[878] | 1 | %'civ_series': PIV function activated by the general GUI series |
---|
[834] | 2 | % --- call the sub-functions: |
---|
| 3 | % civ: PIV function itself |
---|
| 4 | % fix: removes false vectors after detection by various criteria |
---|
| 5 | % filter_tps: make interpolation-smoothing |
---|
| 6 | %------------------------------------------------------------------------ |
---|
| 7 | % function [Data,errormsg,result_conv]= civ_series(Param,ncfile) |
---|
| 8 | % |
---|
| 9 | %OUTPUT |
---|
| 10 | % Data=structure containing the PIV results and information on the processing parameters |
---|
| 11 | % errormsg=error message char string, default='' |
---|
| 12 | % resul_conv: image inter-correlation function for the last grid point (used for tests) |
---|
| 13 | % |
---|
| 14 | %INPUT: |
---|
| 15 | % Param: input images and processing parameters |
---|
| 16 | % .Civ1: for civ1 |
---|
| 17 | % .Fix1: |
---|
| 18 | % .Patch1: |
---|
| 19 | % .Civ2: for civ2 |
---|
| 20 | % .Fix2: |
---|
| 21 | % .Patch2: |
---|
| 22 | % ncfile: name of a netcdf file to be created for the result (extension .nc) |
---|
| 23 | % |
---|
[927] | 24 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
---|
[1071] | 25 | % Copyright 2008-2020, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
---|
[927] | 26 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
---|
| 27 | % This is part of the toolbox UVMAT. |
---|
| 28 | % |
---|
[834] | 29 | % UVMAT is free software; you can redistribute it and/or modify |
---|
[927] | 30 | % it under the terms of the GNU General Public License as published by |
---|
| 31 | % the Free Software Foundation; either version 2 of the License, or |
---|
| 32 | % (at your option) any later version. |
---|
| 33 | % |
---|
[834] | 34 | % UVMAT is distributed in the hope that it will be useful, |
---|
| 35 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
---|
| 36 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
---|
[927] | 37 | % GNU General Public License (open UVMAT/COPYING.txt) for more details. |
---|
| 38 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
---|
[834] | 39 | |
---|
| 40 | function [Data,errormsg,result_conv]= stereo_civ(Param) |
---|
[845] | 41 | Data=[]; |
---|
[834] | 42 | errormsg=''; |
---|
| 43 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed |
---|
| 44 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
---|
[845] | 45 | if size(Param.InputTable,1)<2 |
---|
| 46 | msgbox_uvmat('WARNING','two input file series must be entered') |
---|
| 47 | return |
---|
| 48 | end |
---|
[834] | 49 | path_series=fileparts(which('series')); |
---|
| 50 | addpath(fullfile(path_series,'series')) |
---|
[864] | 51 | Data=stereo_input(Param);% introduce the civ parameters using the GUI civ_input |
---|
[834] | 52 | if isempty(Data) |
---|
| 53 | Data=Param;% if civ_input has been cancelled, keep previous parameters |
---|
| 54 | end |
---|
| 55 | Data.Program=mfilename;%gives the name of the current function |
---|
| 56 | Data.AllowInputSort='on';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
---|
| 57 | Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
---|
| 58 | Data.NbSlice='off'; %nbre of slices ('off' by default) |
---|
| 59 | Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
---|
| 60 | Data.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
---|
| 61 | Data.FieldTransform = 'off';%can use a transform function (use it by force, no input option) |
---|
| 62 | Data.ProjObject='off';%can use projection object(option 'off'/'on', |
---|
| 63 | Data.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
---|
| 64 | Data.OutputDirExt='.stereo';%set the output dir extension |
---|
| 65 | Data.OutputSubDirMode='auto'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default) |
---|
| 66 | Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) |
---|
[927] | 67 | Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) |
---|
| 68 | |
---|
[834] | 69 | return |
---|
| 70 | end |
---|
| 71 | |
---|
| 72 | %% read input parameters from an xml file if input is a file name (batch mode) |
---|
| 73 | checkrun=1; |
---|
| 74 | if ischar(Param) |
---|
| 75 | Param=xml2struct(Param);% read Param as input file (batch case) |
---|
| 76 | checkrun=0; |
---|
| 77 | end |
---|
| 78 | if ~isfield(Param,'ActionInput') |
---|
| 79 | disp_uvmat('ERROR','no parameter set for PIV',checkrun) |
---|
| 80 | return |
---|
| 81 | end |
---|
| 82 | hseries=findobj(allchild(0),'Tag','series'); |
---|
| 83 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
---|
| 84 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
---|
| 85 | |
---|
| 86 | %% input files and indexing |
---|
| 87 | MaxIndex_i=Param.IndexRange.MaxIndex_i; |
---|
| 88 | MinIndex_i=Param.IndexRange.MinIndex_i; |
---|
| 89 | if ~isfield(Param,'InputTable') |
---|
| 90 | disp_uvmat('ERROR', 'no input field',checkrun) |
---|
| 91 | return |
---|
| 92 | end |
---|
| 93 | [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
---|
[985] | 94 | time=[]; |
---|
[834] | 95 | for iview=1:size(Param.InputTable,1) |
---|
[844] | 96 | XmlFileName=find_imadoc(Param.InputTable{iview,1},Param.InputTable{iview,2},Param.InputTable{iview,3},Param.InputTable{iview,5}); |
---|
[834] | 97 | if isempty(XmlFileName) |
---|
| 98 | disp_uvmat('ERROR', [XmlFileName ' not found'],checkrun) |
---|
| 99 | return |
---|
| 100 | end |
---|
| 101 | XmlData{iview}=imadoc2struct(XmlFileName); |
---|
| 102 | if isfield(XmlData{iview},'Time') |
---|
| 103 | time=XmlData{iview}.Time; |
---|
| 104 | TimeSource='xml'; |
---|
| 105 | end |
---|
| 106 | if isfield(XmlData{iview},'Camera') |
---|
| 107 | if isfield(XmlData{iview}.Camera,'NbSlice')&& ~isempty(XmlData{iview}.Camera.NbSlice) |
---|
| 108 | NbSlice_calib{iview}=XmlData{iview}.Camera.NbSlice;% Nbre of slices for Zindex in phys transform |
---|
| 109 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
---|
| 110 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
---|
| 111 | end |
---|
| 112 | end |
---|
| 113 | if isfield(XmlData{iview}.Camera,'TimeUnit')&& ~isempty(XmlData{iview}.Camera.TimeUnit) |
---|
| 114 | TimeUnit=XmlData{iview}.Camera.TimeUnit; |
---|
| 115 | end |
---|
| 116 | end |
---|
| 117 | end |
---|
| 118 | |
---|
| 119 | |
---|
| 120 | iview_A=1;% series index (iview) for the first image series |
---|
| 121 | iview_B=2;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) |
---|
| 122 | |
---|
| 123 | RootPath_A=Param.InputTable{1,1}; |
---|
| 124 | RootFile_A=Param.InputTable{1,3}; |
---|
| 125 | SubDir_A=Param.InputTable{1,2}; |
---|
| 126 | NomType_A=Param.InputTable{1,4}; |
---|
| 127 | FileExt_A=Param.InputTable{1,5}; |
---|
| 128 | RootPath_B=Param.InputTable{2,1}; |
---|
| 129 | RootFile_B=Param.InputTable{2,3}; |
---|
| 130 | SubDir_B=Param.InputTable{2,2}; |
---|
| 131 | NomType_B=Param.InputTable{2,4}; |
---|
| 132 | FileExt_B=Param.InputTable{2,5}; |
---|
| 133 | PairCiv2=''; |
---|
| 134 | |
---|
| 135 | i1_series_Civ1=i1_series{1};i1_series_Civ2=i1_series{1}; |
---|
| 136 | i2_series_Civ1=i1_series{2};i2_series_Civ2=i1_series{2}; |
---|
| 137 | if isempty(j1_series{1}) |
---|
[985] | 138 | FrameIndex_A_Civ1=i1_series_Civ1; |
---|
| 139 | FrameIndex_B_Civ1=i2_series_Civ1; |
---|
[834] | 140 | j1_series_Civ1=ones(size(i1_series{1})); |
---|
| 141 | j2_series_Civ1=ones(size(i1_series{2})); |
---|
| 142 | else |
---|
| 143 | j1_series_Civ1=j1_series{1}; |
---|
| 144 | j2_series_Civ1=j1_series{2}; |
---|
[985] | 145 | FrameIndex_A_Civ1=j1_series_Civ1; |
---|
| 146 | FrameIndex_B_Civ1=j2_series_Civ1; |
---|
[834] | 147 | end |
---|
| 148 | j1_series_Civ2=j1_series_Civ1; |
---|
| 149 | j2_series_Civ2=j2_series_Civ1; |
---|
[985] | 150 | |
---|
| 151 | % if isempty(j1_series_Civ1) |
---|
| 152 | % FrameIndex_A_Civ1=i1_series_Civ1; |
---|
| 153 | % FrameIndex_B_Civ1=i2_series_Civ1; |
---|
| 154 | % j1_series_Civ1=ones(size(i1_series_Civ1)); |
---|
| 155 | % j2_series_Civ1=ones(size(i1_series_Civ1)); |
---|
| 156 | % else |
---|
| 157 | % FrameIndex_A_Civ1=j1_series_Civ1; |
---|
| 158 | % FrameIndex_B_Civ1=j2_series_Civ1; |
---|
| 159 | % end |
---|
[834] | 160 | if isempty(PairCiv2) |
---|
| 161 | FrameIndex_A_Civ2=FrameIndex_A_Civ1; |
---|
| 162 | FrameIndex_B_Civ2=FrameIndex_B_Civ1; |
---|
| 163 | else |
---|
| 164 | if isempty(j1_series_Civ2) |
---|
| 165 | FrameIndex_A_Civ2=i1_series_Civ2; |
---|
| 166 | FrameIndex_B_Civ2=i2_series_Civ2; |
---|
| 167 | j1_series_Civ2=ones(size(i1_series_Civ2)); |
---|
| 168 | j2_series_Civ2=ones(size(i1_series_Civ2)); |
---|
| 169 | else |
---|
| 170 | FrameIndex_A_Civ2=j1_series_Civ2; |
---|
| 171 | FrameIndex_B_Civ2=j2_series_Civ2; |
---|
| 172 | end |
---|
| 173 | end |
