Index: /trunk/src/phys_ima.m =================================================================== --- /trunk/src/phys_ima.m (revision 1128) +++ /trunk/src/phys_ima.m (revision 1129) @@ -11,6 +11,6 @@ % XmlData: cell array of structures defining the calibration parameters for each image % ZIndex: index of the reference plane used to define the phys position in 3D - -function [A_out,Rangx,Rangy]=phys_ima(A,XmlData,ZIndex) +% resolution_factor: factor to control the number of pixels of the new image, default value =1 : same nbre of pixels as the original +function [A_out,Rangx,Rangy]=phys_ima(A,XmlData,ZIndex,resolution_factor) xcorner=[]; ycorner=[]; @@ -21,4 +21,7 @@ if isstruct(XmlData) XmlData={XmlData}; +end +if ~exist('resolution_factor','var') +resolution_factor=1; end @@ -50,6 +53,6 @@ test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths -npX=1+round((Rangx(2)-Rangx(1))/max(dx));% nbre of pixels in the new image (use the largest resolution max(dx) in the set of images) -npY=1+round((Rangy(1)-Rangy(2))/max(dy)); +npX=1+round(resolution_factor*(Rangx(2)-Rangx(1))/max(dx));% nbre of pixels in the new image (use the largest resolution max(dx) in the set of images) +npY=1+round(resolution_factor*(Rangy(1)-Rangy(2))/max(dy)); x=linspace(Rangx(1),Rangx(2),npX); Index: /trunk/src/series/aver_stat.m =================================================================== --- /trunk/src/series/aver_stat.m (revision 1128) +++ /trunk/src/series/aver_stat.m (revision 1129) @@ -298,4 +298,5 @@ for iview=1:NbView % reading input file(s) + filecell{iview,index} [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); if ~isempty(errormsg) @@ -469,5 +470,7 @@ %% writing the result file - OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out); + RootPathOut=fullfile(Param.OutputPath,Param.Experiment,Param.Device); + OutputDir=[Param.OutputSubDir Param.OutputDirExt]; + OutputFile=fullfile_uvmat(RootPathOut,OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out); if strcmp(FileExtOut,'.png') %case of images if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16)) Index: /trunk/src/series/extract_multitif.m =================================================================== --- /trunk/src/series/extract_multitif.m (revision 1128) +++ /trunk/src/series/extract_multitif.m (revision 1129) @@ -1,5 +1,18 @@ %'extract_multitif': read image series from PCO cameras (tiff image series) and write .png images -%------------------------------------------------------------------------ - +% use a single geometric calibration, with information on the slice positions in case of 3D scanning +%------------------------------------------------------ +% the output file indexing is based on the xml file requested by the +% function when it is selected (or possibly inserted in this function in the section TEST) +% This xml file must contain the following information: +% NbDti: the number of 'bursts' -1 +% NbDtj: number of frames in each burst-1, or number of repetition of a burst sequence defined by Dtj +% NbDtk: number of repetitions of a slice scanning process -1 (ignored by default) +% Therefore the total number of frames is (NbDti+1)*(NbDtj+1)*(NbDtk+1) +% The frame series is stored in a single folder with two indices i:(NbDti+1)*(NbDtk+1) +% +% To run the function in the cluster in parallel for each multitif file, indicate nb-slice_i equal to the +% number input multitif files + + % function ParamOut=extract_multitif(Param) % Index: /trunk/src/series/extract_multitif_multislice.m =================================================================== --- /trunk/src/series/extract_multitif_multislice.m (revision 1129) +++ /trunk/src/series/extract_multitif_multislice.m (revision 1129) @@ -0,0 +1,225 @@ +%'extract_multitif_multiplane': read image series from PCO cameras (tiff image series) and write .png images +% case of multislice views with a distinct geometric calibration for each slice +%------------------------------------------------------ +% the output file indexing is based on the xml file requested by the +% function when it is selected (or possibly inserted in this function in the section TEST) +% This xml file must contain the following information: +% NbDti: the number of slices -1 +% NbDtj: number of frames in each slice -1 +% NbDtk: number of repetitions of the slice scanning process -1 +% Therefore the total number of frames is (NbDti+1)*(NbDtj+1)*(NbDtk+1) +% The frame series in each slice is stored in a separate folder labeled by_i, i=1:NbDti+1, +% an xml file with the same name must be created with the appropiate geometric calibration and time interval Dti between +% successive image names in each folder are labeled as _1k_1,_1k_2...._2k_1,_2k_2,... +% +% To run the function in the cluster in parallel