Index: /trunk/src/get_file_index.m =================================================================== --- /trunk/src/get_file_index.m (revision 1171) +++ /trunk/src/get_file_index.m (revision 1172) @@ -1,3 +1,14 @@ -%======================================================================= + +%'get_file_index': determine the frame indexes from ref indices and pair option for civ +% [i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString) +%------------------------------------------------------------------------ +% OUTPUT: +% i1,i2,j1,j2: frem indices i and j for image 1 and 2 +% +% INPUT: +% ref_i,ref_j: reference indices set in the GUI series +% PairString: string defining the choice of pairing: 'Di=..','Dj=..','-' + +%===================================================================== % Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr Index: /trunk/src/mouse_down.m =================================================================== --- /trunk/src/mouse_down.m (revision 1171) +++ /trunk/src/mouse_down.m (revision 1172) @@ -493,4 +493,5 @@ h_ListCoord=hh_geometry_calib.ListCoord; %findobj(h_geometry_calib,'Tag','ListCoord'); Coord=get(h_ListCoord,'Data'); + Coord=Coord(:,1:6); %data=read_geometry_calib(Coord);%transform char cell to numbers xlim=get(haxes,'XLim'); Index: /trunk/src/series/sub_background.m =================================================================== --- /trunk/src/series/sub_background.m (revision 1171) +++ /trunk/src/series/sub_background.m (revision 1172) @@ -229,7 +229,6 @@ NomType=Param.InputTable(:,4); FileExt=Param.InputTable(:,5); -%hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); -[filecell,i1_series,i2_series,j1_series]=get_file_series(Param); -% if ~isempty(hdisp),delete(hdisp),end; +[filecell,i1_series,i2_series,j1_series]=get_file_series(Param);%series of file names organised as a single array + %%%%%%%%%%%% % The cell array filecell is the list of input file names, while @@ -280,6 +279,4 @@ step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst NbSlice_j=1; - %nbfield_i=floor(nbfield_i/NbSlice_i);%total number of indexes in a slice (adjusted to an integer number of slices) - %nbfield=nbfield_i*NbSlice_i; %total number of fields after adjustement nbfield_series=nbfield_i*nbfield_j; end @@ -314,16 +311,30 @@ end - -%%%%%%% LOOP ON SLICES FOR VOLUME SCAN %%%%%%% -for j_slice=1:NbSlice_j +%selection of frame indices +if Param.ActionInput.CheckVolume + nbfield=floor(nbfield/NbSlice_j)*NbSlice_j;% truncate the total number of frames in case of incomplete series + indselect=1:nbfield; + indselect=reshape(indselect,NbSlice_j,[]); + NbSlice=NbSlice_j; +else + NbSlice=NbSlice_i; + nbfield=floor(nbfield/NbSlice)*NbSlice;% truncate the total number of frames in case of incomplete series + indselect=reshape(1:nbfield,NbSlice,[]); + for j_slice=1:NbSlice + indselect(j_slice,:)=j_slice:step*NbSlice:nbfield;% select file indices of the slice + end +end + +%%%%%%% LOOP ON SLICES %%%%%%% +for j_slice=1:NbSlice %% select the series of i indices to process - indselect=j_slice:step*NbSlice_j:nbfield;% select file indices of the slice - for ifield=1:step-1 - indselect=[indselect;indselect(end,:)+NbSlice_j]; - end + % indselect=j_slice:step*NbSlice_j:nbfield;% select file indices of the slice +% for ifield=1:step-1 +% indselect=[indselect;indselect(end,:)+NbSlice]; +% end %% read the first series of nbaver_ima images and sort by luminosity at each pixel for ifield = 1:nbaver_ima - ifile=indselect(ifield); + ifile=indselect(jslice,ifield); filename=filecell{1,ifile}; Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile)); @@ -341,5 +352,5 @@ Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor - ifile=indselect(ifield); + ifile=indselect(jslice,ifield); j1=1; if ~isempty(j1_series{1}) @@ -381,5 +392,5 @@ %incorporate next burst in the current image series for iburst=1:step - ifile=indselect(ifield+iburst+step*halfnbaver); + ifile=indselect(jslice,ifield+iburst+step*halfnbaver); j1=1; if ~isempty(j1_series{1}) @@ -400,5 +411,5 @@ Acor=double(Ak(:,:,step*halfnbaver+iburst))-double(B); %the current image has been already read ans stored as index step*halfnbaver+iburst in the current series Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor - ifile=indselect(ifield+iburst); + ifile=indselect(jslice,ifield+iburst); if ~isempty(j1_series{1}) j1=j1_series{1}(ifile); @@ -428,5 +439,5 @@ Acor=double(Ak(:,:,ifield-nbfield_series+step*(2*halfnbaver+1)))-double(B); Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor - ifile=indselect(ifield); + ifile=indselect(jslice,ifield); if ~isempty(j1_series{1}) j1=j1_series{1}(ifile); Index: unk/src/series/sub_background_special.m =================================================================== --- /trunk/src/series/sub_background_special.m (revision 1171) +++ (revision ) @@ -1,163 +1,0 @@ -%'bed_scan': get the bed shape from laser ipact - -%------------------------------------------------------------------------ -% function GUI_input=bed_scan(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,series -% 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=sub_background_special (Param) - -%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed -if isstruct(Param) && isequal(Param.Action.RUN,0) - ParamOut.NbViewMax=1;% max nbre of input file series (default , no limitation) - 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'; %nbre of slices ('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='.sback';%set the output dir extension - ParamOut.OutputFileMode='NbInput';% ='=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice - %check the type of the existence and type of the first input file: -return -end - -%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% -%% read input parameters from an xml file if input is a file name (batch mode) -ParamOut=[]; -RUNHandle=[]; -WaitbarHandle=[]; -checkrun=1; -if ischar(Param)% case of batch: Param is the name of the xml file containing the input parameters - Param=xml2struct(Param);% read Param as input file (batch case) - checkrun=0; -else% interactive mode in Matlab - 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 -%% estimate the position of bottom and mask for each Z Index -NbSlice=Param.IndexRange.NbSlice; -switch NbSlice - case 11 - BottomIndex=[1900 1800 1700 1650 1650 1600 1600 1600 1600 1600 1600]; - case 4 - BottomIndex=[1950 1850 1740 1700]; -end -MaxIndex=BottomIndex+100; -MinIndex=BottomIndex-100; - -maskindex=[665 1080];% range of x index perturbed by shadows -Bfilter=ones(1,20)/20; -%% root input file names and nomenclature type (cell arrays with one element) -OutputDir=[Param.OutputSubDir Param.OutputDirExt]; -nbj=numel(Param.IndexRange.first_i:Param.IndexRange.last_i); -for i_ind=Param.IndexRange.first_i:Param.IndexRange.last_i - ZIndex=mod(i_ind-1,NbSlice)+1; - for j_ind=Param.IndexRange.first_j:Param.IndexRange.last_j - % read the current image - InputFile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},Param.InputTable{1,4},i_ind,i_ind,j_ind); - A=imread(InputFile); - % get the bottom as the max of luminosity along vertical lines - IndexMax=ones(1,size(A,2));%initiate the index position of the bottom - if j_ind==Param.IndexRange.first_j - indexMax_j=ones(nbj,size(A,2));%initiate the matrix of index position of the bottom - end - for icolumn=1:maskindex(1) - [M,IndexMax(icolumn)] = max(A(MinIndex(ZIndex)+1:MaxIndex(ZIndex),icolumn),[],1); - end - [M,IndexMax(maskindex(2))] = max(A(MinIndex(ZIndex)+1:MaxIndex(ZIndex),maskindex(2)),[],1); - for icolumn=maskindex(1)+1:maskindex(2)-1 % linear interpolation in the masked region - IndexMax(icolumn)= IndexMax(maskindex(1))*(maskindex(2)-icolumn)+IndexMax(maskindex(2))*(icolumn-maskindex(1)); - IndexMax(icolumn)=IndexMax(icolumn)/(maskindex(2)-maskindex(1)); - end - for icolumn=maskindex(2)+1:size(A,2) - [M,IndexMax(icolumn)] = max(A(MinIndex(ZIndex)+1:MaxIndex(ZIndex),icolumn),[],1); - end - IndexFilt=filter(Bfilter,1,IndexMax);% smoothed IndexMax - peakdetect=find(abs(IndexFilt-IndexMax)>5);% detect strong departures from the filtered values - IndexMax(peakdetect)=IndexFilt(peakdetect);%replace the peaks by the filtered values - IndexMax_j(j_ind,:)=round(filter(Bfilter,1,IndexMax));%filter again and take the closest integer - % get the background image as the min at each point in the j series - if j_ind==Param.IndexRange.first_j - Amin=A; - else - Amin=min(Amin,A); - end - end - - for j_ind=Param.IndexRange.first_j:Param.IndexRange.last_j - InputFile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},Param.InputTable{1,4},i_ind,i_ind,j_ind); - A=imread(InputFile); - A=A-Amin; - for icolumn=1:size(A,2) - A(MinIndex(ZIndex)+IndexMax_j(j_ind,icolumn):end,icolumn)=0; - end - OutputFile=fullfile_uvmat(Param.InputTable{1,1},OutputDir,Param.InputTable{1,3},Param.InputTable{1,5},Param.InputTable{1,4},i_ind,i_ind,j_ind); - imwrite(A,OutputFile) - disp([OutputFile ' written']) - end -end - - - - - - - -