---|
| 174 | if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) |
---|
[927] | 175 | disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun) |
---|
[834] | 176 | return |
---|
| 177 | end |
---|
| 178 | |
---|
| 179 | %% check the first image pair |
---|
| 180 | try |
---|
| 181 | if Param.ActionInput.CheckCiv1% Civ1 is performed |
---|
| 182 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1)); |
---|
| 183 | if ~exist(ImageName_A,'file') |
---|
| 184 | disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) |
---|
| 185 | return |
---|
| 186 | end |
---|
| 187 | [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); |
---|
| 188 | FileType_A=FileInfo_A.FileType; |
---|
| 189 | if strcmp(FileInfo_A.FileType,'netcdf') |
---|
| 190 | FieldName_A=Param.InputFields.FieldName; |
---|
| 191 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); |
---|
| 192 | par_civ1.ImageA=DataIn.(FieldName_A); |
---|
| 193 | else |
---|
| 194 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(1)); |
---|
| 195 | end |
---|
| 196 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1),[],j2_series_Civ1(1)); |
---|
| 197 | if ~exist(ImageName_B,'file') |
---|
| 198 | disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) |
---|
| 199 | return |
---|
| 200 | end |
---|
| 201 | [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); |
---|
| 202 | FileType_B=FileInfo_B.FileType; |
---|
| 203 | if strcmp(FileInfo_B.FileType,'netcdf') |
---|
| 204 | FieldName_B=Param.InputFields.FieldName; |
---|
| 205 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); |
---|
| 206 | par_civ1.ImageB=DataIn.(FieldName_B); |
---|
| 207 | else |
---|
| 208 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(1)); |
---|
| 209 | end |
---|
| 210 | NbField=numel(i1_series_Civ1); |
---|
| 211 | elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 |
---|
| 212 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ2(1),[],j1_series_Civ2(1)); |
---|
| 213 | if ~exist(ImageName_A,'file') |
---|
| 214 | disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) |
---|
| 215 | return |
---|
| 216 | end |
---|
| 217 | [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); |
---|
| 218 | FileType_A=FileInfo_A.FileType; |
---|
| 219 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileInfo_A.FileType,VideoObject_A,FrameIndex_A_Civ2(1)); |
---|
| 220 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ2(1),[],j2_series_Civ2(1)); |
---|
| 221 | if ~exist(ImageName_B,'file') |
---|
| 222 | disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) |
---|
| 223 | return |
---|
| 224 | end |
---|
| 225 | [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); |
---|
| 226 | FileType_B=FileInfo_B.FileType; |
---|
| 227 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(1)); |
---|
| 228 | NbField=numel(i1_series_Civ2); |
---|
| 229 | else |
---|
| 230 | NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK |
---|
| 231 | end |
---|
| 232 | catch ME |
---|
| 233 | if ~isempty(ME.message) |
---|
| 234 | disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) |
---|
| 235 | return |
---|
| 236 | end |
---|
| 237 | end |
---|
[985] | 238 | if ismember(FileType_A,{'mmreader','video','cine_phantom'}) |
---|
| 239 | NomTypeNc='_1'; |
---|
| 240 | else |
---|
| 241 | NomTypeNc=NomType_A; |
---|
| 242 | end |
---|
[834] | 243 | |
---|
| 244 | %% Output directory |
---|
| 245 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
---|
| 246 | |
---|
[886] | 247 | ListGlobalAttribute={'Conventions','Program','CivStage'}; |
---|
[834] | 248 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
---|
[846] | 249 | Data.Program=mfilename;%gives the name of the current function; |
---|
[834] | 250 | Data.CivStage=0;%default |
---|
| 251 | maskname='';%default |
---|
| 252 | check_civx=0;%default |
---|
| 253 | |
---|
| 254 | %% get timing from input video |
---|
[985] | 255 | if isempty(time) && ismember(FileType_A,{'mmreader','video','cine_phantom'})% case of video input |
---|
[834] | 256 | time=zeros(FileInfo_A.NumberOfFrames+1,2); |
---|
| 257 | time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; |
---|
| 258 | TimeSource='video'; |
---|
| 259 | ColorType='truecolor'; |
---|
| 260 | end |
---|
| 261 | if isempty(time)% time = index i by default |
---|
| 262 | MaxIndex_i=max(i2_series_Civ1); |
---|
| 263 | MaxIndex_j=max(j2_series_Civ1); |
---|
| 264 | time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); |
---|
| 265 | time=[zeros(1,MaxIndex_j);time];% insert a first line of zeros |
---|
| 266 | time=[zeros(MaxIndex_i+1,1) time];% insert a first column of zeros |
---|
| 267 | end |
---|
| 268 | |
---|
| 269 | if length(FileInfo_A) >1 %case of image with multiple frames |
---|
| 270 | nbfield=length(FileInfo_A); |
---|
| 271 | nbfield_j=1; |
---|
| 272 | end |
---|
| 273 | |
---|
[864] | 274 | tic |
---|
[834] | 275 | %%%%% MAIN LOOP %%%%%% |
---|
[927] | 276 | CheckOverwrite=1;%default |
---|
| 277 | if isfield(Param,'CheckOverwrite') |
---|
| 278 | CheckOverwrite=Param.CheckOverwrite; |
---|
| 279 | end |
---|
| 280 | |
---|
[834] | 281 | for ifield=1:NbField |
---|
| 282 | update_waitbar(WaitbarHandle,ifield/NbField) |
---|
| 283 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
---|
| 284 | disp('program stopped by user') |
---|
| 285 | break |
---|
| 286 | end |
---|
[864] | 287 | % variable for light saving or not. |
---|
| 288 | LSM=Param.ActionInput.CheckLSM; |
---|
| 289 | |
---|
[834] | 290 | Civ1Dir=OutputDir; |
---|
| 291 | |
---|
[985] | 292 | % ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,[RootFile_A,'_All'],'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... |
---|
| 293 | % j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
---|
[864] | 294 | |
---|
| 295 | |
---|
[985] | 296 | ncfile2=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... |
---|
[864] | 297 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
---|
[927] | 298 | |
---|
| 299 | if (~CheckOverwrite && exist(ncfile,'file')) || (~CheckOverwrite && exist(ncfile2,'file')) |
---|
| 300 | disp('existing output file already exists, skip to next field') |
---|
| 301 | result_conv=0; |
---|
| 302 | continue% skip iteration if the mode overwrite is desactivated and the result file already exists |
---|
| 303 | end |
---|
| 304 | |
---|
[864] | 305 | |
---|
[834] | 306 | %% Civ1 |
---|
[878] | 307 | |
---|
| 308 | |
---|
[834] | 309 | % if Civ1 computation is requested |
---|
| 310 | if isfield (Param.ActionInput,'Civ1') |
---|
| 311 | par_civ1=Param.ActionInput.Civ1; |
---|
| 312 | try |
---|
| 313 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); |
---|
| 314 | [A{1},VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); |
---|
| 315 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); |
---|
| 316 | [A{2},VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); |
---|
| 317 | catch ME |
---|
| 318 | if ~isempty(ME.message) |
---|
| 319 | disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) |
---|
| 320 | return |
---|
| 321 | end |
---|
| 322 | end |
---|
[878] | 323 | |
---|
| 324 | |
---|
| 325 | |
---|
[834] | 326 | [A,Rangx,Rangy]=phys_ima(A,XmlData,1); |
---|
[845] | 327 | [Npy,Npx]=size(A{1}); |
---|
[844] | 328 | PhysImageA=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.png','_1a',i1_series_Civ1(ifield),[],1); |
---|
| 329 | PhysImageB=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.png','_1a',i1_series_Civ1(ifield),[],2); |
---|
[864] | 330 | if LSM ~= 1 |
---|
[844] | 331 | imwrite(A{1},PhysImageA) |
---|
| 332 | imwrite(A{2},PhysImageB) |
---|
[864] | 333 | end |
---|
| 334 | |
---|
[834] | 335 | par_civ1.ImageA=A{1}; |
---|
| 336 | par_civ1.ImageB=A{2}; |
---|
| 337 | par_civ1.ImageWidth=size(par_civ1.ImageA,2);%FileInfo_A.Width; |
---|
| 338 | par_civ1.ImageHeight=size(par_civ1.ImageA,1);%FileInfo_A.Height; |
---|
| 339 | list_param=(fieldnames(Param.ActionInput.Civ1))'; |
---|
| 340 | Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param |
---|
| 341 | Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images |
---|
| 342 | %indicate the values of all the global attributes in the output data |
---|
| 343 | Data.Civ1_ImageA=ImageName_A; |
---|
| 344 | Data.Civ1_ImageB=ImageName_B; |
---|
| 345 | i1=i1_series_Civ1(ifield); |
---|
| 346 | i2=i1; |
---|
| 347 | if ~isempty(i2_series_Civ1) |
---|
| 348 | i2=i2_series_Civ1(ifield); |
---|
| 349 | end |
---|
| 350 | j1=1; |
---|
| 351 | if ~isempty(j1_series_Civ1) |
---|
| 352 | j1=j1_series_Civ1(ifield); |
---|
| 353 | end |
---|
| 354 | j2=j1; |
---|
| 355 | if ~isempty(j2_series_Civ1) |
---|
| 356 | j2=j2_series_Civ1(ifield); |
---|
| 357 | end |
---|
