Index: /trunk/src/get_file_info.m =================================================================== --- /trunk/src/get_file_info.m (revision 990) +++ /trunk/src/get_file_info.m (revision 991) @@ -53,4 +53,7 @@ case {'.seq','.sqb'} [A,FileInfo,timestamps,errormsg]=read_rdvision(fileinput,[]); +% %%%%% +% FileInfo.NumberOfFrame=24000; +% %%%%%%%% case '.h5' hinfo=hdf5info(fileinput); @@ -66,4 +69,5 @@ FileInfo.Height=BitmapInfoHeader.biHeight; FileInfo.Width=BitmapInfoHeader.biWidth; + FileInfo.BitDepth=BitmapInfoHeader.biBitCount; otherwise if ~isempty(FileExt)% exclude empty extension Index: /trunk/src/read_cine_phantom.m =================================================================== --- /trunk/src/read_cine_phantom.m (revision 990) +++ /trunk/src/read_cine_phantom.m (revision 991) @@ -22,26 +22,27 @@ fseek(fid, imageLocations( frames(ii) ), 'bof'); if ~BitmapInfoHeader.biCompression +% [A,count]=fread(fid, 10000) imTemp = fread(fid, [BitmapInfoHeader.biWidth BitmapInfoHeader.biHeight],'uint16'); imMat(:,:,ii) = imTemp'; else - imTemp = fread(fid, [BitmapInfoHeader.biWidth BitmapInfoHeader.biHeight], 'ubit10','b'); - im = imTemp'; - im( im < 1 ) = 1; - im =reshape( interp1( 1:1024, lookupTable, im(:) ), BitmapInfoHeader.biHeight, BitmapInfoHeader.biWidth); - im( im < CameraSetup.BlackLevel ) = CameraSetup.BlackLevel; - im( im > 4064 )=4064; - imMat(:,:,ii) = reshape(interp1( CameraSetup.BlackLevel:4064, linspace(0,4095,4064 - CameraSetup.BlackLevel+1), im(:)),... - BitmapInfoHeader.biHeight, BitmapInfoHeader.biWidth); - - if mod( round(0.01*Nf), ii) - if ~exist('dispStr', 'var') - dispStr = ' '; - disp( dispStr ) - end - - lenDispStr = length( dispStr ); - dispStr = ['Reading is ' num2str( round( 100*ii/Nf ) ) '% complete']; - disp( [char(8)*ones(1,lenDispStr+1) dispStr] ) - end + imTemp = fread(fid, [BitmapInfoHeader.biWidth BitmapInfoHeader.biHeight], 'ubit10','b'); + im = imTemp'; + im( im < 1 ) = 1; + im =reshape( interp1( 1:1024, lookupTable, im(:) ), BitmapInfoHeader.biHeight, BitmapInfoHeader.biWidth); + im( im < CameraSetup.BlackLevel ) = CameraSetup.BlackLevel; + im( im > 4064 )=4064; + imMat(:,:,ii) = reshape(interp1( CameraSetup.BlackLevel:4064, linspace(0,4095,4064 - CameraSetup.BlackLevel+1), im(:)),... + BitmapInfoHeader.biHeight, BitmapInfoHeader.biWidth); + + if mod( round(0.01*Nf), ii) + if ~exist('dispStr', 'var') + dispStr = ' '; + disp( dispStr ) + end + + lenDispStr = length( dispStr ); + dispStr = ['Reading is ' num2str( round( 100*ii/Nf ) ) '% complete']; + disp( [char(8)*ones(1,lenDispStr+1) dispStr] ) + end end end @@ -50,5 +51,5 @@ end -function lookupTable = lookupTablePackedFun() +function lookupTable = lookupTablePackedFun() % function to transform the compressed 10 bit images back, close to the 12 bit camera images lookupTable = [ 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 17, 18,... Index: /trunk/src/read_rdvision.m =================================================================== --- /trunk/src/read_rdvision.m (revision 990) +++ /trunk/src/read_rdvision.m (revision 991) @@ -18,18 +18,18 @@ function [A,FileInfo,timestamps,errormsg]=read_rdvision(filename,frame_idx) -% BINREAD_RDV Permet de lire les fichiers bin gï¿œnï¿œrï¿œs par Hiris ï¿œ partir du -% fichier seq associï¿œ. +% BINREAD_RDV Permet de lire les fichiers bin g???n???r???s par Hiris ??? partir du +% fichier seq associ???. % [IMGS,TIMESTAMPS,NB_FRAMES] = BINREAD_RDV(FILENAME,FRAME_IDX) lit -% l'image d'indice FRAME_IDX de la sï¿œquence