|
2404 | |
---|
2405 | detect=1; |
---|
2406 | % while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data |
---|
2407 | for ifile=1:nbfield |
---|
2408 | for j=1:nbslice |
---|
2409 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2410 | detect=exist(filename,'file')==2; |
---|
2411 | filecell.nc.civ2(ifile,j)={filename}; |
---|
2412 | end |
---|
2413 | end |
---|
2414 | %get first image names for checkciv2 |
---|
2415 | if checkbox(1)==1 && isequal(i1_civ1,i1_civ2) && isequal(j1_civ1,j1_civ2) |
---|
2416 | filecell.ima1.civ2=filecell.ima1.civ1; |
---|
2417 | elseif checkbox(4)==1 |
---|
2418 | for ifile=1:nbfield |
---|
2419 | for j=1:nbslice |
---|
2420 | filename=fullfile_uvmat(RootPath,[],RootFile_ima1,ext_ima,NomType_ima1,i1_civ2(ifile),[],j1_civ2(j)); |
---|
2421 | idetect_2(j)=exist(filename,'file')==2; |
---|
2422 | filecell.ima1.civ2(ifile,j)={filename};%first image |
---|
2423 | end |
---|
2424 | [idetectmin,indexj]=min(idetect_2); |
---|
2425 | if idetectmin==0, |
---|
2426 | msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found']) |
---|
2427 | filecell=[]; |
---|
2428 | return |
---|
2429 | end |
---|
2430 | end |
---|
2431 | end |
---|
2432 | |
---|
2433 | %get second image names for checkciv2 |
---|
2434 | if checkbox(1)==1 && isequal(i2_civ1,i2_civ2) && isequal(j2_civ1,j2_civ2) |
---|
2435 | filecell.ima2.civ2=filecell.ima2.civ1; |
---|
2436 | elseif checkbox(4)==1 |
---|
2437 | for ifile=1:nbfield |
---|
2438 | for j=1:nbslice |
---|
2439 | filename=fullfile_uvmat(RootPath,[],RootFile_ima2,ext_ima,NomType_ima2,i2_civ2(ifile),[],j2_civ2(j)); |
---|
2440 | idetect_3(j)=exist(filename,'file')==2; |
---|
2441 | filecell.ima2.civ2(ifile,j)={filename};%first image |
---|
2442 | end |
---|
2443 | [idetectmin,indexj]=min(idetect_3); |
---|
2444 | if idetectmin==0, |
---|
2445 | msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found']) |
---|
2446 | filecell=[]; |
---|
2447 | return |
---|
2448 | end |
---|
2449 | end |
---|
2450 | end |
---|
2451 | end |
---|
2452 | if (checkbox(5) || checkbox(6)) && ~checkbox(4) % need to read an existing netcdf civ2 file |
---|
2453 | if ~testdiff |
---|
2454 | filecell.nc.civ2=filecell.nc.civ1;% file already checked |
---|
2455 | else % check the civ2 files |
---|
2456 | for ifile=1:nbfield |
---|
2457 | for j=1:nbslice |
---|
2458 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2459 | filecell.nc.civ2(ifile,j)={filename}; |
---|
2460 | if ~exist(filename,'file') |
---|
2461 | msgbox_uvmat('ERROR',['input file ' filename ' not found']) |
---|
2462 | filecell=[]; |
---|
2463 | return |
---|
2464 | else |
---|
2465 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2'); |
---|
2466 | if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files |
---|
2467 | msgbox_uvmat('ERROR',['no civ2 data in ' filename]) |
---|
2468 | filecell=[]; |
---|
2469 | return |
---|
2470 | elseif isempty(Data.civ2)||isequal(Data.civ2,0) |
---|
2471 | msgbox_uvmat('ERROR',['no civ2 data in ' filename]) |
---|
2472 | filecell=[]; |
---|
2473 | return |
---|
2474 | end |
---|
2475 | end |
---|
2476 | end |
---|
2477 | end |
---|
2478 | end |
---|
2479 | end |
---|
2480 | |
---|
2481 | %%%%%%%%%%%%% if stereo fields are calculated by PATCH %%%%%%%%%%%%% |
---|
2482 | if strcmp(compare,'stereo PIV') |
---|
2483 | if checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1) |
---|
2484 | for ifile=1:nbfield |
---|
2485 | for j=1:nbslice |
---|
2486 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_AB,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
2487 | filecell.st(ifile,j)={filename}; |
---|
2488 | end |
---|
2489 | end |
---|
2490 | end |
---|
2491 | if checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1) |
---|
2492 | for ifile=1:nbfield |
---|
2493 | for j=1:nbslice |
---|
2494 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_AB,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2495 | filecell.st(ifile,j)={filename}; |
---|
2496 | end |
---|
2497 | end |
---|
2498 | end |
---|
2499 | end |
---|
2500 | set(handles.SubdirCiv1,'String',subdir_civ1);%update the edit box |
---|
2501 | set(handles.SubdirCiv2,'String',subdir_civ2);%update the edit box |
---|
2502 | |
---|
2503 | % For CivX COPY IMAGES TO THE FORMAT .png IF NEEDED |
---|
2504 | if strcmp(CivMode,'CivX') |
---|
2505 | if isequal(NomType_ima1,'*')%case of movie files |
---|
2506 | NomType_imanew1='_i'; |
---|
2507 | else |
---|
2508 | NomType_imanew1=NomType_ima1; |
---|
2509 | end |
---|
2510 | if isequal(NomType_ima2,'*')%case of movie files |
---|
2511 | NomType_imanew2='_i'; |
---|
2512 | else |
---|
2513 | NomType_imanew2=NomType_ima2; |
---|
2514 | end |
---|
2515 | if ~isequal(ext_ima,'.png') |
---|
2516 | %%type of image file |
---|
2517 | type_ima1='none';%default |
---|
2518 | movieobject1=[];%default |
---|
2519 | if strcmpi(ext_ima,'.avi') |
---|
2520 | if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab) |
---|
2521 | type_ima1='movie'; |
---|
2522 | movieobject1=mmreader([filecell.filebase ext_ima]); |
---|
2523 | else |
---|
2524 | type_ima1='avi'; |
---|
2525 | end |
---|
2526 | elseif ischar(ext_ima) && ~isempty(ext_ima(2:end)) |
---|
2527 | form=imformats(ext_ima(2:end)); |
---|
2528 | if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab |
---|
2529 | if isequal(NomType_ima1,'*'); |
---|
2530 | type_ima1='multimage';%image series in a single image file |
---|
2531 | else |
---|
2532 | type_ima1='image'; |
---|
2533 | end |
---|
2534 | end |
---|
2535 | end |
---|
2536 | type_ima2='none';%default |
---|
2537 | movieobject2=[]; |
---|
2538 | if strcmpi(ext_ima,'.avi') |
---|
2539 | if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab) |
---|
2540 | type_ima2='movie'; |
---|
2541 | movieobject2=mmreader([filecell.filebase ext_ima]); |
---|
2542 | else |
---|
2543 | type_ima2='avi'; |
---|
2544 | end |
---|
2545 | elseif ischar(ext_ima) && ~isempty(ext_ima(2:end)) |
---|
2546 | form=imformats(ext_ima(2:end)); |
---|
2547 | if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab |
---|
2548 | if isequal(NomType_ima1,'*'); |
---|
2549 | type_ima2='multimage';%image series in a single image file |
---|
2550 | else |
---|
2551 | type_ima2='image'; |
---|
2552 | end |
---|
2553 | end |
---|
2554 | end |
---|
2555 | if checkbox(1) %if civ1 is performed |
---|
2556 | h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar |
---|
2557 | for ifile=1:nbfield |
---|
2558 | waitbar(ifile/nbfield); |
---|
2559 | for j=1:nbslice |
---|
2560 | filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ1(ifile),[],j1_civ1(j)); |
---|
2561 | if ~exist(filename,'file') |
---|
2562 | A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,i1_civ1(ifile),movieobject1); |
---|
2563 | imwrite(A,filename,'BitDepth',16); |
---|
2564 | end |
---|
2565 | filecell.ima1.civ1(ifile,j)={filename}; |
---|
2566 | filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ1(ifile),[],j2_civ1(j)); |
---|
2567 | if ~exist(filename,'file') |
---|
2568 | A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,i2_civ1(ifile),movieobject2); |
---|
2569 | imwrite(A,filename,'BitDepth',16); |
---|
2570 | end |
---|
2571 | filecell.ima2.civ1(ifile,j)={filename}; |
---|
2572 | end |
---|
2573 | end |
---|
2574 | close(h) |
---|
2575 | end |
---|
2576 | if checkbox(4) %if civ2 is performed |
---|
2577 | h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar |
---|
2578 | for ifile=1:nbfield |
---|
2579 | waitbar(ifile/nbfield); |
---|
2580 | for j=1:nbslice |
---|
2581 | filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ2(ifile),[],j1_civ2(j)); |
---|
2582 | if ~exist(filename,'file') |
---|
2583 | A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,i1_civ2(ifile)); |
---|
2584 | imwrite(A,filename,'BitDepth',16); |
---|
2585 | end |
---|
2586 | filecell.ima1.civ2(ifile,j)={filename}; |
---|
2587 | filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ2(ifile),[],j2_civ2(j)); |
---|
2588 | if ~exist(filename,'file') |
---|
2589 | A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,i2_civ2(ifile)); |
---|
2590 | imwrite(A,filename,'BitDepth',16); |
---|
2591 | end |
---|
2592 | filecell.ima2.civ2(ifile,j)={filename}; |
---|
2593 | end |
---|
2594 | end |
---|
2595 | close(h); |
---|
2596 | end |
---|
2597 | end |
---|
2598 | end |
---|
2599 | |
---|
2600 | %------------------------------------------------------------------------ |
---|
2601 | % --- determine the list of index pairs of processing file |
---|
2602 | function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=... |
---|
2603 | find_pair_indices(handles,ref_i,ref_j,mode) |
---|
2604 | %------------------------------------------------------------------------ |
---|
2605 | |
---|
2606 | list_civ1=get(handles.ListPairCiv1,'String'); |
---|
2607 | index_civ1=get(handles.ListPairCiv1,'Value'); |
---|
2608 | str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1 |
---|
2609 | if isempty(str_civ1)||isequal(str_civ1,'') |
---|
2610 | msgbox_uvmat('ERROR','no image pair selected for civ1') |
---|
2611 | return |
---|
2612 | end |
---|
2613 | list_civ2=get(handles.ListPairCiv2,'String'); |
---|
2614 | index_civ2=get(handles.ListPairCiv2,'Value'); |
---|
2615 | if index_civ2>length(list_civ2) |
---|
2616 | list_civ2=list_civ1; |
---|
2617 | index_civ2=index_civ1; |
---|
2618 | end |
---|
2619 | str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2 |
---|
2620 | |
---|
2621 | if isequal (mode,'series(Di)') |
---|
2622 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
2623 | num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers |
---|
2624 | num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i)); |
---|
2625 | num_a_civ1=ref_j; |
---|
2626 | num_b_civ1=ref_j; |
---|
2627 | num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i)); |
---|
2628 | num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i)); |
---|
2629 | num_a_civ2=ref_j; |
---|
2630 | num_b_civ2=ref_j; |
---|
2631 | |
---|
2632 | % adjust the first and last field number |
---|
2633 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
2634 | if isnan(lastfield) |
---|
2635 | indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1)); |
---|
2636 | else |
---|
2637 | indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1)); |
---|
2638 | end |
---|
2639 | if length(indsel)>=1 |
---|
2640 | firstind=indsel(1); |
---|
2641 | lastind=indsel(end); |
---|
2642 | set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields |
---|
2643 | set(handles.last_i,'String',num2str(ref_i(lastind))) |
---|
2644 | ref_i=ref_i(indsel); |
---|
2645 | num1_civ1=num1_civ1(indsel); |
---|
2646 | num1_civ2=num1_civ2(indsel); |
---|
2647 | num2_civ1=num2_civ1(indsel); |
---|
2648 | num2_civ2=num2_civ2(indsel); |
---|
2649 | end |
---|
2650 | elseif isequal (mode,'series(Dj)') |
---|
2651 | lastfield_j=str2double(get(handles.nb_field2,'String')); |
---|
2652 | num1_civ1=ref_i;% set of first image numbers |
---|
2653 | num2_civ1=ref_i; |
---|
2654 | num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j)); |
---|
2655 | num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j)); |
---|
2656 | num1_civ2=ref_i; |
---|
2657 | num2_civ2=ref_i; |
---|
2658 | num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j)); |
---|
2659 | num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j)); |
---|
2660 | % adjust the first and last field number |
---|
2661 | if isnan(lastfield_j) |
---|
2662 | indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1)); |
---|
2663 | else |
---|
2664 | indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1)); |
---|
2665 | end |
---|
2666 | if length(indsel)>=1 |
---|
2667 | firstind=indsel(1); |
---|
2668 | lastind=indsel(end); |
---|
2669 | set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields |
---|
2670 | set(handles.last_j,'String',num2str(ref_j(lastind))) |
---|
2671 | ref_j=ref_j(indsel); |
---|
2672 | num_a_civ1=num_a_civ1(indsel); |
---|
2673 | num_b_civ1=num_b_civ1(indsel); |
---|
2674 | num_a_civ2=num_a_civ2(indsel); |
---|
2675 | num_b_civ2=num_b_civ2(indsel); |
---|
2676 | end |
---|
2677 | elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) |
---|
2678 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
2679 | num1_civ1=ref_i; |
---|
2680 | num2_civ1=ref_i; |
---|
2681 | num_a_civ1=displ_num(1,index_civ1); |
---|
2682 | num_b_civ1=displ_num(2,index_civ1); |
---|
2683 | num1_civ2=ref_i; |
---|
2684 | num2_civ2=ref_i; |
---|
2685 | num_a_civ2=displ_num(1,index_civ2); |
---|
2686 | num_b_civ2=displ_num(2,index_civ2); |
---|
2687 | elseif isequal(mode,'displacement') |
---|
2688 | num1_civ1=ref_i; |
---|
2689 | num2_civ1=ref_i; |
---|
