Index: trunk/src/plot_field.m =================================================================== --- trunk/src/plot_field.m (revision 1174) +++ trunk/src/plot_field.m (revision 1175) @@ -409,5 +409,9 @@ %% prepare the string for plot command +if isfield(PlotParam,'Type')&& strcmp(PlotParam.Type,'semilogx') + plotstr='hhh=semilogx('; +else plotstr='hhh=plot('; +end xtitle=''; ytitle=''; Index: trunk/src/series/civ_series.m =================================================================== --- trunk/src/series/civ_series.m (revision 1174) +++ trunk/src/series/civ_series.m (revision 1175) @@ -51,4 +51,7 @@ %% 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)% function activated from the GUI series but not RUN + if 0==1 %never satisfied but trigger compilation with the appropriate transform functions ('eval' inactive for compilation) + ima_rescale + end path_series=fileparts(which('series')); addpath(fullfile(path_series,'series')) @@ -66,5 +69,5 @@ Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) - Data.FieldTransform = 'off';%can use a transform function + Data.FieldTransform = 'on';%can use a transform function Data.ProjObject='off';%can use projection object(option 'off'/'on', Data.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) @@ -99,5 +102,5 @@ % CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced) -%% input files and indexing (skipped in Test mode) +%% input files and indexing hseries=findobj(allchild(0),'Tag','series'); RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series @@ -112,5 +115,4 @@ if isfield(Param,'InputTable') [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); - % iview_A=0;% series index (iview) for the first image series iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) if Param.ActionInput.CheckCiv1 @@ -119,5 +121,4 @@ iview_A=2;% the second line is used for the input images end - % if iview_A~=0 RootPath_A=Param.InputTable{iview_A,1}; RootFile_A=Param.InputTable{iview_A,3}; @@ -253,5 +254,12 @@ end end -% end + +%% introduce input image transform +if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) + addpath(Param.FieldTransform.TransformPath) + transform_fct=str2func(Param.FieldTransform.TransformName); + rmpath(Param.FieldTransform.TransformPath) +end + %%%%% MAIN LOOP %%%%%% @@ -276,16 +284,6 @@ end end - % % if CheckInputFile - % if CheckOutputFile OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); - % if iview_A==0 % no nc file has been entered - % ncfile=fullfile_uvmat(OutputPath,Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... - % NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); - % else% an existing nc file has been entered - % if iview_A==1% if Civ1 is performed - % Civ1Dir=OutputDir; - % else - % Civ1Dir=Param.InputTable{1,2}; - % end + if strcmp(Param.ActionInput.ListCompareMode,'PIV') ncfile=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... @@ -295,5 +293,4 @@ j1_series_Civ1(ifield),j2_series_Civ1(ifield)); end - % end ncfile_out=ncfile;% by default @@ -380,4 +377,5 @@ end [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); + catch ME % display errors in reading input images if ~isempty(ME.message) @@ -385,4 +383,8 @@ continue end + end + %% user defined image transform + if ~isempty(transform_fct) + par_civ1 =transform_fct(par_civ1,Param); end @@ -597,4 +599,10 @@ par_civ2.Grid(:,2)=reshape(GridY,[],1);% increases with array index end + + %% user defined image transform + if ~isempty(transform_fct) + par_civ2 =transform_fct(par_civ2,Param); + end + % get the guess from patch1 or patch2 (case 'CheckCiv3') Index: trunk/src/series/sub_background.m =================================================================== --- trunk/src/series/sub_background.m (revision 1174) +++ trunk/src/series/sub_background.m (revision 1175) @@ -151,6 +151,4 @@ end BrightnessRankThreshold=0.1; - % CheckSubmedian='No'; -% SaturationCoeff=0; if isfield(Param,'ActionInput') if isfield(Param.ActionInput,'CheckVolume') && Param.ActionInput.CheckVolume Index: trunk/src/transform_field/ima_rescale.m =================================================================== --- trunk/src/transform_field/ima_rescale.m (revision 1175) +++ trunk/src/transform_field/ima_rescale.m (revision 1175) @@ -0,0 +1,56 @@ +% 'ima_green': take the gree component of a color image +%------------------------------------------------------------------------ +%%%% Use the general syntax for transform fields with a single input %%%% +% OUTPUT: +% DataOut: output field structure +% +%INPUT: +% DataIn: first input field structure + +%======================================================================= +% 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 DataOut=ima_rescale(DataIn,Param) + +%% request input parameters +if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0) + prompt = {'SaturationValue'}; + dlg_title = 'get the maximum image value'; + num_lines= 1; + def = { '1024'}; + if isfield(Param,'TransformInput')&&isfield(Param.TransformInput,'SaturationValue') + def={num2str(Param.TransformInput.SaturationValue)}; + end + answer = inputdlg(prompt,dlg_title,num_lines,def); + DataOut.TransformInput.SaturationValue=str2num(answer{1}); %size of the filtering window + return +end + +Coeff=Param.TransformInput.SaturationValue; +DataOut=DataIn; %default +if isfield(DataOut,'A') + DataOut.A=uint16(Coeff*tanh(double(DataOut.A)/Coeff)); +end +if isfield(DataOut,'ImageA') + DataOut.ImageA=uint16(Coeff*tanh(double(DataOut.ImageA)/Coeff)); +end +if isfield(DataOut,'ImageB') + DataOut.ImageB=uint16(Coeff*tanh(double(DataOut.ImageB)/Coeff)); +end + + Index: trunk/src/uvmat.m =================================================================== --- trunk/src/uvmat.m (revision 1174) +++ trunk/src/uvmat.m (revision 1175) @@ -4019,4 +4019,5 @@ set(handles.Histogram,'Visible','off') set(handles.HistoMenu,'Visible','off') + set(handles.LogLinHisto,'Visible','off') set(handles.HistoAxes,'Visible','off') hlegend=findobj(handles.uvmat,'Tag','HistoLegend'); @@ -4265,4 +4266,5 @@ set(handles.Histogram,'Visible','on') set(handles.HistoMenu,'Visible','on') + set(handles.LogLinHisto,'Visible','on') set(handles.HistoAxes,'Visible','on') HistoMenu_Callback(handles.HistoMenu, [], handles)% plot first histogram @@ -4383,7 +4385,12 @@ C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector Histo.histo(:,col)=hist(C, Histo.(FieldName)); %calculate histogram - end - end - plot_field(Histo,handles.HistoAxes); + if isequal(get(handles.LogLinHisto,'Value'),2) + PlotParam.Type='semilogx'; + else + PlotParam.Type='plot'; + end + end + end + plot_field(Histo,handles.HistoAxes,PlotParam); hlegend=findobj(handles.uvmat,'Tag','HistoLegend'); if isempty(hlegend) @@ -6180,2 +6187,15 @@ + + +% --- Executes on selection change in LogLinHisto. +function LogLinHisto_Callback(hObject, eventdata, handles) + HistoMenu_Callback(hObject, eventdata, handles) +% hObject handle to LogLinHisto (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: contents = cellstr(get(hObject,'String')) returns LogLinHisto contents as cell array +% contents{get(hObject,'Value')} returns selected item from LogLinHisto + +