FILENAME. -% -% Entrï¿œes +% l'image d'indice FRAME_IDX de la s???quence FILENAME. +% +% Entr???es % ------- -% FILENAME : Nom du fichier sï¿œquence (.seq). -% FRAME_IDX : Indice de l'image ï¿œ lire. Si FRAME_IDX vaut -1 alors la -% sï¿œquence est entiï¿œrement lue. Si FRAME_IDX est un tableau d'indices +% FILENAME : Nom du fichier s???quence (.seq). +% FRAME_IDX : Indice de l'image ??? lire. Si FRAME_IDX vaut -1 alors la +% s???quence est enti???rement lue. Si FRAME_IDX est un tableau d'indices % alors toutes les images d'incides correspondant sont lues. Si FRAME_IDX % est un tableau vide alors aucune image n'est lue mais le nombre -% d'images et tous les timestamps sont renvoyï¿œs. Les indices commencent ï¿œ -% 1 et se termines ï¿œ NB_FRAMES. +% d'images et tous les timestamps sont renvoy???s. Les indices commencent ??? +% 1 et se termines ??? NB_FRAMES. % % Sorties @@ -37,5 +37,5 @@ % IMGS : Images de sortie. % TIMESTAMPS : Timestaps des images lues. -% NB_FRAMES : Nombres d'images dans la sï¿œquence. +% NB_FRAMES : Nombres d'images dans la s???quence. errormsg=''; @@ -119,7 +119,8 @@ binrepertoire=regexprep(binrepertoire,'\','/'); [tild,binrepertoire,DirExt]=fileparts(binrepertoire); - binrepertoire=[binrepertoire DirExt]; + binrepertoire=[binrepertoire DirExt]; end % binrepertoire='2014-07-04T10.48.46'% case FJORD5a %%%%%%%%%%%%%%%%%%%%%%%%% + binrepertoire='2017-01-19T22.12.182'% EXP14 %%%%%%%%%%%%%%%%%%%%%%%%% binfile=fullfile(RootPath,binrepertoire,sprintf('%s%.5d.bin',bin_file,data(ii).file_idx)); fid=fopen(binfile,'rb'); Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 990) +++ /trunk/src/series.m (revision 991) @@ -626,11 +626,6 @@ RootFile=''; else %scan the input folder - if strcmp(InputTable{iview,4},'level') - [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=... - find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2},'level0'),[InputTable{iview,3} '0' InputTable{iview,5}]); - else [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=... find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]); - end end % if no file is found, open a browser @@ -654,4 +649,5 @@ set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:)); MaxIndex_i_table=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex + set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:)); MaxIndex_j_table=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex @@ -2081,6 +2077,6 @@ case 'cluster_sge' % for PSMN - % Au PSMN, on ne crée pas 1 job avec plusieurs cœurs, mais N jobs de 1 cœurs - % où N < 1000. + % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs + % o?? N < 1000. %create subdirectory for pbs command and log files @@ -3737,5 +3733,7 @@ % --- Executes on button press in MonitorCluster. function MonitorCluster_Callback(hObject, eventdata, handles) -web('https://www.legi.grenoble-inp.fr/servfill/monika') +disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime') +system('oarstat |grep N=UVmat')% check the list of jobs launched with uvmat + function OutputSubDir_Callback(hObject, eventdata, handles) Index: /trunk/src/series/extract_multitif_parallel.m =================================================================== --- /trunk/src/series/extract_multitif_parallel.m (revision 990) +++ /trunk/src/series/extract_multitif_parallel.m (revision 991) @@ -59,5 +59,5 @@ %======================================================================= -function ParamOut=ima2netcdf(Param) +function ParamOut=extract_multitif_parallel(Param) %%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% @@ -143,4 +143,10 @@ XmlInput=imadoc2struct(XmlInputFile,'Camera'); +%% create the xml file of PCO camera +XmlInput.Camera.CameraName='PCO'; +t=struct2xml(XmlInput.Camera); +t=set(t,1,'name','ImaDoc'); +save(t,fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml'])) + %% Main loop Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 990) +++ /trunk/src/series/extract_rdvision.m (revision 991) @@ -64,22 +64,22 @@ 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=1; ...