2690 | num_a_civ1=ref_j; |
---|
2691 | num_b_civ1=ref_j; |
---|
2692 | num1_civ2=ref_i; |
---|
2693 | num2_civ2=ref_i; |
---|
2694 | num_a_civ2=ref_j; |
---|
2695 | num_b_civ2=ref_j; |
---|
2696 | end |
---|
2697 | |
---|
2698 | %------------------------------------------------------------------------ |
---|
2699 | % --- Executes on button press in ListCompareMode. |
---|
2700 | function ListCompareMode_Callback(hObject, eventdata, handles) |
---|
2701 | %------------------------------------------------------------------------ |
---|
2702 | ListCompareMode=get(handles.ListCompareMode,'String'); |
---|
2703 | option=ListCompareMode{get(handles.ListCompareMode,'Value')}; |
---|
2704 | if ~strcmp(option,'PIV') % case 'displacement' or 'stereo PIV' |
---|
2705 | filebase=get(handles.RootPath,'String'); |
---|
2706 | set(handles.sub_txt,'Visible','on') |
---|
2707 | set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible |
---|
2708 | mode_store=get(handles.ListPairMode,'String');%get the present 'mode' |
---|
2709 | set(handles.ListCompareMode,'UserData',mode_store);%store the mode display |
---|
2710 | set(handles.ListPairMode,'Visible','off') |
---|
2711 | |
---|
2712 | %% open an image file with the browser |
---|
2713 | ind_opening=1;%default |
---|
2714 | browse.incr_pair=[0 0]; %default |
---|
2715 | oldfile=get(handles.RootPath,'String'); |
---|
2716 | menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)'; |
---|
2717 | '*.png','.png image files'; ... |
---|
2718 | '*.jpg',' jpeg image files'; ... |
---|
2719 | '*.tif','.tif image files'; ... |
---|
2720 | '*.avi;*.AVI','.avi movie files'; ... |
---|
2721 | '*.*', 'All Files (*.*)'}; |
---|
2722 | if strcmp(option,'displacement') |
---|
2723 | comment='Pick the reference file for displacements'; |
---|
2724 | else |
---|
2725 | comment='Pick a file of the second series'; |
---|
2726 | end |
---|
2727 | [FileName, PathName] = uigetfile( menu, comment,oldfile); |
---|
2728 | fileinput=[PathName FileName];%complete file name |
---|
2729 | sizf=size(fileinput); |
---|
2730 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
2731 | [path,name,ext]=fileparts(fileinput); |
---|
2732 | [path1]=fileparts(filebase); |
---|
2733 | if isunix |
---|
2734 | [status,path]=system(['readlink ' path]); |
---|
2735 | [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths |
---|
2736 | end |
---|
2737 | if ~strcmp(path1,path) |
---|
2738 | msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one') |
---|
2739 | return |
---|
2740 | end |
---|
2741 | if strcmp(option,'displacement') |
---|
2742 | [tild,RootFile_1]=fileparts(name); |
---|
2743 | else |
---|
2744 | [FilePath,FileName,Ext]=fileparts(fileinput); |
---|
2745 | % detect the file type, get the movie object if relevant, and look for the corresponding file series: |
---|
2746 | % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists |
---|
2747 | [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]); |
---|
2748 | |
---|
2749 | % [tild,tild,RootFile_1,tild,tild,tild,tild,tild,nom_type_1]=fileparts_uvmat(fileinput); |
---|
2750 | %[RootFile_1,i1_series,tild,j1_series,tild,nom_type_1,FileType,Object]=find_file_series(PathName,FileName); |
---|
2751 | %check image nom type |
---|
2752 | if ~strcmp(nom_type_1,get(handles.NomType,'String')) |
---|
2753 | 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') |
---|
2754 | return |
---|
2755 | end |
---|
2756 | end |
---|
2757 | %check image extension |
---|
2758 | if ~strcmp(ext,get(handles.ImaExt,'String')) |
---|
2759 | msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one') |
---|
2760 | return |
---|
2761 | end |
---|
2762 | set(handles.RootFile_1,'String',RootFile_1); |
---|
2763 | else |
---|
2764 | set(handles.ListPairMode,'Visible','on') |
---|
2765 | set(handles.RootFile_1,'Visible','Off'); |
---|
2766 | set(handles.sub_txt,'Visible','off') |
---|
2767 | set(handles.RootFile_1,'String',[]); |
---|
2768 | mode_store=get(handles.ListCompareMode,'UserData'); |
---|
2769 | set(handles.ListPairMode,'Value',1) |
---|
2770 | set(handles.ListPairMode,'String',mode_store) |
---|
2771 | set(handles.CheckStereo,'Value',0) |
---|
2772 | set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default |
---|
2773 | end |
---|
2774 | % if strcmp(option,'stereo PIV') && get(handles.CheckPatch1,'Value') |
---|
2775 | % set(handles.CheckStereo,'Visible','on') |
---|
2776 | % else |
---|
2777 | % set(handles.CheckStereo,'Visible','off') |
---|
2778 | % end |
---|
2779 | % if strcmp(option,'stereo PIV') && get(handles.CheckPatch2,'Value') |
---|
2780 | % set(handles.CheckStereo,'Visible','on') |
---|
2781 | % else |
---|
2782 | % set(handles.CheckStereo,'Visible','off') |
---|
2783 | % end |
---|
2784 | ListPairMode_Callback(hObject, eventdata, handles) |
---|
2785 | |
---|
2786 | |
---|
2787 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
2788 | % Callbacks in the uipanel Pair Indices |
---|
2789 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
2790 | %------------------------------------------------------------------------ |
---|
2791 | % --- Executes on button press in ListPairMode. |
---|
2792 | function ListPairMode_Callback(hObject, eventdata, handles) |
---|
2793 | %------------------------------------------------------------------------ |
---|
2794 | compare_list=get(handles.ListCompareMode,'String'); |
---|
2795 | val=get(handles.ListCompareMode,'Value'); |
---|
2796 | compare=compare_list{val}; |
---|
2797 | if strcmp(compare,'displacement')||strcmp(compare,'shift') |
---|
2798 | mode='displacement'; |
---|
2799 | else |
---|
2800 | mode_list=get(handles.ListPairMode,'String'); |
---|
2801 | if ischar(mode_list) |
---|
2802 | mode_list={mode_list}; |
---|
2803 | end |
---|
2804 | mode_value=get(handles.ListPairMode,'Value'); |
---|
2805 | mode=mode_list{mode_value}; |
---|
2806 | end |
---|
2807 | displ_num=[];%default |
---|
2808 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
2809 | % last_i=str2num(get(handles.last_i,'String')); |
---|
2810 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
2811 | TimeUnit=get(handles.TimeUnit,'String'); |
---|
2812 | checkframe=strcmp(TimeUnit,'frame'); |
---|
2813 | siztime=size(time); |
---|
2814 | nbfield=siztime(1)-1; |
---|
2815 | nbfield2=siztime(2)-1; |
---|
2816 | indchosen=1; %%first pair selected by default |
---|
2817 | %displ_num used to define the indices of the civ pairs |
---|
2818 | % in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices |
---|
2819 | % are relative to the reference indices ref_i and ref_j respectively. |
---|
2820 | if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2') |
---|
2821 | dt=1; |
---|
2822 | displ=''; |
---|
2823 | index=0; |
---|
2824 | numlist_a=[]; |
---|
2825 | numlist_B=[]; |
---|
2826 | %get all the time intervals in bursts |
---|
2827 | displ_dt=1;%default |
---|
2828 | nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10 |
---|
2829 | for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode |
---|
2830 | for numod_b=(numod_a+1):nbfield2 |
---|
2831 | index=index+1; |
---|
2832 | numlist_a(index)=numod_a; |
---|
2833 | numlist_b(index)=numod_b; |
---|
2834 | if size(time,2)>1 && ~checkframe |
---|
2835 | dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%first time interval dt |
---|
2836 | displ_dt(index)=dt(numod_a,numod_b); |
---|
2837 | else |
---|
2838 | displ_dt(index)=1; |
---|
2839 | end |
---|
2840 | end |
---|
2841 | end |
---|
2842 | [dtsort,indsort]=sort(displ_dt); |
---|
2843 | if ~isempty(numlist_a) |
---|
2844 | displ_num(1,:)=numlist_a(indsort); |
---|
2845 | displ_num(2,:)=numlist_b(indsort); |
---|
2846 | end |
---|
2847 | displ_num(3,:)=0; |
---|
2848 | displ_num(4,:)=0; |
---|
2849 | enable_j(handles, 'off') |
---|
2850 | elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') |
---|
2851 | index=1:200; |
---|
2852 | displ_num(1,index)=-floor(index/2); |
---|
2853 | displ_num(2,index)=ceil(index/2); |
---|
2854 | displ_num(3:4,index)=zeros(2,200); |
---|
2855 | enable_j(handles, 'on') |
---|
2856 | elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') |
---|
2857 | index=1:200; |
---|
2858 | displ_num(1:2,index)=zeros(2,200); |
---|
2859 | displ_num(3,index)=-floor(index/2); |
---|
2860 | displ_num(4,index)=ceil(index/2); |
---|
2861 | enable_i(handles, 'on') |
---|
2862 | if nbfield2 > 1 |
---|
2863 | enable_j(handles, 'on') |
---|
2864 | else |
---|
2865 | enable_j(handles, 'off') |
---|
2866 | end |
---|
2867 | elseif isequal(mode,'displacement')%the pairs have the same indices |
---|
2868 | displ_num(1,1)=0; |
---|
2869 | displ_num(2,1)=0; |
---|
2870 | displ_num(3,1)=0; |
---|
2871 | displ_num(4,1)=0; |
---|
2872 | if nbfield > 1 || nbfield==0 |
---|
2873 | enable_i(handles, 'on') |
---|
2874 | else |
---|
2875 | enable_j(handles, 'off') |
---|
2876 | end |
---|
2877 | if nbfield2 > 1 |
---|
2878 | enable_j(handles, 'on') |
---|
2879 | else |
---|
2880 | enable_j(handles, 'off') |
---|
2881 | end |
---|
2882 | end |
---|
2883 | set(handles.ListPairCiv1,'UserData',displ_num); |
---|
2884 | errormsg=find_netcpair_civ( handles,1); |
---|
2885 | if ~isempty(errormsg) |
---|
2886 | msgbox_uvmat('ERROR',errormsg) |
---|
2887 | end |
---|
2888 | % find_netcpair_civ2(handles) |
---|
2889 | |
---|
2890 | function enable_i(handles, state) |
---|
2891 | set(handles.itext,'Visible',state) |
---|
2892 | set(handles.first_i,'Visible',state) |
---|
2893 | set(handles.last_i,'Visible',state) |
---|
2894 | set(handles.incr_i,'Visible',state) |
---|
2895 | set(handles.nb_field,'Visible',state) |
---|
2896 | set(handles.ref_i,'Visible',state) |
---|
2897 | |
---|
2898 | function enable_j(handles, state) |
---|
2899 | set(handles.jtext,'Visible',state) |
---|
2900 | set(handles.first_j,'Visible',state) |
---|
2901 | set(handles.last_j,'Visible',state) |
---|
2902 | set(handles.incr_j,'Visible',state) |
---|
2903 | set(handles.nb_field2,'Visible',state) |
---|
2904 | set(handles.ref_j,'Visible',state) |
---|
2905 | |
---|
2906 | |
---|
2907 | %------------------------------------------------------------------------ |
---|
2908 | % --- Executes on selection change in ListPairCiv1. |
---|
2909 | function ListPairCiv1_Callback(hObject, eventdata, handles) |
---|
2910 | %------------------------------------------------------------------------ |
---|
2911 | %reproduce by default the chosen pair in the checkciv2 menu |
---|
2912 | list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs |
---|
2913 | index_pair=get(handles.ListPairCiv1,'Value'); |
---|
2914 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
2915 | % num_a=displ_num(1,index_pair); |
---|
2916 | % num_b=displ_num(2,index_pair); |
---|
2917 | list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs |
---|
2918 | if index_pair<=length(list_pair2) |
---|
2919 | set(handles.ListPairCiv2,'Value',index_pair); |
---|
2920 | end |
---|
2921 | |
---|
2922 | %update first_i and last_i according to the chosen image pairs |
---|
2923 | mode_list=get(handles.ListPairMode,'String'); |
---|
2924 | mode_value=get(handles.ListPairMode,'Value'); |
---|
2925 | mode=mode_list{mode_value}; |
---|
2926 | if isequal(mode,'series(Di)') |
---|
2927 | first_i=str2double(get(handles.first_i,'String')); |
---|
2928 | last_i=str2double(get(handles.last_i,'String')); |
---|
2929 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
2930 | num1=first_i:incr_i:last_i; |
---|
2931 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
2932 | if ~isnan(lastfield) |
---|
2933 | test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ... |
---|
2934 | (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield); |
---|
2935 | num1=num1(test_find); |
---|
2936 | end |
---|
2937 | set(handles.first_i,'String',num2str(num1(1))); |
---|
2938 | set(handles.last_i,'String',num2str(num1(end))); |
---|
2939 | elseif isequal(mode,'series(Dj)') |
---|
2940 | first_j=str2double(get(handles.first_j,'String')); |
---|
2941 | last_j=str2double(get(handles.last_j,'String')); |
---|
2942 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
2943 | num_j=first_j:incr_j:last_j; |
---|
2944 | lastfield2=str2double(get(handles.nb_field2,'String')); |
---|
2945 | if ~isnan(lastfield2) |
---|
2946 | test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... |
---|
2947 | (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); |
---|
2948 | num1=num_j(test_find); |
---|
2949 | end |
---|
2950 | set(handles.first_j,'String',num2str(num1(1))); |
---|
2951 | set(handles.last_j,'String',num2str(num1(end))); |
---|
2952 | end |
---|
2953 | |
---|
2954 | %------------------------------------------------------------------------ |
---|
