1 | |
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2 | %'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch) |
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3 | %------------------------------------------------------------------------ |
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4 | % provides an interface for the software menucivx |
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5 | % function varargout = civ(varargin) |
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6 | % provides an interface for the software menucivx |
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7 | % |
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8 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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9 | % Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr |
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10 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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11 | % This file is part of the toolbox UVMAT. |
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12 | % |
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13 | % UVMAT is free software; you can redistribute it and/or modify |
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14 | % it under the terms of the GNU General Public License as published by |
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15 | % the Free Software Foundation; either version 2 of the License, or |
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16 | % (at your option) any later version. |
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17 | % |
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18 | % UVMAT is distributed in the hope that it will be useful, |
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19 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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20 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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21 | % GNU General Public License (file UVMAT/COPYING.txt) for more details. |
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22 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
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23 | function varargout = civ(varargin) |
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24 | %TODO: search range |
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25 | |
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26 | % Last Modified by GUIDE v2.5 03-Jun-2012 22:16:42 |
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27 | % Begin initialization code - DO NOT EDIT |
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28 | gui_Singleton = 1; |
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29 | gui_State = struct('gui_Name', mfilename, ... |
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30 | 'gui_Singleton', gui_Singleton, ... |
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31 | 'gui_OpeningFcn', @civ_OpeningFcn, ... |
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32 | 'gui_OutputFcn', @civ_OutputFcn, ... |
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33 | 'gui_LayoutFcn', [] , ... |
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34 | 'gui_Callback', []); |
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35 | if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback$','once')) |
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36 | gui_State.gui_Callback = str2func(varargin{1}); |
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37 | end |
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38 | |
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39 | if nargout |
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40 | [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); |
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41 | else |
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42 | gui_mainfcn(gui_State, varargin{:}); |
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43 | end |
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44 | % End initialization code - DO NOT EDIT |
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45 | |
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46 | %------------------------------------------------------------------------ |
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47 | % --- Executes just before civ is made visible. |
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48 | function civ_OpeningFcn(hObject, eventdata, handles, fileinput) |
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49 | %------------------------------------------------------------------------ |
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50 | % This function has no output args, see OutputFcn. |
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51 | |
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52 | %% General settings |
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53 | handles.output = hObject; |
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54 | guidata(hObject, handles); % Update handles structure |
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55 | set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display) |
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56 | |
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57 | %% Adjust the GUI according to the binaries available in PARAM.xml |
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58 | path_civ=fileparts(which('civ')); %path to civ |
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59 | 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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60 | errormsg=[];%default error message |
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61 | xmlfile='PARAM.xml'; |
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62 | if exist(xmlfile,'file') |
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63 | try |
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64 | t=xmltree(xmlfile); |
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65 | sparam=convert(t); |
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66 | catch ME |
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67 | errormsg={' Unable to read the file PARAM.xml defining the civx binaries:';ME.message}; |
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68 | end |
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69 | else |
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70 | errormsg=[xmlfile ' not found: path to civx binaries undefined']; |
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71 | end |
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72 | if ~isempty(errormsg) |
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73 | msgbox_uvmat('WARNING',errormsg); |
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74 | end |
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75 | test_batch=0;%default: ,no batch mode available |
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76 | if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode') |
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77 | test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod |
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78 | end |
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79 | if test_batch==0 |
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80 | set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated) |
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81 | set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated) |
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82 | end |
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83 | if isfield(sparam.RunParam,'CivBin') |
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84 | if ~exist(sparam.RunParam.CivBin,'file') |
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85 | sparam.RunParam.CivBin=fullfile(path_civ,sparam.RunParam.CivBin); |
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86 | end |
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87 | else |
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88 | sparam.RunParam.CivBin=''; |
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89 | end |
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90 | |
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91 | %% load the list of previously browsed files in the upper bar menu Open/ |
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92 | dir_perso=prefdir; % path to the directory .matlab for personal data |
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93 | profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab |
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94 | if exist(profil_perso,'file') |
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95 | h=load (profil_perso); |
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96 | if isfield(h,'MenuFile') |
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97 | for ifile=1:min(length(h.MenuFile),5) |
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98 | eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});']) |
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99 | end |
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100 | end |
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101 | end |
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102 | |
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103 | %% prepare the GUI with parameters from the input file if opened from uvmat |
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104 | if exist('fileinput','var')% && isfield(param,'RootName') && ~isempty(param.RootName) |
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105 | 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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106 | errormsg=display_file_name(handles,fileinput); |
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107 | if ~isempty(errormsg) |
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108 | msgbox_uvmat('ERROR',errormsg) |
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109 | end |
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110 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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111 | end |
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112 | |
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113 | %------------------------------------------------------------------------ |
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114 | % --- Outputs from this function are returned to the command line. |
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115 | function varargout = civ_OutputFcn(hObject, eventdata, handles) |
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116 | %------------------------------------------------------------------------ |
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117 | % Get default command line output from handles structure |
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118 | varargout{1} = handles.output; |
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119 | |
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120 | %------------------------------------------------------------------------ |
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121 | % --- Function activated by the Open/Browse... option in the upper menu bar. |
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122 | function MenuBrowse_Callback(hObject, eventdata, handles) |
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123 | %------------------------------------------------------------------------ |
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124 | %% get the current input root file name to initiate the browser |
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125 | filebase=get(handles.RootPath,'String'); |
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126 | oldfile=''; %default |
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127 | if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name |
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128 | dir_perso=prefdir; |
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129 | profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); |
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130 | if exist(profil_perso,'file') |
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131 | h=load (profil_perso); |
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132 | if isfield(h,'filebase')&& ischar(h.filebase) |
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133 | oldfile=h.filebase; |
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134 | end |
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135 | if isfield(h,'RootPath') && ischar(h.RootPath) |
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136 | oldfile=h.RootPath; |
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137 | end |
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138 | end |
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139 | else |
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140 | oldfile=filebase; |
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141 | end |
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142 | |
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143 | %% get the new input file with the browser |
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144 | menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)'; |
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145 | '*.xml', '.xml files '; ... |
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146 | '*.civ', '.civ files '; ... |
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147 | '*.png','.png image files'; ... |
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148 | '*.jpg',' jpeg image files'; ... |
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149 | '*.tif','.tif image files'; ... |
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150 | '*.avi;*.AVI','.avi movie files'; ... |
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151 | '*.nc','.netcdf files'; ... |
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152 | '*.*', 'All Files (*.*)'}; |
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153 | [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile); |
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154 | fileinput=[PathName FileName];%complete file name |
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155 | sizf=size(fileinput); |
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156 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
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157 | |
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158 | %% case of the xml file opened as input (TODO: check and see whether it is useful) |
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159 | [path,name,ext]=fileparts(fileinput); |
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160 | testeditxml=0; |
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161 | % if isequal(ext,'.xml') |
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162 | % testeditxml=1; |
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163 | % t_browse=xmltree(fileinput); |
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164 | % head_element=get(t_browse,1); |
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165 | % if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc') |
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166 | % testeditxml=0; |
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167 | % end |
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168 | % end |
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169 | % if testeditxml==1 || isequal(ext,'.xls') |
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170 | % heditxml=editxml({fileinput}); |
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171 | % set(heditxml,'Tag','browser') |
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172 | % waitfor(heditxml,'Tag','idle') |
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173 | % if ~ishandle(heditxml) |
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174 | % return |
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175 | % end |
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176 | % attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes'); |
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177 | % set(handles.browse,'UserData',fileinput)% store for future opening with browser |
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178 | % fileinput=get(attr,'UserData'); |
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179 | % if ~exist(fileinput,'file') |
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180 | % return |
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181 | % end |
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182 | % end |
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183 | [tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput); |
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184 | |
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185 | %% prepare the GUI with parameters from the input file |
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186 | 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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187 | errormsg=display_file_name(handles,fileinput); |
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188 | if ~isempty(errormsg) |
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189 | msgbox_uvmat('ERROR',erromsg) |
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190 | end |
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191 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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192 | |
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193 | %------------------------------------------------------------------------ |
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194 | % --- Open again the file whose name has been recorded in MenuFile_1 |
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195 | function MenuFile_1_Callback(hObject, eventdata, handles) |
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196 | %------------------------------------------------------------------------ |
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197 | 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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198 | fileinput=get(handles.MenuFile_1,'Label'); |
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199 | errormsg=display_file_name(handles,fileinput); |
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200 | if ~isempty(errormsg) |
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201 | msgbox_uvmat('ERROR',errormsg) |
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202 | end |
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203 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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204 | |
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205 | % ----------------------------------------------------------------------- |
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206 | % --- Open again the file whose name has been recorded in MenuFile_2 |
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207 | function MenuFile_2_Callback(hObject, eventdata, handles) |
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208 | %------------------------------------------------------------------------ |
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209 | 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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210 | fileinput=get(handles.MenuFile_2,'Label'); |
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211 | errormsg=display_file_name(handles,fileinput); |
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212 | if ~isempty(errormsg) |
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213 | msgbox_uvmat('ERROR',errormsg) |
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214 | end |
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215 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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216 | |
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217 | % ----------------------------------------------------------------------- |
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218 | % --- Open again the file whose name has been recorded in MenuFile_3 |
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219 | function MenuFile_3_Callback(hObject, eventdata, handles) |
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220 | %------------------------------------------------------------------------ |
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221 | 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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222 | fileinput=get(handles.MenuFile_3,'Label'); |
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223 | errormsg=display_file_name(handles,fileinput); |
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224 | if ~isempty(errormsg) |
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225 | msgbox_uvmat('ERROR',errormsg) |
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226 | end |
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227 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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228 | |
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229 | % ----------------------------------------------------------------------- |
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230 | % --- Open again the file whose name has been recorded in MenuFile_4 |
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231 | function MenuFile_4_Callback(hObject, eventdata, handles) |
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232 | %------------------------------------------------------------------------ |
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233 | 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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234 | fileinput=get(handles.MenuFile_4,'Label'); |
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235 | errormsg=display_file_name(handles,fileinput); |
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236 | if ~isempty(errormsg) |
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237 | msgbox_uvmat('ERROR',errormsg) |
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238 | end |
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239 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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240 | |
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241 | % ----------------------------------------------------------------------- |
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242 | % --- Open again the file whose name has been recorded in MenuFile_5 |
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243 | function MenuFile_5_Callback(hObject, eventdata, handles) |
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244 | %------------------------------------------------------------------------ |
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245 | 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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246 | fileinput=get(handles.MenuFile_5,'Label'); |
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247 | errormsg=display_file_name(handles,fileinput); |
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248 | if ~isempty(errormsg) |
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249 | msgbox_uvmat('ERROR',errormsg) |
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250 | end |
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251 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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252 | |
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253 | % ----------------------------------------------------------------------- |
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254 | % ----------------------------------------------------------------------- |
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255 | % --- Open the help html file |
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256 | function MenuHelp_Callback(hObject, eventdata, handles) |
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257 | % ----------------------------------------------------------------------- |
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258 | path_civ=fileparts(which ('civ')); |
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259 | helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html'); |
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260 | if isempty(dir(helpfile)) |
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261 | 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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262 | else |
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263 | addpath (fullfile(path_civ,'uvmat_doc')) |
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264 | web([helpfile '#civ']) |
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265 | end |
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266 | |
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267 | %------------------------------------------------------------------------ |
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268 | % --- Function activated when a new filebase (image series) is introduced |
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269 | function RootPath_Callback(hObject, eventdata, handles) |
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270 | %------------------------------------------------------------------------ |
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271 | 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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272 | RootPath=get(handles.RootPath,'String'); |
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273 | SubdirImages=get(handles.SubdirImages,'String'); |
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274 | RootFile=get(handles.RootFile,'String'); |
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275 | ref_i=str2num(get(handles.ref_i,'String')); |
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276 | ref_j=str2num(get(handles.ref_j,'String')); |
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277 | NomType=get(handles.NomType,'String'); |
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278 | ImaExt=get(handles.ImaExt,'String'); |
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279 | fileinput=fullfile_uvmat(RootPath,SubdirImages,RootFile,ImaExt,NomType,ref_i,[],ref_j); |
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280 | errormsg=display_file_name(handles,fileinput); |
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281 | if ~isempty(errormsg) |
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282 | msgbox_uvmat('ERROR',errormsg) |
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283 | end |
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284 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
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285 | |
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286 | %------------------------------------------------------------------------ |
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287 | % --- general function activated for an input file series |
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288 | function errormsg=display_file_name(handles,fileinput) |
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289 | %------------------------------------------------------------------------ |
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290 | set(handles.ListCompareMode,'Visible','on') |
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291 | errormsg='';%default empty error message |
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292 | drawnow |
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293 | |
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294 | %% enable RUN, BATCH button and 'status' display |
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295 | set(handles.RUN, 'Enable','On') |
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296 | set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color |
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297 | set(handles.BATCH,'Enable','On') |