| 358 | Data.Civ1_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; |
---|
| 359 | Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1); |
---|
| 360 | for ilist=1:length(list_param) |
---|
| 361 | Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); |
---|
| 362 | end |
---|
[886] | 363 | Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; |
---|
[834] | 364 | Data.CivStage=1; |
---|
| 365 | |
---|
| 366 | % set the list of variables |
---|
[854] | 367 | Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record |
---|
| 368 | Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; |
---|
[834] | 369 | Data.VarAttribute{1}.Role='coord_x'; |
---|
| 370 | Data.VarAttribute{2}.Role='coord_y'; |
---|
| 371 | Data.VarAttribute{3}.Role='vector_x'; |
---|
| 372 | Data.VarAttribute{4}.Role='vector_y'; |
---|
| 373 | Data.VarAttribute{5}.Role='warnflag'; |
---|
| 374 | |
---|
| 375 | |
---|
| 376 | % calculate velocity data (y and v in indices, reverse to y component) |
---|
[864] | 377 | [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); |
---|
[834] | 378 | Data.Civ1_X=reshape(xtable,[],1); |
---|
| 379 | Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1); |
---|
| 380 | % get z from u and v (displacements) |
---|
| 381 | Data.Civ1_U=reshape(utable,[],1); |
---|
[845] | 382 | Data.Civ1_V=reshape(-vtable,[],1); |
---|
[834] | 383 | Data.Civ1_C=reshape(ctable,[],1); |
---|
| 384 | Data.Civ1_F=reshape(F,[],1); |
---|
[864] | 385 | |
---|
[834] | 386 | end |
---|
| 387 | |
---|
| 388 | %% Fix1 |
---|
| 389 | if isfield (Param.ActionInput,'Fix1') |
---|
| 390 | if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1 |
---|
| 391 | Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute)); |
---|
| 392 | Data.ListGlobalAttribute(Fix1_attr)=[]; |
---|
| 393 | for ilist=1:numel(Fix1_attr) |
---|
| 394 | Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)}); |
---|
| 395 | end |
---|
| 396 | end |
---|
| 397 | ListFixParam=fieldnames(Param.ActionInput.Fix1); |
---|
| 398 | for ilist=1:length(ListFixParam) |
---|
| 399 | ParamName=ListFixParam{ilist}; |
---|
| 400 | ListName=['Fix1_' ParamName]; |
---|
| 401 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
| 402 | eval(['Data.' ListName '=Param.ActionInput.Fix1.' ParamName ';']) |
---|
| 403 | end |
---|
| 404 | if check_civx |
---|
| 405 | if ~isfield(Data,'fix') |
---|
| 406 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix']; |
---|
| 407 | Data.fix=1; |
---|
| 408 | Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}]; |
---|
| 409 | Data.VarDimName=[Data.VarDimName {'nb_vectors'}]; |
---|
| 410 | end |
---|
| 411 | Data.vec_FixFlag=fix(Param.ActionInput.Fix1,Data.vec_F,Data.vec_C,Data.vec_U,Data.vec_V,Data.vec_X,Data.vec_Y); |
---|
| 412 | else |
---|
| 413 | Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; |
---|
| 414 | Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; |
---|
| 415 | nbvar=length(Data.ListVarName); |
---|
| 416 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
| 417 | Data.Civ1_FF=fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); |
---|
| 418 | Data.CivStage=2; |
---|
| 419 | end |
---|
| 420 | end |
---|
| 421 | %% Patch1 |
---|
| 422 | if isfield (Param.ActionInput,'Patch1') |
---|
| 423 | if check_civx |
---|
| 424 | errormsg='Civ Matlab input needed for patch'; |
---|
| 425 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 426 | return |
---|
| 427 | end |
---|
| 428 | |
---|
| 429 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}]; |
---|
| 430 | Data.Patch1_FieldSmooth=Param.ActionInput.Patch1.FieldSmooth; |
---|
| 431 | Data.Patch1_MaxDiff=Param.ActionInput.Patch1.MaxDiff; |
---|
| 432 | Data.Patch1_SubDomainSize=Param.ActionInput.Patch1.SubDomainSize; |
---|
| 433 | nbvar=length(Data.ListVarName); |
---|
| 434 | Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; |
---|
| 435 | Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',... |
---|
| 436 | {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; |
---|
| 437 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
| 438 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
| 439 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
| 440 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 441 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
| 442 | Data.Civ1_U_smooth=zeros(size(Data.Civ1_X)); |
---|
| 443 | Data.Civ1_V_smooth=zeros(size(Data.Civ1_X)); |
---|
| 444 | if isfield(Data,'Civ1_FF') |
---|
| 445 | ind_good=find(Data.Civ1_FF==0); |
---|
| 446 | else |
---|
| 447 | ind_good=1:numel(Data.Civ1_X); |
---|
| 448 | end |
---|
| 449 | [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
| 450 | filter_tps([Data.Civ1_X(ind_good) Data.Civ1_Y(ind_good)],Data.Civ1_U(ind_good),Data.Civ1_V(ind_good),[],Data.Patch1_SubDomainSize,Data.Patch1_FieldSmooth,Data.Patch1_MaxDiff); |
---|
| 451 | Data.Civ1_U_smooth(ind_good)=Ures; |
---|
| 452 | Data.Civ1_V_smooth(ind_good)=Vres; |
---|
| 453 | Data.Civ1_FF(ind_good)=FFres; |
---|
| 454 | Data.CivStage=3; |
---|
[1009] | 455 | |
---|
[834] | 456 | end |
---|
| 457 | |
---|
| 458 | %% Civ2 |
---|
| 459 | if isfield (Param.ActionInput,'Civ2') |
---|
| 460 | par_civ2=Param.ActionInput.Civ2; |
---|
[844] | 461 | par_civ2.ImageA=par_civ1.ImageA; |
---|
| 462 | par_civ2.ImageB=par_civ1.ImageB; |
---|
[834] | 463 | % if ~isfield(Param.Civ1,'ImageA') |
---|
| 464 | i1=i1_series_Civ2(ifield); |
---|
| 465 | i2=i1; |
---|
| 466 | if ~isempty(i2_series_Civ2) |
---|
| 467 | i2=i2_series_Civ2(ifield); |
---|
| 468 | end |
---|
| 469 | j1=1; |
---|
| 470 | if ~isempty(j1_series_Civ2) |
---|
| 471 | j1=j1_series_Civ2(ifield); |
---|
| 472 | end |
---|
| 473 | j2=j1; |
---|
| 474 | if ~isempty(j2_series_Civ2) |
---|
| 475 | j2=j2_series_Civ2(ifield); |
---|
| 476 | end |
---|
[864] | 477 | par_civ2.ImageWidth=size(par_civ2.ImageA,2); |
---|
| 478 | par_civ2.ImageHeight=size(par_civ2.ImageA,1); |
---|
| 479 | |
---|
[834] | 480 | if isfield(par_civ2,'Grid')% grid points set as input file |
---|
| 481 | if ischar(par_civ2.Grid)%read the grid file if the input is a file name |
---|
| 482 | par_civ2.Grid=dlmread(par_civ2.Grid); |
---|
| 483 | par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 484 | end |
---|
| 485 | else% automatic grid |
---|
| 486 | minix=floor(par_civ2.Dx/2)-0.5; |
---|
| 487 | maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx); |
---|
| 488 | miniy=floor(par_civ2.Dy/2)-0.5; |
---|
| 489 | maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy); |
---|
| 490 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
---|
| 491 | par_civ2.Grid(:,1)=reshape(GridX,[],1); |
---|
| 492 | par_civ2.Grid(:,2)=reshape(GridY,[],1); |
---|
[864] | 493 | |
---|
| 494 | |
---|
[834] | 495 | end |
---|
| 496 | Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data |
---|
| 497 | Shifty=zeros(size(par_civ2.Grid,1),1); |
---|
| 498 | nbval=zeros(size(par_civ2.Grid,1),1); |
---|
| 499 | if par_civ2.CheckDeformation |
---|
| 500 | DUDX=zeros(size(par_civ2.Grid,1),1); |
---|
| 501 | DUDY=zeros(size(par_civ2.Grid,1),1); |
---|
| 502 | DVDX=zeros(size(par_civ2.Grid,1),1); |
---|
| 503 | DVDY=zeros(size(par_civ2.Grid,1),1); |
---|
| 504 | end |
---|
| 505 | NbSubDomain=size(Data.Civ1_SubRange,3); |
---|
| 506 | % get the guess from patch1 |
---|
| 507 | for isub=1:NbSubDomain% for each sub-domain of Patch1 |
---|
| 508 | nbvec_sub=Data.Civ1_NbCentres(isub);% nbre of Civ1 vectors in the subdomain |
---|
| 509 | ind_sel=find(par_civ2.Grid(:,1)>=Data.Civ1_SubRange(1,1,isub) & par_civ2.Grid(:,1)<=Data.Civ1_SubRange(1,2,isub) &... |
---|
| 510 | par_civ2.Grid(:,2)>=Data.Civ1_SubRange(2,1,isub) & par_civ2.Grid(:,2)<=Data.Civ1_SubRange(2,2,isub)); |
---|
| 511 | epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites |
---|
| 512 | ctrs=Data.Civ1_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
---|
| 513 | nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap) |
---|
| 514 | EM = tps_eval(epoints,ctrs); |
---|
| 515 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
---|
| 516 | Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
---|
| 517 | if par_civ2.CheckDeformation |
---|
| 518 | [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs |
---|
| 519 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
---|
| 520 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
---|
| 521 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
---|
| 522 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
---|
| 523 | end |
---|
| 524 | end |
---|
| 525 | mask=''; |
---|
| 526 | if par_civ2.CheckMask&&~isempty(par_civ2.Mask)&& ~strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 |
---|
| 527 | mask=imread(par_civ2.Mask); |
---|
| 528 | end |
---|