2955 | % --- Executes on selection change in ListPairCiv2. |
---|
2956 | function ListPairCiv2_Callback(hObject, eventdata, handles) |
---|
2957 | %------------------------------------------------------------------------ |
---|
2958 | index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu |
---|
2959 | |
---|
2960 | %update first_i and last_i according to the chosen image pairs |
---|
2961 | mode_list=get(handles.ListPairMode,'String'); |
---|
2962 | mode_value=get(handles.ListPairMode,'Value'); |
---|
2963 | mode=mode_list{mode_value}; |
---|
2964 | if isequal(mode,'series(Di)') |
---|
2965 | first_i=str2double(get(handles.first_i,'String')); |
---|
2966 | last_i=str2double(get(handles.last_i,'String')); |
---|
2967 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
2968 | num1=first_i:incr_i:last_i; |
---|
2969 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
2970 | if ~isnan(lastfield) |
---|
2971 | test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ... |
---|
2972 | (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield); |
---|
2973 | num1=num1(test_find); |
---|
2974 | end |
---|
2975 | set(handles.first_i,'String',num2str(num1(1))); |
---|
2976 | set(handles.last_i,'String',num2str(num1(end))); |
---|
2977 | elseif isequal(mode,'series(Dj)') |
---|
2978 | first_j=str2double(get(handles.first_j,'String')); |
---|
2979 | last_j=str2double(get(handles.last_j,'String')); |
---|
2980 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
2981 | num_j=first_j:incr_j:last_j; |
---|
2982 | lastfield2=str2double(get(handles.nb_field2,'String')); |
---|
2983 | if ~isnan(lastfield2) |
---|
2984 | test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... |
---|
2985 | (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); |
---|
2986 | num1=num_j(test_find); |
---|
2987 | end |
---|
2988 | set(handles.first_j,'String',num2str(num1(1))); |
---|
2989 | set(handles.last_j,'String',num2str(num1(end))); |
---|
2990 | end |
---|
2991 | |
---|
2992 | %------------------------------------------------------------------------ |
---|
2993 | function ref_i_Callback(hObject, eventdata, handles) |
---|
2994 | %------------------------------------------------------------------------ |
---|
2995 | mode_list=get(handles.ListPairMode,'String'); |
---|
2996 | mode_value=get(handles.ListPairMode,'Value'); |
---|
2997 | mode=mode_list{mode_value}; |
---|
2998 | errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files |
---|
2999 | if isequal(mode,'series(Di)') || ...% we do patch2 only |
---|
3000 | (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) |
---|
3001 | errormsg=find_netcpair_civ( handles,2); |
---|
3002 | end |
---|
3003 | if ~isempty(errormsg) |
---|
3004 | msgbox_uvmat('ERROR',errormsg) |
---|
3005 | end |
---|
3006 | |
---|
3007 | %------------------------------------------------------------------------ |
---|
3008 | function ref_j_Callback(hObject, eventdata, handles) |
---|
3009 | %------------------------------------------------------------------------ |
---|
3010 | mode_list=get(handles.ListPairMode,'String'); |
---|
3011 | mode_value=get(handles.ListPairMode,'Value'); |
---|
3012 | mode=mode_list{mode_value}; |
---|
3013 | if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)') |
---|
3014 | errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files |
---|
3015 | end |
---|
3016 | if isequal(mode,'series(Dj)') || ... |
---|
3017 | (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) |
---|
3018 | errormsg=find_netcpair_civ(handles,2); |
---|
3019 | end |
---|
3020 | if ~isempty(errormsg) |
---|
3021 | msgbox_uvmat('ERROR',errormsg) |
---|
3022 | end |
---|
3023 | |
---|
3024 | %------------------------------------------------------------------------ |
---|
3025 | % determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of |
---|
3026 | % the field series set by first_i, incr, last_i |
---|
3027 | % index=1: look for pairs for civ1 |
---|
3028 | % index=2: look for pairs for civ2 |
---|
3029 | function errormsg=find_netcpair_civ(handles,index) |
---|
3030 | %------------------------------------------------------------------------ |
---|
3031 | set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock) |
---|
3032 | |
---|
3033 | %% initialisation |
---|
3034 | errormsg=''; |
---|
3035 | browse=get(handles.RootPath,'UserData'); |
---|
3036 | compare_list=get(handles.ListCompareMode,'String'); |
---|
3037 | val=get(handles.ListCompareMode,'Value'); |
---|
3038 | compare=compare_list{val}; |
---|
3039 | if strcmp(compare,'displacement')||strcmp(compare,'shift') |
---|
3040 | mode='displacement'; |
---|
3041 | else |
---|
3042 | mode_list=get(handles.ListPairMode,'String'); |
---|
3043 | mode_value=get(handles.ListPairMode,'Value'); |
---|
3044 | if isempty(mode_list) |
---|
3045 | return |
---|
3046 | end |
---|
3047 | mode=mode_list{mode_value}; |
---|
3048 | end |
---|
3049 | nom_type_ima=get(handles.NomType,'String'); |
---|
3050 | |
---|
3051 | %% determine nom_type_nc, nomenclature type of the .nc files: |
---|
3052 | [nom_type_nc]=nomtype2pair(nom_type_ima,mode); |
---|
3053 | |
---|
3054 | %% reads .nc subdirectoy and image numbers from the interface |
---|
3055 | subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data |
---|
3056 | subdir_civ2=get(handles.SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data |
---|
3057 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
3058 | if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') |
---|
3059 | ref_j=0; |
---|
3060 | else |
---|
3061 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
3062 | if isnan(ref_j) |
---|
3063 | ref_j=1; |
---|
3064 | end |
---|
3065 | end |
---|
3066 | time=get(handles.ImaDoc,'UserData');%get the set of times |
---|
3067 | TimeUnit=get(handles.TimeUnit,'String'); |
---|
3068 | checkframe=strcmp(TimeUnit,'frame'); |
---|
3069 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
3070 | |
---|
3071 | %% eliminate the first pairs inconsistent with the position |
---|
3072 | if isempty(displ_num) |
---|
3073 | nbpair=0; |
---|
3074 | else |
---|
3075 | nbpair=length(displ_num(1,:));%nbre of displayed pairs |
---|
3076 | if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') |
---|
3077 | nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index |
---|
3078 | elseif isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
3079 | nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index |
---|
3080 | end |
---|
3081 | end |
---|
3082 | nbpair=min(200,nbpair);%limit the number of displayed pairs to 200 |
---|
3083 | |
---|
3084 | %% case with no Civ1 operation, netcdf files need to exist for reading |
---|
3085 | displ_pair={''}; |
---|
3086 | select=ones(size(1:nbpair));%flag for displayed pairs =1 for display |
---|
3087 | testpair=0; |
---|
3088 | RootPath=get(handles.RootPath,'String'); |
---|
3089 | RootFile=get(handles.RootFile,'String'); |
---|
3090 | if index==1 % case civ1 |
---|
3091 | if ~get(handles.CheckCiv1,'Value') % |
---|
3092 | if ~exist(fullfile(RootPath,subdir_civ1),'dir') |
---|
3093 | errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']; |
---|
3094 | set(handles.ListPairCiv1,'String',{}); |
---|
3095 | return |
---|
3096 | end |
---|
3097 | for ipair=1:nbpair |
---|
3098 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,... |
---|
3099 | ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair)); |
---|
3100 | select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist |
---|
3101 | end |
---|
3102 | % case of no displayed pair |
---|
3103 | if isequal(select,zeros(size(1:nbpair))) |
---|
3104 | if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0]) |
---|
3105 | num_i1=ref_i-floor(browse.incr_pair(1)/2); |
---|
3106 | num_i2=ref_i+ceil(browse.incr_pair(1)/2); |
---|
3107 | num_j1=ref_j-floor(browse.incr_pair(2)/2); |
---|
3108 | num_j2=ref_j+ceil(browse.incr_pair(2)/2); |
---|
3109 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2); |
---|
3110 | select(1)=exist(filename,'file')==2; |
---|
3111 | testpair=1; |
---|
3112 | else |
---|
3113 | if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
3114 | errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]; |
---|
3115 | else |
---|
3116 | errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1]; |
---|
3117 | end |
---|
3118 | set(handles.ListPairCiv1,'String',{''}); |
---|
3119 | %COMPLETER CAS STEREO |
---|
3120 | return |
---|
3121 | end |
---|
3122 | end |
---|
3123 | end |
---|
3124 | else %case civ2 alone |
---|
3125 | if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value') |
---|
3126 | if ~exist(fullfile(RootPath,subdir_civ2,ext_dir),'dir') |
---|
3127 | errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist']) |
---|
3128 | set(handles.ListPairCiv2,'Value',1); |
---|
3129 | set(handles.ListPairCiv2,'String',{''}); |
---|
3130 | return |
---|
3131 | end |
---|
3132 | for ipair=1:nbpair |
---|
3133 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,... |
---|
3134 | ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair)); |
---|
3135 | select(ipair)=exist(filename,'file')==2; |
---|
3136 | end |
---|
3137 | if isequal(select,zeros(size(1:nbpair))) |
---|
3138 | if isfield(browse,'incr_pair') |
---|
3139 | num_i1=ref_i-floor(browse.incr_pair(1)/2); |
---|
3140 | num_i2=ref_i+floor((browse.incr_pair(1)+1)/2); |
---|
3141 | num_j1=ref_j-floor(browse.incr_pair(2)/2); |
---|
3142 | num_j2=ref_j+floor((browse.incr_pair(2)+1)/2); |
---|
3143 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2); |
---|
3144 | select(1)=exist(filename,'file')==2; |
---|
3145 | else |
---|
3146 | if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
3147 | errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2]; |
---|
3148 | else |
---|
3149 | errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2]; |
---|
3150 | end |
---|
3151 | set(handles.ListPairCiv2,'Value',1); |
---|
3152 | set(handles.ListPairCiv2,'String',{''}); |
---|
3153 | return |
---|
3154 | end |
---|
3155 | end |
---|
3156 | end |
---|
3157 | end |
---|
3158 | |
---|
3159 | %% determine the menu display in .ListPairCiv1 |
---|
3160 | % the menu depends on the mode defined in ListPairMode_callback through the array displ_num: |
---|
3161 | % displ_num(1,:)=indices j1 |
---|
3162 | % displ_num(2,:)=indices j2 |
---|
3163 | % displ_num(3,:)=indices i1 |
---|
3164 | % displ_num(4,:)=indices i2 |
---|
3165 | % in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices |
---|
3166 | % are relative to the reference indices ref_i and ref_j respectively. |
---|
3167 | if isequal(mode,'series(Di)') |
---|
3168 | if testpair |
---|
3169 | displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; |
---|
3170 | else |
---|
3171 | for ipair=1:nbpair |
---|
3172 | if select(ipair) |
---|
3173 | displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))]; |
---|
3174 | %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 |
---|
3175 | % 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 |
---|
3176 | 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 |
---|
3177 | 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 |
---|
3178 | else |
---|
3179 | dt=1; |
---|
3180 | end |
---|
3181 | displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; |
---|
3182 | else |
---|
3183 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
3184 | end |
---|
3185 | end |
---|
3186 | end |
---|
3187 | elseif isequal(mode,'series(Dj)') |
---|
3188 | if testpair |
---|
3189 | displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; |
---|
3190 | else |
---|
3191 | for ipair=1:nbpair |
---|
3192 | if select(ipair) |
---|
3193 | displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))]; |
---|
3194 | if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair) |
---|
3195 | 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 |
---|
3196 | displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; |
---|
3197 | end |
---|
3198 | else |
---|
3199 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
3200 | end |
---|
3201 | end |
---|
3202 | end |
---|
3203 | elseif isequal(mode,'pair j1-j2')%case of pairs |
---|
3204 | for ipair=1:nbpair |
---|
3205 | if select(ipair) |
---|
3206 | if ~checkframe && size(time,2)>1 |
---|
3207 | 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 |
---|
3208 | else % time set by default to i index |
---|
3209 | dt=1; |
---|
3210 | end |
---|
3211 | displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ... |
---|
3212 | ' :dt= ' num2str(dt*1000)]; |
---|
3213 | else |
---|
3214 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
3215 | end |
---|
3216 | end |
---|
3217 | elseif isequal(mode,'displacement') |
---|
3218 | displ_pair={'Di=Dj=0'}; |