%nbre of slices, 1 prevents splitting in several processes, ('off' by default) - 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='.extract';%set the output dir extension + ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) + ParamOut.NbSlice=1; ...%nbre of slices, 1 prevents splitting in several processes, ('off' by default) + 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='.extract';%set the output dir extension ParamOut.OutputSubDirMode='one'; %output folder given by the folder name of the first input line - % detect the set of image folder + % detect the set of image folder RootPath=Param.InputTable{1,1}; - ListStruct=dir(RootPath); + ListStruct=dir(RootPath); ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files ListDir=ListCells(1,find(check_dir & ~check_bad)); -% InputTable=cell(numel(ListDir),5); -% InputTable(:,2)=ListDir'; + % InputTable=cell(numel(ListDir),5); + % InputTable(:,2)=ListDir'; isel=0; InputTable=Param.InputTable; @@ -90,14 +90,14 @@ seq_index=find(~cellfun('isempty',detect_seq),1); if ~isempty(seq_index) -% msgbox_uvmat('ERROR',['not seq file in ' ListDir{ilist} ': please check the input folders']) -% else - isel=isel+1; - InputTable{isel,1}=RootPath; - InputTable{isel,2}=ListDir{ilist}; + % msgbox_uvmat('ERROR',['not seq file in ' ListDir{ilist} ': please check the input folders']) + % else + isel=isel+1; + InputTable{isel,1}=RootPath; + InputTable{isel,2}=ListDir{ilist}; RootFile=regexprep(ListCellSub{1,seq_index},'.seq$',''); InputTable{isel,3}=RootFile; - InputTable{isel,4}='*'; - InputTable{isel,5}='.seq'; - end + InputTable{isel,4}='*'; + InputTable{isel,5}='.seq'; + end end hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series' @@ -105,5 +105,5 @@ set(hhseries.InputTable,'Data',InputTable) ParamOut.ActionInput.LogPath=RootPath;% indicate the path for the output info: 0_LOG .... -return + return end @@ -239,6 +239,6 @@ SeqData.binrepertoire=regexprep(s.sequenceSettings.bindirectory,'\\$','');%tranform Windows notation to Linux SeqData.binrepertoire=regexprep(SeqData.binrepertoire,'\','/'); - [tild,binrepertoire,DirExt]=fileparts(SeqData.binrepertoire); - SeqData.binrepertoire=[SeqData.binrepertoire DirExt]; + [tild,SeqData.binrepertoire,DirExt]=fileparts(SeqData.binrepertoire); + %SeqData.binrepertoire=[SeqData.binrepertoire DirExt]; end @@ -253,17 +253,18 @@ %%%%%%%BRICOLAGE in case of unreadable .sqb file: remplace lecture du fichier - % ind=[111 114:211];%indices of bin files - % w=1024;%w=width of images in pixels - % h=1024;%h=height of images in pixels - % bpp=2;% nbre of bytes per pixel - % lengthimage=w*h*bpp;% lengthof an image record on the binary file - % nbimages=32; %nbre of images of each camera in a bin file - % for ii=1:32*numel(ind) - % data(ii).offset=mod(ii-1,32)*2*lengthimage+lengthimage;%Dalsa_2 - % %data(ii).offset=mod(ii-1,32)*2*lengthimage;%Dalsa_1 - % data(ii).file_idx=ind(ceil(ii/32)); - % data(ii).timestamp=0.2*(ii-1); - % end - % m.Data=data; +% ind=[8356 