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298 | set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color |
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299 | if isfield(handles,'status') |
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300 | set(handles.status,'Value',0); %suppress the 'status' display |
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301 | status_Callback([], [], handles) |
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302 | end |
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303 | |
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304 | %% determine nomenclature types and extension of the input files |
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305 | [RootPath,SubDir,RootFile,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput); |
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306 | NomTypeNc='';%default |
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307 | |
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308 | %% case of xml file as input, read the civ parameters |
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309 | ind_opening=0;%default |
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310 | if strcmp(ExtInput,'.xml') |
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311 | Param=xml2struct(fileinput); |
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312 | fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file |
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313 | return |
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314 | end |
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315 | |
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316 | %% case of netcdf file as input, get the civ processing stage and look for a coresponding image |
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317 | if strcmp(ExtInput,'.nc') |
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318 | NomTypeNc=NomTypeInput; |
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319 | if isempty(regexp(NomTypeInput,'[ab|AB|-]')) |
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320 | set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs |
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321 | % [RootPath,SubDir]=fileparts(RootPath); |
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322 | set(handles.RootFile_1,'Visible','On'); |
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323 | else |
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324 | set(handles.ListCompareMode,'Value',1) |
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325 | set(handles.RootFile_1,'Visible','Off'); |
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326 | end |
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327 | 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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328 | if isfield(Data,'Txt') |
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329 | errormsg=Data.Txt; |
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330 | return |
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331 | end |
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332 | % settings for new civ data, |
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333 | if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data, |
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334 | set(handles.ListProgram,'Value',2) %select civ/Matlab by default |
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335 | ListProgram_Callback([],[], handles) |
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336 | if ~isempty(Data.CivStage)%test for civ files |
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337 | ind_opening=Data.CivStage; |
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338 | end |
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339 | if ~isempty(Data.Civ2_ImageB)%get the corresponding input image in the netcdf file |
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340 | imageinput=Data.Civ2_ImageB; |
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341 | [tild,ImaName,ImaExt]=fileparts(Data.Civ2_ImageA); |
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342 | set(handles.RootFile_1,'String',[ImaName ImaExt]) |
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343 | elseif ~isempty(Data.Civ1_ImageB) |
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344 | imageinput=Data.Civ1_ImageB; |
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345 | [tild,ImaName,ImaExt]=fileparts(Data.Civ1_ImageA); |
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346 | set(handles.RootFile_1,'String',[ImaName ImaExt]) |
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347 | end |
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348 | % settings for civx data, |
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349 | elseif ~isempty(Data.absolut_time_T0')% case of civx data, |
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350 | set(handles.ListProgram,'Value',1) %select Cix by default |
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351 | ListProgram_Callback([],[], handles) |
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352 | if ~isempty(Data.fix2) |
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353 | ind_opening=5; |
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354 | elseif ~isempty(Data.civ2) |
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355 | ind_opening=4; |
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356 | elseif ~isempty(Data.patch) |
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357 | ind_opening=3; |
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358 | elseif ~isempty(Data.fix) |
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359 | ind_opening=2; |
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360 | end |
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361 | else |
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362 | errormsg='the input netcdf file is not civ data'; |
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363 | return |
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364 | end |
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365 | % look for the corresponding input images |
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366 | check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$','once'));%detect pair label by letter |
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367 | NomTypeIma=NomTypeInput; |
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368 | if check_letter |
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369 | NomTypeIma=NomTypeInput(1:end-1); |
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370 | else |
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371 | r=regexp(NomTypeIma,'.-(?<num2>\d+)$','names'); |
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372 | if ~isempty(r) |
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373 | NomTypeIma=regexprep(NomTypeIma,['-' r.num2],''); |
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374 | end |
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375 | r=regexp(NomTypeIma,'.-(?<num2>\d+)','names'); |
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376 | if ~isempty(r) |
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377 | NomTypeIma=regexprep(NomTypeIma,['-' r.num2],''); |
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378 | end |
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379 | end |
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380 | imageinput=fullfile_uvmat(RootPath,regexprep(SubDir,'.civ(_?)(\d*)$',''),RootFile,'.png',NomTypeIma,i1,[],j1); |
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381 | end |
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382 | |
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383 | %no corresponding image found, select manually with the browser |
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384 | ImaExt=ExtInput; |
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385 | if ~isempty(NomTypeNc) |
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386 | %no corresponding image found, select manually with the browser |
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387 | if ~exist(imageinput,'file') |
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388 | menu={'*.png;*.jpg;*.tif;*.avi;*.AVI', '(*.png,*.jpg ,*.tif, *.avi,*.AVI)'; |
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389 | '*.png','.png image files'; ... |
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390 | '*.jpg',' jpeg image files'; ... |
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391 | '*.tif','.tif image files'; ... |
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392 | '*.avi;*.AVI','.avi movie files'; ... |
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393 | '*.*', 'All Files (*.*)'}; |
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394 | [FileName, PathName] = uigetfile( menu, 'Pick an input image file',fileparts(fileparts(fileinput))); |
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395 | imageinput=[PathName FileName];%complete file name |
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396 | |
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397 | end |
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398 | fileinput=imageinput; |
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399 | end |
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400 | |
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401 | %% scan the image file series |
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402 | [FilePath,FileName,ImaExt]=fileparts(fileinput); |
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403 | % detect the file type, get the movie object if relevant, and look for the corresponding file series: |
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404 | % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists |
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405 | [RootPath,SubdirImages,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName ImaExt]); |
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406 | |
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407 | switch FileType |
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408 | case {'image','multimage','video','mmreader'} |
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409 | otherwise |
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410 | errormsg='invalid input file: enter an image, a movie or civ .nc file'; |
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411 | return |
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412 | end |
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413 | set(handles.RootPath,'String',RootPath) |
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414 | set(handles.SubdirImages,'String',SubdirImages) |
---|
415 | set(handles.RootFile,'String',RootFile) |
---|
416 | if strcmp(ExtInput,'.nc') |
---|
417 | SubDirCiv=regexprep(SubDir,[SuddirImages '^'],'');%suppress the root SuddirImages; |
---|
418 | else |
---|
419 | SubDirCiv= '.civ'; |
---|
420 | end |
---|
421 | set(handles.SubdirCiv1,'String',SubDirCiv) |
---|
422 | set(handles.SubdirCiv2,'String',SubDirCiv) |
---|
423 | browse=get(handles.RootPath,'UserData'); |
---|
424 | browse.incr_pair=[0 0];%default |
---|
425 | |
---|
426 | %% fill reference indices from the input file indices |
---|
427 | num_ref_i=i1;%efaulmt ref index |
---|
428 | if ~isempty(i2) |
---|
429 | num_ref_i=floor((num_ref_i+i2)/2); |
---|
430 | end |
---|
431 | num_ref_j=j1; |
---|
432 | if ~isempty(j2) |
---|
433 | num_ref_j=floor((num_ref_j+j2)/2); |
---|
434 | end |
---|
435 | |
---|
436 | %% scan the images if a civ file has been opened |
---|
437 | MinIndex_i=min(i1_series(i1_series>0)); |
---|
438 | MinIndex_j=min(j1_series(j1_series>0)); |
---|
439 | MaxIndex_i=max(i1_series(i1_series>0)); |
---|
440 | MaxIndex_j=max(j1_series(j1_series>0)); |
---|
441 | |
---|
442 | %% look for an image documentation file |
---|
443 | ext_imadoc='';%default |
---|
444 | SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.' |
---|
445 | filexml=fullfile(RootPath,[SubDirBase '.xml']);% new convention: xml above the image dir |
---|
446 | if ~exist(filexml,'file') |
---|
447 | filexml=fullfile(RootPath,SubDir,[RootFile '.xml']);%old convention: xml within the image directroy |
---|
448 | end |
---|
449 | RootName=fullfile(RootPath,RootFile); |
---|
450 | if exist(filexml,'file') |
---|
451 | ext_imadoc='.xml'; |
---|
452 | elseif exist(fullfile(RootPath,SubDir,[RootFile '.civ']),'file') |
---|
453 | ext_imadoc='.civ'; |
---|
454 | fileciv=fullfile(RootPath,SubDir,[RootFile '.civ']); |
---|
455 | elseif exist([RootName '.avi'],'file') |
---|
456 | ext_imadoc='.avi'; |
---|
457 | elseif exist([RootName '.AVI'],'file') |
---|
458 | ext_imadoc='.AVI'; |
---|
459 | end |
---|
460 | set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used |
---|
461 | |
---|
462 | %% read the time in the image documentation file |
---|
463 | time=[]; |
---|
464 | TimeUnit=''; %default |
---|
465 | CoordUnit='';%default |
---|
466 | pxcm_search=1; |
---|
467 | if ~isempty(ext_imadoc) |
---|
468 | set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning |
---|
469 | drawnow |
---|
470 | switch ext_imadoc |
---|
471 | case '.xml' |
---|
472 | [XmlData,warntext]=imadoc2struct(filexml); |
---|
473 | ext_ima_read=[]; |
---|
474 | nom_type_read=[]; |
---|
475 | if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file |
---|
476 | %[PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName); |
---|
477 | [tild,tild,tild,tild,tild,tild,tild,tild,nom_type_read]=fileparts_uvmat(XmlData.Heading.ImageName); |
---|
478 | fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file, |
---|
479 | if ~exist(fullname,'file') |
---|
480 | msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist']) |
---|
481 | end |
---|
482 | end |
---|
483 | if isfield(XmlData,'Time') |
---|
484 | time=XmlData.Time; |
---|
485 | %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml |
---|
486 | if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector |
---|
487 | if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once')) |
---|
488 | time=time'; |
---|
489 | MaxIndex_i=MaxIndex_j; |
---|
490 | MaxIndex_j=1; |
---|
491 | end |
---|
492 | end |
---|
493 | end |
---|
494 | if isfield(XmlData,'TimeUnit') |
---|
495 | TimeUnit=XmlData.TimeUnit; |
---|
496 | end |
---|
497 | |
---|
498 | if isfield(XmlData,'GeometryCalib') |
---|
499 | tsai=XmlData.GeometryCalib; |
---|
500 | if isfield(tsai,'fx_fy') |
---|
501 | pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range |
---|
502 | end |
---|
503 | if isfield(tsai,'CoordUnit') |
---|
504 | CoordUnit=tsai.CoordUnit; |
---|
505 | end |
---|
506 | end |
---|
507 | case '.civ'% OBSOLETE: case of .civ image documentation file |
---|
508 | [error,time,TimeUnit,mode,npx,npy]=read_imatext(fileciv); |
---|
509 | if error==2, msgbox_uvmat('WARNING',['no file ' fileciv]); |
---|
510 | elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
---|
511 | end |
---|
512 | nom_type_ima='001a'; |
---|
513 | case {'.avi','.AVI'} |
---|
514 | nom_type_ima='*'; |
---|
515 | ImaExt=ext_imadoc; |
---|
516 | set(handles.ListPairMode,'Value',1); |
---|
517 | set(handles.ListPairMode,'String',{'series(Di)'}) |
---|
518 | dt=0.04;%default |
---|
519 | if exist([RootName ext_imadoc],'file')==2 |
---|
520 | hhh=which('videoreader'); |
---|
521 | if isempty(hhh)%use old video function of matlab |
---|
522 | imainfo=aviinfo([RootName ext_imadoc]);%read infos on the avi movie TO REPLACE mmreader |
---|
523 | dt=1/imainfo.FramesPerSecond;%time interval between successive frames |
---|
524 | MaxIndex_i=imainfo.NumFrames;%number of frames |
---|
525 | % XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)'; |
---|
526 | % nbfield=imainfo.NumFrames; |
---|
527 | % set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec |
---|
528 | % ColorType=imainfo.ImageType;%='truecolor' for color images |
---|
529 | else %use video function videoreader of matlab |
---|
530 | imainfo=get(videoreader([RootName ext_imadoc]));%read infos on the avi movie |
---|
531 | dt=1/imainfo.FrameRate;%time interval between successive frames |
---|
532 | MaxIndex_i=imainfo.NumberOfFrames;%number of frames |
---|
533 | % XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)'; |
---|
534 | % nbfield=imainfo.NumberOfFrames; |
---|
535 | % set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec |
---|
536 | % ColorType='truecolor'; |
---|
537 | end |
---|
538 | |
---|
539 | time=(dt*(0:MaxIndex_i-1))';%list of image times |
---|
540 | TimeUnit='s'; |
---|
541 | end |
---|
542 | set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter |
---|
543 | end |
---|
544 | end |
---|
545 | %% timing display |
---|
546 | %show the reference image edit box if relevant (not needed for movies or in the absence of time information |
---|
547 | if numel(time)>=2 % if there are at least two time values to define dt |
---|
548 | MaxIndex_i=min(size(time,1),MaxIndex_i); |
---|
549 | MaxIndex_j=min(size(time,2),MaxIndex_j); |
---|
550 | time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices) |
---|
551 | time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros |
---|
552 | set(handles.ImaDoc,'UserData',time); %store the matrix of times |
---|
553 | set(handles.dt_unit,'String',['dt in m' TimeUnit]); |
---|
554 | set(handles.TimeUnit,'String',TimeUnit); |
---|
555 | else |
---|
556 | set(handles.ImaDoc,'String',''); %xml file not used for timing |
---|
557 | time=(i1_series(:,1)+0:size(i1_series,1)-1);% time=index i |
---|
558 | time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices |
---|
559 | TimeUnit='frame'; |
---|
560 | end |
---|
561 | set(handles.ImaDoc,'UserData',time); %store the matrix of times |
---|
562 | set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms) |
---|
563 | set(handles.TimeUnit,'String',TimeUnit); |
---|
564 | set(handles.nb_field,'String',num2str(MaxIndex_i)); |
---|
565 | set(handles.nb_field2,'String',num2str(MaxIndex_j)); |
---|
566 | set(handles.CoordUnit,'String',CoordUnit) |
---|
567 | set(handles.SearchRange,'UserData', pxcm_search); |
---|
568 | set(handles.ImaExt,'String',ImaExt) |
---|
569 | set(handles.NomType,'String',NomTypeIma) |
---|
570 | set(handles.ref_i,'String',num2str(num_ref_i)) |
---|
571 | set(handles.ref_j,'String',num2str(num_ref_j)) |
---|
572 | |
---|
573 | %% update i and j index range if a nc file has been opened or pb withmin max image indices: |
---|
574 | % then set first and last to the inputfile index by default |
---|
575 | first_i=str2num(get(handles.first_i,'String')); |
---|
576 | last_i=str2num(get(handles.last_i,'String')); |
---|
577 | if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i) |
---|
578 | set(handles.first_i,'String',num2str(num_ref_i)); |
---|
579 | set(handles.last_i,'String',num2str(num_ref_i));% |
---|
580 | end |
---|
581 | if ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i |
---|
582 | set(handles.first_i,'String',num2str(num_ref_i)); |
---|
583 | set(handles.last_i,'String',num2str(num_ref_i));% |
---|
584 | end |
---|
585 | |
---|
586 | %j index range |
---|
587 | first_j=str2num(get(handles.first_j,'String')); |
---|
588 | last_j=str2num(get(handles.last_i,'String')); |
---|
589 | if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j) |
---|
590 | set(handles.first_j,'String',num2str(num_ref_j)); |
---|
591 | set(handles.last_j,'String',num2str(num_ref_j));% |
---|
592 | elseif ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j |
---|
593 | set(handles.first_j,'String',num2str(num_ref_j)); |
---|
594 | set(handles.last_j,'String',num2str(num_ref_j));% |
---|
595 | end |
---|
596 | |
---|
597 | %% set the civ options depending on the input file content when a nc file has been opened |
---|
598 | ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'}; |
---|
599 | if ind_opening~=0 |
---|
600 | for index = 1:ind_opening |
---|
601 | set(handles.(ListOptions{index}),'value',0) |
---|
602 | end |
---|
603 | end |
---|
604 | for index = ind_opening+2:6 |
---|
605 | set(handles.(ListOptions{index}),'value',0) |
---|
606 | end |
---|
607 | set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1) |
---|
608 | update_CivOptions(handles,ind_opening) |
---|
609 | |
---|
610 | %% set the menus of image pairs and default selection for civ %%%%%%%%%%%%%%%%%%% |
---|
611 | %check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter |
---|
612 | if isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1) |
---|
613 | set(handles.ListPairMode,'Value',1) |
---|
614 | set(handles.ListPairMode,'String',{'series(Di)'}) |
---|
615 | elseif MaxIndex_i==1 && MaxIndex_j>1% simple series in j |
---|
616 | set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'}) |
---|
617 | if MaxIndex_j <= 10 |
---|
618 | set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large |
---|
619 | end |
---|
620 | else |
---|
621 | set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice |
---|
622 | if strcmp(NomTypeNc,'_1-2_1') |
---|
623 | set(handles.ListPairMode,'Value',3)% advise 'series(Di)' |
---|
624 | elseif MaxIndex_j <= 10 |
---|
625 | set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large |
---|
626 | end |
---|
627 | end |
---|
628 | |
---|
629 | %% scan files to update the subdirectory list display |
---|
630 | listot=dir(RootPath);%directory of RootPath |
---|
631 | idir=0; |
---|
632 | listdir={''};%default |
---|
633 | % get the list of existing civ subdirectories in the path of theinput root file |
---|
634 | for ilist=1:length(listot) |
---|
635 | if listot(ilist).isdir |
---|
636 | name=listot(ilist).name; |
---|
637 | if ~isequal(name,'.') && ~isequal(name,'..') |
---|
638 | idir=idir+1; |
---|
639 | listdir{idir,1}=listot(ilist).name; |
---|
640 | end |
---|
641 | end |
---|
642 | end |
---|
643 | |
---|
644 | %% store info |
---|
645 | set(handles.RootPath,'UserData',browse)% store the nomenclature type |
---|
646 | |
---|
647 | %% list the possible index pairs, depending on the option set in ListPairMode |
---|
648 | ListPairMode_Callback([], [], handles) |
---|
649 | |
---|
650 | %% store the root input filename for future opening |
---|
651 | profil_perso=fullfile(prefdir,'uvmat_perso.mat'); |
---|
652 | if exist(profil_perso,'file') |
---|
653 | save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat |
---|
654 | else |
---|
655 | txt=ver('MATLAB'); |
---|
656 | Release=txt.Release; |
---|
657 | relnumb=str2double(Release(3:4)); |
---|
658 | if relnumb >= 14 |
---|
659 | save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat |
---|
660 | else |
---|
661 | save (profil_perso,'RootPath'); %store the root name for future opening of uvmat |
---|
662 | end |
---|
663 | end |
---|
664 | set(handles.RootPath,'BackgroundColor',[1 1 1]) |
---|
665 | |
---|
666 | %------------------------------------------------------------------------ |
---|
667 | % --- Executes on carriage return on the subdir checkciv1 edit window |
---|
668 | function SubdirCiv1_Callback(hObject, eventdata, handles) |
---|
669 | %------------------------------------------------------------------------ |
---|
670 | SubDir=get(handles.SubdirCiv1,'String'); |
---|
671 | menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update |
---|
672 | ichoice=find(strcmp(SubDir,menu_str),1); |
---|
673 | if isempty(ichoice) |
---|
674 | ilist=numel(menu_str); %select 'new...' in the menu |
---|
675 | else |
---|
676 | ilist=ichoice; |
---|
677 | end |
---|
678 | set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu |
---|
679 | if get(handles.CheckCiv1,'Value')% if Civ1 is performed |
---|
680 | set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1 |
---|
681 | % set(handles.ListSubdirCiv2,'Value',ilist) |
---|
682 | else % if Civ1 data already exist |
---|
683 | errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory |
---|
684 | if ~isempty(errormsg) |
---|
685 | msgbox_uvmat('ERROR',errormsg) |
---|
686 | end |
---|
687 | end |
---|
688 | |
---|
689 | %------------------------------------------------------------------------ |
---|
690 | % --- Executes on carriage return on the SubDir checkciv1 edit window |
---|
691 | function SubdirCiv2_Callback(hObject, eventdata, handles) |
---|
692 | %------------------------------------------------------------------------ |
---|
693 | SubDir=get(handles.SubdirCiv1,'String'); |
---|
694 | menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update |
---|
695 | ichoice=find(strcmp(SubDir,menu_str),1); |
---|
696 | if isempty(ichoice) |
---|
697 | ilist=numel(menu_str); %select 'new...' in the menu |
---|
698 | else |
---|
699 | ilist=ichoice; |
---|
700 | end |
---|
701 | set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu |
---|
702 | %update the list of available pairs from netcdf files in the new directory |
---|
703 | if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value') |
---|
704 | errormsg=find_netcpair_civ(handles,2); |
---|
705 | if ~isempty(errormsg) |
---|
706 | msgbox_uvmat('ERROR',errormsg) |
---|
707 | end |
---|
708 | end |
---|
709 | |
---|
710 | %------------------------------------------------------------------------ |
---|
711 | % --- Executes on button press in CheckCiv1. |
---|
712 | function CheckCiv1_Callback(hObject, eventdata, handles) |
---|
713 | %------------------------------------------------------------------------ |
---|
714 | update_CivOptions(handles,0) |
---|
715 | |
---|
716 | %------------------------------------------------------------------------ |
---|
717 | % --- Executes on button press in CheckFix1. |
---|
718 | function CheckFix1_Callback(hObject, eventdata, handles) |
---|
719 | %------------------------------------------------------------------------ |
---|
720 | update_CivOptions(handles,0) |
---|
721 | |
---|
722 | %------------------------------------------------------------------------ |
---|
723 | % --- Executes on button press in CheckPatch1. |
---|
724 | function CheckPatch1_Callback(hObject, eventdata, handles) |
---|
725 | %------------------------------------------------------------------------ |
---|
726 | update_CivOptions(handles,0) |
---|
727 | |
---|
728 | %------------------------------------------------------------------------ |
---|
729 | % --- Executes on button press in CheckCiv2. |
---|
730 | function CheckCiv2_Callback(hObject, eventdata, handles) |
---|
731 | %------------------------------------------------------------------------ |
---|
732 | update_CivOptions(handles,0) |
---|
733 | |
---|
734 | %------------------------------------------------------------------------ |
---|
735 | % --- Executes on button press in CheckFix2. |
---|
736 | function CheckFix2_Callback(hObject, eventdata, handles) |
---|
737 | %------------------------------------------------------------------------ |
---|
738 | update_CivOptions(handles,0) |
---|
739 | |
---|
740 | %------------------------------------------------------------------------ |
---|
741 | % --- Executes on button press in CheckPatch2. |
---|
742 | function CheckPatch2_Callback(hObject, eventdata, handles) |
---|
743 | %------------------------------------------------------------------------ |
---|
744 | update_CivOptions(handles,0) |
---|
745 | |
---|
746 | %------------------------------------------------------------------------ |
---|
747 | % --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2 |
---|
748 | function update_CivOptions(handles,opening) |
---|
749 | %------------------------------------------------------------------------ |
---|
750 | checkbox=zeros(1,6); |
---|
751 | checkbox(1)=get(handles.CheckCiv1,'Value'); |
---|
752 | checkbox(2)=get(handles.CheckFix1,'Value'); |
---|
753 | checkbox(3)=get(handles.CheckPatch1,'Value'); |
---|
754 | checkbox(4)=get(handles.CheckCiv2,'Value'); |
---|
755 | checkbox(5)=get(handles.CheckFix2,'Value'); |
---|
756 | checkbox(6)=get(handles.CheckPatch2,'Value'); |
---|
757 | ind_selected=find(checkbox,1); |
---|
758 | if ~isempty(ind_selected) |
---|
759 | RootPath=get(handles.RootPath,'String'); |
---|
760 | if isempty(RootPath) |
---|
761 | msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...') |
---|
762 | return |
---|
763 | end |
---|
764 | end |
---|
765 | set(handles.PairIndices,'Visible','on') |
---|
766 | set(handles.SubdirCiv1,'Visible','on') |
---|
767 | set(handles.TitleSubdirCiv1,'Visible','on') |
---|
768 | if opening==0 |
---|
769 | errormsg=find_netcpair_civ(handles,1); % select the available netcdf files |
---|
770 | if ~isempty(errormsg) |
---|
771 | msgbox_uvmat('ERROR',errormsg) |
---|
772 | end |
---|
773 | end |
---|
774 | if max(checkbox(4:6))% case of civ2 pair choice needed |
---|
775 | set(handles.TitlePairCiv2,'Visible','on') |
---|
776 | set(handles.TitleSubdirCiv2,'Visible','on') |
---|
777 | set(handles.SubdirCiv2,'Visible','on') |
---|