---|
3219 | end |
---|
3220 | if index==1 |
---|
3221 | set(handles.ListPairCiv1,'String',displ_pair'); |
---|
3222 | end |
---|
3223 | |
---|
3224 | %% determine the default selection in the pair menu |
---|
3225 | ichoice=find(select,1);% index of selected pair |
---|
3226 | if (isempty(ichoice) || ichoice < 1); ichoice=1; end; |
---|
3227 | initial=get(handles.ListPairCiv1,'Value');%initial choice of pair |
---|
3228 | if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1)) |
---|
3229 | set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu |
---|
3230 | end |
---|
3231 | initial=get(handles.ListPairCiv2,'Value'); |
---|
3232 | if initial>length(displ_pair')%|~isequal(select(initial),1) |
---|
3233 | if ichoice <= length(displ_pair') |
---|
3234 | set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2 |
---|
3235 | else |
---|
3236 | set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2 |
---|
3237 | end |
---|
3238 | end |
---|
3239 | set(handles.ListPairCiv2,'String',displ_pair'); |
---|
3240 | set(gcf,'Pointer','arrow') |
---|
3241 | |
---|
3242 | |
---|
3243 | |
---|
3244 | % %------------------------------------------------------------------------ |
---|
3245 | % % call 'view_field.fig' to display the field selected in the list of 'status' |
---|
3246 | % function open_view_field(hObject, eventdata) |
---|
3247 | % %------------------------------------------------------------------------ |
---|
3248 | % list=get(hObject,'String'); |
---|
3249 | % index=get(hObject,'Value'); |
---|
3250 | % rootroot=get(hObject,'UserData'); |
---|
3251 | % filename=list{index}; |
---|
3252 | % ind_dot=strfind(filename,'...'); |
---|
3253 | % filename=filename(1:ind_dot-1); |
---|
3254 | % filename=fullfile(rootroot,filename); |
---|
3255 | % delete(get(hObject,'parent'))%delete the display figure to stop the check process |
---|
3256 | % if exist(filename,'file')%visualise the vel field if it exists |
---|
3257 | % uvmat(filename) |
---|
3258 | % set(gcbo,'Value',1) |
---|
3259 | % end |
---|
3260 | |
---|
3261 | |
---|
3262 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3263 | % Callbacks in the uipanel Reference Indices |
---|
3264 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3265 | %------------------------------------------------------------------------ |
---|
3266 | function first_i_Callback(hObject, eventdata, handles) |
---|
3267 | %------------------------------------------------------------------------ |
---|
3268 | first_i=str2double(get(handles.first_i,'String')); |
---|
3269 | set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index |
---|
3270 | ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt) |
---|
3271 | |
---|
3272 | %------------------------------------------------------------------------ |
---|
3273 | function first_j_Callback(hObject, eventdata, handles) |
---|
3274 | %------------------------------------------------------------------------ |
---|
3275 | first_j=str2num(get(handles.first_j,'String')); |
---|
3276 | set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index |
---|
3277 | ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt) |
---|
3278 | |
---|
3279 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3280 | % Callbacks in the uipanel Civ1 |
---|
3281 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3282 | %------------------------------------------------------------------------ |
---|
3283 | % --- Executes on button press in SearchRange: determine the search range num_Searchx,num_Searchy |
---|
3284 | function SearchRange_Callback(hObject, eventdata, handles) |
---|
3285 | %------------------------------------------------------------------------ |
---|
3286 | %determine pair numbers |
---|
3287 | if strcmp(get(handles.num_UMin,'Visible'),'off') |
---|
3288 | set(handles.u_title,'Visible','on') |
---|
3289 | set(handles.v_title,'Visible','on') |
---|
3290 | set(handles.num_UMin,'Visible','on') |
---|
3291 | set(handles.num_UMax,'Visible','on') |
---|
3292 | set(handles.num_VMin,'Visible','on') |
---|
3293 | set(handles.num_VMax,'Visible','on') |
---|
3294 | set(handles.CoordUnit,'Visible','on') |
---|
3295 | set(handles.TimeUnit,'Visible','on') |
---|
3296 | set(handles.slash_title,'Visible','on') |
---|
3297 | set(handles.min_title,'Visible','on') |
---|
3298 | set(handles.max_title,'Visible','on') |
---|
3299 | set(handles.unit_title,'Visible','on') |
---|
3300 | else |
---|
3301 | get_search_range(hObject, eventdata, handles) |
---|
3302 | end |
---|
3303 | |
---|
3304 | %------------------------------------------------------------------------ |
---|
3305 | % --- determine the search range num_Searchx,num_Searchy and shift |
---|
3306 | function get_search_range(hObject, eventdata, handles) |
---|
3307 | %------------------------------------------------------------------------ |
---|
3308 | param_civ1=read_GUI(handles.Civ1); |
---|
3309 | umin=param_civ1.UMin; |
---|
3310 | umax=param_civ1.UMax; |
---|
3311 | vmin=param_civ1.VMin; |
---|
3312 | vmax=param_civ1.VMax; |
---|
3313 | %switch min_title and max_title in case of error |
---|
3314 | if umax<=umin |
---|
3315 | umin_old=umin; |
---|
3316 | umin=umax; |
---|
3317 | umax=umin_old; |
---|
3318 | set(handles.num_UMin,'String', num2str(umin)) |
---|
3319 | set(handles.num_UMax,'String', num2str(umax)) |
---|
3320 | end |
---|
3321 | if vmax<=vmin |
---|
3322 | vmin_old=vmin; |
---|
3323 | vmin=vmax; |
---|
3324 | vmax=vmin_old; |
---|
3325 | set(handles.num_VMin,'String', num2str(vmin)) |
---|
3326 | set(handles.num_VMax,'String', num2str(vmax)) |
---|
3327 | end |
---|
3328 | if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax)) |
---|
3329 | list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs |
---|
3330 | index=get(handles.ListPairCiv1,'Value'); |
---|
3331 | pair_string=list_pair{index}; |
---|
3332 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
3333 | pxcm=get(handles.SearchRange,'UserData'); |
---|
3334 | mode_list=get(handles.ListPairMode,'String'); |
---|
3335 | mode_value=get(handles.ListPairMode,'Value'); |
---|
3336 | mode=mode_list{mode_value}; |
---|
3337 | if isequal (mode, 'series(Di)' ) |
---|
3338 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
3339 | num1=ref_i-floor(index/2);% first image numbers |
---|
3340 | num2=ref_i+ceil(index/2); |
---|
3341 | num_a=1; |
---|
3342 | num_b=1; |
---|
3343 | elseif isequal (mode, 'series(Dj)') |
---|
3344 | num1=1; |
---|
3345 | num2=1; |
---|
3346 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
3347 | num_a=ref_j-floor(index/2);% first image numbers |
---|
3348 | num_b=ref_j+ceil(index/2); |
---|
3349 | elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) |
---|
3350 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
3351 | num1=ref_i; |
---|
3352 | num2=ref_i; |
---|
3353 | r=regexp(pair_string,'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names'); |
---|
3354 | if isempty(r) |
---|
3355 | r=regexp(pair_string,'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names'); |
---|
3356 | end |
---|
3357 | num_a=str2num(r.num1); |
---|
3358 | num_b=str2num(r.num2); |
---|
3359 | end |
---|
3360 | dt=time(num2+1,num_b+1)-time(num1+1,num_a+1); |
---|
3361 | ibx=str2double(get(handles.num_Bx,'String')); |
---|
3362 | iby=str2double(get(handles.num_By,'String')); |
---|
3363 | umin=dt*pxcm*umin; |
---|
3364 | umax=dt*pxcm*umax; |
---|
3365 | vmin=dt*pxcm*vmin; |
---|
3366 | vmax=dt*pxcm*vmax; |
---|
3367 | shiftx=round((umin+umax)/2); |
---|
3368 | shifty=round((vmin+vmax)/2); |
---|
3369 | isx=(umax+2-shiftx)*2+param_civ1.Bx; |
---|
3370 | isx=2*ceil(isx/2)+1; |
---|
3371 | isy=(vmax+2-shifty)*2+param_civ1.Bx; |
---|
3372 | isy=2*ceil(isy/2)+1; |
---|
3373 | set(handles.num_Shiftx,'String',num2str(shiftx)); |
---|
3374 | set(handles.num_Shifty,'String',num2str(shifty)); |
---|
3375 | set(handles.num_Searchx,'String',num2str(isx)); |
---|
3376 | set(handles.num_Searchy,'String',num2str(isy)); |
---|
3377 | end |
---|
3378 | |
---|
3379 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3380 | % Callbacks in the uipanel Fix1 |
---|
3381 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3382 | %------------------------------------------------------------------------ |
---|
3383 | % --- Executes on button press in CheckMask. |
---|
3384 | function get_mask_fix1_Callback(hObject, eventdata, handles) |
---|
3385 | %------------------------------------------------------------------------ |
---|
3386 | maskval=get(handles.CheckMask,'Value'); |
---|
3387 | if isequal(maskval,0) |
---|
3388 | set(handles.Mask,'String','') |
---|
3389 | else |
---|
3390 | mask_displ='no mask'; %default |
---|
3391 | filebase=get(handles.RootPath,'String'); |
---|
3392 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
3393 | if isequal(flag_mask,1) |
---|
3394 | mask_displ=[num2str(nbslice) 'mask']; |
---|
3395 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
3396 | filebase_a=get(handles.RootFile_1,'String'); |
---|
3397 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
3398 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
3399 | mask_displ='no mask'; |
---|
3400 | end |
---|
3401 | end |
---|
3402 | if isequal(mask_displ,'no mask') |
---|
3403 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3404 | {'*.png', ' (*.png)'; |
---|
3405 | '*.png', '.png files '; ... |
---|
3406 | '*.*', 'All Files (*.*)'}, ... |
---|
3407 | 'Pick a mask file *.png',filebase); |
---|
3408 | mask_displ=fullfile(PathName,FileName); |
---|
3409 | if ~exist(mask_displ,'file') |
---|
3410 | mask_displ='no mask'; |
---|
3411 | end |
---|
3412 | end |
---|
3413 | if isequal(mask_displ,'no mask') |
---|
3414 | set(handles.CheckMask,'Value',0) |
---|
3415 | set(handles.CheckMask,'Value',0) |
---|
3416 | set(handles.CheckMask,'Value',0) |
---|
3417 | else |
---|
3418 | %set(handles.CheckMask,'Value',1) |
---|
3419 | set(handles.CheckMask,'Value',1) |
---|
3420 | end |
---|
3421 | set(handles.Mask,'String',mask_displ) |
---|
3422 | set(handles.Mask,'String',mask_displ) |
---|
3423 | set(handles.Mask,'String',mask_displ) |
---|
3424 | end |
---|
3425 | |
---|
3426 | %------------------------------------------------------------------------ |
---|
3427 | % --- Executes on button press in CheckMask: select box for mask option |
---|
3428 | function get_mask_civ2_Callback(hObject, eventdata, handles) |
---|
3429 | %------------------------------------------------------------------------ |
---|
3430 | maskval=get(handles.CheckMask,'Value'); |
---|
3431 | if isequal(maskval,0) |
---|
3432 | set(handles.Mask,'String','') |
---|
3433 | else |
---|
3434 | mask_displ='no mask'; %default |
---|
3435 | filebase=get(handles.RootPath,'String'); |
---|
3436 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
3437 | if isequal(flag_mask,1) |
---|
3438 | mask_displ=[num2str(nbslice) 'mask']; |
---|
3439 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
3440 | filebase_a=get(handles.RootFile_1,'String'); |
---|
3441 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
3442 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
3443 | mask_displ='no mask'; |
---|
3444 | end |
---|
3445 | end |
---|
3446 | if isequal(mask_displ,'no mask') |
---|
3447 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3448 | {'*.png', ' (*.png)'; |
---|
3449 | '*.png', '.png files '; ... |
---|
3450 | '*.*', 'All Files (*.*)'}, ... |
---|
3451 | 'Pick a mask file *.png',filebase); |
---|
3452 | mask_displ=fullfile(PathName,FileName); |
---|
3453 | if ~exist(mask_displ,'file') |
---|
3454 | mask_displ='no mask'; |
---|
3455 | end |
---|
3456 | end |
---|
3457 | if isequal(mask_displ,'no mask') |
---|
3458 | set(handles.CheckMask,'Value',0) |
---|
3459 | set(handles.CheckMask,'Value',0) |
---|
3460 | else |
---|
3461 | set(handles.CheckMask,'Value',1) |
---|
3462 | end |
---|
3463 | set(handles.Mask,'String',mask_displ) |
---|
3464 | set(handles.Mask,'String',mask_displ) |
---|
3465 | end |
---|
3466 | |
---|
3467 | %------------------------------------------------------------------------ |
---|
3468 | % --- Executes on button press in CheckMask. |
---|
3469 | function get_mask_fix2_Callback(hObject, eventdata, handles) |
---|
3470 | %------------------------------------------------------------------------ |
---|
3471 | maskval=get(handles.CheckMask,'Value'); |
---|
3472 | if isequal(maskval,0) |
---|
3473 | set(handles.Mask,'String','') |
---|
3474 | else |
---|
3475 | mask_displ='no mask'; %default |
---|
3476 | filebase=get(handles.RootPath,'String'); |
---|
3477 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
3478 | if isequal(flag_mask,1) |
---|
3479 | mask_displ=[num2str(nbslice) 'mask']; |