8356:8672];%indices of bin files +% w=2432;%w=width of images in pixels +% h=864;%h=height of images in pixels +% bpp=2;% nbre of bytes per pixel +% lengthimage=w*h*bpp;% lengthof an image record on the binary file +% nbimages=15; %nbre of images of each camera in a bin file +% for ii=1:15*numel(ind) +% %data(ii).offset=mod(ii-1,32)*2*lengthimage+lengthimage;%Dalsa_2 +% %data(ii).offset=mod(ii-1,32)*2*lengthimage;%Dalsa_1 +% %data(ii).file_idx=ind(ceil(ii/32)); +% data(ii).file_idx=ind(ceil(ii/15)); +% data(ii).timestamp=0.005*(ii-1); +% end +% m.Data=data; %%%%%%% timestamp=zeros(1,numel(m.Data)); @@ -281,4 +282,8 @@ if ~isempty(errormsg) disp(errormsg) + return + end + if ~isequal(size(XmlData.Time(2:end,2:end)),size(reshape(timestamp(1:end),nbfield2,[])')) + disp(['size of record ' num2str(size(XmlData.Time(2:end,2:end))) ' does not fit with timestamp size ' num2str(size(reshape(timestamp(1:end),nbfield2,[])'))]) return end @@ -327,6 +332,6 @@ for iview=1:size(Param.InputTable,1) fullfile(RootPath,Param.InputTable{iview,2}) - - [SUCCESS,MESSAGE]=rmdir(fullfile(RootPath,Param.InputTable{iview,2}),'s') + source_dir=fullfile(RootPath,Param.InputTable{iview,2}); + [SUCCESS,MESSAGE]=rmdir(source_dir,'s') end end @@ -368,4 +373,11 @@ classname=['*' classname]; BitDepth=8*SeqData.bytesperpixel;%needed to write images (8 or 16 bits) +%%%% +% SeqData.binrepertoire='2017-01-26T11.59.57'; +%SeqData.binrepertoire='2017-01-26T16.57.27'; +%SeqData.binrepertoire='2017-01-26T19.28.05'; +%SeqData.binrepertoire='2017-01-27T09.51.34'; +%SeqData.binrepertoire='2017-01-27T14.21.47' +%%%% binrepertoire=fullfile(PathDir,SeqData.binrepertoire); FileDir=SeqData.sequencename; Index: /trunk/src/transform_field/ima_crop.m =================================================================== --- /trunk/src/transform_field/ima_crop.m (revision 991) +++ /trunk/src/transform_field/ima_crop.m (revision 991) @@ -0,0 +1,53 @@ +% 'ima_crop': removes an upper and lower band to the image + +%------------------------------------------------------------------------ +%%%% Use the general syntax for transform fields with a single input and parameters %%%% +% OUTPUT: +% DataOut: output field structure +% +%INPUT: +% DataIn: input field structure +% Param: matlab structure whose field Param.TransformInput contains the filter parameters +%----------------------------------- + +%======================================================================= +% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France +% http://www.legi.grenoble-inp.fr +% Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.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 DataOut=ima_crop(DataIn,Param) + +%% request input parameters +if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0) + prompt = {'npy_upper';'npy_lower'}; + dlg_title = 'remove image lines above and below'; + num_lines= 2; + def = { '0';'0'}; + if isfield(Param,'TransformInput')&&isfield(Param.TransformInput,'CropUpper')&&... + isfield(Param.TransformInput,'CropLower') + def={num2str(Param.TransformInput.CropUpper);num2str(Param.TransformInput.CropLower)}; + end + answer = inputdlg(prompt,dlg_title,num_lines,def); + DataOut.TransformInput.CropUpper=str2num(answer{1}); %size of the filtering window + DataOut.TransformInput.CropLower=str2num(answer{2}); %size of the filtering window + return +end + +DataOut=DataIn; %default + +DataOut.A(1:Param.TransformInput.CropUpper,:)=[]; +DataOut.A(end-Param.TransformInput.CropLower+1:end,:)=[]; +