778 | %set(handles.ListSubdirCiv2,'Visible','on') |
---|
779 | set(handles.ListPairCiv2,'Visible','on') |
---|
780 | if ~opening |
---|
781 | errormsg=find_netcpair_civ(handles,2); % select the available netcdf files |
---|
782 | if ~isempty(errormsg) |
---|
783 | msgbox_uvmat('ERROR',errormsg) |
---|
784 | end |
---|
785 | end |
---|
786 | else |
---|
787 | set(handles.TitleSubdirCiv2,'Visible','off') |
---|
788 | set(handles.SubdirCiv2,'Visible','off') |
---|
789 | set(handles.ListPairCiv2,'Visible','off') |
---|
790 | end |
---|
791 | options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'}; |
---|
792 | for ilist=1:length(options) |
---|
793 | if checkbox(ilist) |
---|
794 | set(handles.(options{ilist}),'Visible','on') |
---|
795 | else |
---|
796 | set(handles.(options{ilist}),'Visible','off') |
---|
797 | end |
---|
798 | end |
---|
799 | |
---|
800 | %------------------------------------------------------------------------ |
---|
801 | % --- Executes on button press in RUN: processing on local computer |
---|
802 | function RUN_Callback(hObject, eventdata, handles) |
---|
803 | %------------------------------------------------------------------------ |
---|
804 | set(handles.RUN, 'Enable','Off') |
---|
805 | set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784]) |
---|
806 | batch=0; |
---|
807 | errormsg=launch_jobs(hObject, eventdata, handles,batch); |
---|
808 | set(handles.RUN, 'Enable','On') |
---|
809 | set(handles.RUN,'BackgroundColor',[1 0 0]) |
---|
810 | |
---|
811 | % display errors or start status callback to visualise results |
---|
812 | if ~isempty(errormsg) |
---|
813 | display(errormsg) |
---|
814 | msgbox_uvmat('ERROR',errormsg) |
---|
815 | elseif isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3) |
---|
816 | set(handles.status,'Value',1);%suppress status display |
---|
817 | status_Callback(hObject, eventdata, handles) |
---|
818 | end |
---|
819 | |
---|
820 | %------------------------------------------------------------------------ |
---|
821 | % --- Executes on button press in BATCH: remote processing |
---|
822 | function BATCH_Callback(hObject, eventdata, handles) |
---|
823 | % ----------------------------------------------------------------------- |
---|
824 | set(handles.BATCH, 'Enable','Off') |
---|
825 | set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784]) |
---|
826 | batch=1; |
---|
827 | errormsg=launch_jobs(hObject, eventdata, handles, batch); |
---|
828 | set(handles.BATCH, 'Enable','On') |
---|
829 | set(handles.BATCH,'BackgroundColor',[1 0 0]) |
---|
830 | |
---|
831 | % display errors or start status callback to visualise results |
---|
832 | if ~isempty(errormsg) |
---|
833 | display(errormsg) |
---|
834 | msgbox_uvmat('ERROR',errormsg) |
---|
835 | elseif isfield(handles,'status') |
---|
836 | set(handles.status,'Value',1);%suppress status display |
---|
837 | status_Callback(hObject, eventdata, handles) |
---|
838 | end |
---|
839 | |
---|
840 | %------------------------------------------------------------------- |
---|
841 | % --- Executes on button press in status. |
---|
842 | function status_Callback(hObject, eventdata, handles) |
---|
843 | %------------------------------------------------------------------- |
---|
844 | val=get(handles.status,'Value'); |
---|
845 | if val==0 |
---|
846 | set(handles.status,'BackgroundColor',[0 1 0]) |
---|
847 | hfig=findobj(allchild(0),'name','civ_status'); |
---|
848 | if ~isempty(hfig) |
---|
849 | delete(hfig) |
---|
850 | end |
---|
851 | return |
---|
852 | end |
---|
853 | set(handles.status,'BackgroundColor',[1 1 0]) |
---|
854 | drawnow |
---|
855 | listtype={'civ1','fix1','patch1','civ2','fix2','patch2'}; |
---|
856 | Param.CheckCiv1=get(handles.CheckCiv1,'Value'); |
---|
857 | Param.CheckFix1=get(handles.CheckFix1,'Value'); |
---|
858 | Param.CheckPatch1=get(handles.CheckPatch1,'Value'); |
---|
859 | Param.CheckCiv2=get(handles.CheckCiv2,'Value'); |
---|
860 | Param.CheckFix2=get(handles.CheckFix2,'Value'); |
---|
861 | Param.CheckPatch2=get(handles.CheckPatch2,'Value'); |
---|
862 | box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2]; |
---|
863 | |
---|
864 | option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test) |
---|
865 | filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV |
---|
866 | test_new=0; |
---|
867 | if ~isfield(filecell,'nc') |
---|
868 | test_new=1; |
---|
869 | [ref_i,ref_j,errormsg]=find_ref_indices(handles); |
---|
870 | if ~isempty(errormsg) |
---|
871 | msgbox_uvmat('ERROR',errormsg) |
---|
872 | return |
---|
873 | end |
---|
874 | filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status |
---|
875 | end |
---|
876 | if ~isequal(box_test(4:6),[0 0 0]) |
---|
877 | civ_files=filecell.nc.civ2;%case of civ2 operations |
---|
878 | else |
---|
879 | civ_files=filecell.nc.civ1; |
---|
880 | end |
---|
881 | [root,filename,ext]=fileparts(civ_files{1}); |
---|
882 | [rootroot,SubDir,extdir]=fileparts(root); |
---|
883 | hfig=findobj(allchild(0),'name','civ_status'); |
---|
884 | if isempty(hfig) |
---|
885 | hfig=figure('DeleteFcn',@stop_status); |
---|
886 | set(hfig,'MenuBar','none')% suppress the menu bar |
---|
887 | set(hfig,'NumberTitle','off')%suppress the fig number in the title |
---|
888 | set(hfig,'name','civ_status') |
---|
889 | set(hfig,'tag','civ_status') |
---|
890 | set(hfig,'UserData',civ_files) |
---|
891 | hlist= uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list'); |
---|
892 | uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...'); |
---|
893 | uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]); |
---|
894 | 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); |
---|
895 | 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); |
---|
896 | BarPosition=[0.05 0.81 0.01 0.05]; |
---|
897 | uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar'); |
---|
898 | drawnow |
---|
899 | end |
---|
900 | set(hrefresh,'UserData',option_civ) |
---|
901 | filepath=fileparts(civ_files{1}); |
---|
902 | set(hlist,'UserData',fileparts(filepath)) |
---|
903 | refresh_GUI(hrefresh,[]) |
---|
904 | |
---|
905 | %------------------------------------------------------------------------ |
---|
906 | % launched by refreshing the status figure |
---|
907 | function refresh_GUI(hObject, eventdata) |
---|
908 | %------------------------------------------------------------------------ |
---|
909 | Tabchar={}; |
---|
910 | BarPosition=[0.05 0.81 0.01 0.05]; |
---|
911 | hfig=get(hObject,'parent'); |
---|
912 | civ_files=get(hfig,'UserData'); |
---|
913 | [filepath,filename,ext]=fileparts(civ_files{1}); |
---|
914 | [tild,SubDir,extdir]=fileparts(filepath); |
---|
915 | SubDir=[SubDir extdir]; |
---|
916 | option_civ=get(hObject,'UserData'); |
---|
917 | nbfiles=numel(civ_files); |
---|
918 | count=0; |
---|
919 | testrecent=0; |
---|
920 | % while count<nbfiles |
---|
921 | count=0; |
---|
922 | datnum=zeros(1,nbfiles); |
---|
923 | for ifile=1:nbfiles |
---|
924 | detect=exist(civ_files{ifile},'file'); % check the existence of the file |
---|
925 | option=0; |
---|
926 | if detect==0 |
---|
927 | option_str='not created'; |
---|
928 | else |
---|
929 | datfile=dir(civ_files{ifile}); |
---|
930 | if isfield(datfile,'datenum') |
---|
931 | datnum(ifile)=datfile.datenum;%only available in recent matlab versions |
---|
932 | testrecent=1; |
---|
933 | end |
---|
934 | filefound(ifile)={datfile.name}; |
---|
935 | lastfield=''; |
---|
936 | % check the content netcdf file |
---|
937 | Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix'); |
---|
938 | option_list={'civ1','fix1','patch1','civ2','fix2','patch2'}; |
---|
939 | if ~isempty(Data.CivStage) |
---|
940 | option=Data.CivStage;%case of Matlab civ |
---|
941 | else |
---|
942 | if ~isempty(Data.patch2) && isequal(Data.patch2,1) |
---|
943 | option=6; |
---|
944 | elseif ~isempty(Data.fix2) && isequal(Data.fix2,1) |
---|
945 | option=5; |
---|
946 | elseif ~isempty(Data.civ2) && isequal(Data.civ2,1); |
---|
947 | option=4; |
---|
948 | elseif ~isempty(Data.patch) && isequal(Data.patch,1); |
---|
949 | option=3; |
---|
950 | elseif ~isempty(Data.fix) && isequal(Data.fix,1); |
---|
951 | option=2; |
---|
952 | else |
---|
953 | option=1; |
---|
954 | end |
---|
955 | end |
---|
956 | option_str=option_list{option}; |
---|
957 | end |
---|
958 | if option >= option_civ |
---|
959 | count=count+1; |
---|
960 | end |
---|
961 | [filepath,filename,ext]=fileparts(civ_files{ifile}); |
---|
962 | Tabchar{ifile,1}=[fullfile(SubDir,filename) ext '...' option_str]; |
---|
963 | end |
---|
964 | datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files |
---|
965 | if isempty(datnum) |
---|
966 | if testrecent |
---|
967 | message='no civ result created yet'; |
---|
968 | else |
---|
969 | message=''; |
---|
970 | end |
---|
971 | else |
---|
972 | datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files |
---|
973 | [first,ind]=min(datnum); |
---|
974 | [last,indlast]=max(datnum); |
---|
975 | % if test_new |
---|
976 | % message='existing file status, no processing launched yet'; |
---|
977 | % else |
---|
978 | message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification: ' cell2mat(filefound(ind)) ' : ' datestr(first)];... |
---|
979 | ['latest modification: ' cell2mat(filefound(indlast)) ' : ' datestr(last)]}; |
---|
980 | % end |
---|
981 | end |
---|
982 | %hfig=findobj(allchild(0),'name','civ_status'); |
---|
983 | % if isempty(hfig)% the status list has been deleted |
---|
984 | % return |
---|
985 | % else |
---|
986 | hlist=findobj(hfig,'tag','list'); |
---|
987 | hmsgbox=findobj(hfig,'tag','msgbox'); |
---|
988 | hwaitbar=findobj(hfig,'tag','waitbar'); |
---|
989 | set(hlist,'String',Tabchar) |
---|
990 | set(hmsgbox,'String', message) |
---|
991 | if count>0 %&& ~test_new |
---|
992 | BarPosition(3)=0.9*count/nbfiles; |
---|
993 | set(hwaitbar,'Position',BarPosition) |
---|
994 | end |
---|
995 | % end |
---|
996 | % [root,filename,ext]=fileparts(civ_files{1}); |
---|
997 | % [rootroot,SubDir,extdir]=fileparts(root); |
---|
998 | % |
---|
999 | % set(hlist,'UserData',rootroot) |
---|
1000 | % if count<10||(nbfiles-count)<10 |
---|
1001 | % pause(.5)% wait 0.5 seconds for next check |
---|
1002 | % else |
---|
1003 | % pause(10)% wait 10 seconds for next check |
---|
1004 | % end |
---|
1005 | % end |
---|
1006 | |
---|
1007 | %------------------------------------------------------------------------ |
---|
1008 | % launched by deleting the status figure |
---|
1009 | function stop_status(hObject, eventdata) |
---|
1010 | %------------------------------------------------------------------------ |
---|
1011 | hciv=findobj(allchild(0),'tag','civ'); |
---|
1012 | hhciv=guidata(hciv); |
---|
1013 | set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ |
---|
1014 | set(hhciv.status,'BackgroundColor',[0 1 0]) |
---|
1015 | |
---|
1016 | %------------------------------------------------------------------------ |
---|
1017 | % launched by pressing OK on the status figure |
---|
1018 | function close_GUI(hObject, eventdata) |
---|
1019 | %------------------------------------------------------------------------ |
---|
1020 | delete(gcbf) |
---|
1021 | |
---|
1022 | |
---|
1023 | %--------------orm---------------------------------------------------------- |
---|
1024 | % --- Main lauch command, called by RUN and BATCH |
---|
1025 | function errormsg=launch_jobs(hObject, eventdata, handles, batch) |
---|
1026 | %----------------------------------------------------------------------- |
---|
1027 | errormsg='';%default |
---|
1028 | |
---|
1029 | %% read the input parameters from the GUI civ |
---|
1030 | Param=read_GUI(handles.civ); |
---|
1031 | |
---|
1032 | %% check the selected list of operations: |
---|
1033 | operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'}; |
---|
1034 | box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2]; |
---|
1035 | index_first=find(box_test==1,1); |
---|
1036 | if isempty(index_first) |
---|
1037 | errormsg='no selected operation'; |
---|
1038 | return |
---|
1039 | end |
---|
1040 | index_last=find(box_test==1,1,'last'); |
---|
1041 | box_used=box_test(index_first : index_last); |
---|
1042 | [box_missing,ind_missing]=min(box_used); |
---|
1043 | if isequal(box_missing,0); %there is a missing step in the sequence of operations |
---|
1044 | errormsg=['missing' cell2mat(operations(ind_missing))]; |
---|
1045 | return |
---|
1046 | end |
---|
1047 | |
---|
1048 | %% check mask if selecetd |
---|
1049 | %could be included in get_mask callback ? |
---|
1050 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
1051 | maskname=get(handles.Mask,'String'); |
---|
1052 | if ~exist(maskname,'file') |
---|
1053 | get_mask_civ1_Callback(hObject, eventdata, handles); |
---|
1054 | end |
---|
1055 | end |
---|
1056 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
1057 | maskname=get(handles.Mask,'String'); |
---|
1058 | if ~exist(maskname,'file') |
---|
1059 | get_mask_fix1_Callback(hObject, eventdata, handles); |
---|
1060 | end |
---|
1061 | end |
---|
1062 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
1063 | maskname=get(handles.Mask,'String'); |
---|
1064 | if ~exist(maskname,'file') |
---|
1065 | get_mask_civ2_Callback(hObject, eventdata, handles); |
---|
1066 | end |
---|
1067 | end |
---|
1068 | if isequal(get(handles.CheckMask,'Value'),1) |
---|
1069 | maskname=get(handles.Mask,'String'); |
---|
1070 | if ~exist(maskname,'file') |
---|
1071 | get_mask_fix2_Callback(hObject, eventdata, handles); |
---|
1072 | end |
---|
1073 | end |
---|
1074 | |
---|
1075 | %% reinitialise status callback |
---|
1076 | if isfield(handles,'status') |
---|
1077 | set(handles.status,'Value',0);%suppress status display |
---|
1078 | status_Callback(hObject, eventdata, handles) |
---|
1079 | end |
---|
1080 | |
---|
1081 | %% read the PARAM.xml file to get the binaries (and batch_mode if batch) |
---|
1082 | path_civ=fileparts(which('civ')); %path to the source directory of uvmat |
---|
1083 | xmlfile='PARAM.xml'; |
---|
1084 | if exist(xmlfile,'file')% search parameter xml file in the whole matlab path |
---|
1085 | t=xmltree(xmlfile); |
---|
1086 | s=convert(t); |
---|
1087 | else |
---|
1088 | errormsg=['no file ' xmlfile]; |
---|
1089 | return |
---|
1090 | end |
---|
1091 | test_interp=0; %eviter les variables test_ (LG) |
---|
1092 | if batch |
---|
1093 | if isfield(s,'BatchParam') |
---|
1094 | Param.xml=s.BatchParam; |
---|
1095 | if isfield(Param.xml,'BatchMode') |
---|
1096 | batch_mode=Param.xml.BatchMode; |
---|
1097 | if ~ismember(batch_mode,{'sge','oar'}) |
---|
1098 | errormsg=['batch mode ' batch_mode ' not supported by UVMAT']; |
---|
1099 | return |
---|
1100 | end |
---|
1101 | end |
---|
1102 | else |
---|
1103 | errormsg='no batch civ binaries defined in PARAM.xml'; |
---|
1104 | return |
---|
1105 | end |
---|
1106 | else % run |
---|
1107 | if isfield(s,'RunParam') |
---|
1108 | Param.xml=s.RunParam; |
---|
1109 | else |
---|
1110 | errormsg='no run civ binaries defined in PARAM.xml'; |
---|
1111 | return |
---|
1112 | end |
---|
1113 | end |
---|
1114 | |
---|
1115 | %% check batch mode supported |
---|
1116 | if batch |
---|
1117 | switch batch_mode |
---|
1118 | case 'sge' |
---|
1119 | test_command='qstat'; |
---|
1120 | case 'oar' |
---|
1121 | test_command='oarstat'; |
---|
1122 | end |
---|
1123 | [s,w]=system(test_command); |
---|
1124 | if ~isequal(s,0) |
---|
1125 | errormsg=[batch_mode ' batch system not available']; |
---|
1126 | return |
---|
1127 | end |
---|
1128 | end |
---|
1129 | |
---|
1130 | %% check if the binaries exist |
---|
1131 | ListProgram=get(handles.ListProgram,'String'); |
---|
1132 | CivMode=ListProgram{get(handles.ListProgram,'Value')}; |
---|
1133 | binary_list={}; |
---|
1134 | switch CivMode |
---|
1135 | case 'CivX' |
---|
1136 | binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'}; |
---|
1137 | case 'CivAll'% desactivated option |
---|
1138 | binary_list={'Civ'}; |
---|
1139 | case 'Matlab' |
---|
1140 | if batch |
---|
1141 | binary_list={'CivmBin'}; |
---|
1142 | % verifier MenuMatlab installe sur le cluster |
---|
1143 | % difficile a faire a priori |
---|
1144 | end |
---|
1145 | end |
---|
1146 | for bin_name=binary_list %loop on the list of binaries |
---|
1147 | if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list |
---|
1148 | if exist(Param.xml.(bin_name{1}),'file') |
---|
1149 | [path,name,ext]=fileparts(Param.xml.(bin_name{1})); |
---|
1150 | currentdir=pwd; |
---|
1151 | if exist(path,'dir') |
---|
1152 | cd(path); |
---|
1153 | binpath=pwd;%path of the binary |
---|
1154 | Param.xml.(bin_name{1})=fullfile(binpath,[name ext]); |
---|
1155 | cd(currentdir) |
---|
1156 | else |
---|
1157 | errormsg=['path ' path ' for binaries defined in PARAM.xml does not exist']; |
---|
1158 | return |
---|
1159 | end |
---|
1160 | else %look for the full path if the file name has been defined with a relative path in PARAM.xm |
---|
1161 | fullname=fullfile(path_civ,Param.xml.(bin_name{1})); |
---|
1162 | if exist(fullname,'file') |
---|
1163 | Param.xml.(bin_name{1})=fullname; |
---|
1164 | else |
---|
1165 | errormsg=['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist']; |
---|
1166 | return |
---|
1167 | end |
---|
1168 | end |
---|
1169 | end |
---|
1170 | end |
---|
1171 | display('files OK, processing...') |
---|
1172 | |
---|
1173 | %% set the list of files and check them |
---|
1174 | display('checking the files...') |
---|
1175 | [ref_i,ref_j,errormsg]=find_ref_indices(handles); |
---|
1176 | if ~isempty(errormsg) |
---|
1177 | return |
---|
1178 | end |
---|
1179 | [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,tild,tild,compare,errormsg]=... |
---|
1180 | set_civ_filenames(handles,ref_i,ref_j,box_test); |
---|
1181 | if ~isempty(errormsg) |
---|
1182 | return |
---|
1183 | end |
---|
1184 | % if isempty(filecell)% (error message displayed in fct set_civ_filenames) |
---|
1185 | % return |
---|
1186 | % end |
---|
1187 | Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention) |
---|
1188 | set(handles.civ,'UserData',filecell);%store for futur use of status callback |
---|
1189 | nbfield=numel(i1_civ1); |
---|
1190 | nbslice=numel(j1_civ1); |
---|
1191 | if ~strcmp(CivMode,'CivX') |
---|
1192 | if Param.CheckCiv1 |
---|
1193 | [Param.Civ1.FileTypeA,FileInfo,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1}); |
---|
1194 | [Param.Civ1.FileTypeB,FileInfo,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1}); |
---|
1195 | end |
---|
1196 | if Param.CheckCiv2 |
---|
1197 | [Param.Civ2.FileTypeA,FileInfo,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1}); |
---|
1198 | [Param.Civ2.FileTypeB,FileInfo,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1}); |
---|
1199 | end |
---|
1200 | end |
---|
1201 | |
---|
1202 | %% MAIN LOOP |
---|
1203 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
1204 | TimeUnit=get(handles.TimeUnit,'String'); |
---|
1205 | checkframe=strcmp(TimeUnit,'frame'); |
---|
1206 | batch_file_list=[];%should be renamed file_list, can be used for xml or bash files |
---|
1207 | |
---|
1208 | for ifile=1:nbfield |
---|
1209 | for j=1:nbslice |
---|
1210 | % initiate system command |
---|
1211 | switch CivMode |
---|
1212 | case 'CivX' |
---|
1213 | if isunix % check: necessaire aussi en RUN? |
---|
1214 | cmd=['#!/bin/bash \n '... |
---|
1215 | '#$ -cwd \n '... |
---|
1216 | 'hostname && date \n '... |
---|
1217 | 'umask 002 \n'];%allow writting access to created files for user group |
---|
1218 | else |
---|
1219 | cmd=[]; |
---|
1220 | end |
---|
1221 | case 'CivAll' |
---|
1222 | CivAllxml=xmltree;% xml contents, all parameters |
---|
1223 | CivAllCmd=''; |
---|
1224 | CivAllxml=set(CivAllxml,1,'name','CivDoc'); |
---|
1225 | end |
---|
1226 | |
---|
1227 | % define output file name |
---|
1228 | if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1 |
---|
1229 | OutputFile=filecell.nc.civ2{ifile,j}; |
---|
1230 | else |
---|
1231 | OutputFile=filecell.nc.civ1{ifile,j}; |
---|
1232 | end |
---|
1233 | OutputFile=regexprep(OutputFile,'.nc',''); |
---|
1234 | |
---|
1235 | if Param.CheckCiv1 |
---|
1236 | % read image-dependent parameters |
---|
1237 | |
---|
1238 | if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j) |
---|
1239 | Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1)); |
---|
1240 | else |
---|
1241 | Param.Civ1.Dt=1; |
---|
1242 | end |
---|
1243 | Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2); |
---|
1244 | if strcmp(CivMode,'CivX') |
---|
1245 | Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE? |
---|
1246 | Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);% |
---|
1247 | end |
---|
1248 | if isfield(Param.Civ1,'FileTypeA')&&(strcmp(Param.Civ1.FileTypeA,'video')|| strcmp(Param.Civ1.FileTypeA,'mmreader')) |
---|
1249 | % ImageInfo=get(VideoReader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt]))); |
---|
1250 | ImageInfo=get(Param.Civ1.ImageA); |
---|
1251 | % elseif strcmp(Param.Civ1.FileTypeA,'mmreader') |
---|
1252 | % ImageInfo=get(mmreader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt]))); |
---|
1253 | Param.Civ1.ImageBitDepth=ImageInfo.BitsPerPixel/3; |
---|
1254 | if batch |
---|
1255 | Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};%file name must be used for batch instead of video object |
---|
1256 | Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j}; |
---|
1257 | end |
---|
1258 | else |
---|
1259 | Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j}; |
---|
1260 | Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j}; |
---|
1261 | % form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats |
---|
1262 | ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size |
---|
1263 | Param.Civ1.ImageBitDepth=ImageInfo.BitDepth; |
---|
1264 | end |
---|
1265 | Param.Civ1.ImageWidth=ImageInfo.Width; |
---|
1266 | Param.Civ1.ImageHeight=ImageInfo.Height; |
---|
1267 | Param.Civ1.FrameIndexA=i1_civ1(ifile); |
---|
1268 | Param.Civ1.FrameIndexB=i2_civ1(ifile); |
---|
1269 | % read mask )parameters |
---|
1270 | if Param.Civ1.CheckMask % the lines below should be changed with the new gui |
---|
1271 | if ~exist(Param.Civ1.Mask,'file') |
---|
1272 | maskbase=[filecell.filebase '_' Param.Civ1.Mask]; % |
---|
1273 | nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); % |
---|
1274 | i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1; |
---|
1275 | [RootPathMask,RootFileMask]=fileparts(maskbase); |
---|
1276 | Param.Civ1.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask); |
---|
1277 | end |
---|
1278 | end |
---|
1279 | % read grid parameters |
---|
1280 | if Param.Civ1.CheckGrid |
---|
1281 | if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid') |
---|
1282 | nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); % |
---|
1283 | if ~isnan(nbslice_grid) |
---|
1284 | i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1; |
---|
1285 | Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)]; |
---|
1286 | % Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')]; |
---|
1287 | if ~exist(Param.Civ1.GridName,'file') |
---|
1288 | errormsg='grid file absent for civ1'; |
---|
1289 | return |
---|
1290 | end |
---|
1291 | elseif ~exist(Param.Civ1.Grid,'file') |
---|
1292 | errormsg='grid file absent for civ1'; |
---|
1293 | return |
---|
1294 | end |
---|
1295 | end |
---|
1296 | end |
---|
1297 | |
---|
1298 | % send command |
---|
1299 | switch CivMode |
---|
1300 | case 'CivX' |
---|
1301 | [cmd_civ,errormsg]=cmd_civ1(filecell.nc.civ1{ifile,j},Param); |
---|
1302 | cmd=[cmd cmd_civ '\n']; |
---|
1303 | if ~isempty(errormsg) |
---|
1304 | return |
---|
1305 | end |
---|
1306 | case 'CivAll' |
---|
1307 | CivAllCmd=[CivAllCmd ' civ1 ']; |
---|
1308 | str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1); |
---|
1309 | fieldnames=fields(str); |
---|
1310 | [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1'); |
---|
1311 | for ilist=1:length(fieldnames) |
---|
1312 | val=eval(['str.' fieldnames{ilist}]); |
---|
1313 | if ischar(val) |
---|
1314 | [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist}); |
---|
1315 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1316 | end |
---|
1317 | end |
---|
1318 | end |
---|
1319 | end |
---|
1320 | |
---|
1321 | if Param.CheckFix1 |
---|
1322 | switch CivMode |
---|
1323 | case 'CivX' |
---|
1324 | cmd=[cmd... |
---|
1325 | cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n']; |
---|
1326 | case 'CivAll'%to abandon |
---|
1327 | fix1.inputFileName=filecell.nc.civ1{ifile,j} ; |
---|
1328 | fix1.fi1=num2str(param.fix1.flagindex1(1)); |
---|
1329 | fix1.fi2=num2str(param.fix1.flagindex1(2)); |
---|
1330 | fix1.fi3=num2str(param.fix1.flagindex1(3)); |
---|
1331 | fix1.threshC=num2str(param.fix1.thresh_vecC1); |
---|
1332 | fix1.threshV=num2str(param.fix1.thresh_vel1); |
---|
1333 | fieldnames=fields(fix1); |
---|
1334 | [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1'); |
---|
1335 | for ilist=1:length(fieldnames) |
---|
1336 | val=eval(['fix1.' fieldnames{ilist}]); |
---|
1337 | if ischar(val) |
---|
1338 | [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist}); |
---|
1339 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1340 | end |
---|
1341 | end |
---|
1342 | CivAllCmd=[CivAllCmd ' fix1 ']; |
---|
1343 | end |
---|
1344 | end |
---|
1345 | |
---|
1346 | %CheckPatch1 |
---|
1347 | if Param.CheckPatch1==1 |
---|
1348 | switch CivMode |
---|
1349 | case 'CivX' |
---|
1350 | cmd=[cmd... |
---|
1351 | cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n']; |
---|
1352 | case 'CivAll' |
---|
1353 | patch1.inputFileName=filecell.nc.civ1{ifile,j} ; |
---|
1354 | patch1.nopt=subdomain_patch1; |
---|
1355 | patch1.maxdiff=thresh_patch1; |
---|
1356 | patch1.ro=rho_patch1; |
---|
1357 | test_grid=get(handles.get_gridpatch1,'Value'); |
---|
1358 | if test_grid |
---|
1359 | patch1.gridflag='y'; |
---|
1360 | gridname=get(handles.grid_patch1,'String'); |
---|
1361 | if isequal(gridname(end-3:end),'grid') |
---|
1362 | nbslice_grid=str2double(gridname(1:end-4)); % |
---|
1363 | if ~isnan(nbslice_grid) |
---|
1364 | i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1; |
---|
1365 | patch1.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)]; |
---|
1366 | % patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; |
---|
1367 | if ~exist(patch1.gridPatch,'file') |
---|
1368 | errormsg='grid file absent for patch1'; |
---|
1369 | return |
---|
1370 | end |
---|
1371 | elseif exist(gridname,'file') |
---|
1372 | patch1.gridPatch=gridname; |
---|
1373 | else |
---|
1374 | errormsg='grid file absent for patch1'; |
---|
1375 | return |
---|
1376 | end |
---|
1377 | end |
---|
1378 | else |
---|
1379 | patch1.gridPatch='none'; |
---|
1380 | patch1.gridflag='n'; |
---|
1381 | patch1.m=nx_patch1; |
---|
1382 | patch1.n=ny_patch1; |
---|
1383 | end |
---|
1384 | patch1.convectFlow='n'; |
---|
1385 | fieldnames=fields(patch1); |
---|
1386 | [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1'); |
---|
1387 | for ilist=1:length(fieldnames) |
---|
1388 | val=eval(['patch1.' fieldnames{ilist}]); |
---|
1389 | if ischar(val) |
---|
1390 | [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist}); |
---|
1391 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1392 | end |
---|
1393 | end |
---|
1394 | CivAllCmd=[CivAllCmd ' patch1 ']; |
---|
1395 | end |
---|
1396 | end |
---|
1397 | if Param.CheckCiv2==1 |
---|
1398 | if isfield(Param.Civ2,'FileTypeA') &&(strcmp(Param.Civ2.FileTypeA,'video')|| strcmp(Param.Civ2.FileTypeA,'mmreader')) |
---|
1399 | % ImageInfo=get(VideoReader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt]))); |
---|
1400 | ImageInfo=get(Param.Civ2.ImageA); |
---|
1401 | % elseif strcmp(Param.Civ1.FileTypeA,'mmreader') |
---|
1402 | % ImageInfo=get(mmreader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt]))); |
---|
1403 | Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3; |
---|
1404 | if batch |
---|
1405 | Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};%file name must be used for batch instead of video object |
---|
1406 | Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j}; |
---|
1407 | end |
---|
1408 | else |
---|
1409 | Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j}; |
---|
1410 | Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j}; |
---|
1411 | form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats |
---|
1412 | ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size |
---|
1413 | Param.Civ2.ImageBitDepth=ImageInfo.BitDepth; |
---|
1414 | end |
---|
1415 | |
---|
1416 | if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j) |
---|
1417 | Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1); |
---|
1418 | else |
---|
1419 | Param.Civ2.Dt=1; |
---|
1420 | end |
---|
1421 | Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2; |
---|
1422 | if strcmp(CivMode,'CivX') |
---|
1423 | Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc); |
---|
1424 | Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc); |
---|
1425 | end |
---|