---|
3480 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
3481 | filebase_a=get(handles.RootFile_1,'String'); |
---|
3482 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
3483 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
3484 | mask_displ='no mask'; |
---|
3485 | end |
---|
3486 | end |
---|
3487 | if isequal(mask_displ,'no mask') |
---|
3488 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3489 | {'*.png', ' (*.png)'; |
---|
3490 | '*.png', '.png files '; ... |
---|
3491 | '*.*', 'All Files (*.*)'}, ... |
---|
3492 | 'Pick a mask file *.png',filebase); |
---|
3493 | mask_displ=fullfile(PathName,FileName); |
---|
3494 | if ~exist(mask_displ,'file') |
---|
3495 | mask_displ='no mask'; |
---|
3496 | end |
---|
3497 | end |
---|
3498 | if isequal(mask_displ,'no mask') |
---|
3499 | set(handles.CheckMask,'Value',0) |
---|
3500 | end |
---|
3501 | set(handles.Mask,'String',mask_displ) |
---|
3502 | end |
---|
3503 | |
---|
3504 | %------------------------------------------------------------------------ |
---|
3505 | % --- function called to look for mask files |
---|
3506 | function [nbslice, flag_mask]=get_mask(filebase,handles) |
---|
3507 | %------------------------------------------------------------------------ |
---|
3508 | %detect mask files, images with appropriate file base |
---|
3509 | %[filebase '_' xx 'mask'], xx=nbslice |
---|
3510 | %flag_mask=1 indicates detection |
---|
3511 | |
---|
3512 | flag_mask=0;%default |
---|
3513 | nbslice=1; |
---|
3514 | |
---|
3515 | % subdir=get(handles.SubdirCiv1,'String'); |
---|
3516 | [Path,Name]=fileparts(filebase); |
---|
3517 | if ~isdir(Path) |
---|
3518 | msgbox_uvmat('ERROR','no path for input files') |
---|
3519 | return |
---|
3520 | end |
---|
3521 | % currentdir=pwd; |
---|
3522 | % cd(Path);%move in the dir of the root name filebase |
---|
3523 | maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files |
---|
3524 | % cd(currentdir);%come back to the current working directory |
---|
3525 | if ~isempty(maskfiles) |
---|
3526 | % msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat') |
---|
3527 | % else |
---|
3528 | flag_mask=1; |
---|
3529 | maskname=maskfiles(1).name;% take the first mask file in the list |
---|
3530 | [Path2,Name,ext]=fileparts(maskname); |
---|
3531 | Namedouble=double(Name); |
---|
3532 | val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters |
---|
3533 | ind_mask=findstr('mask',Name); |
---|
3534 | i=ind_mask-1; |
---|
3535 | while val(i)==0 && i>0 |
---|
3536 | i=i-1; |
---|
3537 | end |
---|
3538 | nbslice=str2double(Name(i+1:ind_mask-1)); |
---|
3539 | if ~isnan(nbslice) && Name(i)=='_' |
---|
3540 | flag_mask=1; |
---|
3541 | else |
---|
3542 | msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2]) |
---|
3543 | return |
---|
3544 | nbslice=1; |
---|
3545 | end |
---|
3546 | end |
---|
3547 | |
---|
3548 | %------------------------------------------------------------------------ |
---|
3549 | % --- function called to look for grid files |
---|
3550 | function [nbslice, flag_mask]=get_grid(filebase,handles) |
---|
3551 | %------------------------------------------------------------------------ |
---|
3552 | flag_mask=0;%default |
---|
3553 | nbslice=1; |
---|
3554 | [Path,Name]=fileparts(filebase); |
---|
3555 | currentdir=pwd; |
---|
3556 | cd(Path);%move in the dir of the root name filebase |
---|
3557 | maskfiles=dir([Name '_*grid_*.grid']);%look for mask files |
---|
3558 | cd(currentdir);%come back to the current working directory |
---|
3559 | if ~isempty(maskfiles) |
---|
3560 | flag_mask=1; |
---|
3561 | maskname=maskfiles(1).name;% take the first mask file in the list |
---|
3562 | [Path2,Name,ext]=fileparts(maskname); |
---|
3563 | Namedouble=double(Name); |
---|
3564 | val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters |
---|
3565 | ind_mask=findstr('grid',Name); |
---|
3566 | i=ind_mask-1; |
---|
3567 | while val(i)==0 && i>0 |
---|
3568 | i=i-1; |
---|
3569 | end |
---|
3570 | nbslice=str2double(Name(i+1:ind_mask-1)); |
---|
3571 | if ~isnan(nbslice) && Name(i)=='_' |
---|
3572 | flag_mask=1; |
---|
3573 | else |
---|
3574 | msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2]) |
---|
3575 | return |
---|
3576 | nbslice=1; |
---|
3577 | end |
---|
3578 | end |
---|
3579 | |
---|
3580 | %------------------------------------------------------------------------ |
---|
3581 | % --- transform numbers to letters |
---|
3582 | function str=num2stra(num,nom_type) |
---|
3583 | %------------------------------------------------------------------------ |
---|
3584 | if isempty(nom_type) |
---|
3585 | str=''; |
---|
3586 | elseif strcmp(nom_type(end),'a') |
---|
3587 | str=char(96+num); |
---|
3588 | elseif strcmp(nom_type(end),'A') |
---|
3589 | str=char(96+num); |
---|
3590 | elseif isempty(nom_type(2:end))%a single index |
---|
3591 | str=''; |
---|
3592 | else |
---|
3593 | str=num2str(num); |
---|
3594 | end |
---|
3595 | |
---|
3596 | %------------------------------------------------------------------------ |
---|
3597 | % --- Executes on button press in ListSubdirCiv1. |
---|
3598 | function ListSubdirCiv1_Callback(hObject, eventdata, handles) |
---|
3599 | %------------------------------------------------------------------------ |
---|
3600 | list_subdir_civ1=get(handles.ListSubdirCiv1,'String'); |
---|
3601 | val=get(handles.ListSubdirCiv1,'Value'); |
---|
3602 | SubDir=list_subdir_civ1{val}; |
---|
3603 | if strcmp(SubDir,'new...') |
---|
3604 | if get(handles.CheckCiv1,'Value') |
---|
3605 | SubDir='CIV'; %default subdirectory |
---|
3606 | else |
---|
3607 | msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation') |
---|
3608 | return |
---|
3609 | end |
---|
3610 | end |
---|
3611 | set(handles.SubdirCiv1,'String',SubDir); |
---|
3612 | errormsg=find_netcpair_civ(handles,1); |
---|
3613 | if ~isempty(errormsg) |
---|
3614 | msgbox_uvmat('ERROR',errormsg) |
---|
3615 | end |
---|
3616 | |
---|
3617 | %------------------------------------------------------------------------ |
---|
3618 | % --- Executes on button press in ListSubdirCiv2. |
---|
3619 | function ListSubdirCiv2_Callback(hObject, eventdata, handles) |
---|
3620 | %------------------------------------------------------------------------ |
---|
3621 | list_subdir_civ2=get(handles.ListSubdirCiv2,'String'); |
---|
3622 | val=get(handles.ListSubdirCiv2,'Value'); |
---|
3623 | SubDir=list_subdir_civ2{val}; |
---|
3624 | if strcmp(SubDir,'new...') |
---|
3625 | if get(handles.CheckCiv2,'Value') |
---|
3626 | SubDir='CIV'; %default subdirectory |
---|
3627 | else |
---|
3628 | msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation') |
---|
3629 | return |
---|
3630 | end |
---|
3631 | end |
---|
3632 | set(handles.SubdirCiv2,'String',SubDir); |
---|
3633 | |
---|
3634 | %------------------------------------------------------------------------ |
---|
3635 | % --- Executes on button press in CheckGrid. |
---|
3636 | function CheckGrid_Callback(hObject, eventdata, handles) |
---|
3637 | %------------------------------------------------------------------------ |
---|
3638 | value=get(hObject,'Value'); |
---|
3639 | hparent=get(hObject,'parent'); |
---|
3640 | hchildren=get(hparent,'children'); |
---|
3641 | handle_txtbox=findobj(hchildren,'tag','txt_Grid'); |
---|
3642 | handle_dx=findobj(hchildren,'tag','num_Dx'); |
---|
3643 | handle_dy=findobj(hchildren,'tag','num_Dy'); |
---|
3644 | handle_title_dx=findobj(hchildren,'tag','title_Dx'); |
---|
3645 | handle_title_dy=findobj(hchildren,'tag','title_Dy'); |
---|
3646 | testgrid=0; |
---|
3647 | filegrid=''; |
---|
3648 | if value |
---|
3649 | filebase=get(handles.RootPath,'String'); |
---|
3650 | [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name |
---|
3651 | if isequal(flag_grid,1) |
---|
3652 | filegrid=[num2str(nbslice) 'grid']; |
---|
3653 | testgrid=1; |
---|
3654 | else % browse for a grid |
---|
3655 | filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData |
---|
3656 | if exist(filegrid,'file') |
---|
3657 | filebase=filegrid; |
---|
3658 | end |
---|
3659 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3660 | {'*.grid', ' (*.grid)'; |
---|
3661 | '*.grid', '.grid files '; ... |
---|
3662 | '*.*', 'All Files (*.*)'}, ... |
---|
3663 | 'Pick a file',filebase); |
---|
3664 | filegrid=fullfile(PathName,FileName); |
---|
3665 | set(hObject,'UserData',filegrid);%store for future use |
---|
3666 | if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file')) |
---|
3667 | testgrid=1; |
---|
3668 | end |
---|
3669 | end |
---|
3670 | end |
---|
3671 | if testgrid |
---|
3672 | set(handle_dx,'Visible','off'); |
---|
3673 | set(handle_dy,'Visible','off'); |
---|
3674 | set(handle_title_dy,'Visible','off'); |
---|
3675 | set(handle_title_dx,'Visible','off'); |
---|
3676 | set(handle_txtbox,'Visible','on') |
---|
3677 | set(handle_txtbox,'String',filegrid) |
---|
3678 | else |
---|
3679 | set(hObject,'Value',0); |
---|
3680 | set(handle_dx,'Visible','on'); |
---|
3681 | set(handle_dy,'Visible','on'); |
---|
3682 | set(handle_title_dy,'Visible','on'); |
---|
3683 | set(handle_title_dx,'Visible','on'); |
---|
3684 | set(handle_txtbox,'Visible','off') |
---|
3685 | end |
---|
3686 | |
---|
3687 | %% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame |
---|
3688 | PanelName=get(hparent,'tag'); |
---|
3689 | if strcmp(PanelName,'Civ1') |
---|
3690 | hchildren=get(handles.Civ2,'children'); |
---|
3691 | handle_checkbox=findobj(hchildren,'tag','CheckGrid'); |
---|
3692 | handle_txtbox=findobj(hchildren,'tag','txt_Grid'); |
---|
3693 | handle_dx=findobj(hchildren,'tag','num_Dx'); |
---|
3694 | handle_dy=findobj(hchildren,'tag','num_Dy'); |
---|
3695 | handle_title_dx=findobj(hchildren,'tag','title_Dx'); |
---|
3696 | handle_title_dy=findobj(hchildren,'tag','title_Dy'); |
---|
3697 | set(handle_checkbox,'UserData',filegrid);%store for future use |
---|
3698 | if testgrid |
---|
3699 | set(handle_checkbox,'Value',1); |
---|
3700 | set(handle_dx,'Visible','off'); |
---|
3701 | set(handle_dy,'Visible','off'); |
---|
3702 | set(handle_title_dx,'Visible','off'); |
---|
3703 | set(handle_title_dy,'Visible','off'); |
---|
3704 | set(handle_txtbox,'Visible','on') |
---|
3705 | set(handle_txtbox,'String',filegrid) |
---|
3706 | % else |
---|
3707 | % set(handle_checkbox,'Value',0); |
---|
3708 | % set(handles.CheckGrid,'Value',0); |
---|
3709 | % set(handle_dx,'Visible','on'); |
---|
3710 | % set(handle_dy,'Visible','on'); |
---|
3711 | % set(handle_title_dx,'Visible','on'); |
---|
3712 | % set(handle_title_dy,'Visible','on'); |
---|
3713 | % set(handle_txtbox,'Visible','off') |
---|
3714 | end |
---|
3715 | end |
---|
3716 | |
---|
3717 | %------------------------------------------------------------------------ |
---|
3718 | % --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..) |
---|
3719 | function CheckMask_Callback(hObject, eventdata, handles) |
---|
3720 | %------------------------------------------------------------------------ |
---|
3721 | value=get(hObject,'Value'); |
---|
3722 | hparent=get(hObject,'parent'); |
---|
3723 | parent_tag=get(hparent,'Tag'); |
---|
3724 | hchildren=get(hparent,'children'); |
---|
3725 | handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel |
---|
3726 | testmask=0; |
---|
3727 | if value |
---|
3728 | filebase=get(handles.RootPath,'String'); |
---|
3729 | [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name |
---|
3730 | if isequal(flag_mask,1) |
---|
3731 | filemask=[num2str(nbslice) 'mask']; |
---|
3732 | testmask=1; |
---|
3733 | else % browse for a mask |
---|
3734 | filemask=get(hObject,'UserData');%look for previous mask name stored as UserData |
---|
3735 | if exist(filemask,'file') |
---|
3736 | filebase=filemask; |
---|
3737 | end |
---|
3738 | [FileName, PathName] = uigetfile( ... |
---|
3739 | {'*.png', ' (*.png)'; |
---|
3740 | '*.png', '.png files '; ... |
---|
3741 | '*.*', 'All Files (*.*)'}, ... |
---|
3742 | 'Pick a mask file *.png',filebase); |
---|
3743 | filemask=fullfile(PathName,FileName); |
---|
3744 | set(hObject,'UserData',filemask);%store for future use |
---|
3745 | if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file')) |
---|
3746 | testmask=1; |
---|
3747 | end |
---|
3748 | end |
---|
3749 | end |
---|
3750 | if testmask |
---|
3751 | if strcmp(parent_tag,'Civ1') |
---|
3752 | set(handles.Mask,'Visible','on') |
---|
3753 | set(handles.Mask,'String',filemask) |
---|
3754 | set(handles.CheckMask,'Value',1) |
---|
3755 | end |
---|
3756 | % switch parent_tag |
---|
3757 | % % case 'Fix1' |
---|
3758 | % % stage=2; |
---|
3759 | % case 'Civ2' |
---|
3760 | % stage=3; |
---|