[878] | 529 | % ibx2=ceil(par_civ2.CorrBoxSize(1)/2); |
---|
| 530 | % iby2=ceil(par_civ2.CorrBoxSize(2)/2); |
---|
[844] | 531 | par_civ2.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
---|
[834] | 532 | par_civ2.Grid=[par_civ2.Grid(nbval>=1,1)-par_civ2.SearchBoxShift(:,1)/2 par_civ2.Grid(nbval>=1,2)-par_civ2.SearchBoxShift(:,2)/2];% grid taken at the extrapolated origin of the displacement vectors |
---|
| 533 | if par_civ2.CheckDeformation |
---|
[878] | 534 | par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1); |
---|
| 535 | par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1); |
---|
| 536 | par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1); |
---|
| 537 | par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1); |
---|
[834] | 538 | end |
---|
[844] | 539 | % calculate velocity data (y and v in indices, reverse to y component) |
---|
[864] | 540 | [xtable, ytable, utable, vtable, ctable, F] = civ (par_civ2); |
---|
[834] | 541 | list_param=(fieldnames(Param.ActionInput.Civ2))'; |
---|
| 542 | Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before each string in list_param |
---|
| 543 | Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images |
---|
| 544 | %indicate the values of all the global attributes in the output data |
---|
| 545 | Data.Civ2_ImageA=ImageName_A; |
---|
| 546 | Data.Civ2_ImageB=ImageName_B; |
---|
| 547 | Data.Civ2_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; |
---|
[844] | 548 | Data.Civ2_Dt=0; |
---|
[834] | 549 | for ilist=1:length(list_param) |
---|
| 550 | Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist}); |
---|
| 551 | end |
---|
| 552 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; |
---|
| 553 | |
---|
| 554 | nbvar=numel(Data.ListVarName); |
---|
[864] | 555 | Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_F','Civ2_C'}];% cell array containing the names of the fields to record |
---|
| 556 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; |
---|
[834] | 557 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
---|
| 558 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
---|
| 559 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
---|
| 560 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
---|
| 561 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
---|
| 562 | Data.Civ2_X=reshape(xtable,[],1); |
---|
| 563 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
---|
| 564 | Data.Civ2_U=reshape(utable,[],1); |
---|
| 565 | Data.Civ2_V=reshape(-vtable,[],1); |
---|
| 566 | Data.Civ2_C=reshape(ctable,[],1); |
---|
| 567 | Data.Civ2_F=reshape(F,[],1); |
---|
| 568 | Data.CivStage=Data.CivStage+1; |
---|
| 569 | end |
---|
| 570 | |
---|
| 571 | %% Fix2 |
---|
| 572 | if isfield (Param.ActionInput,'Fix2') |
---|
| 573 | ListFixParam=fieldnames(Param.ActionInput.Fix2); |
---|
| 574 | for ilist=1:length(ListFixParam) |
---|
| 575 | ParamName=ListFixParam{ilist}; |
---|
| 576 | ListName=['Fix2_' ParamName]; |
---|
| 577 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
| 578 | eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';']) |
---|
| 579 | end |
---|
| 580 | if check_civx |
---|
| 581 | if ~isfield(Data,'fix2') |
---|
| 582 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; |
---|
| 583 | Data.fix2=1; |
---|
| 584 | Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; |
---|
| 585 | Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; |
---|
| 586 | end |
---|
| 587 | Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y); |
---|
| 588 | else |
---|
| 589 | Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; |
---|
| 590 | Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; |
---|
| 591 | nbvar=length(Data.ListVarName); |
---|
| 592 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
| 593 | Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V)); |
---|
| 594 | Data.CivStage=Data.CivStage+1; |
---|
| 595 | end |
---|
| 596 | |
---|
| 597 | end |
---|
| 598 | |
---|
| 599 | %% Patch2 |
---|
| 600 | if isfield (Param.ActionInput,'Patch2') |
---|
| 601 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}]; |
---|
| 602 | Data.Patch2_FieldSmooth=Param.ActionInput.Patch2.FieldSmooth; |
---|
| 603 | Data.Patch2_MaxDiff=Param.ActionInput.Patch2.MaxDiff; |
---|
| 604 | Data.Patch2_SubDomainSize=Param.ActionInput.Patch2.SubDomainSize; |
---|
| 605 | nbvar=length(Data.ListVarName); |
---|
| 606 | Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; |
---|
| 607 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... |
---|
| 608 | {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; |
---|
| 609 | |
---|
| 610 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
| 611 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
| 612 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
| 613 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 614 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
| 615 | Data.Civ2_U_smooth=zeros(size(Data.Civ2_X)); |
---|
| 616 | Data.Civ2_V_smooth=zeros(size(Data.Civ2_X)); |
---|
| 617 | if isfield(Data,'Civ2_FF') |
---|
| 618 | ind_good=find(Data.Civ2_FF==0); |
---|
| 619 | else |
---|
| 620 | ind_good=1:numel(Data.Civ2_X); |
---|
| 621 | end |
---|
| 622 | [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
| 623 | filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomainSize,Data.Patch2_FieldSmooth,Data.Patch2_MaxDiff); |
---|
| 624 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
| 625 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
| 626 | Data.Civ2_FF(ind_good)=FFres; |
---|
| 627 | Data.CivStage=Data.CivStage+1; |
---|
[864] | 628 | end |
---|
| 629 | |
---|
| 630 | |
---|
| 631 | %% Civ3 |
---|
| 632 | |
---|
| 633 | if isfield (Param.ActionInput,'Civ3') |
---|
| 634 | par_civ3=Param.ActionInput.Civ3; |
---|
| 635 | par_civ3.ImageA=par_civ1.ImageA; |
---|
| 636 | par_civ3.ImageB=par_civ1.ImageB; |
---|
| 637 | par_civ3.ImageWidth=size(par_civ3.ImageA,2); |
---|
| 638 | par_civ3.ImageHeight=size(par_civ3.ImageA,1); |
---|
| 639 | |
---|
| 640 | if isfield(par_civ3,'Grid')% grid points set as input file |
---|
| 641 | if ischar(par_civ3.Grid)%read the grid file if the input is a file name |
---|
| 642 | par_civ3.Grid=dlmread(par_civ3.Grid); |
---|
| 643 | par_civ3.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 644 | end |
---|
| 645 | else% automatic grid |
---|
| 646 | minix=floor(par_civ3.Dx/2)-0.5; |
---|
| 647 | maxix=minix+par_civ3.Dx*floor((par_civ3.ImageWidth-1)/par_civ3.Dx); |
---|
| 648 | miniy=floor(par_civ3.Dy/2)-0.5; |
---|
| 649 | maxiy=minix+par_civ3.Dy*floor((par_civ3.ImageHeight-1)/par_civ3.Dy); |
---|
| 650 | [GridX,GridY]=meshgrid(minix:par_civ3.Dx:maxix,miniy:par_civ3.Dy:maxiy); |
---|
| 651 | par_civ3.Grid(:,1)=reshape(GridX,[],1); |
---|
[878] | 652 | par_civ3.Grid(:,2)=reshape(GridY,[],1); |
---|
[864] | 653 | end |
---|
| 654 | Shiftx=zeros(size(par_civ3.Grid,1),1);% shift expected from civ2 data |
---|
| 655 | Shifty=zeros(size(par_civ3.Grid,1),1); |
---|
| 656 | nbval=zeros(size(par_civ3.Grid,1),1); |
---|
| 657 | if par_civ3.CheckDeformation |
---|
| 658 | DUDX=zeros(size(par_civ3.Grid,1),1); |
---|
| 659 | DUDY=zeros(size(par_civ3.Grid,1),1); |
---|
| 660 | DVDX=zeros(size(par_civ3.Grid,1),1); |
---|
| 661 | DVDY=zeros(size(par_civ3.Grid,1),1); |
---|
| 662 | end |
---|
| 663 | NbSubDomain=size(Data.Civ2_SubRange,3); |
---|
| 664 | % get the guess from patch2 |
---|
| 665 | for isub=1:NbSubDomain% for each sub-domain of Patch2 |
---|
| 666 | nbvec_sub=Data.Civ2_NbCentres(isub);% nbre of Civ2 vectors in the subdomain |
---|
| 667 | ind_sel=find(par_civ3.Grid(:,1)>=Data.Civ2_SubRange(1,1,isub) & par_civ3.Grid(:,1)<=Data.Civ2_SubRange(1,2,isub) &... |
---|
| 668 | par_civ3.Grid(:,2)>=Data.Civ2_SubRange(2,1,isub) & par_civ3.Grid(:,2)<=Data.Civ2_SubRange(2,2,isub)); |
---|
| 669 | epoints = par_civ3.Grid(ind_sel,:);% coordinates of interpolation sites |
---|
| 670 | ctrs=Data.Civ2_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
---|
| 671 | nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap) |
---|
| 672 | EM = tps_eval(epoints,ctrs); |
---|
| 673 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ2_U_tps(1:nbvec_sub+3,isub); |
---|
| 674 | Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ2_V_tps(1:nbvec_sub+3,isub); |
---|
| 675 | if par_civ3.CheckDeformation |
---|
| 676 | [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs |
---|
| 677 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ2_U_tps(1:nbvec_sub+3,isub); |
---|
| 678 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ2_U_tps(1:nbvec_sub+3,isub); |
---|
| 679 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ2_V_tps(1:nbvec_sub+3,isub); |