1426 | Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j}; |
---|
1427 | Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc' |
---|
1428 | |
---|
1429 | % mask |
---|
1430 | if Param.Civ2.CheckMask |
---|
1431 | if ~exist(Param.Civ2.Mask,'file') |
---|
1432 | maskbase=[filecell.filebase '_' Param.Civ2.Mask]; % |
---|
1433 | nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); % |
---|
1434 | i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1; |
---|
1435 | [RootPathMask,RootFileMask]=fileparts(maskbase); |
---|
1436 | Param.Civ2.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask); |
---|
1437 | % Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i'); |
---|
1438 | end |
---|
1439 | end |
---|
1440 | %grid |
---|
1441 | if Param.Civ2.CheckGrid |
---|
1442 | if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid') |
---|
1443 | nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); % |
---|
1444 | if ~isnan(nbslice_grid) |
---|
1445 | i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1; |
---|
1446 | Param.Civ2.Grid=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)]; |
---|
1447 | % Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; |
---|
1448 | end |
---|
1449 | end |
---|
1450 | end |
---|
1451 | form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats |
---|
1452 | if isempty(form) |
---|
1453 | % ImageInfo=get(VideoReader(fullfile()); |
---|
1454 | Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3; |
---|
1455 | else |
---|
1456 | ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size |
---|
1457 | Param.Civ2.ImageBitDepth=ImageInfo.BitDepth; |
---|
1458 | end |
---|
1459 | Param.Civ2.ImageWidth=ImageInfo.Width; |
---|
1460 | Param.Civ2.ImageHeight=ImageInfo.Height; |
---|
1461 | Param.Civ2.FrameIndexA=i1_civ2(ifile); |
---|
1462 | Param.Civ2.FrameIndexB=i2_civ2(ifile); |
---|
1463 | % Param.Civ2.i1=i1_civ2(ifile); |
---|
1464 | % Param.Civ2.i2=i2_civ2(ifile); |
---|
1465 | switch CivMode |
---|
1466 | case 'CivX' |
---|
1467 | cmd=[cmd... |
---|
1468 | cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n']; |
---|
1469 | case 'CivAll' |
---|
1470 | CivAllCmd=[CivAllCmd ' civ2 ']; |
---|
1471 | str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2); |
---|
1472 | fieldnames=fields(str); |
---|
1473 | [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2'); |
---|
1474 | for ilist=1:length(fieldnames) |
---|
1475 | val=eval(['str.' fieldnames{ilist}]); |
---|
1476 | if ischar(val) |
---|
1477 | [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist}); |
---|
1478 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1479 | end |
---|
1480 | end |
---|
1481 | end |
---|
1482 | end |
---|
1483 | |
---|
1484 | % CheckFix2 |
---|
1485 | if Param.CheckFix2==1 |
---|
1486 | switch CivMode |
---|
1487 | case 'CivX' |
---|
1488 | cmd=[cmd... |
---|
1489 | cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n']; |
---|
1490 | case 'CivAll' |
---|
1491 | fix2.inputFileName=filecell.nc.civ2{ifile,j} ; |
---|
1492 | fix2.fi1=num2str(flagindex2(1)); |
---|
1493 | fix2.fi2=num2str(flagindex2(2)); |
---|
1494 | fix2.fi3=num2str(flagindex2(3)); |
---|
1495 | fix2.threshC=num2str(thresh_vec2C); |
---|
1496 | fix2.threshV=num2str(thresh_vel2); |
---|
1497 | fieldnames=fields(fix2); |
---|
1498 | [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2'); |
---|
1499 | for ilist=1:length(fieldnames) |
---|
1500 | val=eval(['fix2.' fieldnames{ilist}]); |
---|
1501 | if ischar(val) |
---|
1502 | [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist}); |
---|
1503 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1504 | end |
---|
1505 | end |
---|
1506 | CivAllCmd=[CivAllCmd ' fix2 ']; |
---|
1507 | end |
---|
1508 | end |
---|
1509 | |
---|
1510 | %CheckPatch2 |
---|
1511 | if Param.CheckPatch2==1 |
---|
1512 | |
---|
1513 | switch CivMode |
---|
1514 | |
---|
1515 | case 'CivX' |
---|
1516 | cmd=[cmd... |
---|
1517 | cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n']; |
---|
1518 | |
---|
1519 | case 'CivAll' |
---|
1520 | patch2.inputFileName=filecell.nc.civ1{ifile,j} ; |
---|
1521 | patch2.nopt=subdomain_patch2; |
---|
1522 | patch2.maxdiff=thresh_patch2; |
---|
1523 | patch2.ro=rho_patch2; |
---|
1524 | test_grid=get(handles.get_gridpatch2,'Value'); |
---|
1525 | if test_grid |
---|
1526 | patch2.gridflag='y'; |
---|
1527 | gridname=get(handles.grid_patch2,'String'); |
---|
1528 | if isequal(gridname(end-3:end),'grid') |
---|
1529 | nbslice_grid=str2double(gridname(1:end-4)); % |
---|
1530 | if ~isnan(nbslice_grid) |
---|
1531 | i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1; |
---|
1532 | patch2.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)]; |
---|
1533 | % patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')]; |
---|
1534 | if ~exist(patch2.gridPatch,'file') |
---|
1535 | errormsg='grid file absent for patch2'; |
---|
1536 | return |
---|
1537 | end |
---|
1538 | elseif exist(gridname,'file') |
---|
1539 | patch2.gridPatch=gridname; |
---|
1540 | else |
---|
1541 | errormsg='grid file absent for patch2'; |
---|
1542 | return |
---|
1543 | end |
---|
1544 | end |
---|
1545 | else |
---|
1546 | patch2.gridPatch='none'; |
---|
1547 | patch2.gridflag='n'; |
---|
1548 | patch2.m=nx_patch2; |
---|
1549 | patch2.n=ny_patch2; |
---|
1550 | end |
---|
1551 | patch2.convectFlow='n'; |
---|
1552 | fieldnames=fields(patch2); |
---|
1553 | [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2'); |
---|
1554 | for ilist=1:length(fieldnames) |
---|
1555 | val=eval(['patch2.' fieldnames{ilist}]); |
---|
1556 | if ischar(val) |
---|
1557 | [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist}); |
---|
1558 | [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val); |
---|
1559 | end |
---|
1560 | end |
---|
1561 | CivAllCmd=[CivAllCmd ' patch2 ']; |
---|
1562 | end |
---|
1563 | end |
---|
1564 | |
---|
1565 | switch CivMode |
---|
1566 | |
---|
1567 | case {'CivX','CivAll'} |
---|
1568 | if isequal(CivMode,'CivAll') |
---|
1569 | save(CivAllxml,[OutputFile '.xml']); |
---|
1570 | cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml ' CivAllCmd ' >' OutputFile '.log' '\n']; |
---|
1571 | end |
---|
1572 | % create the .bat file used in run or batch |
---|
1573 | filename_bat=[OutputFile '.bat']; |
---|
1574 | [fid,message]=fopen(filename_bat,'w'); |
---|
1575 | if isequal(fid,-1) |
---|
1576 | errormsg=['creation of .bat file: ' message]; |
---|
1577 | return |
---|
1578 | end |
---|
1579 | fprintf(fid,cmd); |
---|
1580 | fclose(fid); |
---|
1581 | if isunix |
---|
1582 | system(['chmod +x ' filename_bat]); |
---|
1583 | end |
---|
1584 | batch_file_list{length(batch_file_list)+1}=filename_bat; |
---|
1585 | |
---|
1586 | case 'Matlab' |
---|
1587 | drawnow |
---|
1588 | if ~strcmp(compare,'stereo PIV') |
---|
1589 | filename_xml=[OutputFile '.civ.xml']; |
---|
1590 | t=struct2xml(Param); |
---|
1591 | save(t,filename_xml) |
---|
1592 | if batch |
---|
1593 | path_civ=fileparts(which('civ')); |
---|
1594 | filename_bat=[OutputFile '.bat']; |
---|
1595 | [fid,message]=fopen(filename_bat,'w'); |
---|
1596 | if isequal(fid,-1) |
---|
1597 | errormsg= ['creation of .bat file: ' message]; |
---|
1598 | return |
---|
1599 | end |
---|
1600 | % text_matlabscript=[... |
---|
1601 | % '#!/bin/bash \n'... |
---|
1602 | % '. /etc/sysprofile \n'... |
---|
1603 | % 'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'... |
---|
1604 | % 'cd(''' path_civ '''); \n'... |
---|
1605 | % 'civ_matlab(''' filename_xml ''',''' OutputFile '.nc''); \n'... |
---|
1606 | % 'exit \n'... |
---|
1607 | % 'END_MATLAB \n']; |
---|
1608 | cmd=['#!/bin/bash \n '... |
---|
1609 | '#$ -cwd \n '... |
---|
1610 | 'hostname && date \n '... |
---|
1611 | 'umask 002 \n'... |
---|
1612 | Param.xml.CivmBin ' ' Param.xml.RunTime ' ' filename_xml ' ' OutputFile '.nc'];%allow writting access to created files for user group |
---|
1613 | |
---|
1614 | fprintf(fid,cmd); |
---|
1615 | fclose(fid); |
---|
1616 | if isunix |
---|
1617 | system(['chmod +x ' filename_bat]); |
---|
1618 | end |
---|
1619 | batch_file_list{length(batch_file_list)+1}=filename_bat; |
---|
1620 | else |
---|
1621 | [tild,errormsg]=civ_matlab(Param,filecell.nc.civ1{ifile,j}); |
---|
1622 | if isempty(errormsg) |
---|
1623 | display([filecell.nc.civ1{ifile,j} ' written']) |
---|
1624 | end |
---|
1625 | end |
---|
1626 | end |
---|
1627 | end |
---|
1628 | end |
---|
1629 | end |
---|
1630 | |
---|
1631 | if batch |
---|
1632 | switch batch_mode |
---|
1633 | |
---|
1634 | case 'sge' %at the moment only psmn ENS Lyon uses it |
---|
1635 | for p=1:length(batch_file_list) |
---|
1636 | %cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}]; |
---|
1637 | cmd=['!qsub -q piv1,piv2,piv3 '... |
---|
1638 | '-e ' regexprep(batch_file_list{p},'.bat','.errors') ' -o ' regexprep(batch_file_list{p},'.bat','.log ')... |
---|
1639 | ' -v ' 'LD_LIBRARY_PATH=/home/sjoubaud/matlab_sylvain/civx/lib ' batch_file_list{p}]; |
---|
1640 | display(cmd);eval(cmd); |
---|
1641 | end |
---|
1642 | case 'oar_old' |
---|
1643 | for p=1:length(batch_file_list) |
---|
1644 | oar_command=['!oarsub -n CIVX -q nicejob '... |
---|
1645 | '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')... |
---|
1646 | '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00" ' batch_file_list{p}]; |
---|
1647 | display(oar_command);eval(oar_command); |
---|
1648 | end |
---|
1649 | case 'oar' |
---|
1650 | |
---|
1651 | max_walltime=3600*12; % 12h max |
---|
1652 | oar_modes={'oar-parexec','oar-dispatch','mpilauncher'}; |
---|
1653 | text={'Batch processing on servcalcul3 LEGI';... |
---|
1654 | 'Please choose one of the followint modes';... |
---|
1655 | '* oar-parexec : default and best choice';... |
---|
1656 | '* oar-dispatch : jobs in a container of several cores';... |
---|
1657 | '* mpilauncher : one single parallel mpi job using several cores';... |
---|
1658 | '**********************************'... |
---|
1659 | }; |
---|
1660 | [S,v]=listdlg('PromptString',text,'ListString',oar_modes,... |
---|
1661 | 'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode'); |
---|
1662 | switch oar_modes{S} |
---|
1663 | case 'oar-parexec' %oar-dispatch.pl |
---|
1664 | answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''}); |
---|
1665 | ncores=str2double(answer{1}); |
---|
1666 | extra_oar=answer{2}; |
---|
1667 | walltime_onejob=600;%seconds |
---|
1668 | filename_joblist=fullfile(Rootbat,'job_list.txt'); |
---|
1669 | fid=fopen(filename_joblist,'w'); |
---|
1670 | for p=1:length(batch_file_list) |
---|
1671 | fprintf(fid,[batch_file_list{p} '\n']); |
---|
1672 | end |
---|
1673 | fclose(fid) |
---|
1674 | oar_command=['oarsub -n CIVX '... |
---|
1675 | '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '... |
---|
1676 | '-l /core=' num2str(ncores) ','... |
---|
1677 | 'walltime=' datestr(min(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,max_walltime/86400),13) ' '... |
---|
1678 | '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '... |
---|
1679 | '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '... |
---|
1680 | extra_oar ' '... |
---|
1681 | '"oar-parexec -s -f ' filename_joblist ' '... |
---|
1682 | '-l ' filename_joblist '.log"']; |
---|
1683 | filename_oarcommand=fullfile(Rootbat,'oar_command'); |
---|
1684 | fid=fopen(filename_oarcommand,'w'); |
---|
1685 | fprintf(fid,[oar_command '\n']); |
---|
1686 | fclose(fid); |
---|
1687 | display(oar_command); |
---|
1688 | eval(['! . ' filename_oarcommand]) |
---|
1689 | case 'oar-dispatch' %oar-dispatch.pl |
---|
1690 | ncores=str2double(... |
---|
1691 | inputdlg('Number of cores (max 36)','oarsub parameter',1,{'6'})... |
---|
1692 | ); |
---|
1693 | walltime_onejob=600;%seconds |
---|
1694 | filename_joblist=fullfile(Rootbat,'job_list.txt'); |
---|
1695 | fid=fopen(filename_joblist,'w'); |
---|
1696 | for p=1:length(batch_file_list) |
---|
1697 | oar_command=['oarsub -n CIVX '... |
---|
1698 | '-E ' regexprep(batch_file_list{p},'\.bat\>','.stderr') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.stdout ')... |
---|
1699 | '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '" ' batch_file_list{p}]; |
---|
1700 | fprintf(fid,[oar_command '\n']); |
---|
1701 | end |
---|
1702 | fclose(fid); |
---|
1703 | oar_command=['oarsub -t container -n civx-container '... |
---|
1704 | '-l /core=' num2str(ncores)... |
---|
1705 | ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '... |
---|
1706 | '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '... |
---|
1707 | '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '... |
---|
1708 | '"oar-dispatch -f ' filename_joblist '"']; |
---|
1709 | filename_oarcommand=fullfile(Rootbat,'oar_command'); |
---|
1710 | fid=fopen(filename_oarcommand,'w'); |
---|
1711 | fprintf(fid,[oar_command '\n']); |
---|
1712 | fclose(fid); |
---|
1713 | display(oar_command); |
---|
1714 | eval(['! . ' filename_oarcommand]) |
---|
1715 | case 'mpilauncher' |
---|
1716 | filename_joblist=fullfile(Rootbat,'job_list.txt'); |
---|
1717 | fid=fopen(filename_joblist,'w'); |
---|
1718 | |
---|
1719 | for p=1:length(batch_file_list) |
---|
1720 | fprintf(fid,[batch_file_list{p} '\n']); |
---|
1721 | end |
---|
1722 | fclose(fid) |
---|
1723 | text_oarscript=[... |
---|
1724 | '#!/bin/bash \n'... |
---|
1725 | '#OAR -n Mylauncher \n'... |
---|
1726 | '#OAR -l node=4/core=5,walltime=0:15:00 \n'... |
---|
1727 | '#OAR -E ' fullfile(Rootbat,'stderrfile.log') ' \n'... |
---|
1728 | '#OAR -O ' fullfile(Rootbat,'stdoutfile.log') ' \n'... |
---|
1729 | '# ========================================================= \n'... |
---|
1730 | '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'... |
---|
1731 | '# application for coriolis PIV post-processing. \n'... |
---|
1732 | '# OAR uses oarshmost wrapper to propagate the user environement. \n'... |
---|
1733 | '# This wrapper assert that the user has the same environment on all the \n'... |
---|
1734 | '# allocated nodes (basic behavior needed by most MPI applications). \n'... |
---|
1735 | '# \n'... |
---|
1736 | '# REQUIREMENT: \n'... |
---|
1737 | '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'... |
---|
1738 | '# If a different location is used, change the line following the comment "Bidouille" \n'... |
---|
1739 | '# ========================================================= \n'... |
---|
1740 | '# USER should only modify these 2 lines \n'... |
---|
1741 | 'WORKDIR=' pwd ' \n'... |
---|
1742 | 'COMMANDE="mpilauncher -f ' filename_joblist '" \n'... |
---|
1743 | '# ========================================================= \n'... |
---|
1744 | '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'... |
---|
1745 | 'echo "job starting on: "`hostname` \n'... |
---|
1746 | 'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'... |
---|
1747 | 'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'... |
---|
1748 | '#========== Bidouille ============== \n'... |
---|
1749 | 'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...% 'cd $WORKDIR \n'... |
---|
1750 | 'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'... |
---|
1751 | 'echo "I run: $CMD" \n'... |
---|
1752 | '$CMD \n'... |
---|
1753 | 'echo "job ending" \n'... |
---|
1754 | ]; |
---|
1755 | % oarsub -S ./oar.sub |
---|
1756 | filename_oarscript=fullfile(Rootbat,'oar_command'); |
---|
1757 | fid=fopen(filename_oarscript,'w'); |
---|
1758 | fprintf(fid,[text_oarscript]); |
---|
1759 | fclose(fid); |
---|
1760 | eval(['!chmod +x ' filename_oarscript]); |
---|
1761 | eval(['!oarsub -S ' filename_oarscript]); |
---|
1762 | end |
---|
1763 | end |
---|
1764 | else |
---|
1765 | if ~isequal(CivMode,'Matlab') |
---|
1766 | filename_superbat=fullfile(Rootbat,'job_list.bat'); |
---|
1767 | fid=fopen(filename_superbat,'w'); |
---|
1768 | if fid==-1 |
---|
1769 | msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat]) |
---|
1770 | return |
---|
1771 | end |
---|
1772 | for p=1:length(batch_file_list) |
---|
1773 | if isunix |
---|
1774 | fprintf(fid,['sh ' batch_file_list{p} '\n']); |
---|
1775 | else |
---|
1776 | fprintf(fid,['@call "' regexprep(batch_file_list{p},'\\','\\\\') '"' '\n']); |
---|
1777 | end |
---|
1778 | end |
---|
1779 | fclose(fid); |
---|
1780 | if(isunix) |
---|
1781 | system(['chmod +x ' filename_superbat]); |
---|
1782 | end |
---|
1783 | system([filename_superbat ' &']);% execute main commmand |
---|
1784 | end |
---|
1785 | end |
---|
1786 | |
---|
1787 | |
---|
1788 | %% save interface state |
---|
1789 | if isfield(filecell,'nc') |
---|
1790 | if isfield(filecell.nc,'civ2') |
---|
1791 | fileresu=filecell.nc.civ2{1,1}; |
---|
1792 | else |
---|
1793 | fileresu=filecell.nc.civ1{1,1}; |
---|
1794 | end |
---|
1795 | end |
---|
1796 | [RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu); |
---|
1797 | namedoc=fullfile(RootPath,SubDir,RootFile); |
---|
1798 | detect=1; |
---|
1799 | while detect==1 |
---|
1800 | namefigfull=[namedoc '.fig']; |
---|
1801 | hh=dir(namefigfull); |
---|
1802 | if ~isempty(hh) |
---|
1803 | detect=1; |
---|
1804 | namedoc=[namedoc '.0']; |
---|
1805 | else |
---|
1806 | detect=0; |
---|
1807 | end |
---|
1808 | end |
---|
1809 | Param=rmfield(Param,'status'); |
---|
1810 | Param=rmfield(Param,'xml'); |
---|
1811 | t=struct2xml(Param); |
---|
1812 | t=set(t,1,'name','Civ');% set the head label |
---|
1813 | save(t,[namedoc '.civ.xml']); %save GUI parameters as xml file |
---|
1814 | saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml) |
---|
1815 | |
---|
1816 | %Save info in personal profile (initiate browser next time) TODO |
---|
1817 | MenuFile={}; |
---|
1818 | dir_perso=prefdir; |
---|
1819 | profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); |
---|
1820 | if exist(profil_perso,'file') |
---|
1821 | hh=load (profil_perso); |
---|
1822 | if isfield(hh,'MenuFile') |
---|
1823 | MenuFile=hh.MenuFile; |
---|
1824 | end |
---|
1825 | if isfield(filecell.nc,'civ2') |
---|
1826 | MenuFile=[filecell.nc.civ2{1,1}; MenuFile]; |
---|
1827 | else |
---|
1828 | MenuFile=[filecell.nc.civ1{1,1}; MenuFile]; |
---|
1829 | end |
---|
1830 | save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat |
---|
1831 | else |
---|
1832 | MenuFile=filecell.ima1.civ1(1,1); |
---|
1833 | save (profil_perso,'MenuFile') |
---|
1834 | end |
---|
1835 | |
---|
1836 | %------------------------------------------------------------------------ |
---|
1837 | % --- determine the list of reference indices of processing file |
---|
1838 | function [ref_i,ref_j,errormsg]=find_ref_indices(handles) |
---|
1839 | %------------------------------------------------------------------------ |
---|
1840 | errormsg=''; %default error message |
---|
1841 | first_i=str2double(get(handles.first_i,'String'));%first index i |
---|
1842 | last_i=str2double(get(handles.last_i,'String'));%last index i |
---|
1843 | incr_i=str2double(get(handles.incr_i,'String'));% increment |
---|
1844 | if isequal(get(handles.first_j,'Visible'),'on') |
---|
1845 | first_j=str2double(get(handles.first_j,'String'));%first index j |
---|
1846 | last_j=str2double(get(handles.last_j,'String'));%last index j |
---|
1847 | incr_j=str2double(get(handles.incr_j,'String'));% increment |
---|
1848 | else |
---|
1849 | first_j=1; |
---|
1850 | last_j=1; |
---|
1851 | incr_j=1; |
---|
1852 | end |
---|
1853 | ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair) |
---|
1854 | ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair) |
---|
1855 | if isnan(first_i)||isnan(first_j) |
---|
1856 | errormsg='first field number not defined'; |
---|
1857 | elseif isnan(last_i)||isnan(last_j) |
---|
1858 | errormsg='last field number not defined'; |
---|
1859 | elseif isnan(incr_i)||isnan(incr_j) |
---|
1860 | errormsg='increment in field number not defined'; |
---|
1861 | elseif last_i < first_i || last_j < first_j |
---|
1862 | errormsg='last field number must be larger than the first one'; |
---|
1863 | end |
---|
1864 | |
---|
1865 | %------------------------------------------------------------------------ |
---|
1866 | % --- determine the list of filenames and indices needed for launch_job |
---|
1867 | %------------------------------------------------------------------------ |
---|
1868 | % OUTPUT: |
---|
1869 | % filecell: structure of cell arrays {ref_i,ref_j} containing all the filenames involved in the civ process |
---|
1870 | % the indices ref_i and ref_j correspond to the list of reference indices |
---|
1871 | % .filebase=fullfile(RootPath,RootFile) used to construct mask names, grid names, CivDoc xml file |
---|
1872 | % .ima1.civ1,.ima1.civ2: first image for civ1 and civ2 respectively (possibly different) |
---|
1873 | % .ima2.civ1,.ima2.civ2: second image for civ1 and civ2 respectively (possibly different) |
---|
1874 | % .nc.civ1,.nc.civ2: netcdf files containing civ1 and civ2 data respectively (possibly different) |
---|
1875 | % i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2: arrays of files indices, needed for timing records |
---|
1876 | function [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,NomType_nc,file_ref_fix1,file_ref_fix2,compare,errormsg]=... |
---|
1877 | set_civ_filenames(handles,ref_i,ref_j,checkbox) |
---|
1878 | %------------------------------------------------------------------------ |
---|
1879 | filecell=[];%default |
---|
1880 | errormsg=''; |
---|
1881 | ListProgram=get(handles.ListProgram,'String'); |
---|
1882 | CivMode=ListProgram{get(handles.ListProgram,'Value')};%Program to use , CivX or Matlab |
---|
1883 | |
---|
1884 | %% get the root name and check dir |
---|
1885 | RootPath=get(handles.RootPath,'String'); |
---|
1886 | SubdirImages=get(handles.SubdirImages,'String'); |
---|
1887 | RootFile=get(handles.RootFile,'String'); |
---|
1888 | filecell.filebase=fullfile(RootPath,SubdirImages,RootFile); |
---|
1889 | if isempty(filecell.filebase) |
---|
1890 | errormsg='please open an image with the upper menu option Open/Browse...'; |
---|
1891 | return |
---|
1892 | end |
---|
1893 | if ~exist(RootPath,'dir') |
---|
1894 | errormsg=['path to images ' RootPath ' not found']; |
---|
1895 | return |
---|
1896 | end |
---|
1897 | [tild,message]=fileattrib(RootPath); |
---|
1898 | if ~isempty(message) && ~isequal(message.UserWrite,1) |
---|
1899 | errormsg=['No writting access to ' RootPath]; |
---|
1900 | return |
---|
1901 | end |
---|
1902 | %check result directory |
---|
1903 | subdir_civ1=regexprep(get(handles.SubdirCiv1,'String'),'^.','');%subdirectory subdir_civ1 for the netcdf output data |
---|
1904 | subdir_civ2=regexprep(get(handles.SubdirCiv2,'String'),'^.',''); |
---|
1905 | if isequal(subdir_civ1,''),subdir_civ1='civ'; end% put default subdir |
---|
1906 | % subdir_civ1=[ '.' subdir_civ1]; |
---|
1907 | % subdir_civ2=[ '.' subdir_civ2]; |
---|
1908 | if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir |
---|
1909 | subdir_civ1=[SubdirImages '.' subdir_civ1]; |
---|
1910 | subdir_civ2=[SubdirImages '.' subdir_civ2]; |
---|
1911 | |
---|
1912 | %% choose root names depending on ListCompareMode =displacement, shift, PIV or stereo PIV |
---|
1913 | ListCompareMode=get(handles.ListCompareMode,'String'); |
---|
1914 | compare=ListCompareMode{get(handles.ListCompareMode,'Value')}; |
---|
1915 | |
---|
1916 | % set the nomenclature type of the nc files depending on the pair mode |
---|
1917 | if strcmp(compare,'displacement')||strcmp(compare,'shift') |
---|
1918 | mode='displacement'; |
---|
1919 | else |
---|
1920 | mode_list=get(handles.ListPairMode,'String'); |
---|
1921 | mode_value=get(handles.ListPairMode,'Value'); |
---|
1922 | mode=mode_list{mode_value}; |
---|
1923 | end |
---|
1924 | NomType_ima2=get(handles.NomType,'String'); |
---|
1925 | NomType_nc=nomtype2pair(NomType_ima2,mode); |
---|
1926 | |
---|
1927 | % set the rootfile and image indexing |
---|
1928 | RootFile_ima2=get(handles.RootFile,'String');%root file for the second image series |
---|
1929 | ext_ima=get(handles.ImaExt,'String'); % image extension (the same for all images) |
---|
1930 | switch compare |
---|
1931 | case 'PIV' |
---|
1932 | RootFile_ima1=RootFile_ima2;% root name of the two image series is the same |
---|
1933 | NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one |
---|
1934 | RootFile_nc=RootFile_ima2; |
---|
1935 | case 'displacement' |
---|
1936 | RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1 |
---|
1937 | NomType_ima1='';% no indexing of the first image, a fixed reference for the whole series |
---|
1938 | RootFile_nc=RootFile_ima2; |
---|
1939 | case 'shift' |
---|
1940 | RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1 |
---|
1941 | NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one |
---|
1942 | RootFile_nc=[RootFile_ima1 '-' RootFile_ima2]; |
---|
1943 | end |
---|
1944 | |
---|
1945 | %determine the list of file indices involved |
---|
1946 | [i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=... |
---|
1947 | find_pair_indices(handles,ref_i,ref_j,mode); |
---|
1948 | |
---|
1949 | %determine the new filebase for 'displacement' ListPairMode (comparison of two series) |
---|
1950 | %filebase_B=filebase;% root name of the second field series for stereo |
---|
1951 | % filebase_A=filebase;%default |
---|
1952 | % if strcmp(compare,'PIV') |
---|
1953 | % filebase_AB=filebase; |
---|
1954 | % else |
---|
1955 | % [Path2,Name2]=fileparts(filebase_B); |
---|
1956 | % Name1=RootFile_ima1; |
---|
1957 | % filebase_AB=fullfile(Path2,[Name2 '-' Name1]); |
---|
1958 | % end |
---|
1959 | % [RootPath_AB,RootFile_AB]=fileparts(filebase_AB); |
---|
1960 | % % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B); |
---|
1961 | % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B); |
---|
1962 | % [RootPath_nc,RootFile_nc]=fileparts(filebase_B);%default |
---|
1963 | % if strcmp(compare,'displacement') |
---|
1964 | % % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B); |
---|
1965 | % % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B); |
---|
1966 | % [RootPath_nc,RootFile_nc]=fileparts(filebase_B); |
---|
1967 | % elseif strcmp(compare,'shift') |
---|
1968 | % RootPath_nc=RootPath_AB; |
---|
1969 | % RootFile_nc=RootFile_AB; |
---|
1970 | % end |
---|
1971 | % else |
---|
1972 | % filebase_ima1=filebase_B; |
---|
1973 | % filebase_ima2=filebase_B; |
---|
1974 | % filebase_nc=filebase_B; |
---|
1975 | % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1); |
---|
1976 | % [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2); |
---|
1977 | % [RootPath_nc,RootFile_nc]=fileparts(filebase_nc); |
---|
1978 | % [RootPath_A,RootFile_A]=fileparts(filebase_A); |
---|
1979 | |
---|
1980 | |
---|
1981 | %% determine reference files for fix: |
---|
1982 | file_ref_fix1={};%default |
---|
1983 | file_ref_fix2={}; |
---|
1984 | nbfield=length(i1_civ1); |
---|
1985 | nbslice=length(j1_civ1); |
---|
1986 | if checkbox(2)==1% fix1 performed |
---|
1987 | ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback |
---|
1988 | if ~isempty(ref) |
---|
1989 | first_i=str2double(get(handles.first_i,'String')); |
---|
1990 | last_i=str2double(get(handles.last_i,'String')); |
---|
1991 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
1992 | first_j=str2double(get(handles.first_j,'String')); |
---|
1993 | last_j=str2double(get(handles.last_j,'String')); |
---|
1994 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
1995 | num_i_ref=first_i:incr_i:last_i; |
---|
1996 | num_j_ref=first_j:incr_j:last_j; |
---|
1997 | if isequal(mode,'displacement') |
---|
1998 | num_i1=num_i_ref; |
---|
1999 | num_i2=num_i_ref; |
---|
2000 | num_j1=num_j_ref; |
---|
2001 | num_j2=num_j_ref; |
---|
2002 | elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2') |
---|
2003 | num_i1=num_i_ref; |
---|
2004 | num_i2=num_i1; |
---|
2005 | num_j1=ref.num_a*ones(size(num_i_ref)); |
---|
2006 | num_j2=ref.num_b*ones(size(num_i_ref)); |
---|
2007 | elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)') |
---|
2008 | delta1=floor((ref.num2-ref.num1)/2); |
---|
2009 | delta2=ceil((ref.num2-ref.num1)/2); |
---|
2010 | num_i1=num_i_ref-delta1*ones(size(num_i_ref)); |
---|
2011 | num_i2=num_i_ref+delta2*ones(size(num_i_ref)); |
---|
2012 | if isempty(ref.num_a) |
---|
2013 | ref.num_a=1; |
---|
2014 | end |
---|
2015 | num_j1=ref.num_a*ones(size(num_i1)); |
---|
2016 | num_j2=num_j1; |
---|
2017 | elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)') |
---|
2018 | delta1=floor((ref.num_b-ref.num_a)/2); |
---|
2019 | delta2=ceil((ref.num_b-ref.num_a)/2); |
---|
2020 | num_i1=ref.num1*ones(size(num_i_ref)); |
---|
2021 | num_i2=num_i1; |
---|
2022 | num_j1=num_j_ref-delta1*ones(size(num_j_ref)); |
---|
2023 | num_j2=num_j_ref+delta2*ones(size(num_j_ref)); |
---|
2024 | end |
---|
2025 | for ifile=1:nbfield |
---|
2026 | for j=1:nbslice |
---|
2027 | [RootPathRef,RootFile]=fileparts(ref.filebase); |
---|
2028 | file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j)); |
---|
2029 | file_ref_fix1(ifile,j)={file_ref}; |
---|
2030 | if ~exist(file_ref,'file') |
---|
2031 | errormsg=['reference file ' file_ref ' not found for fix1']; |
---|
2032 | return |
---|
