%'ima2vol': concatene image series to form a 'volume' image, make vertical cuts along x and y %------------------------------------------------------------------------ % function GUI_input=ima2vol(num_i1,num_i2,num_j1,num_j2,Series) % %OUTPUT % GUI_input=list of options in the GUI series.fig needed for the function % %INPUT: %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) %Series: Matlab structure containing information set by the series interface % %---------------------------------------------------------------------- %======================================================================= % 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=ima2vol(Param) %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed 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='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) ParamOut.NbSlice='off'; %nbre of slices ('off' by default) ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) ParamOut.FieldTransform = 'on';%can use a transform function ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) ParamOut.ProjObject='on';%can use projection object(option 'off'/'on', ParamOut.Mask='on';%can use mask option (option 'off'/'on', 'off' by default) ParamOut.OutputDirExt='.vol';%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 input files ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) first_j=[]; if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_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); 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) 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 %% subdirectory for output files SubdirOut=[Param.OutputSubDir Param.OutputDirExt]; %% root input file names and nomenclature type (cell arrays with one element) RootPath=Param.InputTable(:,1); RootFile=Param.InputTable(:,3); SubDir=Param.InputTable(:,2); NomType=Param.InputTable(:,4); FileExt=Param.InputTable(:,5); %% get the set of input file names (cell array filecell), and file indices [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); % filecell{iview,fileindex}: cell array representing the list of file names % iview: line in the table corresponding to a given file series % fileindex: file index within the file series, % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) nbfield_i=size(i1_series{1},2); %nb of fields for the i index nbfield=nbfield_j*nbfield_i; %total number of fields [FileInfo{1},VideoObject{1}]=get_file_info(filecell{1,1});% type of input file FileType{1}=FileInfo{1}.FileType; %% calibration data and timing: read the ImaDoc files [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); if ~isempty(errormsg) disp_uvmat('WARNING',errormsg,checkrun) end %% coordinate transform or other user defined transform transform_fct='';%default fct handle if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) currentdir=pwd; cd(Param.FieldTransform.TransformPath) transform_fct=str2func(Param.FieldTransform.TransformName); cd (currentdir) end %% main loop for ifile=1:nbfield_i update_waitbar(WaitbarHandle,ifile/nbfield) if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') return end for jfile=1:nbfield_j if ~isempty(j1_series)&&~isequal(j1_series,{[]}) j1=j1_series{1}(jfile,ifile); end filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(jfile,ifile),[],j1) [Data,tild,errormsg] = read_field(filename,'image'); % transform the input field (e.g; phys) if requested (no transform involving two input fields) if ~isempty(transform_fct) Data.ZIndex=jfile; Data=transform_fct(Data,XmlData{1}); end if jfile==1 VolData.A=zeros(nbfield_j,size(Data.A,1),size(Data.A,2)); VolData.Coord_z=1:nbfield_j;%default Z values end VolData.A(jfile,:,:)=Data.A;%concacene along y VolData.Coord_z(jfile)=XmlData{1}.GeometryCalib.SliceCoord(jfile,3); end % npx=size(Data.A,2); % npy=size(Data.A,1); % npz=256; % ind_x=round(npx/2)-10:round(npx/2)+10;%image index at the mid x position % ind_y=round(npy/2)-10:round(npy/2)+10;%image index at the mid y position % ind_y=ind_y-100;% shift to avoid the injector % %write xml calibration file, using the first file % Rangx=Data.Coord_x; % Rangy=Data.Coord_y; % Rangz=[Z(end) Z(1)]; % % GeometryCal.CalibrationType='rescale'; % GeometryCal.CoordUnit=Data.CoordUnit; % GeometryCal.focal=1; % %scaling along x, y and z % pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); % pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); % pxcmz=(npz-1)/(Rangz(2)-Rangz(1)); % T_x=-pxcmx*Rangx(1)+0.5; % T_y=-pxcmy*Rangy(2)+0.5; % T_z=-pxcmz*Rangz(2)+0.5; % % xml file for x cut % GeometryCal.R=[pxcmx,0,0;0,pxcmz,0;0,0,1]; % GeometryCal.Tx_Ty_Tz=[T_x T_z 1]; % ImaDoc.GeometryCalib=GeometryCal; % t=struct2xml(ImaDoc); % t=set(t,1,'name','ImaDoc'); % save(t,fullfile(RootPath{1},SubdirOut,'cut_x.xml')) % % xml file for y cut % GeometryCal.R=[pxcmy,0,0;0,pxcmz,0;0,0,1]; % GeometryCal.Tx_Ty_Tz=[T_y T_z 1]; % ImaDoc.GeometryCalib=GeometryCal; % t=struct2xml(ImaDoc); % t=set(t,1,'name','ImaDoc'); % save(t,fullfile(RootPath{1},SubdirOut,'cut_y.xml')) % end filename=fullfile_uvmat(RootPath{1},SubdirOut,RootFile{1},'.nc','_1',i1_series{1}(jfile,ifile),[],j1); VolData.ListVarName={'Coord_z','Coord_y','Coord_x','A'}; VolData.VarDimName={'Coord_z','Coord_y','Coord_x',{'Coord_z','Coord_y','Coord_x'}}; VolData.Coord_x=Data.Coord_x; VolData.Coord_y=Data.Coord_y; struct2nc(filename,VolData) disp([filename ' written']) end