3761 | % % case 'Fix2' |
---|
3762 | % % stage=4; |
---|
3763 | % end |
---|
3764 | % set(handles.Mask(stage:end),'Visible','on') |
---|
3765 | % set(handles.Mask(stage:end),'String',filemask) |
---|
3766 | % set(handles.CheckMask(stage:end),'Value',1) |
---|
3767 | else |
---|
3768 | set(hObject,'Value',0); |
---|
3769 | set(handle_txtbox,'Visible','off') |
---|
3770 | end |
---|
3771 | |
---|
3772 | |
---|
3773 | % --- Executes on button press in get_gridpatch1. |
---|
3774 | function get_gridpatch1_Callback(hObject, eventdata, handles) |
---|
3775 | filebase=get(handles.RootPath,'String'); |
---|
3776 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3777 | {'*.grid', ' (*.grid)'; |
---|
3778 | '*.grid', '.grid files '; ... |
---|
3779 | '*.*', 'All Files (*.*)'}, ... |
---|
3780 | 'Pick a file',filebase); |
---|
3781 | filegrid=fullfile(PathName,FileName); |
---|
3782 | set(handles.grid_patch1,'string',filegrid); |
---|
3783 | |
---|
3784 | |
---|
3785 | %------------------------------------------------------------------------ |
---|
3786 | % --- Executes on button press in get_gridpatch2. |
---|
3787 | function get_gridpatch2_Callback(hObject, eventdata, handles) |
---|
3788 | %------------------------------------------------------------------------ |
---|
3789 | |
---|
3790 | |
---|
3791 | %------------------------------------------------------------------------ |
---|
3792 | % --- STEREO Interp |
---|
3793 | 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) |
---|
3794 | %------------------------------------------------------------------------ |
---|
3795 | namelog=[filename_nc(1:end-3) '_stinterp.log']; |
---|
3796 | cmd=[stinterpBin ' -f1 ' filename_A_nc ' -f2 ' filename_B_nc ' -f ' filename_nc ... |
---|
3797 | ' -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 |
---|
3798 | |
---|
3799 | %------------------------------------------------------------------------ |
---|
3800 | %--read images and convert them to the uint16 format used for PIV |
---|
3801 | function A=read_image(filename,type_ima,num,movieobject) |
---|
3802 | %------------------------------------------------------------------------ |
---|
3803 | %num is the view number needed for an avi movie |
---|
3804 | switch type_ima |
---|
3805 | case 'movie' |
---|
3806 | A=read(movieobject,num); |
---|
3807 | case 'avi' |
---|
3808 | mov=aviread(filename,num); |
---|
3809 | A=frame2im(mov(1)); |
---|
3810 | case 'multimage' |
---|
3811 | A=imread(filename,num); |
---|
3812 | case 'image' |
---|
3813 | A=imread(filename); |
---|
3814 | end |
---|
3815 | siz=size(A); |
---|
3816 | if length(siz)==3;%color images |
---|
3817 | A=sum(double(A),3); |
---|
3818 | A=uint16(A); |
---|
3819 | end |
---|
3820 | |
---|
3821 | |
---|
3822 | %------------------------------------------------------------------------ |
---|
3823 | % --- Executes on button press in get_ref_fix1. |
---|
3824 | function get_ref_fix1_Callback(hObject, eventdata, handles) |
---|
3825 | %------------------------------------------------------------------------ |
---|
3826 | filebase=get(handles.RootPath,'String'); |
---|
3827 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3828 | {'*.nc', ' (*.nc)'; |
---|
3829 | '*.nc', 'netcdf files '; ... |
---|
3830 | '*.*', 'All Files (*.*)'}, ... |
---|
3831 | 'Pick a file',filebase); |
---|
3832 | |
---|
3833 | fileinput=[PathName FileName]; |
---|
3834 | sizf=size(fileinput); |
---|
3835 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
3836 | %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); |
---|
3837 | [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput); |
---|
3838 | ref.filebase=fullfile(Path,File); |
---|
3839 | % ref.num_a=stra2num(str_a); |
---|
3840 | % ref.num_b=stra2num(str_b); |
---|
3841 | % ref.num1=str2double(field_count); |
---|
3842 | % ref.num2=str2double(str2); |
---|
3843 | browse=[];%initialisation |
---|
3844 | if ~isequal(ref.ext,'.nc') |
---|
3845 | msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') |
---|
3846 | return |
---|
3847 | end |
---|
3848 | set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']); |
---|
3849 | set(handles.ref_fix1,'UserData',ref) |
---|
3850 | menu_field{1}='civ1'; |
---|
3851 | Data=nc2struct(fileinput,[]); |
---|
3852 | if isfield(Data,'patch') && isequal(Data.patch,1) |
---|
3853 | menu_field{2}='filter1'; |
---|
3854 | end |
---|
3855 | if isfield(Data,'civ2') && isequal(Data.civ2,1) |
---|
3856 | menu_field{3}='civ2'; |
---|
3857 | end |
---|
3858 | if isfield(Data,'patch2') && isequal(Data.patch2,1) |
---|
3859 | menu_field{4}='filter2'; |
---|
3860 | end |
---|
3861 | set(handles.field_ref1,'String',menu_field); |
---|
3862 | set(handles.field_ref1,'Value',length(menu_field)); |
---|
3863 | set(handles.num_MinVel,'Value',2); |
---|
3864 | set(handles.num_MinVel,'String','1');%default threshold |
---|
3865 | set(handles.ref_fix1,'Enable','on') |
---|
3866 | |
---|
3867 | %------------------------------------------------------------------------ |
---|
3868 | % --- Executes on button press in get_ref_fix2. |
---|
3869 | function get_ref_fix2_Callback(hObject, eventdata, handles) |
---|
3870 | %------------------------------------------------------------------------ |
---|
3871 | if isequal(get(handles.get_ref_fix2,'Value'),1) |
---|
3872 | filebase=get(handles.RootPath,'String'); |
---|
3873 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3874 | {'*.nc', ' (*.nc)'; |
---|
3875 | '*.nc', 'netcdf files '; ... |
---|
3876 | '*.*', 'All Files (*.*)'}, ... |
---|
3877 | 'Pick a file',filebase); |
---|
3878 | fileinput=[PathName FileName]; |
---|
3879 | sizf=size(fileinput); |
---|
3880 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
3881 | %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); |
---|
3882 | [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput); |
---|
3883 | ref.filebase=fullfile(Path,File); |
---|
3884 | % ref.num_a=stra2num(str_a); |
---|
3885 | % ref.num_b=stra2num(str_b); |
---|
3886 | % ref.num1=str2num(field_count); |
---|
3887 | % ref.num2=str2num(str2); |
---|
3888 | browse=[];%initialisation |
---|
3889 | if ~isequal(ref.ext,'.nc') |
---|
3890 | msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') |
---|
3891 | return |
---|
3892 | end |
---|
3893 | set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']); |
---|
3894 | set(handles.ref_fix2,'UserData',ref) |
---|
3895 | menu_field{1}='civ1'; |
---|
3896 | Data=nc2struct(fileinput,[]); |
---|
3897 | if isfield(Data,'patch') && isequal(Data.patch,1) |
---|
3898 | menu_field{2}='filter1'; |
---|
3899 | end |
---|
3900 | if isfield(Data,'civ2') && isequal(Data.civ2,1) |
---|
3901 | menu_field{3}='civ2'; |
---|
3902 | end |
---|
3903 | if isfield(Data,'patch2') && isequal(Data.patch2,1) |
---|
3904 | menu_field{4}='filter2'; |
---|
3905 | end |
---|
3906 | set(handles.field_ref2,'String',menu_field); |
---|
3907 | set(handles.field_ref2,'Value',length(menu_field)); |
---|
3908 | set(handles.num_MinVel,'Value',2); |
---|
3909 | set(handles.num_MinVel,'String','1');%default threshold |
---|
3910 | set(handles.ref_fix2,'Enable','on') |
---|
3911 | set(handles.ref_fix2,'Visible','on') |
---|
3912 | set(handles.field_ref2,'Visible','on') |
---|
3913 | else |
---|
3914 | set(handles.ref_fix2,'Visible','off') |
---|
3915 | set(handles.field_ref2,'Visible','off') |
---|
3916 | end |
---|
3917 | |
---|
3918 | %------------------------------------------------------------------------ |
---|
3919 | function ref_fix1_Callback(hObject, eventdata, handles) |
---|
3920 | %------------------------------------------------------------------------ |
---|
3921 | set(handles.num_MinVel,'Value',1); |
---|
3922 | set(handles.field_ref1,'Value',1) |
---|
3923 | set(handles.field_ref1,'String',{' '}) |
---|
3924 | set(handles.ref_fix1,'UserData',[]); |
---|
3925 | set(handles.ref_fix1,'String',''); |
---|
3926 | set(handles.thresh_vel1,'String','0'); |
---|
3927 | |
---|
3928 | %------------------------------------------------------------------------ |
---|
3929 | function ref_fix2_Callback(hObject, eventdata, handles) |
---|
3930 | %------------------------------------------------------------------------ |
---|
3931 | set(handles.num_MinVel,'Value',1); |
---|
3932 | set(handles.field_ref2,'Value',1) |
---|
3933 | set(handles.field_ref2,'String',{' '}) |
---|
3934 | set(handles.ref_fix2,'UserData',[]); |
---|
3935 | set(handles.ref_fix2,'String',''); |
---|
3936 | set(handles.num_MinVel,'String','0'); |
---|
3937 | |
---|
3938 | %------------------------------------------------------------------------ |
---|
3939 | % --- TO ABANDON Executes on button press in test_stereo1. |
---|
3940 | function CheckStereo_Callback(hObject, eventdata, handles) |
---|
3941 | %------------------------------------------------------------------------ |
---|
3942 | hparent=get(hObject,'parent'); |
---|
3943 | parent_tag=get(hparent,'Tag'); |
---|
3944 | hchildren=get(hparent,'children'); |
---|
3945 | handle_txtbox=findobj(hchildren,'tag','txt_Mask'); |
---|
3946 | if isequal(get(hObject,'Value'),0) |
---|
3947 | set(handles.num_SubdomainSize,'Visible','on') |
---|
3948 | set(handles.num_SmoothingParam,'Visible','on') |
---|
3949 | else |
---|
3950 | set(handles.num_SubdomainSize,'Visible','off') |
---|
3951 | set(handles.num_SmoothingParam,'Visible','off') |
---|
3952 | end |
---|
3953 | |
---|
3954 | % %------------------------------------------------------------------------ |
---|
3955 | % % --- Executes on button press in CheckStereo. |
---|
3956 | % function StereoCheck_Callback(hObject, eventdata, handles) |
---|
3957 | % %------------------------------------------------------------------------ |
---|
3958 | % if isequal(get(handles.CheckStereo,'Value'),0) |
---|
3959 | % set(handles.num_SubdomainSize,'Visible','on') |
---|
3960 | % set(handles.num_SmoothingParam,'Visible','on') |
---|
3961 | % else |
---|
3962 | % set(handles.num_SubdomainSize,'Visible','off') |
---|
3963 | % set(handles.num_SmoothingParam,'Visible','off') |
---|
3964 | % end |
---|
3965 | |
---|
3966 | %------------------------------------------------------------------------ |
---|
3967 | % --- Executes on button press in TestCiv1: prepare the image correlation function |
---|
3968 | % activated by mouse motion |
---|
3969 | function TestCiv1_Callback(hObject, eventdata, handles) |
---|
3970 | %------------------------------------------------------------------------ |
---|
3971 | drawnow |
---|
3972 | if get(handles.TestCiv1,'Value') |
---|
3973 | set(handles.TestCiv1,'BackgroundColor',[0.7 0.7 0.7])% paint TestCiv1 button to grey to confirm civ launch |
---|
3974 | ref_i=str2double(get(handles.ref_i,'String'));% read reference i index |
---|
3975 | if strcmp(get(handles.ref_j,'Visible'),'on') |
---|
3976 | ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant |
---|
3977 | else |
---|
3978 | ref_j=1;%default j index |
---|
3979 | end |
---|
3980 | [filecell,i1,i2,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=... |
---|
3981 | set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices |
---|
3982 | Data.ListVarName={'ny','nx','A'}; |
---|
3983 | Data.VarDimName= {'ny','nx',{'ny','nx'}}; |
---|
3984 | Data.A=imread(filecell.ima1.civ1{1}); % read the first image |
---|
3985 | if ndims(Data.A)==3 %case of color image |
---|
3986 | Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}}; |
---|
3987 | end |
---|
3988 | Data.ny=[size(Data.A,1) 1]; |
---|
3989 | Data.nx=[1 size(Data.A,2)]; |
---|
3990 | Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly |
---|
3991 | par_civ1=read_GUI(handles.Civ1); |
---|
3992 | par_civ1.ImageWidth=size(Data.A,2); |
---|
3993 | par_civ1.ImageHeight=size(Data.A,1); |
---|
3994 | par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation |
---|
3995 | par_civ1.i1=i1; |
---|
3996 | par_civ1.i2=i2; |
---|
3997 | Param.Civ1=par_civ1; |
---|
3998 | Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV |
---|
3999 | hview_field=view_field(Data); %view the image in the GUI view_field |
---|
4000 | set(0,'CurrentFigure',hview_field) |
---|
4001 | hhview_field=guihandles(hview_field); |
---|
4002 | set(hview_field,'CurrentAxes',hhview_field.axes3) |
---|
4003 | ViewData=get(hview_field,'UserData'); |
---|
4004 | ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field |
---|
4005 | ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field |
---|
4006 | ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory |
---|
4007 | ViewData.axes3.Y=Grid.Civ1_Y; |
---|
4008 | set(hview_field,'UserData',ViewData) |
---|
4009 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
4010 | if isempty(corrfig) |
---|
4011 | corrfig=figure; |