2033 | end |
---|
2034 | end |
---|
2035 | end |
---|
2036 | end |
---|
2037 | end |
---|
2038 | |
---|
2039 | %% determine reference files for fix2: |
---|
2040 | if checkbox(5)==1% fix2 performed |
---|
2041 | ref=get(handles.ref_fix2,'UserData'); |
---|
2042 | if ~isempty(ref) |
---|
2043 | first_i=str2double(get(handles.first_i,'String')); |
---|
2044 | last_i=str2double(get(handles.last_i,'String')); |
---|
2045 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
2046 | first_j=str2double(get(handles.first_j,'String')); |
---|
2047 | last_j=str2double(get(handles.last_j,'String')); |
---|
2048 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
2049 | num_i_ref=first_i:incr_i:last_i; |
---|
2050 | num_j_ref=first_j:incr_j:last_j; |
---|
2051 | if isequal(mode,'displacement') |
---|
2052 | num_i1=num_i_ref; |
---|
2053 | num_i2=num_i_ref; |
---|
2054 | num_j1=num_j_ref; |
---|
2055 | num_j2=num_j_ref; |
---|
2056 | elseif isequal(mode,'pair j1-j2') |
---|
2057 | num_i1=num_i_ref; |
---|
2058 | num_i2=num_i1; |
---|
2059 | num_j1=ref.num_a; |
---|
2060 | num_j2=ref.num_b; |
---|
2061 | elseif isequal(mode,'series(Di)') |
---|
2062 | delta1=floor((ref.num2-ref.num1)/2); |
---|
2063 | delta2=ceil((ref.num2-ref.num1)/2); |
---|
2064 | num_i1=num_i_ref-delta1*ones(size(num_i_ref)); |
---|
2065 | num_i2=num_i_ref+delta2*ones(size(num_i_ref)); |
---|
2066 | num_j1=ref.num_a*ones(size(num_i1)); |
---|
2067 | num_j2=num_j1; |
---|
2068 | elseif isequal(mode,'series(Dj)') |
---|
2069 | delta1=floor((ref.num_b-ref.num_a)/2); |
---|
2070 | delta2=ceil((ref.num_b-ref.num_a)/2); |
---|
2071 | num_i1=ref.num1*ones(size(num_i_ref)); |
---|
2072 | num_i2=num_i1; |
---|
2073 | num_j1=num_j_ref-delta1*ones(size(num_j_ref)); |
---|
2074 | num_j2=num_j_ref+delta2*ones(size(num_j_ref)); |
---|
2075 | end |
---|
2076 | for ifile=1:nbfield |
---|
2077 | for j=1:nbslice |
---|
2078 | [RootPathRef,RootFile]=fileparts(ref.filebase); |
---|
2079 | file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j)); |
---|
2080 | file_ref_fix2(ifile,j)={file_ref}; |
---|
2081 | if ~exist(file_ref,'file') |
---|
2082 | errormsg=['reference file ' file_ref ' not found for fix2']; |
---|
2083 | return |
---|
2084 | end |
---|
2085 | end |
---|
2086 | end |
---|
2087 | end |
---|
2088 | end |
---|
2089 | |
---|
2090 | %% check the existence of the netcdf and image files involved |
---|
2091 | % %%%%%%%%%%%% case CheckCiv1 activated %%%%%%%%%%%%% |
---|
2092 | if checkbox(1)==1; |
---|
2093 | detect=1; |
---|
2094 | vers=0; |
---|
2095 | subdir_civ1_new=subdir_civ1; |
---|
2096 | while detect==1 %create a new subdir if the netcdf files already exist |
---|
2097 | for ifile=1:nbfield |
---|
2098 | for j=1:nbslice |
---|
2099 | filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
2100 | detect=exist(filename,'file')==2; |
---|
2101 | if detect% if a netcdf file already exists |
---|
2102 | r=regexp(subdir_civ1_new,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number |
---|
2103 | if isempty(r) |
---|
2104 | r(1).root=[subdir_civ1_new '_']; |
---|
2105 | r(1).num1='0'; |
---|
2106 | end |
---|
2107 | subdir_civ1_new=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1 |
---|
2108 | % indstr=regexp(subdir_civ1_new,'\D'); |
---|
2109 | % if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number |
---|
2110 | % vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1; |
---|
2111 | % subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)]; |
---|
2112 | % else |
---|
2113 | % vers=vers+1; |
---|
2114 | % subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)]; |
---|
2115 | % end |
---|
2116 | subdir_civ2=subdir_civ1_new; |
---|
2117 | break |
---|
2118 | end |
---|
2119 | filecell.nc.civ1(ifile,j)={filename}; |
---|
2120 | end |
---|
2121 | if detect% if a netcdf file already exists |
---|
2122 | break |
---|
2123 | end |
---|
2124 | end |
---|
2125 | |
---|
2126 | %create the new SubdirCiv1 |
---|
2127 | if ~exist(fullfile(RootPath,subdir_civ1_new),'dir') |
---|
2128 | [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new)); |
---|
2129 | if ~strcmp(msg1,'') |
---|
2130 | errormsg=['cannot create ' subdir_civ1_new ': ' msg1];%error message for directory creation |
---|
2131 | return |
---|
2132 | elseif isunix |
---|
2133 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
2134 | if ~strcmp(msg2,'') |
---|
2135 | errormsg=['pb of permission for ' fullfile(RootPath,subdir_civ1_new) ': ' msg2];%error message for directory creation |
---|
2136 | return |
---|
2137 | end |
---|
2138 | end |
---|
2139 | end |
---|
2140 | if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series |
---|
2141 | for ifile=1:nbfield |
---|
2142 | for j=1:nbslice |
---|
2143 | filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
2144 | % filename=name_generator(filebase_A,i1_civ1(ifile),j1_civ1(j),'.nc',NomType_nc,1,i2_civ1(ifile),j2_civ1(j),subdir_civ1_new);% |
---|
2145 | detect=exist(filename,'file')==2; |
---|
2146 | if detect% if a netcdf file already exists |
---|
2147 | indstr=regexp(subdir_civ1_new,'\D'); |
---|
2148 | if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number |
---|
2149 | vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1; |
---|
2150 | subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)]; |
---|
2151 | else |
---|
2152 | vers=vers+1; |
---|
2153 | subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)]; |
---|
2154 | end |
---|
2155 | subdir_civ2=subdir_civ1; |
---|
2156 | break |
---|
2157 | end |
---|
2158 | filecell.ncA.civ1(ifile,j)={filename}; |
---|
2159 | end |
---|
2160 | if detect% if a netcdf file already exists |
---|
2161 | break |
---|
2162 | end |
---|
2163 | end |
---|
2164 | %create the new SubdirCiv1 |
---|
2165 | if ~exist(fullfile(RootPath,subdir_civ1_new),'dir') |
---|
2166 | [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new)); |
---|
2167 | if ~strcmp(msg1,'') |
---|
2168 | errormsg=['cannot create ' subdir_civ1_new ': ' msg1]; |
---|
2169 | return |
---|
2170 | else |
---|
2171 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
2172 | if ~strcmp(msg2,'') |
---|
2173 | errormsg=['pb of permission for ' subdir_civ1_new ': ' msg2];%error message for directory creation |
---|
2174 | return |
---|
2175 | end |
---|
2176 | end |
---|
2177 | end |
---|
2178 | end |
---|
2179 | end |
---|
2180 | subdir_civ1=subdir_civ1_new; |
---|
2181 | % get image names |
---|
2182 | for ifile=1:nbfield |
---|
2183 | for j=1:nbslice |
---|
2184 | filename=fullfile_uvmat(RootPath,SubdirImages,RootFile_ima1,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j)); |
---|
2185 | idetect(j)=exist(filename,'file')==2; |
---|
2186 | filecell.ima1.civ1(ifile,j)={filename}; %first image |
---|
2187 | filename=fullfile_uvmat(RootPath,SubdirImages,RootFile_ima2,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j)); |
---|
2188 | idetect_1(j)=exist(filename,'file')==2; |
---|
2189 | filecell.ima2.civ1(ifile,j)={filename};%second image |
---|
2190 | end |
---|
2191 | [idetectmin,indexj]=min(idetect); |
---|
2192 | if idetectmin==0, |
---|
2193 | errormsg=[filecell.ima1.civ1{ifile,indexj} ' not found']; |
---|
2194 | return |
---|
2195 | end |
---|
2196 | [idetectmin,indexj]=min(idetect_1); |
---|
2197 | if idetectmin==0, |
---|
2198 | errormsg=[filecell.ima2.civ1{ifile,indexj} ' not found']; |
---|
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 | errormsg=[filecell.imaA1.civ1{ifile,indexj} ' not found']; |
---|
2215 | return |
---|
2216 | end |
---|
2217 | [idetectmin,indexj]=min(idetect_1); |
---|
2218 | if idetectmin==0, |
---|
2219 | errormsg=[filecell.imaA2.civ1{ifile,indexj} ' not found']; |
---|
2220 | return |
---|
2221 | end |
---|
2222 | end |
---|
2223 | end |
---|
2224 | |
---|
2225 | %%%%%%%%%%%%% checkfix1 or checkpatch1 activated but no checkciv1 %%%%%%%%%%%%% |
---|
2226 | elseif (checkbox(2)==1 || checkbox(3)==1); |
---|
2227 | for ifile=1:nbfield |
---|
2228 | for j=1:nbslice |
---|
2229 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
2230 | detect=exist(filename,'file')==2; |
---|
2231 | if detect==0 |
---|
2232 | errormsg=[filename ' not found']; |
---|
2233 | return |
---|
2234 | end |
---|
2235 | filecell.nc.civ1(ifile,j)={filename}; |
---|
2236 | end |
---|
2237 | end |
---|
2238 | if strcmp(compare,'stereo PIV') |
---|
2239 | for ifile=1:nbfield |
---|
2240 | for j=1:nbslice |
---|
2241 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
2242 | filecell.ncA.civ1(ifile,j)={filename}; |
---|
2243 | if ~exist(filename,'file') |
---|
2244 | errormsg=['input file ' filename ' not found']; |
---|
2245 | return |
---|
2246 | end |
---|
2247 | end |
---|
2248 | end |
---|
2249 | end |
---|
2250 | end |
---|
2251 | |
---|
2252 | %%%%%%%%%%%%% if checkciv2 performed with pairs different than checkciv1 %%%%%%%%%%%%% |
---|
2253 | testdiff=0; |
---|
2254 | if (checkbox(4)==1)&&... |
---|
2255 | ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1)) |
---|
2256 | testdiff=1; |
---|
2257 | detect=1; |
---|
2258 | vers=0; |
---|
2259 | subdir_civ2_new=subdir_civ2; |
---|
2260 | while detect==1 %create a new subdir if the netcdf files already exist |
---|
2261 | for ifile=1:nbfield |
---|
2262 | for j=1:nbslice |
---|
2263 | filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2264 | detect=exist(filename,'file')==2; |
---|
2265 | if detect% if a netcdf file already exists |
---|
2266 | indstr=regexp(subdir_civ2,'\D'); |
---|
2267 | if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number |
---|
2268 | vers=str2double(subdir_civ2(indstr(end)+1:end))+1; |
---|
2269 | subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)]; |
---|
2270 | else |
---|
2271 | vers=vers+1; |
---|
2272 | subdir_civ2_new=[subdir_civ1 '_' num2str(vers)]; |
---|
2273 | end |
---|
2274 | break |
---|
2275 | end |
---|
2276 | filecell.nc.civ2(ifile,j)={filename}; |
---|
2277 | end |
---|
2278 | if detect% if a netcdf file already exists |
---|
2279 | break |
---|
2280 | end |
---|
2281 | end |
---|
2282 | %create the new subdir_civ2_new |
---|
2283 | if ~exist(fullfile(RootPath,subdir_civ2_new),'dir') |
---|
2284 | [xx,m2]=mkdir(fullfile(RootPath,subdir_civ2_new)); |
---|
2285 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
2286 | if ~isequal(m2,'') |
---|
2287 | errormsg=['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2]; |
---|
2288 | return |
---|
2289 | end |
---|
2290 | end |
---|
2291 | if strcmp(compare,'stereo PIV')%check second nc series |
---|
2292 | for ifile=1:nbfield |
---|
2293 | for j=1:nbslice |
---|
2294 | filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2295 | detect=exist(filename,'file')==2; |
---|
2296 | if detect% if a netcdf file already exists |
---|
2297 | indstr=regexp(subdir_civ2,'\D'); |
---|
2298 | if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number |
---|
2299 | vers=str2double(subdir_civ2(indstr(end)+1:end))+1; |
---|
2300 | subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)]; |
---|
2301 | else |
---|
2302 | vers=vers+1; |
---|
2303 | subdir_civ2_new=[subdir_civ1 '_' num2str(vers)]; |
---|
2304 | end |
---|
2305 | break |
---|
2306 | end |
---|
2307 | filecell.ncA.civ2(ifile,j)={filename}; |
---|
2308 | end |
---|
2309 | if detect% if a netcdf file already exists |
---|
2310 | break |
---|
2311 | end |
---|
2312 | end |
---|
2313 | subdir_civ2=subdir_civ2_new; |
---|
2314 | %create the new SubdirCiv1 |
---|
2315 | if ~exist(fullfile(RootPath,subdir_civ2_new),'dir') |
---|
2316 | [xx,m2]=mkdir(subdir_civ2_new); |
---|
2317 | [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g) |
---|
2318 | if ~isequal(m2,'') |
---|
2319 | errormsg= ['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2];%error message for directory creation |
---|
2320 | return |
---|
2321 | end |
---|
2322 | end |
---|
2323 | end |
---|
2324 | end |
---|
2325 | subdir_civ2=subdir_civ2_new; |
---|
2326 | end |
---|
2327 | |
---|
2328 | %%%%%%%%%%%%% if checkciv2 results are obtained or used %%%%%%%%%%%%% |
---|
2329 | if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2 |
---|
2330 | %check source netcdf file of checkciv1 estimates |
---|
2331 | if checkbox(1)==0; %no civ1 performed |
---|
2332 | for ifile=1:nbfield |
---|
2333 | for j=1:nbslice |
---|
2334 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));% |
---|
2335 | filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file |
---|
2336 | if ~exist(filename,'file') |
---|
2337 | errormsg=['input file ' filename ' not found']; |
---|
2338 | return |
---|
2339 | end |
---|
2340 | if ~testdiff % civ2 or patch2 are written in the same file as civ1 |
---|
2341 | if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated |
---|
2342 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2'); |
---|
2343 | if isfield(Data,'Txt') |
---|
2344 | errormsg=Data.Txt; |
---|
2345 | return |
---|
2346 | elseif ~isempty(Data.CivStage)% case of new civ files |
---|
2347 | if Data.CivStage<4 %test for civ files |
---|
2348 | errormsg=['no civ2 data in ' filename]; |
---|
2349 | return |
---|
2350 | end |
---|
2351 | elseif isempty(Data.civ2)||isequal(Data.civ2,0) |
---|
2352 | errormsg=['no civ2 data in ' filename]; |
---|
2353 | return |
---|
2354 | end |
---|
2355 | elseif checkbox(3)==0; %check the existence of patch if it is not calculated |
---|
2356 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch'); |
---|
2357 | if isfield(Data,'Txt') |
---|
2358 | errormsg=Data.Txt; |
---|
2359 | return |
---|
2360 | elseif ~isempty(Data.CivStage) |
---|
2361 | if Data.CivStage<3 %test for civ files |
---|
2362 | errormsg=['no patch data in ' filename]; |
---|
2363 | return |
---|
2364 | end |
---|
2365 | elseif isempty(Data.patch)||isequal(Data.patch,0) |
---|
2366 | errormsg=['no patch data in ' filename]; |
---|
2367 | return |
---|
2368 | end |
---|
2369 | end |
---|
2370 | end |
---|
2371 | end |
---|
2372 | end |
---|
2373 | if strcmp(compare,'stereo PIV') |
---|
2374 | for ifile=1:nbfield |
---|
2375 | for j=1:nbslice |
---|
2376 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2377 | filecell.ncA.civ2(ifile,j)={filename}; |
---|
2378 | if ~exist(filename,'file') |
---|
2379 | errormsg=['input file ' filename ' not found']; |
---|
2380 | return |
---|
2381 | end |
---|
2382 | end |
---|
2383 | end |
---|
2384 | end |
---|
2385 | end |
---|
2386 | |
---|
2387 | detect=1; |
---|
2388 | % while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data |
---|
2389 | for ifile=1:nbfield |
---|
2390 | for j=1:nbslice |
---|
2391 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2392 | detect=exist(filename,'file')==2; |
---|
2393 | filecell.nc.civ2(ifile,j)={filename}; |
---|
2394 | end |
---|
2395 | end |
---|
2396 | %get first image names for checkciv2 |
---|
2397 | if checkbox(1)==1 && isequal(i1_civ1,i1_civ2) && isequal(j1_civ1,j1_civ2) |
---|
2398 | filecell.ima1.civ2=filecell.ima1.civ1; |
---|
2399 | elseif checkbox(4)==1 |
---|
2400 | for ifile=1:nbfield |
---|
2401 | for j=1:nbslice |
---|
2402 | filename=fullfile_uvmat(RootPath,[],RootFile_ima1,ext_ima,NomType_ima1,i1_civ2(ifile),[],j1_civ2(j)); |
---|
2403 | idetect_2(j)=exist(filename,'file')==2; |
---|
2404 | filecell.ima1.civ2(ifile,j)={filename};%first image |
---|
2405 | end |
---|
2406 | [idetectmin,indexj]=min(idetect_2); |
---|
2407 | if idetectmin==0, |
---|
2408 | errormsg=['input image ' filecell.ima1.civ2{ifile,indexj} ' not found']; |
---|
2409 | return |
---|
2410 | end |
---|
2411 | end |
---|
2412 | end |
---|
2413 | |
---|
2414 | %get second image names for checkciv2 |
---|
2415 | if checkbox(1)==1 && isequal(i2_civ1,i2_civ2) && isequal(j2_civ1,j2_civ2) |
---|
2416 | filecell.ima2.civ2=filecell.ima2.civ1; |
---|
2417 | elseif checkbox(4)==1 |
---|
2418 | for ifile=1:nbfield |
---|
2419 | for j=1:nbslice |
---|
2420 | filename=fullfile_uvmat(RootPath,[],RootFile_ima2,ext_ima,NomType_ima2,i2_civ2(ifile),[],j2_civ2(j)); |
---|
2421 | idetect_3(j)=exist(filename,'file')==2; |
---|
2422 | filecell.ima2.civ2(ifile,j)={filename};%first image |
---|
2423 | end |
---|
2424 | [idetectmin,indexj]=min(idetect_3); |
---|
2425 | if idetectmin==0, |
---|
2426 | errormsg=['input image ' filecell.ima2.civ2{ifile,indexj} ' not found']; |
---|
2427 | return |
---|
2428 | end |
---|
2429 | end |
---|
2430 | end |
---|
2431 | end |
---|
2432 | if (checkbox(5) || checkbox(6)) && ~checkbox(4) % need to read an existing netcdf civ2 file |
---|
2433 | if ~testdiff |
---|
2434 | filecell.nc.civ2=filecell.nc.civ1;% file already checked |
---|
2435 | else % check the civ2 files |
---|
2436 | for ifile=1:nbfield |
---|
2437 | for j=1:nbslice |
---|
2438 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2439 | filecell.nc.civ2(ifile,j)={filename}; |
---|
2440 | if ~exist(filename,'file') |
---|
2441 | errormsg=['input file ' filename ' not found']; |
---|
2442 | return |
---|
2443 | else |
---|
2444 | Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2'); |
---|
2445 | if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files |
---|
2446 | errormsg=['no civ2 data in ' filename]; |
---|
2447 | return |
---|
2448 | elseif isempty(Data.civ2)||isequal(Data.civ2,0) |
---|
2449 | errormsg=['no civ2 data in ' filename]; |
---|
2450 | return |
---|
2451 | end |
---|
2452 | end |
---|
2453 | end |
---|
2454 | end |
---|
2455 | end |
---|
2456 | end |
---|
2457 | |
---|
2458 | %%%%%%%%%%%%% if stereo fields are calculated by PATCH %%%%%%%%%%%%% |
---|
2459 | if strcmp(compare,'stereo PIV') |
---|
2460 | if checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1) |
---|
2461 | for ifile=1:nbfield |
---|
2462 | for j=1:nbslice |
---|
2463 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_AB,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j)); |
---|
2464 | filecell.st(ifile,j)={filename}; |
---|
2465 | end |
---|
2466 | end |
---|
2467 | end |
---|
2468 | if checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1) |
---|
2469 | for ifile=1:nbfield |
---|
2470 | for j=1:nbslice |
---|
2471 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_AB,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j)); |
---|
2472 | filecell.st(ifile,j)={filename}; |
---|
2473 | end |
---|
2474 | end |
---|
2475 | end |
---|
2476 | end |
---|
2477 | set(handles.SubdirCiv1,'String',regexprep(subdir_civ1,['^' SubdirImages],''));%suppress the root SuddirImages;);%update the edit box |
---|
2478 | set(handles.SubdirCiv2,'String',regexprep(subdir_civ2,['^' SubdirImages],''));%update the edit box |
---|
2479 | |
---|
2480 | % For CivX COPY IMAGES TO THE FORMAT .png IF NEEDED |
---|
2481 | if strcmp(CivMode,'CivX') |
---|
2482 | if isequal(NomType_ima1,'*')%case of movie files |
---|
2483 | NomType_imanew1='_i'; |
---|
2484 | else |
---|
2485 | NomType_imanew1=NomType_ima1; |
---|
2486 | end |
---|
2487 | if isequal(NomType_ima2,'*')%case of movie files |
---|
2488 | NomType_imanew2='_i'; |
---|
2489 | else |
---|
2490 | NomType_imanew2=NomType_ima2; |
---|
2491 | end |
---|
2492 | if ~isequal(ext_ima,'.png') |
---|
2493 | %%type of image file |
---|
2494 | type_ima1='none';%default |
---|
2495 | movieobject1=[];%default |
---|
2496 | if strcmpi(ext_ima,'.avi') |
---|
2497 | if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab) |
---|
2498 | type_ima1='movie'; |
---|
2499 | movieobject1=mmreader([filecell.filebase ext_ima]); |
---|
2500 | else |
---|
2501 | type_ima1='avi'; |
---|
2502 | end |
---|
2503 | elseif ischar(ext_ima) && ~isempty(ext_ima(2:end)) |
---|
2504 | form=imformats(ext_ima(2:end)); |
---|
2505 | if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab |
---|
2506 | if isequal(NomType_ima1,'*'); |
---|
2507 | type_ima1='multimage';%image series in a single image file |
---|
2508 | else |
---|
2509 | type_ima1='image'; |
---|
2510 | end |
---|
2511 | end |
---|
2512 | end |
---|
2513 | type_ima2='none';%default |
---|
2514 | movieobject2=[]; |
---|
2515 | if strcmpi(ext_ima,'.avi') |
---|
2516 | if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab) |
---|
2517 | type_ima2='movie'; |
---|
2518 | movieobject2=mmreader([filecell.filebase ext_ima]); |
---|
2519 | else |
---|
2520 | type_ima2='avi'; |
---|
2521 | end |
---|
2522 | elseif ischar(ext_ima) && ~isempty(ext_ima(2:end)) |
---|
2523 | form=imformats(ext_ima(2:end)); |
---|
2524 | if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab |
---|
2525 | if isequal(NomType_ima1,'*'); |
---|
2526 | type_ima2='multimage';%image series in a single image file |
---|
2527 | else |
---|
2528 | type_ima2='image'; |
---|
2529 | end |
---|
2530 | end |
---|
2531 | end |
---|
2532 | if checkbox(1) %if civ1 is performed |
---|
2533 | h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar |
---|
2534 | for ifile=1:nbfield |
---|
2535 | waitbar(ifile/nbfield); |
---|
2536 | for j=1:nbslice |
---|
2537 | filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ1(ifile),[],j1_civ1(j)); |
---|
2538 | if ~exist(filename,'file') |
---|
2539 | A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,i1_civ1(ifile),movieobject1); |
---|
2540 | imwrite(A,filename,'BitDepth',16); |
---|
2541 | end |
---|
2542 | filecell.ima1.civ1(ifile,j)={filename}; |
---|
2543 | filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ1(ifile),[],j2_civ1(j)); |
---|
2544 | if ~exist(filename,'file') |
---|
2545 | A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,i2_civ1(ifile),movieobject2); |
---|
2546 | imwrite(A,filename,'BitDepth',16); |
---|
2547 | end |
---|
2548 | filecell.ima2.civ1(ifile,j)={filename}; |
---|
2549 | end |
---|
2550 | end |
---|
2551 | close(h) |
---|
2552 | end |
---|
2553 | if checkbox(4) %if civ2 is performed |
---|
2554 | h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar |
---|
2555 | for ifile=1:nbfield |
---|
2556 | waitbar(ifile/nbfield); |
---|
2557 | for j=1:nbslice |
---|
2558 | filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ2(ifile),[],j1_civ2(j)); |
---|
2559 | if ~exist(filename,'file') |
---|
2560 | A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,i1_civ2(ifile)); |
---|
2561 | imwrite(A,filename,'BitDepth',16); |
---|
2562 | end |
---|
2563 | filecell.ima1.civ2(ifile,j)={filename}; |
---|
2564 | filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ2(ifile),[],j2_civ2(j)); |
---|
2565 | if ~exist(filename,'file') |
---|
2566 | A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,i2_civ2(ifile)); |
---|
2567 | imwrite(A,filename,'BitDepth',16); |
---|
2568 | end |
---|
2569 | filecell.ima2.civ2(ifile,j)={filename}; |
---|
2570 | end |
---|
2571 | end |
---|
2572 | close(h); |
---|
2573 | end |
---|
2574 | end |
---|
2575 | end |
---|
2576 | |
---|
2577 | %------------------------------------------------------------------------ |
---|
2578 | % --- determine the list of index pairs of processing file |
---|
2579 | function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=... |
---|
2580 | find_pair_indices(handles,ref_i,ref_j,mode) |
---|
2581 | %------------------------------------------------------------------------ |
---|
2582 | |
---|
2583 | list_civ1=get(handles.ListPairCiv1,'String'); |
---|
2584 | index_civ1=get(handles.ListPairCiv1,'Value'); |
---|
2585 | str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1 |
---|
2586 | if isempty(str_civ1)||isequal(str_civ1,'') |
---|
2587 | msgbox_uvmat('ERROR','no image pair selected for civ1') |
---|
2588 | return |
---|
2589 | end |
---|
2590 | list_civ2=get(handles.ListPairCiv2,'String'); |
---|
2591 | index_civ2=get(handles.ListPairCiv2,'Value'); |
---|
2592 | if index_civ2>length(list_civ2) |
---|
2593 | list_civ2=list_civ1; |
---|
2594 | index_civ2=index_civ1; |
---|
2595 | end |
---|
2596 | str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2 |
---|
2597 | |
---|
2598 | if isequal (mode,'series(Di)') |
---|
2599 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
2600 | num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers |
---|
2601 | num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i)); |
---|
2602 | num_a_civ1=ref_j; |
---|
2603 | num_b_civ1=ref_j; |
---|
2604 | num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i)); |
---|
2605 | num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i)); |
---|
2606 | num_a_civ2=ref_j; |
---|
2607 | num_b_civ2=ref_j; |
---|
2608 | |
---|
2609 | % adjust the first and last field number |
---|
2610 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
2611 | if isnan(lastfield) |
---|
2612 | indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1)); |
---|
2613 | else |
---|
2614 | indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1)); |
---|
2615 | end |
---|
2616 | if length(indsel)>=1 |
---|
2617 | firstind=indsel(1); |
---|
2618 | lastind=indsel(end); |
---|
2619 | set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields |
---|
2620 | set(handles.last_i,'String',num2str(ref_i(lastind))) |
---|
2621 | ref_i=ref_i(indsel); |
---|
2622 | num1_civ1=num1_civ1(indsel); |
---|
2623 | num1_civ2=num1_civ2(indsel); |
---|
2624 | num2_civ1=num2_civ1(indsel); |
---|
2625 | num2_civ2=num2_civ2(indsel); |
---|
2626 | end |
---|
2627 | elseif isequal (mode,'series(Dj)') |
---|
2628 | lastfield_j=str2double(get(handles.nb_field2,'String')); |
---|
2629 | num1_civ1=ref_i;% set of first image numbers |
---|
2630 | num2_civ1=ref_i; |
---|
2631 | num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j)); |
---|
2632 | num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j)); |
---|
2633 | num1_civ2=ref_i; |
---|
2634 | num2_civ2=ref_i; |
---|
2635 | num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j)); |
---|
2636 | num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j)); |
---|
2637 | % adjust the first and last field number |
---|
2638 | if isnan(lastfield_j) |
---|
2639 | indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1)); |
---|
2640 | else |
---|
2641 | indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1)); |
---|
2642 | end |
---|
2643 | if length(indsel)>=1 |
---|
2644 | firstind=indsel(1); |
---|
2645 | lastind=indsel(end); |
---|
2646 | set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields |
---|
2647 | set(handles.last_j,'String',num2str(ref_j(lastind))) |
---|
2648 | ref_j=ref_j(indsel); |
---|
2649 | num_a_civ1=num_a_civ1(indsel); |
---|
2650 | num_b_civ1=num_b_civ1(indsel); |
---|
2651 | num_a_civ2=num_a_civ2(indsel); |
---|
2652 | num_b_civ2=num_b_civ2(indsel); |
---|
2653 | end |
---|
2654 | elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) |
---|
2655 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
2656 | num1_civ1=ref_i; |
---|
2657 | num2_civ1=ref_i; |
---|
2658 | num_a_civ1=displ_num(1,index_civ1); |
---|
2659 | num_b_civ1=displ_num(2,index_civ1); |
---|
2660 | num1_civ2=ref_i; |
---|
2661 | num2_civ2=ref_i; |
---|
2662 | num_a_civ2=displ_num(1,index_civ2); |
---|
2663 | num_b_civ2=displ_num(2,index_civ2); |
---|
2664 | elseif isequal(mode,'displacement') |
---|
2665 | num1_civ1=ref_i; |
---|
2666 | num2_civ1=ref_i; |
---|
2667 | num_a_civ1=ref_j; |
---|
2668 | num_b_civ1=ref_j; |
---|
2669 | num1_civ2=ref_i; |
---|
2670 | num2_civ2=ref_i; |
---|
2671 | num_a_civ2=ref_j; |
---|
2672 | num_b_civ2=ref_j; |
---|
2673 | end |
---|
2674 | |
---|
2675 | %------------------------------------------------------------------------ |
---|
2676 | % --- Executes on button press in ListCompareMode. |
---|
2677 | function ListCompareMode_Callback(hObject, eventdata, handles) |
---|
2678 | %------------------------------------------------------------------------ |
---|
2679 | ListCompareMode=get(handles.ListCompareMode,'String'); |
---|
2680 | option=ListCompareMode{get(handles.ListCompareMode,'Value')}; |
---|
2681 | if ~strcmp(option,'PIV') % case 'displacement' or 'stereo PIV' |
---|
2682 | filebase=get(handles.RootPath,'String'); |
---|
2683 | set(handles.sub_txt,'Visible','on') |
---|
2684 | set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible |
---|
2685 | mode_store=get(handles.ListPairMode,'String');%get the present 'mode' |
---|
2686 | set(handles.ListCompareMode,'UserData',mode_store);%store the mode display |
---|
2687 | set(handles.ListPairMode,'Visible','off') |
---|
2688 | |
---|
2689 | %% open an image file with the browser |
---|
2690 | ind_opening=1;%default |
---|
2691 | browse.incr_pair=[0 0]; %default |
---|
2692 | oldfile=get(handles.RootPath,'String'); |
---|
2693 | menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)'; |
---|
2694 | '*.png','.png image files'; ... |
---|
2695 | '*.jpg',' jpeg image files'; ... |
---|
2696 | '*.tif','.tif image files'; ... |
---|
2697 | '*.avi;*.AVI','.avi movie files'; ... |
---|
2698 | '*.*', 'All Files (*.*)'}; |
---|
2699 | if strcmp(option,'displacement') |
---|
2700 | comment='Pick the reference file for displacements'; |
---|
2701 | else |
---|
2702 | comment='Pick a file of the second series'; |
---|
2703 | end |
---|
2704 | [FileName, PathName] = uigetfile( menu, comment,oldfile); |
---|
2705 | fileinput=[PathName FileName];%complete file name |
---|
2706 | sizf=size(fileinput); |
---|
2707 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
2708 | [path,name,ext]=fileparts(fileinput); |