for each multitif file, indicate nb-slice_i equal to the +% number input multitif files + +%------------------------------------------------------------------------ + +% function ParamOut=extract_multitif_multiplane(Param) +% +%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% +% +%OUTPUT +% ParamOut: sets options in the GUI series.fig needed for the function +% +%INPUT: +% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. +% In batch mode, Param is the name of the corresponding xml file containing the same information +% when Param.Action.RUN=0 (as activated when the current Action is selected +% in series), the function ouput paramOut set the activation of the needed GUI elements +% +% Param contains the elements:(use the menu bar command 'export/GUI config' in series to +% see the current structure Param) +% .InputTable: cell of input file names, (several lines for multiple input) +% each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} +% .OutputSubDir: name of the subdirectory for data outputs +% .OutputDirExt: directory extension for data outputs +% .Action: .ActionName: name of the current activated function +% .ActionPath: path of the current activated function +% .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct +% .RUN =0 for GUI input, =1 for function activation +% .RunMode='local','background', 'cluster': type of function use +% +% .IndexRange: set the file or frame indices on which the action must be performed +% .FieldTransform: .TransformName: name of the selected transform function +% .TransformPath: path of the selected transform function +% .InputFields: sub structure describing the input fields withfields +% .FieldName: name(s) of the field +% .VelType: velocity type +% .FieldName_1: name of the second field in case of two input series +% .VelType_1: velocity type of the second field in case of two input series +% .Coord_y: name of y coordinate variable +% .Coord_x: name of x coordinate variable +% .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +%======================================================================= +% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France +% http://www.legi.grenoble-inp.fr +% Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr +% +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published +% by the Free Software Foundation; either version 2 of the license, +% or (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (see LICENSE.txt) for more details. +%======================================================================= + +function ParamOut=extract_multitif(Param) + +%%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% +if isstruct(Param) && isequal(Param.Action.RUN,0) + ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) + ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) + ParamOut.NbSlice='on'; % impose calculation in a single process (no parallel processing to avoid 'holes')) + ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldTransform = 'off';%can use a transform function + ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', + ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) + ParamOut.OutputDirExt='.png';%set the output dir extension + ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice + ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) + ParamOut.CPUTime=10;% expected time for writting the output of one source image ( in minute) + %% root input file(s) and type + % check the existence of the first file in the series + first_j=[];% note that the function will propose to cover the whole range of indices + if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end + last_j=[]; + if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end + PairString=''; + if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end + [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); + FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... + Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); + if ~exist(FirstFileName,'file') + msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) + end + + %% check the validity of input file types + FileInfo=get_file_info(FirstFileName); + if ~strcmp(FileInfo.FileType,'multimage') + msgbox_uvmat('ERROR',['invalid file type input: ' FileInfo.FileType ' not an image']) + return + end + ParamOut.ActionInput.XmlFile=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml'); + return +end +%%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% + +%% read input parameters from an xml file if input is a file name (batch mode) +checkrun=1; +RUNHandle=[]; +WaitbarHandle=[]; +if ischar(Param) + Param=xml2struct(Param);% read Param as input file (batch case) + checkrun=0; +else + hseries=findobj(allchild(0),'Tag','series'); + RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series + WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series +end + +%% Timing +XmlInputFile=Param.ActionInput.XmlFile; +[XmlInput,errormsg]=imadoc2struct(XmlInputFile,'Camera'); +if ~isempty(errormsg) + disp(['bad xml input file: ' errormsg]) + return +end +ImagesPerLevel=size(XmlInput.Time,2)-1;%100;%use the xmlinformation to get the nbre of j indices + +%% output directory +Nbre_level=XmlInput.Camera.BurstTiming.NbDti+1; +for idir=1:Nbre_level +OutputDir{idir}=fullfile(Param.InputTable{1,1},[Param.OutputSubDir '_' num2str(idir) Param.OutputDirExt]); +if ~exist(OutputDir{idir},'dir') + mkdir(OutputDir{idir}) +end +end + +%% create the xml file for timing if it does not exist : example to adapt +TEST=0; +if TEST + count0=14; + Dtj=0.05;% time interval between frames + ImagesPerLevel=455;% total number of images per position, ImagesPerLevel-Nbj images skiiped during motion between two positions + Nbj=390; %Nbre of images kept at a given position + Dti=Dtj*ImagesPerLevel; + NbLevel=11; + NbScan=3; + TimeReturn=268.5; %time needed to return back to the first position (in sec) + NbReturn=round(TimeReturn/Dtj); + NbSkipReturn=NbReturn+1-NbLevel*ImagesPerLevel; + + Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']); + if ~exist(Newxml,'file') + XmlInput.Camera.CameraName='PCO'; + XmlInput.Camera.TimeUnit='s'; + XmlInput.Camera.BurstTiming.FrameFrequency=1; + XmlInput.Camera.BurstTiming.Time=0;% for 200 + XmlInput.Camera.BurstTiming.Dtj=Dtj; + XmlInput.Camera.BurstTiming.NbDtj=Nbj-1; + XmlInput.Camera.BurstTiming.Dti=Dti; + XmlInput.Camera.BurstTiming.NbDti=NbLevel-1; + XmlInput.Camera.BurstTiming.Dtk=TimeReturn; + XmlInput.Camera.BurstTiming.NbDtk=NbScan-1; + t=struct2xml(XmlInput); + t=set(t,1,'name','ImaDoc'); + save(t,Newxml); + end +end + +%% loop on the files +% include the first tiff file with no index in the first iteration +if Param.IndexRange.first_i==1% first slice of processing + firstindex=0;% to read the first multitif with no number + count=0; +else + firstindex=Param.IndexRange.first_i; + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif'); + NbFrames=numel(imfinfo(ImageName));%nbre of frames in each multitif image + count=Param.IndexRange.first_i*NbFrames; +end +for ifile=firstindex:Param.IndexRange.last_i + tic + if firstindex==0 && ifile==0% first slice of processing + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif') + else + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},['im@' num2str(ifile,'%04d') '.tif']) + end + NbFrames=numel(imfinfo(ImageName));% nbre of frames in each multitif file + for iframe=1:NbFrames + if isequal(ImagesPerLevel,1)% mode series + OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); + else % indices i and j + i_index=fix(count/ImagesPerLevel)+1; + dir_index=mod(i_index-1,XmlInput.Camera.BurstTiming.NbDti+1)+1; + inew=floor((i_index-1)/(XmlInput.Camera.BurstTiming.NbDti+1))+1; + j_index=mod(count,ImagesPerLevel)+1; + OutputFile=fullfile(OutputDir{dir_index},['img_' num2str(inew) 'k_' num2str(j_index) '.png']); + end + if Param.CheckOverwrite ||~exist(OutputFile,'file') + A=imread(ImageName,iframe); + imwrite(A,OutputFile,'BitDepth',16); + disp([OutputFile ' written']) + else + disp([OutputFile ' already exists']) + end + count=count+1; + end + tt=toc; + disp(['elapsed time (in min.) for the file im@' num2str(ifile,'%04d')]) + disp(num2str(tt/60)) +end + + + Index: /trunk/src/series/stereo_input.m =================================================================== --- /trunk/src/series/stereo_input.m (revision 1128) +++ /trunk/src/series/stereo_input.m (revision 1129) @@ -243,5 +243,5 @@ %show the reference image edit box if relevant (not needed for movies or in the absence of time information if numel(time)>=2 % if there are at least two time values to define dt - if size(time,1)0).*A; %replaces zeros by ones @@ -1734,4 +1735,6 @@ gamma_coeff=NaN(1,npy); fitlength=NaN(1,npy); +%[ThetaMask,RMask] = cart2pol(MaskData.Coord(:,1)-x0,MaskData.Coord(:,2)-y0); +%ThetaMask=ThetaMask*180/pi for iY=1:npy% loop on the y index of the image in polar coordinate ALine=A(iY,:);%profile of image luminosity log (vs radial index) @@ -1752,6 +1755,13 @@ p = polyfit(RLine,ALine,1); gamma_coeff(iY)=-p(1); - fitlength(iY)=numel(find(check_good)); -end + fitlength(iY)=numel(find(check_good)); +end + +%% plot the decay coef versus theta +figure(13) +plot(Theta(:,1),100*gamma_coeff) +xlabel('angle(degree)') +ylabel('decay coeff(m-1)') + %% show and store the rescaled image @@ -1760,8 +1770,5 @@ view_field(DataPol); imwrite(DataPol.A,NewImageName,'BitDepth',16) -figure(13) -plot(Theta(:,1),100*gamma_coeff) -xlabel('angle(degree)') -ylabel('decay coeff(m-1)') + %% keep the average of gamma_coeff