---|
4012 | set(corrfig,'tag','corrfig') |
---|
4013 | set(corrfig,'name','image correlation') |
---|
4014 | set(corrfig,'DeleteFcn',{@closeview_field})% |
---|
4015 | end |
---|
4016 | set(handles.TestCiv1,'BackgroundColor',[1 0 0]) |
---|
4017 | else |
---|
4018 | set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red |
---|
4019 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
4020 | if ~isempty(corrfig) |
---|
4021 | delete(corrfig) |
---|
4022 | end |
---|
4023 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
4024 | if ~isempty(hview_field) |
---|
4025 | delete(hview_field) |
---|
4026 | end |
---|
4027 | end |
---|
4028 | |
---|
4029 | %------------------------------------------------------------------------ |
---|
4030 | %----function introduced for the correlation window figure, activated by deleting this window |
---|
4031 | function closeview_field(gcbo,eventdata) |
---|
4032 | %------------------------------------------------------------------------ |
---|
4033 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
4034 | if ~isempty(hview_field) |
---|
4035 | delete(hview_field) |
---|
4036 | end |
---|
4037 | |
---|
4038 | %------------------------------------------------------------------------ |
---|
4039 | % --- Executes on button press in CheckThreshold. |
---|
4040 | function CheckThreshold_Callback(hObject, eventdata, handles) |
---|
4041 | %------------------------------------------------------------------------ |
---|
4042 | huipanel=get(hObject,'parent'); |
---|
4043 | obj(1)=findobj(huipanel,'Tag','num_MinIma'); |
---|
4044 | obj(2)=findobj(huipanel,'Tag','num_MaxIma'); |
---|
4045 | obj(3)=findobj(huipanel,'Tag','title_Threshold'); |
---|
4046 | if get(hObject,'Value') |
---|
4047 | set(obj,'Visible','on') |
---|
4048 | else |
---|
4049 | set(obj,'Visible','off') |
---|
4050 | end |
---|
4051 | |
---|
4052 | %------------------------------------------------------------------------ |
---|
4053 | function [cmd,errormsg]=cmd_civ1(filename,Param) |
---|
4054 | %------------------------------------------------------------------------ |
---|
4055 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
4056 | %changes : filename_cmx -> filename ( no extension ) |
---|
4057 | cmd=''; |
---|
4058 | filename=regexprep(filename,'.nc',''); %file name for the result |
---|
4059 | if isequal(Param.Civ1.Dt,0) |
---|
4060 | Param.Civ1.Dt=1 ;%case of 'displacement' mode |
---|
4061 | end |
---|
4062 | Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png',''); |
---|
4063 | Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png',''); |
---|
4064 | [fid,errormsg]=fopen([filename '.civ1.cmx'],'w'); |
---|
4065 | if isequal(fid,-1) |
---|
4066 | errormsg=['cmd file ' filename ' cannot be created: ' errormsg]; |
---|
4067 | return |
---|
4068 | end |
---|
4069 | fprintf(fid,['############## CMX file' '\n' ]); |
---|
4070 | fprintf(fid, ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
4071 | fprintf(fid, ['LastImage ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
4072 | fprintf(fid, ['XX' '\n' ]); |
---|
4073 | if isfield(Param.Civ1,'Mask') |
---|
4074 | fprintf(fid, ['Mask ' 'y' '\n' ]); |
---|
4075 | fprintf(fid, ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]); |
---|
4076 | else |
---|
4077 | fprintf(fid, ['Mask ' 'n' '\n' ]); |
---|
4078 | fprintf(fid, ['MaskName ' 'noFile use default' '\n' ]); |
---|
4079 | end |
---|
4080 | fprintf(fid, ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]); %VERIFIER CAS GENERAL ? |
---|
4081 | fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ1.Bx) ' ' num2str(Param.Civ1.By) '\n' ]); |
---|
4082 | fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ1.Searchx) ' ' num2str(Param.Civ1.Searchy) '\n' ]); |
---|
4083 | fprintf(fid, ['RO ' num2str(Param.Civ1.Rho) '\n' ]); |
---|
4084 | if isfield(Param.Civ1,'Grid') |
---|
4085 | fprintf(fid, ['GridSpacing ' '25' ' ' '25' '\n' ]); |
---|
4086 | else |
---|
4087 | fprintf(fid, ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]); |
---|
4088 | end |
---|
4089 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4090 | fprintf(fid, ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]); |
---|
4091 | fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]); |
---|
4092 | fprintf(fid, ['XX 1' '\n' ]); |
---|
4093 | fprintf(fid, ['ShiftXY ' num2str(Param.Civ1.Shiftx) ' ' num2str(Param.Civ1.Shifty) '\n' ]); |
---|
4094 | if isfield(Param.Civ1,'Grid') |
---|
4095 | fprintf(fid, ['Grid ' 'y' '\n' ]); |
---|
4096 | fprintf(fid, ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]); |
---|
4097 | else |
---|
4098 | fprintf(fid, ['Grid ' 'n' '\n' ]); |
---|
4099 | fprintf(fid, ['GridName ' 'noFile use default' '\n' ]); |
---|
4100 | end |
---|
4101 | fprintf(fid, ['XX 85' '\n' ]); |
---|
4102 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4103 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4104 | fprintf(fid, ['Hart 1' '\n' ]); |
---|
4105 | fprintf(fid, [ 'DecimalShift 0' '\n' ]); |
---|
4106 | fprintf(fid, ['Deformation 0' '\n' ]); |
---|
4107 | fprintf(fid, ['CorrelationMin 0' '\n' ]); |
---|
4108 | fprintf(fid, ['IntensityMin 0' '\n' ]); |
---|
4109 | if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated |
---|
4110 | fprintf(fid, ['SeuilImage n' '\n' ]); |
---|
4111 | fprintf(fid, ['SeuilImageValues 0 4096' '\n' ]);%not used in principle |
---|
4112 | else% Image threshold activated |
---|
4113 | if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma) |
---|
4114 | Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default |
---|
4115 | end |
---|
4116 | fprintf(fid, ['SeuilImage y' '\n' ]); |
---|
4117 | fprintf(fid, ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]); |
---|
4118 | end |
---|
4119 | fprintf(fid, ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ? |
---|
4120 | fprintf(fid, ['ImageUsedBefore null null' '\n' ]); |
---|
4121 | fclose(fid); |
---|
4122 | |
---|
4123 | if(isunix) %unix (or Mac) system |
---|
4124 | cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file |
---|
4125 | cmd=[cmd Param.xml.Civ1Bin ' -f ' filename '.cmx >' filename '.civ1.log \n ' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx |
---|
4126 | cmd=[cmd 'rm ' filename '.cmx']; |
---|
4127 | else %Windows system |
---|
4128 | filename=regexprep(filename,'\\','\\\\'); |
---|
4129 | cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n ']; |
---|
4130 | cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')... |
---|
4131 | '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file |
---|
4132 | cmd=[cmd 'del "' filename '.cmx"']; |
---|
4133 | end |
---|
4134 | |
---|
4135 | |
---|
4136 | function cmd=cmd_fix(filename,Param,fixname) |
---|
4137 | %% |
---|
4138 | switch fixname |
---|
4139 | case 'Fix1' |
---|
4140 | fi2_value=num2str(Param.(fixname).CheckF2); |
---|
4141 | case 'Fix2' |
---|
4142 | fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why... |
---|
4143 | end |
---|
4144 | filename=regexprep(filename,'.nc',''); |
---|
4145 | MaskName_string='';%default |
---|
4146 | MaxVel_string='';%default |
---|
4147 | if ~isempty(Param.(fixname).MaxVel) |
---|
4148 | MaxVel_string=[' -threshV ' num2str(Param.(fixname).MaxVel)]; |
---|
4149 | end |
---|
4150 | if isunix |
---|
4151 | cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ... |
---|
4152 | ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ... |
---|
4153 | ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string... |
---|
4154 | ' >' filename '.' lower(fixname) '.log 2>&1']; |
---|
4155 | else |
---|
4156 | cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)... |
---|
4157 | ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ... |
---|
4158 | ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string... |
---|
4159 | ' > "' filename '.' lower(fixname) '.log"']; |
---|
4160 | cmd=regexprep(cmd,'\\','\\\\'); |
---|
4161 | end |
---|
4162 | |
---|
4163 | |
---|
4164 | function cmd=cmd_patch(filename,Param,patchname) |
---|
4165 | %% ------------------------------------------------------------------------ |
---|
4166 | filename=regexprep(filename,'.nc',''); |
---|
4167 | if isunix |
---|
4168 | cmd=[Param.xml.PatchBin... |
---|
4169 | ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)... |
---|
4170 | ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)... |
---|
4171 | ' -nopt ' num2str(Param.(patchname).SubdomainSize) ... |
---|
4172 | ' > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file |
---|
4173 | else |
---|
4174 | cmd=['"' Param.xml.PatchBin... |
---|
4175 | '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)... |
---|
4176 | ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)... |
---|
4177 | ' -nopt ' num2str(Param.(patchname).SubdomainSize)... |
---|
4178 | ' > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file |
---|
4179 | cmd=regexprep(cmd,'\\','\\\\'); |
---|
4180 | end |
---|
4181 | |
---|
4182 | %------------------------------------------------------------------------ |
---|
4183 | % --- CheckCiv2 CheckCiv2 CheckCiv2 CheckCiv2 |
---|
4184 | function [cmd,errormsg]=cmd_civ2(filename,Param) |
---|
4185 | %------------------------------------------------------------------------ |
---|
4186 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
4187 | % global civ2Bin sge%name of the executable for checkciv1 calculation |
---|
4188 | cmd=''; |
---|
4189 | filename=regexprep(filename,'.nc',''); |
---|
4190 | if isequal(Param.Civ2.Dt,'0') |
---|
4191 | Param.Civ2.Dt='1' ;%case of 'displacement' mode |
---|
4192 | end |
---|
4193 | Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png',''); |
---|
4194 | Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ? |
---|
4195 | [fid,errormsg]=fopen([filename '.civ2.cmx'],'w'); |
---|
4196 | if isequal(fid,-1) |
---|
4197 | return |
---|
4198 | end |
---|
4199 | fprintf(fid,['############## CMX file' '\n' ]); |
---|
4200 | fprintf(fid, ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
4201 | fprintf(fid, ['LastImage ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
4202 | fprintf(fid, ['XX' '\n' ]); |
---|
4203 | if isfield(Param.Civ2,'Mask') |
---|
4204 | fprintf(fid, ['Mask ' 'y' '\n' ]); |
---|
4205 | fprintf(fid, ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]); |
---|
4206 | else |
---|
4207 | fprintf(fid, ['Mask ' 'n' '\n' ]); |
---|
4208 | fprintf(fid, ['MaskName ' 'noFile use default' '\n' ]); |
---|
4209 | end |
---|
4210 | % fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]); |
---|
4211 | % fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
4212 | fprintf(fid, ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); |
---|
4213 | % fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]); %VERIFIER CAS GENERAL ? |
---|
4214 | fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n' ]); |
---|
4215 | fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n']); |
---|
4216 | fprintf(fid, ['RO ' num2str(Param.Civ2.Rho) '\n']); |
---|
4217 | if isfield(Param.Civ2,'Grid') |
---|
4218 | fprintf(fid, ['GridSpacing ' '25' ' ' '25' '\n' ]); |
---|
4219 | else |
---|
4220 | fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]); |
---|
4221 | end |
---|
4222 | % fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']); |
---|
4223 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4224 | fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]); |
---|
4225 | fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]); |
---|
4226 | fprintf(fid, ['XX 1' '\n' ]); |
---|
4227 | fprintf(fid, 'ShiftXY 0 0\n'); |
---|
4228 | if isfield(Param.Civ2,'Grid') |
---|
4229 | fprintf(fid, ['Grid ' 'y' '\n' ]); |
---|
4230 | fprintf(fid, ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]); |
---|
4231 | else |
---|
4232 | fprintf(fid, ['Grid ' 'n' '\n' ]); |
---|
4233 | fprintf(fid, ['GridName ' 'noFile use default' '\n' ]); |
---|
4234 | end |
---|
4235 | % fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]); |
---|
4236 | % fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']); |
---|
4237 | fprintf(fid, ['XX 85' '\n' ]); |
---|
4238 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4239 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4240 | fprintf(fid, ['Hart 1' '\n' ]); |
---|
4241 | fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']); |
---|
4242 | fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']); |
---|
4243 | fprintf(fid, ['CorrelationMin 0' '\n' ]); |
---|
4244 | fprintf(fid, ['IntensityMin 0' '\n' ]); |
---|
4245 | |
---|
4246 | if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated |
---|
4247 | fprintf(fid, ['SeuilImage n' '\n' ]); |
---|
4248 | fprintf(fid, ['SeuilImageValues 0 4096' '\n' ]);%not used in principle |