---|
2709 | [path1]=fileparts(filebase); |
---|
2710 | if isunix |
---|
2711 | [status,path]=system(['readlink ' path]); |
---|
2712 | [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths |
---|
2713 | end |
---|
2714 | if ~strcmp(path1,path) |
---|
2715 | msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one') |
---|
2716 | return |
---|
2717 | end |
---|
2718 | if strcmp(option,'displacement') |
---|
2719 | [tild,RootFile_1]=fileparts(name); |
---|
2720 | else |
---|
2721 | [FilePath,FileName,Ext]=fileparts(fileinput); |
---|
2722 | % detect the file type, get the movie object if relevant, and look for the corresponding file series: |
---|
2723 | % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists |
---|
2724 | [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]); |
---|
2725 | |
---|
2726 | % [tild,tild,RootFile_1,tild,tild,tild,tild,tild,nom_type_1]=fileparts_uvmat(fileinput); |
---|
2727 | %[RootFile_1,i1_series,tild,j1_series,tild,nom_type_1,FileType,Object]=find_file_series(PathName,FileName); |
---|
2728 | %check image nom type |
---|
2729 | if ~strcmp(nom_type_1,get(handles.NomType,'String')) |
---|
2730 | 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') |
---|
2731 | return |
---|
2732 | end |
---|
2733 | end |
---|
2734 | %check image extension |
---|
2735 | if ~strcmp(ext,get(handles.ImaExt,'String')) |
---|
2736 | msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one') |
---|
2737 | return |
---|
2738 | end |
---|
2739 | set(handles.RootFile_1,'String',RootFile_1); |
---|
2740 | else |
---|
2741 | set(handles.ListPairMode,'Visible','on') |
---|
2742 | set(handles.RootFile_1,'Visible','Off'); |
---|
2743 | set(handles.sub_txt,'Visible','off') |
---|
2744 | set(handles.RootFile_1,'String',[]); |
---|
2745 | mode_store=get(handles.ListCompareMode,'UserData'); |
---|
2746 | set(handles.ListPairMode,'Value',1) |
---|
2747 | set(handles.ListPairMode,'String',mode_store) |
---|
2748 | set(handles.CheckStereo,'Value',0) |
---|
2749 | set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default |
---|
2750 | end |
---|
2751 | % if strcmp(option,'stereo PIV') && get(handles.CheckPatch1,'Value') |
---|
2752 | % set(handles.CheckStereo,'Visible','on') |
---|
2753 | % else |
---|
2754 | % set(handles.CheckStereo,'Visible','off') |
---|
2755 | % end |
---|
2756 | % if strcmp(option,'stereo PIV') && get(handles.CheckPatch2,'Value') |
---|
2757 | % set(handles.CheckStereo,'Visible','on') |
---|
2758 | % else |
---|
2759 | % set(handles.CheckStereo,'Visible','off') |
---|
2760 | % end |
---|
2761 | ListPairMode_Callback(hObject, eventdata, handles) |
---|
2762 | |
---|
2763 | |
---|
2764 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
2765 | % Callbacks in the uipanel Pair Indices |
---|
2766 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
2767 | %------------------------------------------------------------------------ |
---|
2768 | % --- Executes on button press in ListPairMode. |
---|
2769 | function ListPairMode_Callback(hObject, eventdata, handles) |
---|
2770 | %------------------------------------------------------------------------ |
---|
2771 | compare_list=get(handles.ListCompareMode,'String'); |
---|
2772 | val=get(handles.ListCompareMode,'Value'); |
---|
2773 | compare=compare_list{val}; |
---|
2774 | if strcmp(compare,'displacement')||strcmp(compare,'shift') |
---|
2775 | mode='displacement'; |
---|
2776 | else |
---|
2777 | mode_list=get(handles.ListPairMode,'String'); |
---|
2778 | if ischar(mode_list) |
---|
2779 | mode_list={mode_list}; |
---|
2780 | end |
---|
2781 | mode_value=get(handles.ListPairMode,'Value'); |
---|
2782 | mode=mode_list{mode_value}; |
---|
2783 | end |
---|
2784 | displ_num=[];%default |
---|
2785 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
2786 | % last_i=str2num(get(handles.last_i,'String')); |
---|
2787 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
2788 | TimeUnit=get(handles.TimeUnit,'String'); |
---|
2789 | checkframe=strcmp(TimeUnit,'frame'); |
---|
2790 | siztime=size(time); |
---|
2791 | nbfield=siztime(1)-1; |
---|
2792 | nbfield2=siztime(2)-1; |
---|
2793 | indchosen=1; %%first pair selected by default |
---|
2794 | %displ_num used to define the indices of the civ pairs |
---|
2795 | % in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices |
---|
2796 | % are relative to the reference indices ref_i and ref_j respectively. |
---|
2797 | if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2') |
---|
2798 | dt=1; |
---|
2799 | displ=''; |
---|
2800 | index=0; |
---|
2801 | numlist_a=[]; |
---|
2802 | numlist_B=[]; |
---|
2803 | %get all the time intervals in bursts |
---|
2804 | displ_dt=1;%default |
---|
2805 | nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10 |
---|
2806 | for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode |
---|
2807 | for numod_b=(numod_a+1):nbfield2 |
---|
2808 | index=index+1; |
---|
2809 | numlist_a(index)=numod_a; |
---|
2810 | numlist_b(index)=numod_b; |
---|
2811 | if size(time,2)>1 && ~checkframe |
---|
2812 | dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%first time interval dt |
---|
2813 | displ_dt(index)=dt(numod_a,numod_b); |
---|
2814 | else |
---|
2815 | displ_dt(index)=1; |
---|
2816 | end |
---|
2817 | end |
---|
2818 | end |
---|
2819 | [dtsort,indsort]=sort(displ_dt); |
---|
2820 | if ~isempty(numlist_a) |
---|
2821 | displ_num(1,:)=numlist_a(indsort); |
---|
2822 | displ_num(2,:)=numlist_b(indsort); |
---|
2823 | end |
---|
2824 | displ_num(3,:)=0; |
---|
2825 | displ_num(4,:)=0; |
---|
2826 | enable_j(handles, 'off') |
---|
2827 | elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') |
---|
2828 | index=1:200; |
---|
2829 | displ_num(1,index)=-floor(index/2); |
---|
2830 | displ_num(2,index)=ceil(index/2); |
---|
2831 | displ_num(3:4,index)=zeros(2,200); |
---|
2832 | enable_j(handles, 'on') |
---|
2833 | elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') |
---|
2834 | index=1:200; |
---|
2835 | displ_num(1:2,index)=zeros(2,200); |
---|
2836 | displ_num(3,index)=-floor(index/2); |
---|
2837 | displ_num(4,index)=ceil(index/2); |
---|
2838 | enable_i(handles, 'on') |
---|
2839 | if nbfield2 > 1 |
---|
2840 | enable_j(handles, 'on') |
---|
2841 | else |
---|
2842 | enable_j(handles, 'off') |
---|
2843 | end |
---|
2844 | elseif isequal(mode,'displacement')%the pairs have the same indices |
---|
2845 | displ_num(1,1)=0; |
---|
2846 | displ_num(2,1)=0; |
---|
2847 | displ_num(3,1)=0; |
---|
2848 | displ_num(4,1)=0; |
---|
2849 | if nbfield > 1 || nbfield==0 |
---|
2850 | enable_i(handles, 'on') |
---|
2851 | else |
---|
2852 | enable_j(handles, 'off') |
---|
2853 | end |
---|
2854 | if nbfield2 > 1 |
---|
2855 | enable_j(handles, 'on') |
---|
2856 | else |
---|
2857 | enable_j(handles, 'off') |
---|
2858 | end |
---|
2859 | end |
---|
2860 | set(handles.ListPairCiv1,'UserData',displ_num); |
---|
2861 | errormsg=find_netcpair_civ( handles,1); |
---|
2862 | if ~isempty(errormsg) |
---|
2863 | msgbox_uvmat('ERROR',errormsg) |
---|
2864 | end |
---|
2865 | % find_netcpair_civ2(handles) |
---|
2866 | |
---|
2867 | function enable_i(handles, state) |
---|
2868 | set(handles.itext,'Visible',state) |
---|
2869 | set(handles.first_i,'Visible',state) |
---|
2870 | set(handles.last_i,'Visible',state) |
---|
2871 | set(handles.incr_i,'Visible',state) |
---|
2872 | set(handles.nb_field,'Visible',state) |
---|
2873 | set(handles.ref_i,'Visible',state) |
---|
2874 | |
---|
2875 | function enable_j(handles, state) |
---|
2876 | set(handles.jtext,'Visible',state) |
---|
2877 | set(handles.first_j,'Visible',state) |
---|
2878 | set(handles.last_j,'Visible',state) |
---|
2879 | set(handles.incr_j,'Visible',state) |
---|
2880 | set(handles.nb_field2,'Visible',state) |
---|
2881 | set(handles.ref_j,'Visible',state) |
---|
2882 | |
---|
2883 | |
---|
2884 | %------------------------------------------------------------------------ |
---|
2885 | % --- Executes on selection change in ListPairCiv1. |
---|
2886 | function ListPairCiv1_Callback(hObject, eventdata, handles) |
---|
2887 | %------------------------------------------------------------------------ |
---|
2888 | %reproduce by default the chosen pair in the checkciv2 menu |
---|
2889 | list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs |
---|
2890 | index_pair=get(handles.ListPairCiv1,'Value'); |
---|
2891 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
2892 | % num_a=displ_num(1,index_pair); |
---|
2893 | % num_b=displ_num(2,index_pair); |
---|
2894 | list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs |
---|
2895 | if index_pair<=length(list_pair2) |
---|
2896 | set(handles.ListPairCiv2,'Value',index_pair); |
---|
2897 | end |
---|
2898 | |
---|
2899 | %update first_i and last_i according to the chosen image pairs |
---|
2900 | mode_list=get(handles.ListPairMode,'String'); |
---|
2901 | mode_value=get(handles.ListPairMode,'Value'); |
---|
2902 | mode=mode_list{mode_value}; |
---|
2903 | if isequal(mode,'series(Di)') |
---|
2904 | first_i=str2double(get(handles.first_i,'String')); |
---|
2905 | last_i=str2double(get(handles.last_i,'String')); |
---|
2906 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
2907 | num1=first_i:incr_i:last_i; |
---|
2908 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
2909 | if ~isnan(lastfield) |
---|
2910 | test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ... |
---|
2911 | (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield); |
---|
2912 | num1=num1(test_find); |
---|
2913 | end |
---|
2914 | set(handles.first_i,'String',num2str(num1(1))); |
---|
2915 | set(handles.last_i,'String',num2str(num1(end))); |
---|
2916 | elseif isequal(mode,'series(Dj)') |
---|
2917 | first_j=str2double(get(handles.first_j,'String')); |
---|
2918 | last_j=str2double(get(handles.last_j,'String')); |
---|
2919 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
2920 | num_j=first_j:incr_j:last_j; |
---|
2921 | lastfield2=str2double(get(handles.nb_field2,'String')); |
---|
2922 | if ~isnan(lastfield2) |
---|
2923 | test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... |
---|
2924 | (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); |
---|
2925 | num1=num_j(test_find); |
---|
2926 | end |
---|
2927 | set(handles.first_j,'String',num2str(num1(1))); |
---|
2928 | set(handles.last_j,'String',num2str(num1(end))); |
---|
2929 | end |
---|
2930 | |
---|
2931 | %------------------------------------------------------------------------ |
---|
2932 | % --- Executes on selection change in ListPairCiv2. |
---|
2933 | function ListPairCiv2_Callback(hObject, eventdata, handles) |
---|
2934 | %------------------------------------------------------------------------ |
---|
2935 | index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu |
---|
2936 | |
---|
2937 | %update first_i and last_i according to the chosen image pairs |
---|
2938 | mode_list=get(handles.ListPairMode,'String'); |
---|
2939 | mode_value=get(handles.ListPairMode,'Value'); |
---|
2940 | mode=mode_list{mode_value}; |
---|
2941 | if isequal(mode,'series(Di)') |
---|
2942 | first_i=str2double(get(handles.first_i,'String')); |
---|
2943 | last_i=str2double(get(handles.last_i,'String')); |
---|
2944 | incr_i=str2double(get(handles.incr_i,'String')); |
---|
2945 | num1=first_i:incr_i:last_i; |
---|
2946 | lastfield=str2double(get(handles.nb_field,'String')); |
---|
2947 | if ~isnan(lastfield) |
---|
2948 | test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ... |
---|
2949 | (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield); |
---|
2950 | num1=num1(test_find); |
---|
2951 | end |
---|
2952 | set(handles.first_i,'String',num2str(num1(1))); |
---|
2953 | set(handles.last_i,'String',num2str(num1(end))); |
---|
2954 | elseif isequal(mode,'series(Dj)') |
---|
2955 | first_j=str2double(get(handles.first_j,'String')); |
---|
2956 | last_j=str2double(get(handles.last_j,'String')); |
---|
2957 | incr_j=str2double(get(handles.incr_j,'String')); |
---|
2958 | num_j=first_j:incr_j:last_j; |
---|
2959 | lastfield2=str2double(get(handles.nb_field2,'String')); |
---|
2960 | if ~isnan(lastfield2) |
---|
2961 | test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... |
---|
2962 | (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); |
---|
2963 | num1=num_j(test_find); |
---|
2964 | end |
---|
2965 | set(handles.first_j,'String',num2str(num1(1))); |
---|
2966 | set(handles.last_j,'String',num2str(num1(end))); |
---|
2967 | end |
---|
2968 | |
---|
2969 | %------------------------------------------------------------------------ |
---|
2970 | function ref_i_Callback(hObject, eventdata, handles) |
---|
2971 | %------------------------------------------------------------------------ |
---|
2972 | mode_list=get(handles.ListPairMode,'String'); |
---|
2973 | mode_value=get(handles.ListPairMode,'Value'); |
---|
2974 | mode=mode_list{mode_value}; |
---|
2975 | errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files |
---|
2976 | if isequal(mode,'series(Di)') || ...% we do patch2 only |
---|
2977 | (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) |
---|
2978 | errormsg=find_netcpair_civ( handles,2); |
---|
2979 | end |
---|
2980 | if ~isempty(errormsg) |
---|
2981 | msgbox_uvmat('ERROR',errormsg) |
---|
2982 | end |
---|
2983 | |
---|
2984 | %------------------------------------------------------------------------ |
---|
2985 | function ref_j_Callback(hObject, eventdata, handles) |
---|
2986 | %------------------------------------------------------------------------ |
---|
2987 | mode_list=get(handles.ListPairMode,'String'); |
---|
2988 | mode_value=get(handles.ListPairMode,'Value'); |
---|
2989 | mode=mode_list{mode_value}; |
---|
2990 | if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)') |
---|
2991 | errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files |
---|
2992 | end |
---|
2993 | if isequal(mode,'series(Dj)') || ... |
---|
2994 | (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0) |
---|
2995 | errormsg=find_netcpair_civ(handles,2); |
---|
2996 | end |
---|
2997 | if ~isempty(errormsg) |
---|
2998 | msgbox_uvmat('ERROR',errormsg) |
---|
2999 | end |
---|
3000 | |
---|
3001 | %------------------------------------------------------------------------ |
---|
3002 | % determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of |
---|
3003 | % the field series set by first_i, incr, last_i |
---|
3004 | % index=1: look for pairs for civ1 |
---|
3005 | % index=2: look for pairs for civ2 |
---|
3006 | function errormsg=find_netcpair_civ(handles,index) |
---|
3007 | %------------------------------------------------------------------------ |
---|
3008 | set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock) |
---|
3009 | |
---|
3010 | %% initialisation |
---|
3011 | errormsg=''; |
---|
3012 | browse=get(handles.RootPath,'UserData'); |
---|
3013 | compare_list=get(handles.ListCompareMode,'String'); |
---|
3014 | val=get(handles.ListCompareMode,'Value'); |
---|
3015 | compare=compare_list{val}; |
---|
3016 | if strcmp(compare,'displacement')||strcmp(compare,'shift') |
---|
3017 | mode='displacement'; |
---|
3018 | else |
---|
3019 | mode_list=get(handles.ListPairMode,'String'); |
---|
3020 | mode_value=get(handles.ListPairMode,'Value'); |
---|
3021 | if isempty(mode_list) |
---|
3022 | return |
---|
3023 | end |
---|
3024 | mode=mode_list{mode_value}; |
---|
3025 | end |
---|
3026 | nom_type_ima=get(handles.NomType,'String'); |
---|
3027 | |
---|
3028 | %% determine nom_type_nc, nomenclature type of the .nc files: |
---|
3029 | [nom_type_nc]=nomtype2pair(nom_type_ima,mode); |
---|
3030 | |
---|
3031 | %% reads .nc subdirectoy and image numbers from the interface |
---|
3032 | subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data |
---|
3033 | subdir_civ2=get(handles.SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data |
---|
3034 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
3035 | if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') |
---|
3036 | ref_j=0; |
---|
3037 | else |
---|
3038 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
3039 | if isnan(ref_j) |
---|
3040 | ref_j=1; |
---|
3041 | end |
---|
3042 | end |
---|
3043 | time=get(handles.ImaDoc,'UserData');%get the set of times |
---|
3044 | TimeUnit=get(handles.TimeUnit,'String'); |
---|
3045 | checkframe=strcmp(TimeUnit,'frame'); |
---|
3046 | displ_num=get(handles.ListPairCiv1,'UserData'); |
---|
3047 | |
---|
3048 | %% eliminate the first pairs inconsistent with the position |
---|
3049 | if isempty(displ_num) |
---|
3050 | nbpair=0; |
---|
3051 | else |
---|
3052 | nbpair=length(displ_num(1,:));%nbre of displayed pairs |
---|
3053 | if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') |
---|
3054 | nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index |
---|
3055 | elseif isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
3056 | nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index |
---|
3057 | end |
---|
3058 | end |
---|
3059 | nbpair=min(200,nbpair);%limit the number of displayed pairs to 200 |
---|
3060 | |
---|
3061 | %% case with no Civ1 operation, netcdf files need to exist for reading |
---|
3062 | displ_pair={''}; |
---|
3063 | select=ones(size(1:nbpair));%flag for displayed pairs =1 for display |
---|
3064 | testpair=0; |
---|
3065 | RootPath=get(handles.RootPath,'String'); |
---|
3066 | RootFile=get(handles.RootFile,'String'); |
---|
3067 | if index==1 % case civ1 |
---|
3068 | if ~get(handles.CheckCiv1,'Value') % |
---|
3069 | if ~exist(fullfile(RootPath,subdir_civ1),'dir') |
---|
3070 | errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']; |
---|
3071 | set(handles.ListPairCiv1,'String',{}); |
---|
3072 | return |
---|
3073 | end |
---|
3074 | for ipair=1:nbpair |
---|
3075 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,... |
---|
3076 | ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair)); |
---|
3077 | select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist |
---|
3078 | end |
---|
3079 | % case of no displayed pair |
---|
3080 | if isequal(select,zeros(size(1:nbpair))) |
---|
3081 | if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0]) |
---|
3082 | num_i1=ref_i-floor(browse.incr_pair(1)/2); |
---|
3083 | num_i2=ref_i+ceil(browse.incr_pair(1)/2); |
---|
3084 | num_j1=ref_j-floor(browse.incr_pair(2)/2); |
---|
3085 | num_j2=ref_j+ceil(browse.incr_pair(2)/2); |
---|
3086 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2); |
---|
3087 | select(1)=exist(filename,'file')==2; |
---|
3088 | testpair=1; |
---|
3089 | else |
---|
3090 | if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
3091 | errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]; |
---|
3092 | else |
---|
3093 | errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1]; |
---|
3094 | end |
---|
3095 | set(handles.ListPairCiv1,'String',{''}); |
---|
3096 | %COMPLETER CAS STEREO |
---|
3097 | return |
---|
3098 | end |
---|
3099 | end |
---|
3100 | end |
---|
3101 | else %case civ2 alone |
---|
3102 | if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value') |
---|
3103 | if ~exist(fullfile(RootPath,subdir_civ2),'dir') |
---|
3104 | msgbox_uvmat('ERROR',['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist']) |
---|
3105 | set(handles.ListPairCiv2,'Value',1); |
---|
3106 | set(handles.ListPairCiv2,'String',{''}); |
---|
3107 | return |
---|
3108 | end |
---|
3109 | for ipair=1:nbpair |
---|
3110 | filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,... |
---|
3111 | ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair)); |
---|
3112 | select(ipair)=exist(filename,'file')==2; |
---|
3113 | end |
---|
3114 | if isequal(select,zeros(size(1:nbpair))) |
---|
3115 | if isfield(browse,'incr_pair') |
---|
3116 | num_i1=ref_i-floor(browse.incr_pair(1)/2); |
---|
3117 | num_i2=ref_i+floor((browse.incr_pair(1)+1)/2); |
---|
3118 | num_j1=ref_j-floor(browse.incr_pair(2)/2); |
---|
3119 | num_j2=ref_j+floor((browse.incr_pair(2)+1)/2); |
---|
3120 | filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2); |
---|
3121 | select(1)=exist(filename,'file')==2; |
---|
3122 | else |
---|
3123 | if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') |
---|
3124 | errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2]; |
---|
3125 | else |
---|
3126 | errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2]; |
---|
3127 | end |
---|
3128 | set(handles.ListPairCiv2,'Value',1); |
---|
3129 | set(handles.ListPairCiv2,'String',{''}); |
---|
3130 | return |
---|
3131 | end |
---|
3132 | end |
---|
3133 | end |
---|
3134 | end |
---|
3135 | |
---|
3136 | %% determine the menu display in .ListPairCiv1 |
---|
3137 | % the menu depends on the mode defined in ListPairMode_callback through the array displ_num: |
---|
3138 | % displ_num(1,:)=indices j1 |
---|
3139 | % displ_num(2,:)=indices j2 |
---|
3140 | % displ_num(3,:)=indices i1 |
---|
3141 | % displ_num(4,:)=indices i2 |
---|
3142 | % in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices |
---|
3143 | % are relative to the reference indices ref_i and ref_j respectively. |
---|
3144 | if isequal(mode,'series(Di)') |
---|
3145 | if testpair |
---|
3146 | displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; |
---|
3147 | else |
---|
3148 | for ipair=1:nbpair |
---|
3149 | if select(ipair) |
---|
3150 | displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))]; |
---|
3151 | %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 |
---|
3152 | % 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 |
---|
3153 | 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 |
---|
3154 | 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 |
---|
3155 | else |
---|
3156 | dt=1; |
---|
3157 | end |
---|
3158 | displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; |
---|
3159 | else |
---|
3160 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
3161 | end |
---|
3162 | end |
---|
3163 | end |
---|
3164 | elseif isequal(mode,'series(Dj)') |
---|
3165 | if testpair |
---|
3166 | displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; |
---|
3167 | else |
---|
3168 | for ipair=1:nbpair |
---|
3169 | if select(ipair) |
---|
3170 | displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))]; |
---|
3171 | if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair) |
---|
3172 | 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 |
---|
3173 | displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)]; |
---|
3174 | end |
---|
3175 | else |
---|
3176 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
3177 | end |
---|
3178 | end |
---|
3179 | end |
---|
3180 | elseif isequal(mode,'pair j1-j2')%case of pairs |
---|
3181 | for ipair=1:nbpair |
---|
3182 | if select(ipair) |
---|
3183 | if ~checkframe && size(time,2)>1 |
---|
3184 | 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 |
---|
3185 | else % time set by default to i index |
---|
3186 | dt=1; |
---|
3187 | end |
---|
3188 | displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ... |
---|
3189 | ' :dt= ' num2str(dt*1000)]; |
---|
3190 | else |
---|
3191 | displ_pair{ipair}='...'; %pair not displayed in the menu |
---|
3192 | end |
---|
3193 | end |
---|
3194 | elseif isequal(mode,'displacement') |
---|
3195 | displ_pair={'Di=Dj=0'}; |
---|
3196 | end |
---|
3197 | if index==1 |
---|
3198 | set(handles.ListPairCiv1,'String',displ_pair'); |
---|
3199 | end |
---|
3200 | |
---|
3201 | %% determine the default selection in the pair menu |
---|
3202 | ichoice=find(select,1);% index of selected pair |
---|
3203 | if (isempty(ichoice) || ichoice < 1); ichoice=1; end; |
---|
3204 | initial=get(handles.ListPairCiv1,'Value');%initial choice of pair |
---|
3205 | if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1)) |
---|
3206 | set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu |
---|
3207 | end |
---|
3208 | initial=get(handles.ListPairCiv2,'Value'); |
---|
3209 | if initial>length(displ_pair')%|~isequal(select(initial),1) |
---|
3210 | if ichoice <= length(displ_pair') |
---|
3211 | set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2 |
---|
3212 | else |
---|
3213 | set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2 |
---|
3214 | end |
---|
3215 | end |
---|
3216 | set(handles.ListPairCiv2,'String',displ_pair'); |
---|
3217 | set(gcf,'Pointer','arrow') |
---|
3218 | |
---|
3219 | |
---|
3220 | |
---|
3221 | % %------------------------------------------------------------------------ |
---|
3222 | % % call 'view_field.fig' to display the field selected in the list of 'status' |
---|
3223 | % function open_view_field(hObject, eventdata) |
---|
3224 | % %------------------------------------------------------------------------ |
---|
3225 | % list=get(hObject,'String'); |
---|
3226 | % index=get(hObject,'Value'); |
---|
3227 | % rootroot=get(hObject,'UserData'); |
---|
3228 | % filename=list{index}; |
---|
3229 | % ind_dot=strfind(filename,'...'); |
---|
3230 | % filename=filename(1:ind_dot-1); |
---|
3231 | % filename=fullfile(rootroot,filename); |
---|
3232 | % delete(get(hObject,'parent'))%delete the display figure to stop the check process |
---|
3233 | % if exist(filename,'file')%visualise the vel field if it exists |
---|
3234 | % uvmat(filename) |
---|
3235 | % set(gcbo,'Value',1) |
---|
3236 | % end |
---|
3237 | |
---|
3238 | |
---|
3239 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3240 | % Callbacks in the uipanel Reference Indices |
---|
3241 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3242 | %------------------------------------------------------------------------ |
---|
3243 | function first_i_Callback(hObject, eventdata, handles) |
---|
3244 | %------------------------------------------------------------------------ |
---|
3245 | first_i=str2double(get(handles.first_i,'String')); |
---|
3246 | set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index |
---|
3247 | ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt) |
---|
3248 | |
---|
3249 | %------------------------------------------------------------------------ |
---|
3250 | function first_j_Callback(hObject, eventdata, handles) |
---|
3251 | %------------------------------------------------------------------------ |
---|
3252 | first_j=str2num(get(handles.first_j,'String')); |
---|
3253 | set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index |
---|
3254 | ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt) |
---|
3255 | |
---|
3256 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3257 | % Callbacks in the uipanel Civ1 |
---|
3258 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3259 | %------------------------------------------------------------------------ |
---|
3260 | % --- Executes on button press in SearchRange: determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 |
---|
3261 | function SearchRange_Callback(hObject, eventdata, handles) |
---|
3262 | %------------------------------------------------------------------------ |
---|
3263 | %determine pair numbers |
---|
3264 | if strcmp(get(handles.num_UMin,'Visible'),'off') |
---|
3265 | set(handles.u_title,'Visible','on') |
---|
3266 | set(handles.v_title,'Visible','on') |
---|
3267 | set(handles.num_UMin,'Visible','on') |
---|
3268 | set(handles.num_UMax,'Visible','on') |
---|
3269 | set(handles.num_VMin,'Visible','on') |
---|
3270 | set(handles.num_VMax,'Visible','on') |
---|
3271 | set(handles.CoordUnit,'Visible','on') |
---|
3272 | set(handles.TimeUnit,'Visible','on') |
---|
3273 | set(handles.slash_title,'Visible','on') |
---|
3274 | set(handles.min_title,'Visible','on') |
---|
3275 | set(handles.max_title,'Visible','on') |
---|
3276 | set(handles.unit_title,'Visible','on') |
---|
3277 | else |
---|
3278 | get_search_range(hObject, eventdata, handles) |
---|
3279 | end |
---|
3280 | |
---|
3281 | %------------------------------------------------------------------------ |
---|
3282 | % --- determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 and shift |
---|
3283 | function get_search_range(hObject, eventdata, handles) |
---|
3284 | %------------------------------------------------------------------------ |
---|
3285 | param_civ1=read_GUI(handles.Civ1); |
---|
3286 | umin=param_civ1.UMin; |
---|
3287 | umax=param_civ1.UMax; |
---|
3288 | vmin=param_civ1.VMin; |
---|
3289 | vmax=param_civ1.VMax; |
---|
3290 | %switch min_title and max_title in case of error |
---|
3291 | if umax<=umin |
---|
3292 | umin_old=umin; |
---|
3293 | umin=umax; |
---|
3294 | umax=umin_old; |
---|
3295 | set(handles.num_UMin,'String', num2str(umin)) |
---|
3296 | set(handles.num_UMax,'String', num2str(umax)) |
---|
3297 | end |
---|
3298 | if vmax<=vmin |
---|
3299 | vmin_old=vmin; |
---|
3300 | vmin=vmax; |
---|
3301 | vmax=vmin_old; |
---|
3302 | set(handles.num_VMin,'String', num2str(vmin)) |
---|
3303 | set(handles.num_VMax,'String', num2str(vmax)) |
---|
3304 | end |
---|
3305 | if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax)) |
---|
3306 | list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs |
---|
3307 | index=get(handles.ListPairCiv1,'Value'); |
---|