---|
| 680 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ2_V_tps(1:nbvec_sub+3,isub); |
---|
| 681 | end |
---|
| 682 | end |
---|
| 683 | mask=''; |
---|
| 684 | if par_civ3.CheckMask&&~isempty(par_civ3.Mask)&& ~strcmp(maskname,par_civ3.Mask)% mask exist, not already read in Civ2 |
---|
| 685 | mask=imread(par_civ3.Mask); |
---|
| 686 | end |
---|
[878] | 687 | % ibx2=ceil(par_civ3.CorrBoxSize(1)/2); |
---|
| 688 | % iby2=ceil(par_civ3.CorrBoxSize(2)/2); |
---|
[864] | 689 | par_civ3.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
---|
| 690 | par_civ3.Grid=[par_civ3.Grid(nbval>=1,1)-par_civ3.SearchBoxShift(:,1)/2 par_civ3.Grid(nbval>=1,2)-par_civ3.SearchBoxShift(:,2)/2];% grid taken at the extrapolated origin of the displacement vectors |
---|
| 691 | if par_civ3.CheckDeformation |
---|
[878] | 692 | par_civ3.DUDX=DUDX(nbval>=1)./nbval(nbval>=1); |
---|
| 693 | par_civ3.DUDY=DUDY(nbval>=1)./nbval(nbval>=1); |
---|
| 694 | par_civ3.DVDX=DVDX(nbval>=1)./nbval(nbval>=1); |
---|
| 695 | par_civ3.DVDY=DVDY(nbval>=1)./nbval(nbval>=1); |
---|
[864] | 696 | end |
---|
| 697 | % calculate velocity data (y and v in indices, reverse to y component) |
---|
| 698 | [xtable, ytable, utable, vtable, ctable, F] = civ (par_civ3); |
---|
| 699 | list_param=(fieldnames(Param.ActionInput.Civ3))'; |
---|
| 700 | Civ3_param=regexprep(list_param,'^.+','Civ3_$0');% insert 'Civ3_' before each string in list_param |
---|
| 701 | Civ3_param=[{'Civ3_ImageA','Civ3_ImageB','Civ3_Time','Civ3_Dt'} Civ3_param]; %insert the names of the two input images |
---|
| 702 | %indicate the values of all the global attributes in the output data |
---|
| 703 | Data.Civ3_ImageA=ImageName_A; |
---|
| 704 | Data.Civ3_ImageB=ImageName_B; |
---|
| 705 | Data.Civ3_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; |
---|
| 706 | Data.Civ3_Dt=0; |
---|
| 707 | for ilist=1:length(list_param) |
---|
| 708 | Data.(Civ3_param{4+ilist})=Param.ActionInput.Civ3.(list_param{ilist}); |
---|
| 709 | end |
---|
| 710 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ3_param]; |
---|
| 711 | |
---|
| 712 | nbvar=numel(Data.ListVarName); |
---|
[878] | 713 | Data.ListVarName=[Data.ListVarName {'Civ3_X','Civ3_Y','Civ3_U','Civ3_V','Civ3_F','Civ3_C','Xphys','Yphys','Zphys'}];% cell array containing the names of the fields to record |
---|
| 714 | Data.VarDimName=[Data.VarDimName {'nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3'}]; |
---|
[864] | 715 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
---|
| 716 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
---|
| 717 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
---|
| 718 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
---|
| 719 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
---|
| 720 | Data.Civ3_X=reshape(xtable,[],1); |
---|
| 721 | Data.Civ3_Y=reshape(size(par_civ3.ImageA,1)-ytable+1,[],1); |
---|
| 722 | Data.Civ3_U=reshape(utable,[],1); |
---|
| 723 | Data.Civ3_V=reshape(-vtable,[],1); |
---|
| 724 | Data.Civ3_C=reshape(ctable,[],1); |
---|
| 725 | Data.Civ3_F=reshape(F,[],1); |
---|
| 726 | Data.CivStage=Data.CivStage+1; |
---|
| 727 | end |
---|
| 728 | |
---|
| 729 | %% Fix3 |
---|
| 730 | if isfield (Param.ActionInput,'Fix3') |
---|
| 731 | ListFixParam=fieldnames(Param.ActionInput.Fix3); |
---|
| 732 | for ilist=1:length(ListFixParam) |
---|
| 733 | ParamName=ListFixParam{ilist}; |
---|
| 734 | ListName=['Fix3_' ParamName]; |
---|
| 735 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
| 736 | eval(['Data.' ListName '=Param.ActionInput.Fix3.' ParamName ';']) |
---|
| 737 | end |
---|
| 738 | if check_civx |
---|
| 739 | if ~isfield(Data,'fix3') |
---|
| 740 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix3']; |
---|
| 741 | Data.fix3=1; |
---|
| 742 | Data.ListVarName=[Data.ListVarName {'vec3_FixFlag'}]; |
---|
| 743 | Data.VarDimName=[Data.VarDimName {'nb_vectors3'}]; |
---|
| 744 | end |
---|
| 745 | Data.vec_FixFlag=fix(Param.Fix3,Data.vec3_F,Data.vec3_C,Data.vec3_U,Data.vec3_V,Data.vec3_X,Data.vec3_Y); |
---|
| 746 | else |
---|
| 747 | Data.ListVarName=[Data.ListVarName {'Civ3_FF'}]; |
---|
| 748 | Data.VarDimName=[Data.VarDimName {'nb_vec_3'}]; |
---|
| 749 | nbvar=length(Data.ListVarName); |
---|
| 750 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
| 751 | Data.Civ3_FF=double(fix(Param.ActionInput.Fix3,Data.Civ3_F,Data.Civ3_C,Data.Civ3_U,Data.Civ3_V)); |
---|
| 752 | Data.CivStage=Data.CivStage+1; |
---|
| 753 | end |
---|
| 754 | |
---|
| 755 | end |
---|
| 756 | |
---|
| 757 | |
---|
| 758 | %% Patch3 |
---|
| 759 | if isfield (Param.ActionInput,'Patch3') |
---|
| 760 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch3_Rho','Patch3_Threshold','Patch3_SubDomain'}]; |
---|
| 761 | Data.Patch3_FieldSmooth=Param.ActionInput.Patch3.FieldSmooth; |
---|
| 762 | Data.Patch3_MaxDiff=Param.ActionInput.Patch3.MaxDiff; |
---|
| 763 | Data.Patch3_SubDomainSize=Param.ActionInput.Patch3.SubDomainSize; |
---|
| 764 | nbvar=length(Data.ListVarName); |
---|
[878] | 765 | Data.ListVarName=[Data.ListVarName {'Civ3_U_smooth','Civ3_V_smooth','Civ3_SubRange','Civ3_NbCentres','Civ3_Coord_tps','Civ3_U_tps','Civ3_V_tps','Xmid','Ymid','Uphys','Vphys','Error'}]; |
---|
[864] | 766 | Data.VarDimName=[Data.VarDimName {'nb_vec_3','nb_vec_3',{'nb_coord','nb_bounds','nb_subdomain_3'},{'nb_subdomain_3'},... |
---|
[878] | 767 | {'nb_tps_3','nb_coord','nb_subdomain_3'},{'nb_tps_3','nb_subdomain_3'},{'nb_tps_3','nb_subdomain_3'},'nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3'}]; |
---|
[864] | 768 | |
---|
| 769 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
| 770 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
| 771 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
| 772 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
| 773 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
| 774 | Data.Civ3_U_smooth=zeros(size(Data.Civ3_X)); |
---|
| 775 | Data.Civ3_V_smooth=zeros(size(Data.Civ3_X)); |
---|
| 776 | if isfield(Data,'Civ3_FF') |
---|
| 777 | ind_good=find(Data.Civ3_FF==0); |
---|
| 778 | else |
---|
| 779 | ind_good=1:numel(Data.Civ3_X); |
---|
| 780 | end |
---|
| 781 | [Data.Civ3_SubRange,Data.Civ3_NbCentres,Data.Civ3_Coord_tps,Data.Civ3_U_tps,Data.Civ3_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
| 782 | filter_tps([Data.Civ3_X(ind_good) Data.Civ3_Y(ind_good)],Data.Civ3_U(ind_good),Data.Civ3_V(ind_good),[],Data.Patch3_SubDomainSize,Data.Patch3_FieldSmooth,Data.Patch3_MaxDiff); |
---|
| 783 | Data.Civ3_U_smooth(ind_good)=Ures; |
---|
| 784 | Data.Civ3_V_smooth(ind_good)=Vres; |
---|
| 785 | Data.Civ3_FF(ind_good)=FFres; |
---|
| 786 | Data.CivStage=Data.CivStage+1; |
---|
| 787 | |
---|
| 788 | |
---|
[854] | 789 | % get z from u and v (displacements) |
---|
| 790 | |
---|
[864] | 791 | Data.Xmid=Rangx(1)+(Rangx(2)-Rangx(1))*(Data.Civ3_X-0.5)/(Npx-1);%temporary coordinate (velocity taken at the point middle from imgae 1 and 2) |
---|
| 792 | Data.Ymid=Rangy(2)+(Rangy(1)-Rangy(2))*(Data.Civ3_Y-0.5)/(Npy-1);%temporary coordinate (velocity taken at the point middle from imgae 1 and 2) |
---|
| 793 | Data.Uphys=Data.Civ3_U_smooth*(Rangx(2)-Rangx(1))/(Npx-1); |
---|
[878] | 794 | Data.Vphys=Data.Civ3_V_smooth*(Rangy(1)-Rangy(2))/(Npy-1); |
---|
| 795 | [Data.Zphys,Data.Xphys,Data.Yphys,Data.Error]=shift2z(Data.Xmid,Data.Ymid,Data.Uphys,Data.Vphys,XmlData); %Data.Xphys and Data.Xphys are real coordinate (geometric correction more accurate than xtemp/ytemp) |
---|
[854] | 796 | if ~isempty(errormsg) |
---|
| 797 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
| 798 | return |
---|
| 799 | end |
---|
[851] | 800 | |
---|
[834] | 801 | end |
---|
[878] | 802 | |
---|
[834] | 803 | |
---|
| 804 | %% write result in a netcdf file if requested |
---|
[985] | 805 | % if LSM ~= 1 % store all data |
---|
| 806 | % if exist('ncfile','var') |
---|
| 807 | % errormsg=struct2nc(ncfile,Data); |
---|
| 808 | % if isempty(errormsg) |
---|
| 809 | % disp([ncfile ' written']) |
---|
| 810 | % else |
---|
| 811 | % disp(errormsg) |
---|
| 812 | % end |
---|
| 813 | % end |
---|
| 814 | % else |
---|
[864] | 815 | % store only phys data |
---|
[1009] | 816 | % Data_light.ListVarName={'Xphys','Yphys','Zphys','Civ3_C','Xmid','Ymid','Uphys','Vphys','Error'}; |
---|
| 817 | % Data_light.VarDimName={'nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3'}; |
---|
| 818 | Data_light.ListVarName={'Xphys','Yphys','Zphys','Civ3_C','DX','DY','Error'}; |
---|
| 819 | Data_light.VarDimName={'nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3','nb_vec_3'}; |
---|
| 820 | Data_light.VarAttribute{1}.Role='coord_x'; |
---|
| 821 | Data_light.VarAttribute{2}.Role='coord_y'; |
---|