---|
4249 | else% Image threshold activated |
---|
4250 | if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma) |
---|
4251 | Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default |
---|
4252 | end |
---|
4253 | fprintf(fid, ['SeuilImage y' '\n' ]); |
---|
4254 | fprintf(fid, ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]); |
---|
4255 | end |
---|
4256 | fprintf(fid, ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ? |
---|
4257 | fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']); |
---|
4258 | fclose(fid); |
---|
4259 | |
---|
4260 | if(isunix) |
---|
4261 | cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'... |
---|
4262 | Param.xml.Civ2Bin ' -f ' filename '.cmx >' filename '.civ2.log \n '... % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx |
---|
4263 | 'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx |
---|
4264 | else |
---|
4265 | filename=regexprep(filename,'\\','\\\\'); |
---|
4266 | cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'... |
---|
4267 | '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename '.cmx" >"' filename '.civ2.log" \n'... |
---|
4268 | 'del "' filename '.cmx" \n']; |
---|
4269 | end |
---|
4270 | |
---|
4271 | %------------------------------------------------------------------------ |
---|
4272 | % --- CheckCiv1 Unified: TO ABADON |
---|
4273 | function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par) |
---|
4274 | %------------------------------------------------------------------------ |
---|
4275 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
4276 | %global CivBin%name of the executable for checkciv1 calculation |
---|
4277 | |
---|
4278 | civ1.image1=par.ImageA; |
---|
4279 | civ1.image2=par.ImageB; |
---|
4280 | civ1.imageSize_X=par.npx; |
---|
4281 | civ1.imageSize_Y=par.npy; |
---|
4282 | civ1.outputFileName=[filename '.nc']; |
---|
4283 | civ1.correlationBoxesSize_X=par.ibx; |
---|
4284 | civ1.correlationBoxesSize_Y=par.iby; |
---|
4285 | civ1.searchBoxesSize_X=par.isx; |
---|
4286 | civ1.searchBoxesSize_Y=par.isy; |
---|
4287 | civ1.globalShift_X=par.shiftx; |
---|
4288 | civ1.globalShift_Y=par.shifty; |
---|
4289 | civ1.ro=par.rho; |
---|
4290 | civ1.hart='y'; |
---|
4291 | if isequal(par.gridflag,'y') |
---|
4292 | civ1.grid=par.gridname; |
---|
4293 | else |
---|
4294 | civ1.grid='n'; |
---|
4295 | civ1.gridSpacing_X=par.dx; |
---|
4296 | civ1.gridSpacing_Y=par.dy; |
---|
4297 | end |
---|
4298 | if isequal(par.maskflag,'y') |
---|
4299 | civ1.mask=par.maskname; |
---|
4300 | end |
---|
4301 | civ1.dt=par.Dt; |
---|
4302 | civ1.unit='pixel'; |
---|
4303 | civ1.absolut_time_T0=par.Time; |
---|
4304 | civ1.pixcmx='1'; |
---|
4305 | civ1.pixcmy='1'; |
---|
4306 | civ1.convectFlow='n'; |
---|
4307 | |
---|
4308 | xml_civ1_parameters=civ1; |
---|
4309 | |
---|
4310 | %------------------------------------------------------------------------ |
---|
4311 | % --- CheckCiv2 Unified: TO ABADON |
---|
4312 | function civ2=CIV2_CMD_Unified(filename,namelog,par) |
---|
4313 | %------------------------------------------------------------------------ |
---|
4314 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
4315 | %global CivBin%name of the executable for checkciv1 calculation |
---|
4316 | |
---|
4317 | filename=regexprep(filename,'.nc',''); |
---|
4318 | |
---|
4319 | civ2.image1=par.ImageA; |
---|
4320 | civ2.image2=par.ImageB; |
---|
4321 | civ2.imageSize_X=par.npx; |
---|
4322 | civ2.imageSize_Y=par.npy; |
---|
4323 | civ2.inputFileName=[par.filename_nc1 '.nc']; |
---|
4324 | civ2.outputFileName=[filename '.nc']; |
---|
4325 | civ2.correlationBoxesSize_X=par.ibx; |
---|
4326 | civ2.correlationBoxesSize_Y=par.iby; |
---|
4327 | civ2.ro=par.rho; |
---|
4328 | %checkciv2.decimalShift=par.CheckDecimal; |
---|
4329 | %checkciv2.CheckDeformation=par.CheckDeformation; |
---|
4330 | if isequal(par.decimal,'1') |
---|
4331 | civ2.decimalShift='y'; |
---|
4332 | else |
---|
4333 | civ2.decimalShift='n'; |
---|
4334 | end |
---|
4335 | if isequal(par.deformation,'1') |
---|
4336 | civ2.deformation='y'; |
---|
4337 | else |
---|
4338 | civ2.deformation='n'; |
---|
4339 | end |
---|
4340 | if isequal(par.gridflag,'y') |
---|
4341 | civ2.grid=par.gridname; |
---|
4342 | else |
---|
4343 | civ2.grid='n'; |
---|
4344 | civ2.gridSpacing_X=par.dx; |
---|
4345 | civ2.gridSpacing_Y=par.dy; |
---|
4346 | end |
---|
4347 | civ2.gridSpacing_X='10'; |
---|
4348 | civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee |
---|
4349 | if isequal(par.maskflag,'y') |
---|
4350 | civ2.mask=par.maskname; |
---|
4351 | else |
---|
4352 | civ2.mask='n'; |
---|
4353 | end |
---|
4354 | civ2.dt=par.Dt; |
---|
4355 | civ2.unit='pixel'; |
---|
4356 | civ2.absolut_time_T0=par.Time; |
---|
4357 | civ2.pixcmx='1'; |
---|
4358 | civ2.pixcmy='1'; |
---|
4359 | civ2.convectFlow='n'; |
---|
4360 | |
---|
4361 | |
---|
4362 | % --- Executes on button press in TestPatch1. |
---|
4363 | function TestPatch1_Callback(hObject, eventdata, handles) |
---|
4364 | set(handles.TestPatch1,'BackgroundColor',[1 1 0]) |
---|
4365 | drawnow |
---|
4366 | if get(handles.TestPatch1,'Value') |
---|
4367 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
4368 | if strcmp(get(handles.ref_j,'Visible'),'on') |
---|
4369 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
4370 | else |
---|
4371 | ref_j=1;%default |
---|
4372 | end |
---|
4373 | [filecell,i1,i21,j1,j2,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=... |
---|
4374 | set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]); |
---|
4375 | |
---|
4376 | Data.ListVarName={'ny','nx','A'}; |
---|
4377 | Data.VarDimName= {'ny','nx',{'ny','nx'}}; |
---|
4378 | |
---|
4379 | param_patch1=read_GUI(handles.Patch1); |
---|
4380 | param_patch1.CivFile=filecell.nc.civ1{1}; |
---|
4381 | Param.Patch1=param_patch1; |
---|
4382 | for irho=1:7 |
---|
4383 | [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV |
---|
4384 | if ~isempty(errormsg) |
---|
4385 | msgbox_uvmat('ERROR',errormsg) |
---|
4386 | return |
---|
4387 | end |
---|
4388 | SmoothingParam(irho)=Param.Patch1.SmoothingParam; |
---|
4389 | Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0); |
---|
4390 | Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0); |
---|
4391 | DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff)) |
---|
4392 | NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff); |
---|
4393 | Param.Patch1.SmoothingParam=2*Param.Patch1.SmoothingParam; |
---|
4394 | end |
---|
4395 | figure |
---|
4396 | plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r') |
---|
4397 | set(handles.TestPatch1,'BackgroundColor',[1 0 0]) |
---|
4398 | else |
---|
4399 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
4400 | if ~isempty(corrfig) |
---|
4401 | delete(corrfig) |
---|
4402 | end |
---|
4403 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
4404 | if ~isempty(hview_field) |
---|
4405 | delete(hview_field) |
---|
4406 | end |
---|
4407 | end |
---|
4408 | %'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature |
---|
4409 | %--------------------------------------------------------------------- |
---|
4410 | % [nom_type_pair]=nomtype2pair(nom_type,Dti,Dtj); |
---|
4411 | %--------------------------------------------------------------------- |
---|
4412 | |
---|
4413 | % OUTPUT: |
---|
4414 | %nom_type_nc |
---|
4415 | |
---|
4416 | %--------------------------------------------------------------------- |
---|
4417 | % INPUT: |
---|
4418 | % 'nom_type': string defining the kind of nomenclature used: |
---|
4419 | %nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined) |
---|
4420 | %nom_type='*': the same file [filebase ext] contains successive fields (ex avi movies) |
---|
4421 | %nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png'). |
---|
4422 | %nom_type='#' series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif' |
---|
4423 | %nom_type='_i_j' matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png') |
---|
4424 | %nom_type='_i1-i2' from pairs from a single index (e.g. 'aa_45-47.nc') |
---|
4425 | %nom_type='_i_j1-j2'pairs of j indices (e.g. 'aa_45_2-3.nc') |
---|
4426 | %nom_type='_i1-i2_j' pairs of i indices (e.g. 'aa_45-46_2.nc') |
---|
4427 | %nom_type='#a','#A', with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j') |
---|
4428 | %nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif' |
---|
4429 | %nom_type='_%03d', '_%04d', or '_%05d', series of indexed images with _ and numbers completed with zeros to 3, 4 or 5 digits, e.g.'aa_045.tif' |
---|
4430 | %nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE |
---|
4431 | %nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D') |
---|
4432 | %nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D') |
---|
4433 | % Dti: ~=0 if i index pairs are used |
---|
4434 | % Dtj: ~=0 if i index pairs are used |
---|
4435 | |
---|
4436 | function NomTypeNc=nomtype2pair(NomTypeIma,mode) |
---|
4437 | |
---|
4438 | %determine nom_type_nc: |
---|
4439 | NomTypeNc=NomTypeIma;%default |
---|
4440 | switch mode |
---|
4441 | case 'pair j1-j2' |
---|
4442 | if ~isempty(regexp(NomTypeIma,'a$')) |
---|
4443 | NomTypeNc=[NomTypeIma 'b']; |
---|
4444 | elseif ~isempty(regexp(NomTypeIma,'A$')) |
---|
4445 | NomTypeNc=[NomTypeIma 'B']; |
---|
4446 | else |
---|
4447 | r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); |
---|
4448 | if ~isempty(r) |
---|
4449 | NomTypeNc='_1_1-2'; |
---|
4450 | end |
---|
4451 | end |
---|
4452 | case 'series(Dj)' |
---|
4453 | r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); |
---|
4454 | if ~isempty(r) |
---|
4455 | NomTypeNc='_1_1-2'; |
---|
4456 | end |
---|
4457 | case 'series(Di)' |
---|
4458 | r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); |
---|
4459 | if ~isempty(r) |
---|
4460 | NomTypeNc='_1-2_1'; |
---|
4461 | else |
---|
4462 | NomTypeNc='_1-2'; |
---|
4463 | end |
---|
4464 | end |
---|
4465 | |
---|
4466 | function NomType_Callback(hObject, eventdata, handles) |
---|
4467 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
---|
4468 | RootPath=get(handles.RootPath,'String'); |
---|
4469 | RootFile=get(handles.RootFile,'String'); |
---|
4470 | ref_i=str2num(get(handles.ref_i,'String')); |
---|
4471 | ref_j=str2num(get(handles.ref_j,'String')); |
---|
4472 | NomType=get(handles.NomType,'String'); |
---|
4473 | ImaExt=get(handles.ImaExt,'String'); |
---|
4474 | fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j); |
---|
4475 | errormsg=display_file_name(handles,fileinput); |
---|
4476 | if ~isempty(errormsg) |
---|
4477 | msgbox_uvmat('ERROR',errormsg) |
---|
4478 | end |
---|
4479 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
---|
4480 | |
---|
4481 | % --- Executes on selection change in ListProgram. |
---|
4482 | function ListProgram_Callback(hObject, eventdata, handles) |
---|
4483 | ListProgram=get(handles.ListProgram,'String'); |
---|
4484 | Program=ListProgram{get(handles.ListProgram,'value')}; |
---|
4485 | switch Program |
---|
4486 | case 'CivX' |
---|
4487 | set(handles.num_MaxDiff,'Visible','off') |
---|
4488 | set(handles.num_Nx,'Visible','on') |
---|
4489 | set(handles.num_Ny,'Visible','on') |
---|
4490 | set(handles.title_Nx,'Visible','on') |
---|
4491 | set(handles.title_Ny,'Visible','on') |
---|
4492 | set(handles.title_MaxDiff,'Visible','off') |
---|
4493 | set(handles.num_Rho,'Style','edit') |
---|
4494 | set(handles.num_Rho,'String','1') |
---|
4495 | set(handles.BATCH,'Enable','on') |
---|
4496 | set(handles.CheckThreshold,'Visible','off') |
---|
4497 | set(handles.CheckDeformation,'Value',1) |
---|
4498 | set(handles.CheckDecimal,'Value',1) |
---|
4499 | case 'Matlab' |
---|
4500 | set(handles.num_MaxDiff,'Visible','on') |
---|
4501 | set(handles.title_MaxDiff,'Visible','on') |
---|
4502 | set(handles.num_Nx,'Visible','off') |
---|
4503 | set(handles.num_Ny,'Visible','off') |
---|
4504 | set(handles.title_Nx,'Visible','off') |
---|
4505 | set(handles.title_Ny,'Visible','off') |
---|
4506 | set(handles.num_Rho,'Style','popupmenu') |
---|
4507 | set(handles.num_Rho,'Value',1) |
---|
4508 | set(handles.num_Rho,'String',{'1';'2'}) |
---|
4509 | set(handles.CheckThreshold,'Visible','on') |
---|
4510 | set(handles.CheckDeformation,'Value',0)% desactivate (work in progress) |
---|
4511 | set(handles.CheckDecimal,'Value',0)% desactivate (work in progress) |
---|
4512 | end |
---|
4513 | |
---|
4514 | |
---|
4515 | % --- Executes on button press in TestCiv2. |
---|
4516 | function TestCiv2_Callback(hObject, eventdata, handles) |
---|
4517 | |
---|
4518 | |
---|
4519 | |
---|
4520 | function RootFile_Callback(hObject, eventdata, handles) |
---|