3308 | pair_string=list_pair{index}; |
---|
3309 | time=get(handles.ImaDoc,'UserData'); %get the set of times |
---|
3310 | pxcm=get(handles.SearchRange,'UserData'); |
---|
3311 | mode_list=get(handles.ListPairMode,'String'); |
---|
3312 | mode_value=get(handles.ListPairMode,'Value'); |
---|
3313 | mode=mode_list{mode_value}; |
---|
3314 | if isequal (mode, 'series(Di)' ) |
---|
3315 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
3316 | num1=ref_i-floor(index/2);% first image numbers |
---|
3317 | num2=ref_i+ceil(index/2); |
---|
3318 | num_a=1; |
---|
3319 | num_b=1; |
---|
3320 | elseif isequal (mode, 'series(Dj)') |
---|
3321 | num1=1; |
---|
3322 | num2=1; |
---|
3323 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
3324 | num_a=ref_j-floor(index/2);% first image numbers |
---|
3325 | num_b=ref_j+ceil(index/2); |
---|
3326 | elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) |
---|
3327 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
3328 | num1=ref_i; |
---|
3329 | num2=ref_i; |
---|
3330 | r=regexp(pair_string,'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names'); |
---|
3331 | if isempty(r) |
---|
3332 | r=regexp(pair_string,'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names'); |
---|
3333 | end |
---|
3334 | num_a=str2num(r.num1); |
---|
3335 | num_b=str2num(r.num2); |
---|
3336 | end |
---|
3337 | dt=time(num2+1,num_b+1)-time(num1+1,num_a+1); |
---|
3338 | ibx=str2double(get(handles.num_CorrBoxSize_1,'String')); |
---|
3339 | iby=str2double(get(handles.num_CorrBoxSize_2,'String')); |
---|
3340 | umin=dt*pxcm*umin; |
---|
3341 | umax=dt*pxcm*umax; |
---|
3342 | vmin=dt*pxcm*vmin; |
---|
3343 | vmax=dt*pxcm*vmax; |
---|
3344 | shiftx=round((umin+umax)/2); |
---|
3345 | shifty=round((vmin+vmax)/2); |
---|
3346 | isx=(umax+2-shiftx)*2+param_civ1.Bx; |
---|
3347 | isx=2*ceil(isx/2)+1; |
---|
3348 | isy=(vmax+2-shifty)*2+param_civ1.Bx; |
---|
3349 | isy=2*ceil(isy/2)+1; |
---|
3350 | set(handles.num_SearchBoxShift_1,'String',num2str(shiftx)); |
---|
3351 | set(handles.num_SearchBoxShift_2,'String',num2str(shifty)); |
---|
3352 | set(handles.num_SearchBoxSize_1,'String',num2str(isx)); |
---|
3353 | set(handles.num_SearchBoxSize_2,'String',num2str(isy)); |
---|
3354 | end |
---|
3355 | |
---|
3356 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3357 | % Callbacks in the uipanel Fix1 |
---|
3358 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
3359 | %------------------------------------------------------------------------ |
---|
3360 | % --- Executes on button press in CheckMask. |
---|
3361 | function get_mask_fix1_Callback(hObject, eventdata, handles) |
---|
3362 | %------------------------------------------------------------------------ |
---|
3363 | maskval=get(handles.CheckMask,'Value'); |
---|
3364 | if isequal(maskval,0) |
---|
3365 | set(handles.Mask,'String','') |
---|
3366 | else |
---|
3367 | mask_displ='no mask'; %default |
---|
3368 | filebase=get(handles.RootPath,'String'); |
---|
3369 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
3370 | if isequal(flag_mask,1) |
---|
3371 | mask_displ=[num2str(nbslice) 'mask']; |
---|
3372 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
3373 | filebase_a=get(handles.RootFile_1,'String'); |
---|
3374 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
3375 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
3376 | mask_displ='no mask'; |
---|
3377 | end |
---|
3378 | end |
---|
3379 | if isequal(mask_displ,'no mask') |
---|
3380 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3381 | {'*.png', ' (*.png)'; |
---|
3382 | '*.png', '.png files '; ... |
---|
3383 | '*.*', 'All Files (*.*)'}, ... |
---|
3384 | 'Pick a mask file *.png',filebase); |
---|
3385 | mask_displ=fullfile(PathName,FileName); |
---|
3386 | if ~exist(mask_displ,'file') |
---|
3387 | mask_displ='no mask'; |
---|
3388 | end |
---|
3389 | end |
---|
3390 | if isequal(mask_displ,'no mask') |
---|
3391 | set(handles.CheckMask,'Value',0) |
---|
3392 | set(handles.CheckMask,'Value',0) |
---|
3393 | set(handles.CheckMask,'Value',0) |
---|
3394 | else |
---|
3395 | %set(handles.CheckMask,'Value',1) |
---|
3396 | set(handles.CheckMask,'Value',1) |
---|
3397 | end |
---|
3398 | set(handles.Mask,'String',mask_displ) |
---|
3399 | set(handles.Mask,'String',mask_displ) |
---|
3400 | set(handles.Mask,'String',mask_displ) |
---|
3401 | end |
---|
3402 | |
---|
3403 | %------------------------------------------------------------------------ |
---|
3404 | % --- Executes on button press in CheckMask: select box for mask option |
---|
3405 | function get_mask_civ2_Callback(hObject, eventdata, handles) |
---|
3406 | %------------------------------------------------------------------------ |
---|
3407 | maskval=get(handles.CheckMask,'Value'); |
---|
3408 | if isequal(maskval,0) |
---|
3409 | set(handles.Mask,'String','') |
---|
3410 | else |
---|
3411 | mask_displ='no mask'; %default |
---|
3412 | filebase=get(handles.RootPath,'String'); |
---|
3413 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
3414 | if isequal(flag_mask,1) |
---|
3415 | mask_displ=[num2str(nbslice) 'mask']; |
---|
3416 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
3417 | filebase_a=get(handles.RootFile_1,'String'); |
---|
3418 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
3419 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
3420 | mask_displ='no mask'; |
---|
3421 | end |
---|
3422 | end |
---|
3423 | if isequal(mask_displ,'no mask') |
---|
3424 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3425 | {'*.png', ' (*.png)'; |
---|
3426 | '*.png', '.png files '; ... |
---|
3427 | '*.*', 'All Files (*.*)'}, ... |
---|
3428 | 'Pick a mask file *.png',filebase); |
---|
3429 | mask_displ=fullfile(PathName,FileName); |
---|
3430 | if ~exist(mask_displ,'file') |
---|
3431 | mask_displ='no mask'; |
---|
3432 | end |
---|
3433 | end |
---|
3434 | if isequal(mask_displ,'no mask') |
---|
3435 | set(handles.CheckMask,'Value',0) |
---|
3436 | set(handles.CheckMask,'Value',0) |
---|
3437 | else |
---|
3438 | set(handles.CheckMask,'Value',1) |
---|
3439 | end |
---|
3440 | set(handles.Mask,'String',mask_displ) |
---|
3441 | set(handles.Mask,'String',mask_displ) |
---|
3442 | end |
---|
3443 | |
---|
3444 | %------------------------------------------------------------------------ |
---|
3445 | % --- Executes on button press in CheckMask. |
---|
3446 | function get_mask_fix2_Callback(hObject, eventdata, handles) |
---|
3447 | %------------------------------------------------------------------------ |
---|
3448 | maskval=get(handles.CheckMask,'Value'); |
---|
3449 | if isequal(maskval,0) |
---|
3450 | set(handles.Mask,'String','') |
---|
3451 | else |
---|
3452 | mask_displ='no mask'; %default |
---|
3453 | filebase=get(handles.RootPath,'String'); |
---|
3454 | [nbslice, flag_mask]=get_mask(filebase,handles); |
---|
3455 | if isequal(flag_mask,1) |
---|
3456 | mask_displ=[num2str(nbslice) 'mask']; |
---|
3457 | elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series |
---|
3458 | filebase_a=get(handles.RootFile_1,'String'); |
---|
3459 | [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); |
---|
3460 | if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice) |
---|
3461 | mask_displ='no mask'; |
---|
3462 | end |
---|
3463 | end |
---|
3464 | if isequal(mask_displ,'no mask') |
---|
3465 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3466 | {'*.png', ' (*.png)'; |
---|
3467 | '*.png', '.png files '; ... |
---|
3468 | '*.*', 'All Files (*.*)'}, ... |
---|
3469 | 'Pick a mask file *.png',filebase); |
---|
3470 | mask_displ=fullfile(PathName,FileName); |
---|
3471 | if ~exist(mask_displ,'file') |
---|
3472 | mask_displ='no mask'; |
---|
3473 | end |
---|
3474 | end |
---|
3475 | if isequal(mask_displ,'no mask') |
---|
3476 | set(handles.CheckMask,'Value',0) |
---|
3477 | end |
---|
3478 | set(handles.Mask,'String',mask_displ) |
---|
3479 | end |
---|
3480 | |
---|
3481 | %------------------------------------------------------------------------ |
---|
3482 | % --- function called to look for mask files |
---|
3483 | function [nbslice, flag_mask]=get_mask(filebase,handles) |
---|
3484 | %------------------------------------------------------------------------ |
---|
3485 | %detect mask files, images with appropriate file base |
---|
3486 | %[filebase '_' xx 'mask'], xx=nbslice |
---|
3487 | %flag_mask=1 indicates detection |
---|
3488 | |
---|
3489 | flag_mask=0;%default |
---|
3490 | nbslice=1; |
---|
3491 | |
---|
3492 | % subdir=get(handles.SubdirCiv1,'String'); |
---|
3493 | [Path,Name]=fileparts(filebase); |
---|
3494 | if ~isdir(Path) |
---|
3495 | msgbox_uvmat('ERROR','no path for input files') |
---|
3496 | return |
---|
3497 | end |
---|
3498 | % currentdir=pwd; |
---|
3499 | % cd(Path);%move in the dir of the root name filebase |
---|
3500 | maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files |
---|
3501 | % cd(currentdir);%come back to the current working directory |
---|
3502 | if ~isempty(maskfiles) |
---|
3503 | % msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat') |
---|
3504 | % else |
---|
3505 | flag_mask=1; |
---|
3506 | maskname=maskfiles(1).name;% take the first mask file in the list |
---|
3507 | [Path2,Name,ext]=fileparts(maskname); |
---|
3508 | Namedouble=double(Name); |
---|
3509 | val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters |
---|
3510 | ind_mask=findstr('mask',Name); |
---|
3511 | i=ind_mask-1; |
---|
3512 | while val(i)==0 && i>0 |
---|
3513 | i=i-1; |
---|
3514 | end |
---|
3515 | nbslice=str2double(Name(i+1:ind_mask-1)); |
---|
3516 | if ~isnan(nbslice) && Name(i)=='_' |
---|
3517 | flag_mask=1; |
---|
3518 | else |
---|
3519 | msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2]) |
---|
3520 | return |
---|
3521 | nbslice=1; |
---|
3522 | end |
---|
3523 | end |
---|
3524 | |
---|
3525 | %------------------------------------------------------------------------ |
---|
3526 | % --- function called to look for grid files |
---|
3527 | function [nbslice, flag_mask]=get_grid(filebase,handles) |
---|
3528 | %------------------------------------------------------------------------ |
---|
3529 | flag_mask=0;%default |
---|
3530 | nbslice=1; |
---|
3531 | [Path,Name]=fileparts(filebase); |
---|
3532 | currentdir=pwd; |
---|
3533 | cd(Path);%move in the dir of the root name filebase |
---|
3534 | maskfiles=dir([Name '_*grid_*.grid']);%look for mask files |
---|
3535 | cd(currentdir);%come back to the current working directory |
---|
3536 | if ~isempty(maskfiles) |
---|
3537 | flag_mask=1; |
---|
3538 | maskname=maskfiles(1).name;% take the first mask file in the list |
---|
3539 | [Path2,Name,ext]=fileparts(maskname); |
---|
3540 | Namedouble=double(Name); |
---|
3541 | val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters |
---|
3542 | ind_mask=findstr('grid',Name); |
---|
3543 | i=ind_mask-1; |
---|
3544 | while val(i)==0 && i>0 |
---|
3545 | i=i-1; |
---|
3546 | end |
---|
3547 | nbslice=str2double(Name(i+1:ind_mask-1)); |
---|
3548 | if ~isnan(nbslice) && Name(i)=='_' |
---|
3549 | flag_mask=1; |
---|
3550 | else |
---|
3551 | msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2]) |
---|
3552 | return |
---|
3553 | nbslice=1; |
---|
3554 | end |
---|
3555 | end |
---|
3556 | |
---|
3557 | %------------------------------------------------------------------------ |
---|
3558 | % --- transform numbers to letters |
---|
3559 | function str=num2stra(num,nom_type) |
---|
3560 | %------------------------------------------------------------------------ |
---|
3561 | if isempty(nom_type) |
---|
3562 | str=''; |
---|
3563 | elseif strcmp(nom_type(end),'a') |
---|
3564 | str=char(96+num); |
---|
3565 | elseif strcmp(nom_type(end),'A') |
---|
3566 | str=char(96+num); |
---|
3567 | elseif isempty(nom_type(2:end))%a single index |
---|
3568 | str=''; |
---|
3569 | else |
---|
3570 | str=num2str(num); |
---|
3571 | end |
---|
3572 | |
---|
3573 | % %------------------------------------------------------------------------ |
---|
3574 | % % --- Executes on button press in ListSubdirCiv1. |
---|
3575 | % function ListSubdirCiv1_Callback(hObject, eventdata, handles) |
---|
3576 | % %------------------------------------------------------------------------ |
---|
3577 | % list_subdir_civ1=get(handles.ListSubdirCiv1,'String'); |
---|
3578 | % val=get(handles.ListSubdirCiv1,'Value'); |
---|
3579 | % SubDir=list_subdir_civ1{val}; |
---|
3580 | % if strcmp(SubDir,'new...') |
---|
3581 | % if get(handles.CheckCiv1,'Value') |
---|
3582 | % SubDir='CIV'; %default subdirectory |
---|
3583 | % else |
---|
3584 | % msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation') |
---|
3585 | % return |
---|
3586 | % end |
---|
3587 | % end |
---|
3588 | % set(handles.SubdirCiv1,'String',SubDir); |
---|
3589 | % errormsg=find_netcpair_civ(handles,1); |
---|
3590 | % if ~isempty(errormsg) |
---|
3591 | % msgbox_uvmat('ERROR',errormsg) |
---|
3592 | % end |
---|
3593 | % |
---|
3594 | %------------------------------------------------------------------------ |
---|
3595 | % % --- Executes on button press in ListSubdirCiv2. |
---|
3596 | % function ListSubdirCiv2_Callback(hObject, eventdata, handles) |
---|
3597 | % %------------------------------------------------------------------------ |
---|
3598 | % list_subdir_civ2=get(handles.ListSubdirCiv2,'String'); |
---|
3599 | % val=get(handles.ListSubdirCiv2,'Value'); |
---|
3600 | % SubDir=list_subdir_civ2{val}; |
---|
3601 | % if strcmp(SubDir,'new...') |
---|
3602 | % if get(handles.CheckCiv2,'Value') |
---|
3603 | % SubDir='CIV'; %default subdirectory |
---|
3604 | % else |
---|
3605 | % msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation') |
---|
3606 | % return |
---|
3607 | % end |
---|
3608 | % end |
---|
3609 | % set(handles.SubdirCiv2,'String',SubDir); |
---|
3610 | |
---|
3611 | %------------------------------------------------------------------------ |
---|
3612 | % --- Executes on button press in CheckGrid. |
---|
3613 | function CheckGrid_Callback(hObject, eventdata, handles) |
---|
3614 | %------------------------------------------------------------------------ |
---|
3615 | value=get(hObject,'Value'); |
---|
3616 | hparent=get(hObject,'parent'); |
---|
3617 | hchildren=get(hparent,'children'); |
---|
3618 | handle_txtbox=findobj(hchildren,'tag','txt_Grid'); |
---|
3619 | handle_dx=findobj(hchildren,'tag','num_Dx'); |
---|
3620 | handle_dy=findobj(hchildren,'tag','num_Dy'); |
---|
3621 | handle_title_dx=findobj(hchildren,'tag','title_Dx'); |
---|
3622 | handle_title_dy=findobj(hchildren,'tag','title_Dy'); |
---|
3623 | testgrid=0; |
---|
3624 | filegrid=''; |
---|
3625 | if value |
---|
3626 | filebase=get(handles.RootPath,'String'); |
---|
3627 | [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name |
---|
3628 | if isequal(flag_grid,1) |
---|
3629 | filegrid=[num2str(nbslice) 'grid']; |
---|
3630 | testgrid=1; |
---|
3631 | else % browse for a grid |
---|
3632 | filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData |
---|
3633 | if exist(filegrid,'file') |
---|
3634 | filebase=filegrid; |
---|
3635 | end |
---|
3636 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3637 | {'*.grid', ' (*.grid)'; |
---|
3638 | '*.grid', '.grid files '; ... |
---|
3639 | '*.*', 'All Files (*.*)'}, ... |
---|
3640 | 'Pick a file',filebase); |
---|
3641 | filegrid=fullfile(PathName,FileName); |
---|
3642 | set(hObject,'UserData',filegrid);%store for future use |
---|
3643 | if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file')) |
---|
3644 | testgrid=1; |
---|
3645 | end |
---|
3646 | end |
---|
3647 | end |
---|
3648 | if testgrid |
---|
3649 | set(handle_dx,'Visible','off'); |
---|
3650 | set(handle_dy,'Visible','off'); |
---|
3651 | set(handle_title_dy,'Visible','off'); |
---|
3652 | set(handle_title_dx,'Visible','off'); |
---|
3653 | set(handle_txtbox,'Visible','on') |
---|
3654 | set(handle_txtbox,'String',filegrid) |
---|
3655 | else |
---|
3656 | set(hObject,'Value',0); |
---|
3657 | set(handle_dx,'Visible','on'); |
---|
3658 | set(handle_dy,'Visible','on'); |
---|
3659 | set(handle_title_dy,'Visible','on'); |
---|
3660 | set(handle_title_dx,'Visible','on'); |
---|
3661 | set(handle_txtbox,'Visible','off') |
---|
3662 | end |
---|
3663 | |
---|
3664 | %% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame |
---|
3665 | PanelName=get(hparent,'tag'); |
---|
3666 | if strcmp(PanelName,'Civ1') |
---|
3667 | hchildren=get(handles.Civ2,'children'); |
---|
3668 | handle_checkbox=findobj(hchildren,'tag','CheckGrid'); |
---|
3669 | handle_txtbox=findobj(hchildren,'tag','txt_Grid'); |
---|
3670 | handle_dx=findobj(hchildren,'tag','num_Dx'); |
---|
3671 | handle_dy=findobj(hchildren,'tag','num_Dy'); |
---|
3672 | handle_title_dx=findobj(hchildren,'tag','title_Dx'); |
---|
3673 | handle_title_dy=findobj(hchildren,'tag','title_Dy'); |
---|
3674 | set(handle_checkbox,'UserData',filegrid);%store for future use |
---|
3675 | if testgrid |
---|
3676 | set(handle_checkbox,'Value',1); |
---|
3677 | set(handle_dx,'Visible','off'); |
---|
3678 | set(handle_dy,'Visible','off'); |
---|
3679 | set(handle_title_dx,'Visible','off'); |
---|
3680 | set(handle_title_dy,'Visible','off'); |
---|
3681 | set(handle_txtbox,'Visible','on') |
---|
3682 | set(handle_txtbox,'String',filegrid) |
---|
3683 | % else |
---|
3684 | % set(handle_checkbox,'Value',0); |
---|
3685 | % set(handles.CheckGrid,'Value',0); |
---|
3686 | % set(handle_dx,'Visible','on'); |
---|
3687 | % set(handle_dy,'Visible','on'); |
---|
3688 | % set(handle_title_dx,'Visible','on'); |
---|
3689 | % set(handle_title_dy,'Visible','on'); |
---|
3690 | % set(handle_txtbox,'Visible','off') |
---|
3691 | end |
---|
3692 | end |
---|
3693 | |
---|
3694 | %------------------------------------------------------------------------ |
---|
3695 | % --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..) |
---|
3696 | function CheckMask_Callback(hObject, eventdata, handles) |
---|
3697 | %------------------------------------------------------------------------ |
---|
3698 | value=get(hObject,'Value'); |
---|
3699 | hparent=get(hObject,'parent'); |
---|
3700 | parent_tag=get(hparent,'Tag'); |
---|
3701 | hchildren=get(hparent,'children'); |
---|
3702 | handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel |
---|
3703 | testmask=0; |
---|
3704 | if value |
---|
3705 | filebase=get(handles.RootPath,'String'); |
---|
3706 | [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name |
---|
3707 | if isequal(flag_mask,1) |
---|
3708 | filemask=[num2str(nbslice) 'mask']; |
---|
3709 | testmask=1; |
---|
3710 | else % browse for a mask |
---|
3711 | filemask=get(hObject,'UserData');%look for previous mask name stored as UserData |
---|
3712 | if exist(filemask,'file') |
---|
3713 | filebase=filemask; |
---|
3714 | end |
---|
3715 | [FileName, PathName] = uigetfile( ... |
---|
3716 | {'*.png', ' (*.png)'; |
---|
3717 | '*.png', '.png files '; ... |
---|
3718 | '*.*', 'All Files (*.*)'}, ... |
---|
3719 | 'Pick a mask file *.png',filebase); |
---|
3720 | filemask=fullfile(PathName,FileName); |
---|
3721 | set(hObject,'UserData',filemask);%store for future use |
---|
3722 | if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file')) |
---|
3723 | testmask=1; |
---|
3724 | end |
---|
3725 | end |
---|
3726 | end |
---|
3727 | if testmask |
---|
3728 | if strcmp(parent_tag,'Civ1') |
---|
3729 | set(handles.Mask,'Visible','on') |
---|
3730 | set(handles.Mask,'String',filemask) |
---|
3731 | set(handles.CheckMask,'Value',1) |
---|
3732 | end |
---|
3733 | % switch parent_tag |
---|
3734 | % % case 'Fix1' |
---|
3735 | % % stage=2; |
---|
3736 | % case 'Civ2' |
---|
3737 | % stage=3; |
---|
3738 | % % case 'Fix2' |
---|
3739 | % % stage=4; |
---|
3740 | % end |
---|
3741 | % set(handles.Mask(stage:end),'Visible','on') |
---|
3742 | % set(handles.Mask(stage:end),'String',filemask) |
---|
3743 | % set(handles.CheckMask(stage:end),'Value',1) |
---|
3744 | else |
---|
3745 | set(hObject,'Value',0); |
---|
3746 | set(handle_txtbox,'Visible','off') |
---|
3747 | end |
---|
3748 | |
---|
3749 | |
---|
3750 | % --- Executes on button press in get_gridpatch1. |
---|
3751 | function get_gridpatch1_Callback(hObject, eventdata, handles) |
---|
3752 | filebase=get(handles.RootPath,'String'); |
---|
3753 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3754 | {'*.grid', ' (*.grid)'; |
---|
3755 | '*.grid', '.grid files '; ... |
---|
3756 | '*.*', 'All Files (*.*)'}, ... |
---|
3757 | 'Pick a file',filebase); |
---|
3758 | filegrid=fullfile(PathName,FileName); |
---|
3759 | set(handles.grid_patch1,'string',filegrid); |
---|
3760 | |
---|
3761 | |
---|
3762 | %------------------------------------------------------------------------ |
---|
3763 | % --- Executes on button press in get_gridpatch2. |
---|
3764 | function get_gridpatch2_Callback(hObject, eventdata, handles) |
---|
3765 | %------------------------------------------------------------------------ |
---|
3766 | |
---|
3767 | |
---|
3768 | %------------------------------------------------------------------------ |
---|
3769 | % --- STEREO Interp |
---|
3770 | 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) |
---|
3771 | %------------------------------------------------------------------------ |
---|
3772 | namelog=[filename_nc(1:end-3) '_stinterp.log']; |
---|
3773 | cmd=[stinterpBin ' -f1 ' filename_A_nc ' -f2 ' filename_B_nc ' -f ' filename_nc ... |
---|
3774 | ' -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 |
---|
3775 | |
---|
3776 | %------------------------------------------------------------------------ |
---|
3777 | %--read images and convert them to the uint16 format used for PIV |
---|
3778 | function A=read_image(filename,type_ima,num,movieobject) |
---|
3779 | %------------------------------------------------------------------------ |
---|
3780 | %num is the view number needed for an avi movie |
---|
3781 | switch type_ima |
---|
3782 | case 'movie' |
---|
3783 | A=read(movieobject,num); |
---|
3784 | case 'avi' |
---|
3785 | mov=aviread(filename,num); |
---|
3786 | A=frame2im(mov(1)); |
---|
3787 | case 'multimage' |
---|
3788 | A=imread(filename,num); |
---|
3789 | case 'image' |
---|
3790 | A=imread(filename); |
---|
3791 | end |
---|
3792 | siz=size(A); |
---|
3793 | if length(siz)==3;%color images |
---|
3794 | A=sum(double(A),3); |
---|
3795 | A=uint16(A); |
---|
3796 | end |
---|
3797 | |
---|
3798 | |
---|
3799 | %------------------------------------------------------------------------ |
---|
3800 | % --- Executes on button press in get_ref_fix1. |
---|
3801 | function get_ref_fix1_Callback(hObject, eventdata, handles) |
---|
3802 | %------------------------------------------------------------------------ |
---|
3803 | filebase=get(handles.RootPath,'String'); |
---|
3804 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3805 | {'*.nc', ' (*.nc)'; |
---|
3806 | '*.nc', 'netcdf files '; ... |
---|
3807 | '*.*', 'All Files (*.*)'}, ... |
---|
3808 | 'Pick a file',filebase); |
---|
3809 | |
---|
3810 | fileinput=[PathName FileName]; |
---|
3811 | sizf=size(fileinput); |
---|
3812 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
3813 | %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); |
---|
3814 | [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput); |
---|
3815 | ref.filebase=fullfile(Path,File); |
---|
3816 | % ref.num_a=stra2num(str_a); |
---|
3817 | % ref.num_b=stra2num(str_b); |
---|
3818 | % ref.num1=str2double(field_count); |
---|
3819 | % ref.num2=str2double(str2); |
---|
3820 | browse=[];%initialisation |
---|
3821 | if ~isequal(ref.ext,'.nc') |
---|
3822 | msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') |
---|
3823 | return |
---|
3824 | end |
---|
3825 | set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']); |
---|
3826 | set(handles.ref_fix1,'UserData',ref) |
---|
3827 | menu_field{1}='civ1'; |
---|
3828 | Data=nc2struct(fileinput,[]); |
---|
3829 | if isfield(Data,'patch') && isequal(Data.patch,1) |
---|
3830 | menu_field{2}='filter1'; |
---|
3831 | end |
---|
3832 | if isfield(Data,'civ2') && isequal(Data.civ2,1) |
---|
3833 | menu_field{3}='civ2'; |
---|
3834 | end |
---|
3835 | if isfield(Data,'patch2') && isequal(Data.patch2,1) |
---|
3836 | menu_field{4}='filter2'; |
---|
3837 | end |
---|
3838 | set(handles.field_ref1,'String',menu_field); |
---|
3839 | set(handles.field_ref1,'Value',length(menu_field)); |
---|
3840 | set(handles.num_MinVel,'Value',2); |
---|
3841 | set(handles.num_MinVel,'String','1');%default threshold |
---|
3842 | set(handles.ref_fix1,'Enable','on') |
---|
3843 | |
---|
3844 | %------------------------------------------------------------------------ |
---|
3845 | % --- Executes on button press in get_ref_fix2. |
---|
3846 | function get_ref_fix2_Callback(hObject, eventdata, handles) |
---|
3847 | %------------------------------------------------------------------------ |
---|
3848 | if isequal(get(handles.get_ref_fix2,'Value'),1) |
---|
3849 | filebase=get(handles.RootPath,'String'); |
---|
3850 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
3851 | {'*.nc', ' (*.nc)'; |
---|
3852 | '*.nc', 'netcdf files '; ... |
---|
3853 | '*.*', 'All Files (*.*)'}, ... |
---|
3854 | 'Pick a file',filebase); |
---|
3855 | fileinput=[PathName FileName]; |
---|
3856 | sizf=size(fileinput); |
---|
3857 | if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string |
---|
3858 | %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); |
---|
3859 | [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput); |
---|
3860 | ref.filebase=fullfile(Path,File); |
---|
3861 | % ref.num_a=stra2num(str_a); |
---|
3862 | % ref.num_b=stra2num(str_b); |
---|
3863 | % ref.num1=str2num(field_count); |
---|
3864 | % ref.num2=str2num(str2); |
---|
3865 | browse=[];%initialisation |
---|
3866 | if ~isequal(ref.ext,'.nc') |
---|
3867 | msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') |
---|
3868 | return |
---|
3869 | end |
---|
3870 | set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']); |
---|
3871 | set(handles.ref_fix2,'UserData',ref) |
---|
3872 | menu_field{1}='civ1'; |
---|
3873 | Data=nc2struct(fileinput,[]); |
---|
3874 | if isfield(Data,'patch') && isequal(Data.patch,1) |
---|
3875 | menu_field{2}='filter1'; |
---|
3876 | end |
---|
3877 | if isfield(Data,'civ2') && isequal(Data.civ2,1) |
---|
3878 | menu_field{3}='civ2'; |
---|
3879 | end |
---|
3880 | if isfield(Data,'patch2') && isequal(Data.patch2,1) |
---|
3881 | menu_field{4}='filter2'; |
---|
3882 | end |
---|
3883 | set(handles.field_ref2,'String',menu_field); |
---|
3884 | set(handles.field_ref2,'Value',length(menu_field)); |
---|
3885 | set(handles.num_MinVel,'Value',2); |
---|
3886 | set(handles.num_MinVel,'String','1');%default threshold |
---|
3887 | set(handles.ref_fix2,'Enable','on') |
---|
3888 | set(handles.ref_fix2,'Visible','on') |
---|
3889 | set(handles.field_ref2,'Visible','on') |
---|
3890 | else |
---|
3891 | set(handles.ref_fix2,'Visible','off') |
---|
3892 | set(handles.field_ref2,'Visible','off') |
---|
3893 | end |
---|
3894 | |
---|
3895 | %------------------------------------------------------------------------ |
---|
3896 | function ref_fix1_Callback(hObject, eventdata, handles) |
---|
3897 | %------------------------------------------------------------------------ |
---|
3898 | set(handles.num_MinVel,'Value',1); |
---|
3899 | set(handles.field_ref1,'Value',1) |
---|
3900 | set(handles.field_ref1,'String',{' '}) |
---|
3901 | set(handles.ref_fix1,'UserData',[]); |
---|
3902 | set(handles.ref_fix1,'String',''); |
---|
3903 | set(handles.thresh_vel1,'String','0'); |
---|
3904 | |
---|
3905 | %------------------------------------------------------------------------ |
---|
3906 | function ref_fix2_Callback(hObject, eventdata, handles) |
---|
3907 | %------------------------------------------------------------------------ |
---|
3908 | set(handles.num_MinVel,'Value',1); |
---|
3909 | set(handles.field_ref2,'Value',1) |
---|
3910 | set(handles.field_ref2,'String',{' '}) |
---|
3911 | set(handles.ref_fix2,'UserData',[]); |
---|
3912 | set(handles.ref_fix2,'String',''); |
---|
3913 | set(handles.num_MinVel,'String','0'); |
---|
3914 | |
---|
3915 | %------------------------------------------------------------------------ |
---|
3916 | % --- TO ABANDON Executes on button press in test_stereo1. |
---|
3917 | function CheckStereo_Callback(hObject, eventdata, handles) |
---|
3918 | %------------------------------------------------------------------------ |
---|
3919 | hparent=get(hObject,'parent'); |
---|
3920 | parent_tag=get(hparent,'Tag'); |
---|
3921 | hchildren=get(hparent,'children'); |
---|
3922 | handle_txtbox=findobj(hchildren,'tag','txt_Mask'); |
---|
3923 | if isequal(get(hObject,'Value'),0) |
---|
3924 | set(handles.num_SubdomainSize,'Visible','on') |
---|
3925 | set(handles.num_FieldSmooth,'Visible','on') |
---|
3926 | else |
---|
3927 | set(handles.num_SubdomainSize,'Visible','off') |
---|
3928 | set(handles.num_FieldSmooth,'Visible','off') |
---|
3929 | end |
---|
3930 | |
---|