| 822 | Data_light.VarAttribute{3}.Role='scalar'; |
---|
| 823 | Data_light.VarAttribute{5}.Role='vector_x'; |
---|
| 824 | Data_light.VarAttribute{6}.Role='vector_y'; |
---|
| 825 | ind_good=find(Data.Civ3_FF==0); |
---|
| 826 | Data_light.Zphys=Data.Zphys(ind_good); |
---|
| 827 | Data_light.Yphys=Data.Yphys(ind_good); |
---|
| 828 | Data_light.Xphys=Data.Xphys(ind_good); |
---|
| 829 | Data_light.Civ3_C=Data.Civ3_C(ind_good); |
---|
| 830 | % Data_light.Xmid=Data.Xmid(ind_good); |
---|
| 831 | % Data_light.Ymid=Data.Ymid(ind_good); |
---|
| 832 | Data_light.DX=Data.Uphys(ind_good); |
---|
| 833 | Data_light.DY=Data.Vphys(ind_good); |
---|
| 834 | Data_light.Error=Data.Error(ind_good); |
---|
[864] | 835 | if exist('ncfile2','var') |
---|
| 836 | errormsg=struct2nc(ncfile2,Data_light); |
---|
| 837 | if isempty(errormsg) |
---|
| 838 | disp([ncfile2 ' written']) |
---|
| 839 | else |
---|
| 840 | disp(errormsg) |
---|
| 841 | end |
---|
| 842 | end |
---|
| 843 | |
---|
[985] | 844 | % end |
---|
[927] | 845 | end |
---|
| 846 | disp(['ellapsed time for the loop ' num2str(toc) ' s']) |
---|
| 847 | tic |
---|
| 848 | while toc < rand(1)*10 |
---|
| 849 | for i = 1:100000, sqrt(1237); end |
---|
| 850 | end |
---|
[834] | 851 | |
---|
[864] | 852 | |
---|
| 853 | |
---|
[834] | 854 | % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ |
---|
| 855 | %-------------------------------------------------------------------------- |
---|
| 856 | % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) |
---|
| 857 | % |
---|
| 858 | % OUTPUT: |
---|
| 859 | % xtable: set of x coordinates |
---|
| 860 | % ytable: set of y coordiantes |
---|
| 861 | % utable: set of u displacements (along x) |
---|
| 862 | % vtable: set of v displacements (along y) |
---|
| 863 | % ctable: max image correlation for each vector |
---|
| 864 | % typevector: set of flags, =1 for good, =0 for NaN vectors |
---|
| 865 | % |
---|
| 866 | %INPUT: |
---|
| 867 | % par_civ: structure of input parameters, with fields: |
---|
| 868 | % .CorrBoxSize |
---|
| 869 | % .SearchBoxSize |
---|
| 870 | % .SearchBoxShift |
---|
| 871 | % .ImageHeight |
---|
| 872 | % .ImageWidth |
---|
| 873 | % .Dx, Dy |
---|
| 874 | % .Grid |
---|
| 875 | % .Mask |
---|
| 876 | % .MinIma |
---|
| 877 | % .MaxIma |
---|
| 878 | % .image1:first image (matrix) |
---|
| 879 | % image2: second image (matrix) |
---|
| 880 | % ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1) |
---|
| 881 | % isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1) |
---|
| 882 | % shiftx, shifty: shift of the search box (in pixel index, yshift reversed) |
---|
| 883 | % step: mesh of the measurement points (in px) |
---|
| 884 | % subpixfinder=1 or 2 controls the curve fitting of the image correlation |
---|
| 885 | % mask: =[] for no mask |
---|
| 886 | % roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[]; |
---|
| 887 | function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ) |
---|
| 888 | %this funtion performs the DCC PIV analysis. Recent window-deformation |
---|
| 889 | %methods perform better and will maybe be implemented in the future. |
---|
| 890 | |
---|
| 891 | %% prepare measurement grid |
---|
| 892 | if isfield(par_civ,'Grid')% grid points set as input |
---|
| 893 | if ischar(par_civ.Grid)%read the drid file if the input is a file name |
---|
| 894 | par_civ.Grid=dlmread(par_civ.Grid); |
---|
| 895 | par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
| 896 | end |
---|
| 897 | else% automatic grid |
---|
| 898 | minix=floor(par_civ.Dx/2)-0.5; |
---|
| 899 | maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); |
---|
| 900 | miniy=floor(par_civ.Dy/2)-0.5; |
---|
| 901 | maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); |
---|
| 902 | [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
| 903 | par_civ.Grid(:,1)=reshape(GridX,[],1); |
---|
| 904 | par_civ.Grid(:,2)=reshape(GridY,[],1); |
---|
| 905 | end |
---|
| 906 | nbvec=size(par_civ.Grid,1); |
---|
| 907 | |
---|
[879] | 908 | %% prepare correlation and search boxes |
---|
[878] | 909 | ibx2=floor(par_civ.CorrBoxSize(1)/2); |
---|
| 910 | iby2=floor(par_civ.CorrBoxSize(2)/2); |
---|
| 911 | isx2=floor(par_civ.SearchBoxSize(1)/2); |
---|
| 912 | isy2=floor(par_civ.SearchBoxSize(2)/2); |
---|
[834] | 913 | shiftx=round(par_civ.SearchBoxShift(:,1)); |
---|
| 914 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
---|
| 915 | if numel(shiftx)==1% case of a unique shift for the whole field( civ1) |
---|
| 916 | shiftx=shiftx*ones(nbvec,1); |
---|
| 917 | shifty=shifty*ones(nbvec,1); |
---|
| 918 | end |
---|
| 919 | |
---|
| 920 | %% Default output |
---|
| 921 | xtable=par_civ.Grid(:,1); |
---|
| 922 | ytable=par_civ.Grid(:,2); |
---|
| 923 | utable=zeros(nbvec,1); |
---|
| 924 | vtable=zeros(nbvec,1); |
---|
| 925 | ctable=zeros(nbvec,1); |
---|
| 926 | F=zeros(nbvec,1); |
---|
| 927 | result_conv=[]; |
---|
| 928 | errormsg=''; |
---|
| 929 | |
---|
| 930 | %% prepare mask |
---|
| 931 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
| 932 | if strcmp(par_civ.Mask,'all') |
---|
| 933 | return % get the grid only, no civ calculation |
---|
| 934 | elseif ischar(par_civ.Mask) |
---|
| 935 | par_civ.Mask=imread(par_civ.Mask); |
---|
| 936 | end |
---|
| 937 | end |
---|
| 938 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
| 939 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
| 940 | |
---|
| 941 | par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images |
---|
| 942 | par_civ.ImageB=sum(double(par_civ.ImageB),3); |
---|
| 943 | [npy_ima npx_ima]=size(par_civ.ImageA); |
---|
| 944 | if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) |
---|
| 945 | errormsg='image pair with unequal size'; |
---|
| 946 | return |
---|
| 947 | end |
---|
| 948 | |
---|
| 949 | %% Apply mask |
---|
[879] | 950 | % Convention for mask IDEAS TO IMPLEMENT ? |
---|
| 951 | % mask >200 : velocity calculated |
---|
| 952 | % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) |
---|
| 953 | % 150>=mask >100: velocity not calculated, nor interpolated |
---|
| 954 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
| 955 | % 20>=mask: velocity=0 |
---|
[834] | 956 | checkmask=0; |
---|
| 957 | MinA=min(min(par_civ.ImageA)); |
---|
[879] | 958 | %MinB=min(min(par_civ.ImageB)); |
---|
| 959 | %check_undefined=false(size(par_civ.ImageA)); |
---|
[834] | 960 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
[879] | 961 | checkmask=1; |
---|
| 962 | if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) |
---|
[834] | 963 | errormsg='mask must be an image with the same size as the images'; |
---|
| 964 | return |
---|
[879] | 965 | end |
---|
| 966 | % check_noflux=(par_civ.Mask<100) ;%TODO: to implement |
---|
[834] | 967 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
[879] | 968 | % par_civ.ImageA(check_undefined)=MinA;% put image A to zero (i.e. the min image value) in the undefined area |
---|
| 969 | % par_civ.ImageB(check_undefined)=MinB;% put image B to zero (i.e. the min image value) in the undefined area |
---|
[834] | 970 | end |
---|
| 971 | |
---|
| 972 | %% compute image correlations: MAINLOOP on velocity vectors |
---|
| 973 | corrmax=0; |
---|
| 974 | sum_square=1;% default |
---|
| 975 | mesh=1;% default |
---|
[878] | 976 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
| 977 | if CheckDeformation |
---|
| 978 | mesh=0.25;%mesh in pixels for subpixel image interpolation |
---|
[834] | 979 | end |
---|
| 980 | % vector=[0 0];%default |
---|
[864] | 981 | |
---|
[834] | 982 | for ivec=1:nbvec |
---|
| 983 | iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box |
---|
| 984 | jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box |
---|
[864] | 985 | |
---|
[834] | 986 | %if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask |
---|
| 987 | % if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||... |
---|
| 988 | % jref+shifty(ivec)-isy2<1||jref+shifty(ivec)+isy2>par_civ.ImageHeight|| iref+shiftx(ivec)-isx2<1 || iref+shiftx(ivec)+isx2>par_civ.ImageWidth % we are outside the image |
---|
| 989 | % F(ivec)=3; |
---|
| 990 | % else |
---|
| 991 | F(ivec)=0; |
---|
| 992 | subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage |
---|
| 993 | subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage |
---|
| 994 | subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage |
---|
| 995 | subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage |
---|
| 996 | image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A |
---|
| 997 | image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A |
---|
[878] | 998 | mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask |
---|