3931 | % %------------------------------------------------------------------------ |
---|
3932 | % % --- Executes on button press in CheckStereo. |
---|
3933 | % function StereoCheck_Callback(hObject, eventdata, handles) |
---|
3934 | % %------------------------------------------------------------------------ |
---|
3935 | % if isequal(get(handles.CheckStereo,'Value'),0) |
---|
3936 | % set(handles.num_SubdomainSize,'Visible','on') |
---|
3937 | % set(handles.num_FieldSmooth,'Visible','on') |
---|
3938 | % else |
---|
3939 | % set(handles.num_SubdomainSize,'Visible','off') |
---|
3940 | % set(handles.num_FieldSmooth,'Visible','off') |
---|
3941 | % end |
---|
3942 | |
---|
3943 | %------------------------------------------------------------------------ |
---|
3944 | % --- Executes on button press in TestCiv1: prepare the image correlation function |
---|
3945 | % activated by mouse motion |
---|
3946 | function TestCiv1_Callback(hObject, eventdata, handles) |
---|
3947 | %------------------------------------------------------------------------ |
---|
3948 | drawnow |
---|
3949 | if get(handles.TestCiv1,'Value') |
---|
3950 | set(handles.TestCiv1,'BackgroundColor',[0.7 0.7 0.7])% paint TestCiv1 button to grey to confirm civ launch |
---|
3951 | ref_i=str2double(get(handles.ref_i,'String'));% read reference i index |
---|
3952 | if strcmp(get(handles.ref_j,'Visible'),'on') |
---|
3953 | ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant |
---|
3954 | else |
---|
3955 | ref_j=1;%default j index |
---|
3956 | end |
---|
3957 | [filecell,i1,i2]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices |
---|
3958 | Data.ListVarName={'ny','nx','A'}; |
---|
3959 | Data.VarDimName= {'ny','nx',{'ny','nx'}}; |
---|
3960 | |
---|
3961 | Data.A=imread(filecell.ima1.civ1{1}); % read the first image |
---|
3962 | if ndims(Data.A)==3 %case of color image |
---|
3963 | Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}}; |
---|
3964 | end |
---|
3965 | Data.ny=[size(Data.A,1) 1]; |
---|
3966 | Data.nx=[1 size(Data.A,2)]; |
---|
3967 | Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly |
---|
3968 | par_civ1=read_GUI(handles.Civ1); |
---|
3969 | par_civ1.FileTypeA=get_file_type(filecell.ima1.civ1{1}); |
---|
3970 | par_civ1.ImageWidth=size(Data.A,2); |
---|
3971 | par_civ1.ImageHeight=size(Data.A,1); |
---|
3972 | par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation |
---|
3973 | par_civ1.FrameIndexA=num2str(i1); |
---|
3974 | par_civ1.FrameIndexB=num2str(i2); |
---|
3975 | Param.Civ1=par_civ1; |
---|
3976 | Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV |
---|
3977 | hview_field=view_field(Data); %view the image in the GUI view_field |
---|
3978 | set(0,'CurrentFigure',hview_field) |
---|
3979 | hhview_field=guihandles(hview_field); |
---|
3980 | set(hview_field,'CurrentAxes',hhview_field.axes3) |
---|
3981 | ViewData=get(hview_field,'UserData'); |
---|
3982 | ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field |
---|
3983 | ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field |
---|
3984 | ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory |
---|
3985 | ViewData.axes3.Y=Grid.Civ1_Y; |
---|
3986 | set(hview_field,'UserData',ViewData) |
---|
3987 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
3988 | if isempty(corrfig) |
---|
3989 | corrfig=figure; |
---|
3990 | set(corrfig,'tag','corrfig') |
---|
3991 | set(corrfig,'name','image correlation') |
---|
3992 | set(corrfig,'DeleteFcn',{@closeview_field})% |
---|
3993 | end |
---|
3994 | set(handles.TestCiv1,'BackgroundColor',[1 0 0]) |
---|
3995 | else |
---|
3996 | set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red |
---|
3997 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
3998 | if ~isempty(corrfig) |
---|
3999 | delete(corrfig) |
---|
4000 | end |
---|
4001 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
4002 | if ~isempty(hview_field) |
---|
4003 | delete(hview_field) |
---|
4004 | end |
---|
4005 | end |
---|
4006 | |
---|
4007 | %------------------------------------------------------------------------ |
---|
4008 | %----function introduced for the correlation window figure, activated by deleting this window |
---|
4009 | function closeview_field(gcbo,eventdata) |
---|
4010 | %------------------------------------------------------------------------ |
---|
4011 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
4012 | if ~isempty(hview_field) |
---|
4013 | delete(hview_field) |
---|
4014 | end |
---|
4015 | |
---|
4016 | %------------------------------------------------------------------------ |
---|
4017 | % --- Executes on button press in CheckThreshold. |
---|
4018 | function CheckThreshold_Callback(hObject, eventdata, handles) |
---|
4019 | %------------------------------------------------------------------------ |
---|
4020 | huipanel=get(hObject,'parent'); |
---|
4021 | obj(1)=findobj(huipanel,'Tag','num_MinIma'); |
---|
4022 | obj(2)=findobj(huipanel,'Tag','num_MaxIma'); |
---|
4023 | obj(3)=findobj(huipanel,'Tag','title_Threshold'); |
---|
4024 | if get(hObject,'Value') |
---|
4025 | set(obj,'Visible','on') |
---|
4026 | else |
---|
4027 | set(obj,'Visible','off') |
---|
4028 | end |
---|
4029 | |
---|
4030 | %------------------------------------------------------------------------ |
---|
4031 | function [cmd,errormsg]=cmd_civ1(filename,Param) |
---|
4032 | %------------------------------------------------------------------------ |
---|
4033 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
4034 | %changes : filename_cmx -> filename ( no extension ) |
---|
4035 | cmd=''; |
---|
4036 | filename=regexprep(filename,'.nc',''); %file name for the result |
---|
4037 | if isequal(Param.Civ1.Dt,0) |
---|
4038 | Param.Civ1.Dt=1 ;%case of 'displacement' mode |
---|
4039 | end |
---|
4040 | Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png',''); |
---|
4041 | Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png',''); |
---|
4042 | [fid,errormsg]=fopen([filename '.civ1.cmx'],'w'); |
---|
4043 | if isequal(fid,-1) |
---|
4044 | errormsg=['cmd file ' filename ' cannot be created: ' errormsg]; |
---|
4045 | return |
---|
4046 | end |
---|
4047 | fprintf(fid,['############## CMX file' '\n' ]); |
---|
4048 | fprintf(fid, ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
4049 | fprintf(fid, ['LastImage ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
4050 | fprintf(fid, ['XX' '\n' ]); |
---|
4051 | if isfield(Param.Civ1,'Mask') |
---|
4052 | fprintf(fid, ['Mask ' 'y' '\n' ]); |
---|
4053 | fprintf(fid, ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]); |
---|
4054 | else |
---|
4055 | fprintf(fid, ['Mask ' 'n' '\n' ]); |
---|
4056 | fprintf(fid, ['MaskName ' 'noFile use default' '\n' ]); |
---|
4057 | end |
---|
4058 | fprintf(fid, ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]); %VERIFIER CAS GENERAL ? |
---|
4059 | fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ1.CorrBoxSize(1)) ' ' num2str(Param.Civ1.CorrBoxSize(2)) '\n' ]); |
---|
4060 | fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ1.SearchBoxSize(1)) ' ' num2str(Param.Civ1.SearchBoxSize(2)) '\n' ]); |
---|
4061 | fprintf(fid, ['RO ' num2str(Param.Civ1.CorrSmooth) '\n' ]); |
---|
4062 | if isfield(Param.Civ1,'Grid') |
---|
4063 | fprintf(fid, ['GridSpacing ' '25' ' ' '25' '\n' ]); |
---|
4064 | else |
---|
4065 | fprintf(fid, ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]); |
---|
4066 | end |
---|
4067 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4068 | fprintf(fid, ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]); |
---|
4069 | fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]); |
---|
4070 | fprintf(fid, ['XX 1' '\n' ]); |
---|
4071 | fprintf(fid, ['ShiftXY ' num2str(Param.Civ1.SearchBoxShift(1)) ' ' num2str(Param.Civ1.SearchBoxShift(2)) '\n' ]); |
---|
4072 | if isfield(Param.Civ1,'Grid') |
---|
4073 | fprintf(fid, ['Grid ' 'y' '\n' ]); |
---|
4074 | fprintf(fid, ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]); |
---|
4075 | else |
---|
4076 | fprintf(fid, ['Grid ' 'n' '\n' ]); |
---|
4077 | fprintf(fid, ['GridName ' 'noFile use default' '\n' ]); |
---|
4078 | end |
---|
4079 | fprintf(fid, ['XX 85' '\n' ]); |
---|
4080 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4081 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4082 | fprintf(fid, ['Hart 1' '\n' ]); |
---|
4083 | fprintf(fid, [ 'DecimalShift 0' '\n' ]); |
---|
4084 | fprintf(fid, ['Deformation 0' '\n' ]); |
---|
4085 | fprintf(fid, ['CorrelationMin 0' '\n' ]); |
---|
4086 | fprintf(fid, ['IntensityMin 0' '\n' ]); |
---|
4087 | if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated |
---|
4088 | fprintf(fid, ['SeuilImage n' '\n' ]); |
---|
4089 | fprintf(fid, ['SeuilImageValues 0 4096' '\n' ]);%not used in principle |
---|
4090 | else% Image threshold activated |
---|
4091 | if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma) |
---|
4092 | Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default |
---|
4093 | end |
---|
4094 | fprintf(fid, ['SeuilImage y' '\n' ]); |
---|
4095 | fprintf(fid, ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]); |
---|
4096 | end |
---|
4097 | fprintf(fid, ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ? |
---|
4098 | fprintf(fid, ['ImageUsedBefore null null' '\n' ]); |
---|
4099 | fclose(fid); |
---|
4100 | |
---|
4101 | if(isunix) %unix (or Mac) system |
---|
4102 | cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file |
---|
4103 | cmd=[cmd Param.xml.Civ1Bin ' -f ' filename '.cmx >' filename '.civ1.log \n ' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx |
---|
4104 | cmd=[cmd 'rm ' filename '.cmx']; |
---|
4105 | else %Windows system |
---|
4106 | filename=regexprep(filename,'\\','\\\\'); |
---|
4107 | cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n ']; |
---|
4108 | cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')... |
---|
4109 | '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file |
---|
4110 | cmd=[cmd 'del "' filename '.cmx"']; |
---|
4111 | end |
---|
4112 | |
---|
4113 | |
---|
4114 | function cmd=cmd_fix(filename,Param,fixname) |
---|
4115 | %% |
---|
4116 | switch fixname |
---|
4117 | case 'Fix1' |
---|
4118 | fi2_value=num2str(Param.(fixname).CheckF2); |
---|
4119 | case 'Fix2' |
---|
4120 | fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why... |
---|
4121 | end |
---|
4122 | filename=regexprep(filename,'.nc',''); |
---|
4123 | MaskName_string='';%default |
---|
4124 | MaxVel_string='';%default |
---|
4125 | if ~isempty(Param.(fixname).MinVel) |
---|
4126 | MaxVel_string=[' -threshV ' num2str(Param.(fixname).MinVel)]; |
---|
4127 | end |
---|
4128 | if isunix |
---|
4129 | cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ... |
---|
4130 | ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ... |
---|
4131 | ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string... |
---|
4132 | ' >' filename '.' lower(fixname) '.log 2>&1']; |
---|
4133 | else |
---|
4134 | cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)... |
---|
4135 | ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ... |
---|
4136 | ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string... |
---|
4137 | ' > "' filename '.' lower(fixname) '.log"']; |
---|
4138 | cmd=regexprep(cmd,'\\','\\\\'); |
---|
4139 | end |
---|
4140 | |
---|
4141 | |
---|
4142 | function cmd=cmd_patch(filename,Param,patchname) |
---|
4143 | %% ------------------------------------------------------------------------ |
---|
4144 | filename=regexprep(filename,'.nc',''); |
---|
4145 | if isunix |
---|
4146 | cmd=[Param.xml.PatchBin... |
---|
4147 | ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)... |
---|
4148 | ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).FieldSmooth)... |
---|
4149 | ' -nopt ' num2str(Param.(patchname).SubdomainSize) ... |
---|
4150 | ' > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file |
---|
4151 | else |
---|
4152 | cmd=['"' Param.xml.PatchBin... |
---|
4153 | '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)... |
---|
4154 | ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).FieldSmooth)... |
---|
4155 | ' -nopt ' num2str(Param.(patchname).SubdomainSize)... |
---|
4156 | ' > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file |
---|
4157 | cmd=regexprep(cmd,'\\','\\\\'); |
---|
4158 | end |
---|
4159 | |
---|
4160 | %------------------------------------------------------------------------ |
---|
4161 | % --- CheckCiv2 CheckCiv2 CheckCiv2 CheckCiv2 |
---|
4162 | function [cmd,errormsg]=cmd_civ2(filename,Param) |
---|
4163 | %------------------------------------------------------------------------ |
---|
4164 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
4165 | % global civ2Bin sge%name of the executable for checkciv1 calculation |
---|
4166 | cmd=''; |
---|
4167 | filename=regexprep(filename,'.nc',''); |
---|
4168 | if isequal(Param.Civ2.Dt,'0') |
---|
4169 | Param.Civ2.Dt='1' ;%case of 'displacement' mode |
---|
4170 | end |
---|
4171 | Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png',''); |
---|
4172 | Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ? |
---|
4173 | [fid,errormsg]=fopen([filename '.civ2.cmx'],'w'); |
---|
4174 | if isequal(fid,-1) |
---|
4175 | return |
---|
4176 | end |
---|
4177 | fprintf(fid,['############## CMX file' '\n' ]); |
---|
4178 | fprintf(fid, ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
4179 | fprintf(fid, ['LastImage ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
4180 | fprintf(fid, ['XX' '\n' ]); |
---|
4181 | if isfield(Param.Civ2,'Mask') |
---|
4182 | fprintf(fid, ['Mask ' 'y' '\n' ]); |
---|
4183 | fprintf(fid, ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]); |
---|
4184 | else |
---|
4185 | fprintf(fid, ['Mask ' 'n' '\n' ]); |
---|
4186 | fprintf(fid, ['MaskName ' 'noFile use default' '\n' ]); |
---|
4187 | end |
---|
4188 | % fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]); |
---|
4189 | % fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility |
---|
4190 | fprintf(fid, ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); |
---|
4191 | % fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]); %VERIFIER CAS GENERAL ? |
---|
4192 | fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.CorrBoxSize(1)) ' ' num2str(Param.Civ2.CorrBoxSize(2)) '\n' ]); |
---|
4193 | fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.CorrBoxSize(1)) ' ' num2str(Param.Civ2.CorrBoxSize(2)) '\n']); |
---|
4194 | fprintf(fid, ['RO ' num2str(Param.Civ2.CorrSmooth) '\n']); |
---|
4195 | if isfield(Param.Civ2,'Grid') |
---|
4196 | fprintf(fid, ['GridSpacing ' '25' ' ' '25' '\n' ]); |
---|
4197 | else |
---|
4198 | fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]); |
---|
4199 | end |
---|
4200 | % fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']); |
---|
4201 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4202 | fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]); |
---|
4203 | fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]); |
---|
4204 | fprintf(fid, ['XX 1' '\n' ]); |
---|
4205 | fprintf(fid, 'ShiftXY 0 0\n'); |
---|
4206 | if isfield(Param.Civ2,'Grid') |
---|
4207 | fprintf(fid, ['Grid ' 'y' '\n' ]); |
---|
4208 | fprintf(fid, ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]); |
---|
4209 | else |
---|
4210 | fprintf(fid, ['Grid ' 'n' '\n' ]); |
---|
4211 | fprintf(fid, ['GridName ' 'noFile use default' '\n' ]); |
---|
4212 | end |
---|
4213 | % fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]); |
---|
4214 | % fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']); |
---|
4215 | fprintf(fid, ['XX 85' '\n' ]); |
---|
4216 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4217 | fprintf(fid, ['XX 1.0' '\n' ]); |
---|
4218 | fprintf(fid, ['Hart 1' '\n' ]); |
---|
4219 | fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']); |
---|
4220 | fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']); |
---|
4221 | fprintf(fid, ['CorrelationMin 0' '\n' ]); |
---|
4222 | fprintf(fid, ['IntensityMin 0' '\n' ]); |
---|
4223 | |
---|
4224 | if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated |
---|
4225 | fprintf(fid, ['SeuilImage n' '\n' ]); |
---|
4226 | fprintf(fid, ['SeuilImageValues 0 4096' '\n' ]);%not used in principle |
---|
4227 | else% Image threshold activated |
---|
4228 | if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma) |
---|
4229 | Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default |
---|
4230 | end |
---|
4231 | fprintf(fid, ['SeuilImage y' '\n' ]); |
---|
4232 | fprintf(fid, ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]); |
---|
4233 | end |
---|
4234 | fprintf(fid, ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ? |
---|
4235 | fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']); |
---|
4236 | fclose(fid); |
---|
4237 | |
---|
4238 | if(isunix) |
---|
4239 | cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'... |
---|
4240 | 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 |
---|
4241 | 'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx |
---|
4242 | else |
---|
4243 | filename=regexprep(filename,'\\','\\\\'); |
---|
4244 | cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'... |
---|
4245 | '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename '.cmx" >"' filename '.civ2.log" \n'... |
---|
4246 | 'del "' filename '.cmx" \n']; |
---|
4247 | end |
---|
4248 | |
---|
4249 | %------------------------------------------------------------------------ |
---|
4250 | % --- CheckCiv1 Unified: TO ABADON |
---|
4251 | function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par) |
---|
4252 | %------------------------------------------------------------------------ |
---|
4253 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
4254 | %global CivBin%name of the executable for checkciv1 calculation |
---|
4255 | |
---|
4256 | civ1.image1=par.ImageA; |
---|
4257 | civ1.image2=par.ImageB; |
---|
4258 | civ1.imageSize_X=par.npx; |
---|
4259 | civ1.imageSize_Y=par.npy; |
---|
4260 | civ1.outputFileName=[filename '.nc']; |
---|
4261 | civ1.correlationBoxesSize_X=par.ibx; |
---|
4262 | civ1.correlationBoxesSize_Y=par.iby; |
---|
4263 | civ1.searchBoxesSize_X=par.isx; |
---|
4264 | civ1.searchBoxesSize_Y=par.isy; |
---|
4265 | civ1.globalShift_X=par.shiftx; |
---|
4266 | civ1.globalShift_Y=par.shifty; |
---|
4267 | civ1.ro=par.rho; |
---|
4268 | civ1.hart='y'; |
---|
4269 | if isequal(par.gridflag,'y') |
---|
4270 | civ1.grid=par.gridname; |
---|
4271 | else |
---|
4272 | civ1.grid='n'; |
---|
4273 | civ1.gridSpacing_X=par.dx; |
---|
4274 | civ1.gridSpacing_Y=par.dy; |
---|
4275 | end |
---|
4276 | if isequal(par.maskflag,'y') |
---|
4277 | civ1.mask=par.maskname; |
---|
4278 | end |
---|
4279 | civ1.dt=par.Dt; |
---|
4280 | civ1.unit='pixel'; |
---|
4281 | civ1.absolut_time_T0=par.Time; |
---|
4282 | civ1.pixcmx='1'; |
---|
4283 | civ1.pixcmy='1'; |
---|
4284 | civ1.convectFlow='n'; |
---|
4285 | |
---|
4286 | xml_civ1_parameters=civ1; |
---|
4287 | |
---|
4288 | %------------------------------------------------------------------------ |
---|
4289 | % --- CheckCiv2 Unified: TO ABADON |
---|
4290 | function civ2=CIV2_CMD_Unified(filename,namelog,par) |
---|
4291 | %------------------------------------------------------------------------ |
---|
4292 | %pixels per cm and matrix of the image times, read from the .civ file by uvmat |
---|
4293 | %global CivBin%name of the executable for checkciv1 calculation |
---|
4294 | |
---|
4295 | filename=regexprep(filename,'.nc',''); |
---|
4296 | |
---|
4297 | civ2.image1=par.ImageA; |
---|
4298 | civ2.image2=par.ImageB; |
---|
4299 | civ2.imageSize_X=par.npx; |
---|
4300 | civ2.imageSize_Y=par.npy; |
---|
4301 | civ2.inputFileName=[par.filename_nc1 '.nc']; |
---|
4302 | civ2.outputFileName=[filename '.nc']; |
---|
4303 | civ2.correlationBoxesSize_X=par.ibx; |
---|
4304 | civ2.correlationBoxesSize_Y=par.iby; |
---|
4305 | civ2.ro=par.rho; |
---|
4306 | %checkciv2.decimalShift=par.CheckDecimal; |
---|
4307 | %checkciv2.CheckDeformation=par.CheckDeformation; |
---|
4308 | if isequal(par.decimal,'1') |
---|
4309 | civ2.decimalShift='y'; |
---|
4310 | else |
---|
4311 | civ2.decimalShift='n'; |
---|
4312 | end |
---|
4313 | if isequal(par.deformation,'1') |
---|
4314 | civ2.deformation='y'; |
---|
4315 | else |
---|
4316 | civ2.deformation='n'; |
---|
4317 | end |
---|
4318 | if isequal(par.gridflag,'y') |
---|
4319 | civ2.grid=par.gridname; |
---|
4320 | else |
---|
4321 | civ2.grid='n'; |
---|
4322 | civ2.gridSpacing_X=par.dx; |
---|
4323 | civ2.gridSpacing_Y=par.dy; |
---|
4324 | end |
---|
4325 | civ2.gridSpacing_X='10'; |
---|
4326 | civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee |
---|
4327 | if isequal(par.maskflag,'y') |
---|
4328 | civ2.mask=par.maskname; |
---|
4329 | else |
---|
4330 | civ2.mask='n'; |
---|
4331 | end |
---|
4332 | civ2.dt=par.Dt; |
---|
4333 | civ2.unit='pixel'; |
---|
4334 | civ2.absolut_time_T0=par.Time; |
---|
4335 | civ2.pixcmx='1'; |
---|
4336 | civ2.pixcmy='1'; |
---|
4337 | civ2.convectFlow='n'; |
---|
4338 | |
---|
4339 | |
---|
4340 | % --- Executes on button press in TestPatch1. |
---|
4341 | function TestPatch1_Callback(hObject, eventdata, handles) |
---|
4342 | set(handles.TestPatch1,'BackgroundColor',[1 1 0]) |
---|
4343 | drawnow |
---|
4344 | if get(handles.TestPatch1,'Value') |
---|
4345 | ref_i=str2double(get(handles.ref_i,'String')); |
---|
4346 | if strcmp(get(handles.ref_j,'Visible'),'on') |
---|
4347 | ref_j=str2double(get(handles.ref_j,'String')); |
---|
4348 | else |
---|
4349 | ref_j=1;%default |
---|
4350 | end |
---|
4351 | filecell=set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]); |
---|
4352 | Data.ListVarName={'ny','nx','A'}; |
---|
4353 | Data.VarDimName= {'ny','nx',{'ny','nx'}}; |
---|
4354 | param_patch1=read_GUI(handles.Patch1); |
---|
4355 | param_patch1.CivFile=filecell.nc.civ1{1}; |
---|
4356 | Param.Patch1=param_patch1; |
---|
4357 | for irho=1:7 |
---|
4358 | [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV |
---|
4359 | if ~isempty(errormsg) |
---|
4360 | msgbox_uvmat('ERROR',errormsg) |
---|
4361 | return |
---|
4362 | end |
---|
4363 | SmoothingParam(irho)=Param.Patch1.FieldSmooth; |
---|
4364 | Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0); |
---|
4365 | Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0); |
---|
4366 | DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff)) |
---|
4367 | NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff); |
---|
4368 | Param.Patch1.SmoothingParam=2*Param.Patch1.FieldSmooth; |
---|
4369 | end |
---|
4370 | figure |
---|
4371 | plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r') |
---|
4372 | set(handles.TestPatch1,'BackgroundColor',[1 0 0]) |
---|
4373 | else |
---|
4374 | corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display |
---|
4375 | if ~isempty(corrfig) |
---|
4376 | delete(corrfig) |
---|
4377 | end |
---|
4378 | hview_field=findobj(allchild(0),'tag','view_field');% look for view_field |
---|
4379 | if ~isempty(hview_field) |
---|
4380 | delete(hview_field) |
---|
4381 | end |
---|
4382 | end |
---|
4383 | %'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature |
---|
4384 | %--------------------------------------------------------------------- |
---|
4385 | % [nom_type_pair]=nomtype2pair(nom_type,Dti,Dtj); |
---|
4386 | %--------------------------------------------------------------------- |
---|
4387 | |
---|
4388 | % OUTPUT: |
---|
4389 | %nom_type_nc |
---|
4390 | |
---|
4391 | %--------------------------------------------------------------------- |
---|
4392 | % INPUT: |
---|
4393 | % 'nom_type': string defining the kind of nomenclature used: |
---|
4394 | %nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined) |
---|
4395 | %nom_type='*': the same file [filebase ext] contains successive fields (ex avi movies) |
---|
4396 | %nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png'). |
---|
4397 | %nom_type='#' series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif' |
---|
4398 | %nom_type='_i_j' matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png') |
---|
4399 | %nom_type='_i1-i2' from pairs from a single index (e.g. 'aa_45-47.nc') |
---|
4400 | %nom_type='_i_j1-j2'pairs of j indices (e.g. 'aa_45_2-3.nc') |
---|
4401 | %nom_type='_i1-i2_j' pairs of i indices (e.g. 'aa_45-46_2.nc') |
---|
4402 | %nom_type='#a','#A', with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j') |
---|
4403 | %nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif' |
---|
4404 | %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' |
---|
4405 | %nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE |
---|
4406 | %nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D') |
---|
4407 | %nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D') |
---|
4408 | % Dti: ~=0 if i index pairs are used |
---|
4409 | % Dtj: ~=0 if i index pairs are used |
---|
4410 | |
---|
4411 | function NomTypeNc=nomtype2pair(NomTypeIma,mode) |
---|
4412 | |
---|
4413 | %determine nom_type_nc: |
---|
4414 | NomTypeNc=NomTypeIma;%default |
---|
4415 | switch mode |
---|
4416 | case 'pair j1-j2' |
---|
4417 | if ~isempty(regexp(NomTypeIma,'a$')) |
---|
4418 | NomTypeNc=[NomTypeIma 'b']; |
---|
4419 | elseif ~isempty(regexp(NomTypeIma,'A$')) |
---|
4420 | NomTypeNc=[NomTypeIma 'B']; |
---|
4421 | else |
---|
4422 | r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); |
---|
4423 | if ~isempty(r) |
---|
4424 | NomTypeNc='_1_1-2'; |
---|
4425 | end |
---|
4426 | end |
---|
4427 | case 'series(Dj)' |
---|
4428 | r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); |
---|
4429 | if ~isempty(r) |
---|
4430 | NomTypeNc='_1_1-2'; |
---|
4431 | end |
---|
4432 | case 'series(Di)' |
---|
4433 | r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); |
---|
4434 | if ~isempty(r) |
---|
4435 | NomTypeNc='_1-2_1'; |
---|
4436 | else |
---|
4437 | NomTypeNc='_1-2'; |
---|
4438 | end |
---|
4439 | end |
---|
4440 | |
---|
4441 | function NomType_Callback(hObject, eventdata, handles) |
---|
4442 | set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding |
---|
4443 | RootPath=get(handles.RootPath,'String'); |
---|
4444 | RootFile=get(handles.RootFile,'String'); |
---|
4445 | ref_i=str2num(get(handles.ref_i,'String')); |
---|
4446 | ref_j=str2num(get(handles.ref_j,'String')); |
---|
4447 | NomType=get(handles.NomType,'String'); |
---|
4448 | ImaExt=get(handles.ImaExt,'String'); |
---|
4449 | fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j); |
---|
4450 | errormsg=display_file_name(handles,fileinput); |
---|
4451 | if ~isempty(errormsg) |
---|
4452 | msgbox_uvmat('ERROR',errormsg) |
---|
4453 | end |
---|
4454 | set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished |
---|
4455 | |
---|
4456 | % --- Executes on selection change in ListProgram. |
---|
4457 | function ListProgram_Callback(hObject, eventdata, handles) |
---|
4458 | ListProgram=get(handles.ListProgram,'String'); |
---|
4459 | Program=ListProgram{get(handles.ListProgram,'value')}; |
---|
4460 | switch Program |
---|
4461 | case 'CivX' |
---|
4462 | set(handles.num_MaxDiff,'Visible','off') |
---|
4463 | set(handles.num_MaxVel,'Visible','off') |
---|
4464 | set(handles.title_MaxVel,'Visible','off') |
---|
4465 | set(handles.num_Nx,'Visible','on') |
---|
4466 | set(handles.num_Ny,'Visible','on') |
---|
4467 | set(handles.title_Nx,'Visible','on') |
---|
4468 | set(handles.title_Ny,'Visible','on') |
---|
4469 | set(handles.title_MaxDiff,'Visible','off') |
---|
4470 | set(handles.num_CorrSmooth,'Style','edit') |
---|
4471 | set(handles.num_CorrSmooth,'String','1') |
---|
4472 | set(handles.BATCH,'Enable','on') |
---|
4473 | set(handles.CheckThreshold,'Visible','off') |
---|
4474 | set(handles.CheckDeformation,'Value',1) |
---|
4475 | set(handles.CheckDecimal,'Value',1) |
---|
4476 | case 'Matlab' |
---|
4477 | set(handles.num_MaxDiff,'Visible','on') |
---|
4478 | set(handles.num_MaxVel,'Visible','on') |
---|
4479 | set(handles.title_MaxVel,'Visible','on') |
---|
4480 | set(handles.title_MaxDiff,'Visible','on') |
---|
4481 | set(handles.num_Nx,'Visible','off') |
---|
4482 | set(handles.num_Ny,'Visible','off') |
---|
4483 | set(handles.title_Nx,'Visible','off') |
---|
4484 | set(handles.title_Ny,'Visible','off') |
---|
4485 | set(handles.num_CorrSmooth,'Style','popupmenu') |
---|
4486 | set(handles.num_CorrSmooth,'Value',1) |
---|
4487 | set(handles.num_CorrSmooth,'String',{'1';'2'}) |
---|
4488 | set(handles.CheckThreshold,'Visible','on') |
---|
4489 | set(handles.CheckDeformation,'Value',0)% desactivate (work in progress) |
---|
4490 | set(handles.CheckDecimal,'Value',0)% desactivate (work in progress) |
---|
4491 | end |
---|
4492 | |
---|
4493 | |
---|
4494 | % --- Executes on button press in TestCiv2. |
---|
4495 | function TestCiv2_Callback(hObject, eventdata, handles) |
---|
4496 | |
---|
4497 | |
---|
4498 | |
---|
4499 | function RootFile_Callback(hObject, eventdata, handles) |
---|
4500 | |
---|
4501 | |
---|
4502 | |
---|
4503 | function SubdirImages_Callback(hObject, eventdata, handles) |
---|