| 999 | mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask |
---|
[834] | 1000 | check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1 |
---|
| 1001 | check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight; |
---|
| 1002 | check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2 |
---|
[879] | 1003 | check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight; |
---|
[834] | 1004 | image1_crop(check1_y,check1_x)=par_civ.ImageA(subrange1_y(check1_y),subrange1_x(check1_x));%extract a subimage (correlation box) from image A |
---|
| 1005 | image2_crop(check2_y,check2_x)=par_civ.ImageB(subrange2_y(check2_y),subrange2_x(check2_x));%extract a larger subimage (search box) from image B |
---|
[879] | 1006 | if checkmask |
---|
| 1007 | mask1_crop(check1_y,check1_x)=check_undefined(subrange1_y(check1_y),subrange1_x(check1_x));%extract a mask subimage (correlation box) from image A |
---|
| 1008 | mask2_crop(check2_y,check2_x)=check_undefined(subrange2_y(check2_y),subrange2_x(check2_x));%extract a mask subimage (search box) from imag |
---|
| 1009 | sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image |
---|
[878] | 1010 | if sizemask > 1/2% eliminate point if more than half of the correlation box is masked |
---|
| 1011 | F(ivec)=3; % |
---|
| 1012 | else |
---|
| 1013 | image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1) |
---|
| 1014 | image2_crop=image2_crop.*~mask2_crop; |
---|
| 1015 | image1_mean=mean(mean(image1_crop))/(1-sizemask); |
---|
| 1016 | image2_mean=mean(mean(image2_crop))/(1-sizemask); |
---|
[879] | 1017 | end |
---|
| 1018 | else |
---|
| 1019 | image1_mean=mean(mean(image1_crop)); |
---|
| 1020 | image2_mean=mean(mean(image2_crop)); |
---|
| 1021 | end |
---|
[834] | 1022 | %threshold on image minimum |
---|
| 1023 | if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) |
---|
| 1024 | F(ivec)=3; |
---|
| 1025 | end |
---|
| 1026 | %threshold on image maximum |
---|
| 1027 | if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) |
---|
| 1028 | F(ivec)=3; |
---|
| 1029 | end |
---|
| 1030 | if F(ivec)~=3 |
---|
[879] | 1031 | image1_crop=(image1_crop-image1_mean);%substract the mean, put to zero the masked parts |
---|
| 1032 | image2_crop=(image2_crop-image2_mean); |
---|
| 1033 | if checkmask |
---|
| 1034 | image1_crop=image1_crop.*~mask1_crop;% put to zero the masked parts |
---|
| 1035 | image2_crop=image2_crop.*~mask2_crop; |
---|
| 1036 | end |
---|
[878] | 1037 | if CheckDeformation |
---|
[879] | 1038 | xi=(1:mesh:size(image1_crop,2)); |
---|
| 1039 | yi=(1:mesh:size(image1_crop,1))'; |
---|
| 1040 | [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); |
---|
| 1041 | XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); |
---|
| 1042 | YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); |
---|
| 1043 | image1_crop=interp2(image1_crop,XIant,YIant); |
---|
| 1044 | image1_crop(isnan(image1_crop))=0; |
---|
| 1045 | xi=(1:mesh:size(image2_crop,2)); |
---|
| 1046 | yi=(1:mesh:size(image2_crop,1))'; |
---|
| 1047 | image2_crop=interp2(image2_crop,xi,yi,'*spline'); |
---|
| 1048 | image2_crop(isnan(image2_crop))=0; |
---|
[834] | 1049 | end |
---|
[864] | 1050 | sum_square=(sum(sum(image1_crop.*image1_crop)));%+sum(sum(image2_crop.*image2_crop)))/2; |
---|
[834] | 1051 | %reference: Oliver Pust, PIV: Direct Cross-Correlation |
---|
| 1052 | result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); |
---|
| 1053 | corrmax= max(max(result_conv)); |
---|
| 1054 | result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 |
---|
| 1055 | %Find the correlation max, at 255 |
---|
| 1056 | [y,x] = find(result_conv==255,1); |
---|
[878] | 1057 | subimage2_crop=image2_crop(y:y+2*iby2/mesh,x:x+2*ibx2/mesh);%subimage of image 2 corresponding to the optimum displacement of first image |
---|
[879] | 1058 | sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2 |
---|
| 1059 | sum_square=sqrt(sum_square);% sqrt of the variance product to normalise correlation |
---|
[834] | 1060 | if ~isempty(y) && ~isempty(x) |
---|
| 1061 | try |
---|
| 1062 | if par_civ.CorrSmooth==1 |
---|
| 1063 | [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); |
---|
| 1064 | elseif par_civ.CorrSmooth==2 |
---|
| 1065 | [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); |
---|
| 1066 | end |
---|
[864] | 1067 | |
---|
[879] | 1068 | |
---|
[864] | 1069 | utable(ivec)=vector(1)*mesh+shiftx(ivec); |
---|
[834] | 1070 | vtable(ivec)=vector(2)*mesh+shifty(ivec); |
---|
[864] | 1071 | |
---|
[879] | 1072 | |
---|
[864] | 1073 | xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
---|
| 1074 | ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
---|
| 1075 | |
---|
[834] | 1076 | iref=round(xtable(ivec));% image index for the middle of the vector |
---|
| 1077 | jref=round(ytable(ivec)); |
---|
| 1078 | if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100 |
---|
| 1079 | utable(ivec)=0; |
---|
| 1080 | vtable(ivec)=0; |
---|
| 1081 | F(ivec)=3; |
---|
| 1082 | end |
---|
| 1083 | ctable(ivec)=corrmax/sum_square;% correlation value |
---|
| 1084 | catch ME |
---|
| 1085 | F(ivec)=3; |
---|
| 1086 | end |
---|
| 1087 | else |
---|
| 1088 | F(ivec)=3; |
---|
| 1089 | end |
---|
| 1090 | end |
---|
| 1091 | end |
---|
| 1092 | result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output |
---|
| 1093 | |
---|
| 1094 | %------------------------------------------------------------------------ |
---|
| 1095 | % --- Find the maximum of the correlation function after interpolation |
---|
| 1096 | function [vector,F] = SUBPIXGAUSS (result_conv,x,y) |
---|
| 1097 | %------------------------------------------------------------------------ |
---|
| 1098 | vector=[0 0]; %default |
---|
| 1099 | F=0; |
---|
| 1100 | [npy,npx]=size(result_conv); |
---|
| 1101 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) |
---|
[927] | 1102 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology |
---|
[834] | 1103 | %http://urapiv.wordpress.com |
---|
| 1104 | peaky = y; |
---|
| 1105 | if y <= npy-1 && y >= 1 |
---|
| 1106 | f0 = log(result_conv(y,x)); |
---|
| 1107 | f1 = log(result_conv(y-1,x)); |
---|
| 1108 | f2 = log(result_conv(y+1,x)); |
---|
| 1109 | peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 1110 | else |
---|
| 1111 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 1112 | end |
---|
| 1113 | peakx=x; |
---|
| 1114 | if x <= npx-1 && x >= 1 |
---|
| 1115 | f0 = log(result_conv(y,x)); |
---|
| 1116 | f1 = log(result_conv(y,x-1)); |
---|
| 1117 | f2 = log(result_conv(y,x+1)); |
---|
| 1118 | peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
| 1119 | else |
---|
| 1120 | F=-2; % warning flag for vector truncated by the limited search box |
---|
| 1121 | end |
---|
| 1122 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
| 1123 | |
---|
| 1124 | %------------------------------------------------------------------------ |
---|
| 1125 | % --- Find the maximum of the correlation function after interpolation |
---|
| 1126 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
| 1127 | %------------------------------------------------------------------------ |
---|
| 1128 | vector=[0 0]; %default |
---|
| 1129 | F=-2; |
---|
| 1130 | peaky=y; |
---|
| 1131 | peakx=x; |
---|
| 1132 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) |
---|
| 1133 | [npy,npx]=size(result_conv); |
---|
| 1134 | if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1) |
---|
| 1135 | F=0; |
---|
| 1136 | for i=-1:1 |
---|
| 1137 | for j=-1:1 |
---|
| 1138 | %following 15 lines based on |
---|
[927] | 1139 | %H. Nobach ??? M. Honkanen (2005) |
---|
[834] | 1140 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
| 1141 | %estimation in particle image velocimetry or particle position |
---|
| 1142 | %estimation in particle tracking velocimetry |
---|
[927] | 1143 | %Experiments in Fluids (2005) 38: 511???515 |
---|
[834] | 1144 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
| 1145 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
| 1146 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
| 1147 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
| 1148 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
| 1149 | end |
---|
| 1150 | end |
---|
| 1151 | c10=(1/6)*sum(sum(c10)); |
---|
| 1152 | c01=(1/6)*sum(sum(c01)); |
---|
| 1153 | c11=(1/4)*sum(sum(c11)); |
---|
| 1154 | c20=(1/6)*sum(sum(c20)); |
---|
| 1155 | c02=(1/6)*sum(sum(c02)); |
---|
| 1156 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
| 1157 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
| 1158 | if abs(deltax)<1 |
---|
| 1159 | peakx=x+deltax; |
---|
| 1160 | end |
---|
| 1161 | if abs(deltay)<1 |
---|
| 1162 | peaky=y+deltay; |
---|
| 1163 | end |
---|
| 1164 | end |
---|
| 1165 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
| 1166 | |
---|
| 1167 | %'RUN_FIX': function for fixing velocity fields: |
---|
| 1168 | %----------------------------------------------- |
---|
| 1169 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) |
---|
| 1170 | % |
---|
| 1171 | %filename: name of the netcdf file (used as input and output) |
---|
| 1172 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) |
---|
| 1173 | %.vel_type='civ1' or 'civ2'; |
---|
| 1174 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); |
---|
| 1175 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) |
---|
| 1176 | %flagindex: flag specifying which values of vec_f are removed: |
---|
| 1177 | % if flagindex(1)=1: vec_f=-2 vectors are removed |
---|
| 1178 | % if flagindex(2)=1: vec_f=3 vectors are removed |
---|
| 1179 | % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) |
---|
| 1180 | %iter=1 for civ1 fields and iter=2 for civ2 fields |
---|
| 1181 | %thresh_vecC: threshold in the image correlation vec_C |
---|
| 1182 | %flag_mask: =1 mask used to remove vectors (0 else) |
---|
| 1183 | %maskname: name of the mask image file for fix |
---|
| 1184 | %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists |
---|
| 1185 | %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold |
---|
| 1186 | %fileref: .nc file name for a reference velocity (='': refrence 0 used) |
---|
| 1187 | %fieldref: 'civ1','filter1'...feld used in fileref |
---|
| 1188 | |
---|
| 1189 | function FF=fix(Param,F,C,U,V,X,Y) |
---|
| 1190 | FF=zeros(size(F));%default |
---|
| 1191 | |
---|
| 1192 | %criterium on warn flags |
---|
| 1193 | FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; |
---|
| 1194 | FlagVal=[-2 2 3 4]; |
---|
| 1195 | for iflag=1:numel(FlagName) |
---|
| 1196 | if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) |
---|
| 1197 | FF=(FF==1| F==FlagVal(iflag)); |
---|
| 1198 | end |
---|
| 1199 | end |
---|
| 1200 | %criterium on correlation values |
---|
| 1201 | if isfield (Param,'MinCorr') |
---|
| 1202 | FF=FF==1 | C<Param.MinCorr; |
---|
| 1203 | end |
---|
| 1204 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
| 1205 | Umod= U.*U+V.*V; |
---|
| 1206 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
| 1207 | FF=FF==1 | Umod<(Param.MinVel*Param.MinVel); |
---|
| 1208 | end |
---|
| 1209 | if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel) |
---|
| 1210 | FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel); |
---|
| 1211 | end |
---|
| 1212 | end |
---|
| 1213 | |
---|
| 1214 | |
---|
| 1215 | %------------------------------------------------------------------------ |
---|
| 1216 | % --- determine the list of index pairs of processing file |
---|
| 1217 | function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=... |
---|
| 1218 | find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j) |
---|
| 1219 | %------------------------------------------------------------------------ |
---|
| 1220 | i1_series=i_series;% set of first image indexes |
---|
| 1221 | i2_series=i_series; |
---|
| 1222 | j1_series=j_series;%ones(size(i_series));% set of first image numbers |
---|
| 1223 | j2_series=j_series;%ones(size(i_series)); |
---|
| 1224 | r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names'); |
---|
| 1225 | if ~isempty(r) |
---|
| 1226 | mode=['D' r.ind]; |
---|
| 1227 | ind1=str2num(r.num1); |
---|
| 1228 | ind2=str2num(r.num2); |
---|
| 1229 | else |
---|
| 1230 | mode='j1-j2'; |
---|
| 1231 | r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names'); |
---|
| 1232 | if ~isempty(r) |
---|
| 1233 | NomTypeNc='_1ab'; |
---|
| 1234 | else |
---|
| 1235 | r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names'); |
---|
| 1236 | if ~isempty(r) |
---|
| 1237 | NomTypeNc='_1AB'; |
---|
| 1238 | else |
---|
| 1239 | r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names'); |
---|
| 1240 | if ~isempty(r) |
---|
| 1241 | NomTypeNc='_1_1-2'; |
---|
| 1242 | end |
---|
| 1243 | end |
---|
| 1244 | end |
---|
| 1245 | if isempty(r) |
---|
| 1246 | display('wrong pair mode input option') |
---|
| 1247 | else |
---|
| 1248 | ind1=stra2num(r.num1); |
---|
| 1249 | ind2=stra2num(r.num2); |
---|
| 1250 | end |
---|
| 1251 | end |
---|
| 1252 | switch mode |
---|
| 1253 | case 'Di' |
---|
| 1254 | i1_series=i_series-ind1;% set of first image numbers |
---|
| 1255 | i2_series=i_series+ind2; |
---|
| 1256 | check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i; |
---|
| 1257 | if isempty(j_series) |
---|
| 1258 | NomTypeNc='_1-2'; |
---|
| 1259 | else |
---|
| 1260 | j1_series=j_series; |
---|
| 1261 | j2_series=j_series; |
---|
| 1262 | NomTypeNc='_1-2_1'; |
---|
| 1263 | end |
---|
| 1264 | case 'Dj' |
---|
| 1265 | j1_series=j_series-ind1; |
---|
| 1266 | j2_series=j_series+ind2; |
---|
| 1267 | check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j; |
---|
| 1268 | NomTypeNc='_1_1-2'; |
---|
| 1269 | otherwise %bursts |
---|
| 1270 | i1_series=i_series(1,:);% do not sweep the j index |
---|
| 1271 | i2_series=i_series(1,:); |
---|
| 1272 | j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice |
---|
| 1273 | j2_series=ind2*ones(1,size(i_series,2)); |
---|
| 1274 | check_bounds=zeros(size(i1_series));% no limitations due to min-max indices |
---|
| 1275 | end |
---|
| 1276 | |
---|
[845] | 1277 | %INPUT: |
---|
| 1278 | % xmid- u/2: set of apparent phys x coordinates in the ref plane, image A |
---|
| 1279 | % ymid- v/2: set of apparent phys y coordinates in the ref plane, image A |
---|
| 1280 | % xmid+ u/2: set of apparent phys x coordinates in the ref plane, image B |
---|
| 1281 | % ymid+ v/2: set of apparent phys y coordinates in the ref plane, image B |
---|
| 1282 | % XmlData: content of the xml files containing geometric calibration parameters |
---|
[878] | 1283 | function [z,Xphy,Yphy,Error]=shift2z(xmid, ymid, u, v,XmlData) |
---|
[845] | 1284 | z=0; |
---|
| 1285 | error=0; |
---|
[834] | 1286 | |
---|
[851] | 1287 | |
---|
[845] | 1288 | %% first image |
---|
| 1289 | Calib_A=XmlData{1}.GeometryCalib; |
---|
| 1290 | R=(Calib_A.R)'; |
---|
[864] | 1291 | x_a=xmid- u/2; |
---|
[878] | 1292 | y_a=ymid- v/2; |
---|
[851] | 1293 | z_a=R(7)*x_a+R(8)*y_a+Calib_A.Tx_Ty_Tz(1,3); |
---|
| 1294 | Xa=(R(1)*x_a+R(2)*y_a+Calib_A.Tx_Ty_Tz(1,1))./z_a; |
---|
| 1295 | Ya=(R(4)*x_a+R(5)*y_a+Calib_A.Tx_Ty_Tz(1,2))./z_a; |
---|
| 1296 | |
---|
| 1297 | A_1_1=R(1)-R(7)*Xa; |
---|
| 1298 | A_1_2=R(2)-R(8)*Xa; |
---|
| 1299 | A_1_3=R(3)-R(9)*Xa; |
---|
| 1300 | A_2_1=R(4)-R(7)*Ya; |
---|
| 1301 | A_2_2=R(5)-R(8)*Ya; |
---|
| 1302 | A_2_3=R(6)-R(9)*Ya; |
---|
[845] | 1303 | Det=A_1_1.*A_2_2-A_1_2.*A_2_1; |
---|
| 1304 | Dxa=(A_1_2.*A_2_3-A_2_2.*A_1_3)./Det; |
---|
| 1305 | Dya=(A_2_1.*A_1_3-A_1_1.*A_2_3)./Det; |
---|
[834] | 1306 | |
---|
[845] | 1307 | %% second image |
---|
[878] | 1308 | %loading shift angle |
---|
| 1309 | |
---|
[851] | 1310 | Calib_B=XmlData{2}.GeometryCalib; |
---|
| 1311 | R=(Calib_B.R)'; |
---|
[878] | 1312 | |
---|
| 1313 | |
---|
[864] | 1314 | x_b=xmid+ u/2; |
---|
| 1315 | y_b=ymid+ v/2; |
---|
[851] | 1316 | z_b=R(7)*x_b+R(8)*y_b+Calib_B.Tx_Ty_Tz(1,3); |
---|
| 1317 | Xb=(R(1)*x_b+R(2)*y_b+Calib_B.Tx_Ty_Tz(1,1))./z_b; |
---|
| 1318 | Yb=(R(4)*x_b+R(5)*y_b+Calib_B.Tx_Ty_Tz(1,2))./z_b; |
---|
| 1319 | B_1_1=R(1)-R(7)*Xb; |
---|
| 1320 | B_1_2=R(2)-R(8)*Xb; |
---|
| 1321 | B_1_3=R(3)-R(9)*Xb; |
---|
| 1322 | B_2_1=R(4)-R(7)*Yb; |
---|
| 1323 | B_2_2=R(5)-R(8)*Yb; |
---|
| 1324 | B_2_3=R(6)-R(9)*Yb; |
---|
| 1325 | Det=B_1_1.*B_2_2-B_1_2.*B_2_1; |
---|
| 1326 | Dxb=(B_1_2.*B_2_3-B_2_2.*B_1_3)./Det; |
---|
| 1327 | Dyb=(B_2_1.*B_1_3-B_1_1.*B_2_3)./Det; |
---|
[834] | 1328 | |
---|
[845] | 1329 | %% result |
---|
| 1330 | Den=(Dxb-Dxa).*(Dxb-Dxa)+(Dyb-Dya).*(Dyb-Dya); |
---|
[878] | 1331 | mfx=(XmlData{1}.GeometryCalib.fx_fy(1)+XmlData{2}.GeometryCalib.fx_fy(1))/2; |
---|
| 1332 | mfy=(XmlData{1}.GeometryCalib.fx_fy(2)+XmlData{2}.GeometryCalib.fx_fy(2))/2; |
---|
| 1333 | mtz=(XmlData{1}.GeometryCalib.Tx_Ty_Tz(1,3)+XmlData{2}.GeometryCalib.Tx_Ty_Tz(1,3))/2; |
---|
[864] | 1334 | |
---|
[878] | 1335 | Error=(sqrt(mfx^2+mfy^2)/(2*sqrt(2)*mtz)).*(((Dyb-Dya).*(-u)-(Dxb-Dxa).*(-v))./Den); |
---|
| 1336 | |
---|
| 1337 | z=((Dxb-Dxa).*(-u)+(Dyb-Dya).*(-v))./Den; |
---|
| 1338 | |
---|
[864] | 1339 | xnew(1,:)=Dxa.*z+x_a; |
---|
| 1340 | xnew(2,:)=Dxb.*z+x_b; |
---|
| 1341 | ynew(1,:)=Dya.*z+y_a; |
---|
| 1342 | ynew(2,:)=Dyb.*z+y_b; |
---|
[878] | 1343 | Xphy=mean(xnew,1); |
---|
[864] | 1344 | Yphy=mean(ynew,1); |
---|
[851] | 1345 | |
---|
[864] | 1346 | |
---|
| 1347 | |
---|
| 1348 | |
---|
[878] | 1349 | |
---|