Changeset 457 for trunk/src/series/merge_proj.m

Timestamp:

Jun 17, 2012, 10:52:04 PM (12 years ago)

Author:

sommeria

Message:

merg_i_j transformed to the new standards.
Various improvements

File:

• trunk/src/series/merge_proj.m (modified) (2 diffs)

trunk/src/series/merge_proj.m

@@ -1 @@
-
-
-
-
-
-%'merge_proj': project and concatene fields, used with series.fig
+%'merge_proj': project and concatene fieldsmerge_proj
+% can be used as a template for applying an operation (here projection and concateantion) on each field of an input series
 %------------------------------------------------------------------------
-% function GUI_input=merge_proj(Param)
+% function GUI_config=merge_proj(Param)
+%------------------------------------------------------------------------
+
+%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
 %
+% This function is used in four modes by the GUI series:
+%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
+%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
+%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced. 
+%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
+%
+% This function is used in four modes by the GUI series:
+%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
+%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
+%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced. 
+%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
+%
+%OUTPUT
+% GUI_input=list of 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
+% In the absence of input (as activated when the current Action is selected
+% in series), the function ouput GUI_input 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
+%    .OutputDir: directory for data outputs, including path
+%    .Action: .ActionName: name of the current activated function
+%             .ActionPath:   path of the current activated function
+%    .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
+%                     .TransformHandle: corresponding function handle
+%    .InputFields: sub structure describing the input fields withfields
+%              .FieldName: name 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
+%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function GUI_input=merge_proj(Param)
+
+%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
+if ~exist('Param','var') % case with no input parameter 
+    GUI_input={'NbViewMax';2;...% max nbre of input file series (default='' , no limitation)
+        'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default)
+        'NbSlice';'on'; ...%nbre of slices ('off' by default)
+        'VelType';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
+        'FieldName';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
+        'FieldTransform'; 'on';...%can use a transform function
+        'ProjObject';'on';...%can use projection object(option 'off'/'on',
+        'Mask';'on';...%can use mask option   (option 'off'/'on', 'off' by default)
+        'OutputDirExt';'.proj';...%set the output dir extension
+               ''};
+        return
+end
+
+%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
+%% select different modes,  RUN, parameter input, BATCH
+% BATCH  case: read the xml file for batch case
+if ischar(Param)
+    if strcmp(Param,'input?')
+        checkrun=1;% will inly search input parameters (preparation of BATCH mode)
+    else
+        Param=xml2struct(Param);
+        checkrun=0;
+    end
+% RUN case: parameters introduced as the input structure Param
+else
+    hseries=guidata(Param.hseries);%handles of the GUI series
+    WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series
+    checkrun=2; % indicate the RUN option is used
+end
+
+%% root input file(s) and type
+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 the lists of
+% input file or frame indices i1_series,i2_series,j1_series,j2_series
+[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
+% set of frame indices used for movie or multimage input 
+% numbers of slices and file indices
+
+NbSlice=1;%default
+if isfield(Param.IndexRange,'NbSlice')
+    NbSlice=Param.IndexRange.NbSlice;
+end
+nbview=numel(i1_series);%number of input file series (lines in InputTable)
+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
+nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices) 
+nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
+
+%determine the file type on each line from the first input file 
+ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)
+
+[FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1});
+CheckImage{1}=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images
+if ~isempty(j1_series{1})
+    frame_index{1}=j1_series{1};
+else
+    frame_index{1}=i1_series{1};
+end
+
+%% calibration data and timing: read the ImaDoc files
+mode=''; %default
+timecell={};
+itime=0;
+NbSlice_calib={};
+for iview=1:nbview%Loop on views
+    XmlData{iview}=[];%default
+    filebase{iview}=fullfile(RootPath{iview},RootFile{iview});
+    if exist([filebase{iview} '.xml'],'file')
+        [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); 
+        if isfield(XmlData{iview},'Time')
+            itime=itime+1;
+            timecell{itime}=XmlData{iview}.Time;
+        end
+        if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord')
+            NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform
+            if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
+                msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
+            end
+        end 
+    elseif exist([filebase{iview} '.civ'],'file')
+        [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']);
+        itime=itime+1;
+        timecell{itime}=time;
+        XmlData{iview}.Time=time;
+        GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
+        GeometryCalib.Tx=0;
+        GeometryCalib.Ty=0;
+        GeometryCalib.Tz=1;
+        GeometryCalib.dpx=1;
+        GeometryCalib.dpy=1;
+        GeometryCalib.sx=1;
+        GeometryCalib.Cx=0;
+        GeometryCalib.Cy=0;
+        GeometryCalib.f=1;
+        GeometryCalib.kappa1=0;
+        GeometryCalib.CoordUnit='cm';
+        XmlData{iview}.GeometryCalib=GeometryCalib;
+        if error==1
+            msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
+        end
+    end
+end
+
+%% check coincidence in time for several input file series
+multitime=0;
+if isempty(timecell)
+    time=[];
+elseif length(timecell)==1
+    time=timecell{1};
+elseif length(timecell)>1
+    multitime=1;
+    for icell=1:length(timecell)
+        if ~isequal(size(timecell{icell}),size(timecell{1}))
+            msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used')
+            time=timecell{1};
+            multitime=0;
+            break
+        end
+    end
+end
+if multitime
+    for icell=1:length(timecell)
+        time(icell,:,:)=timecell{icell};
+    end
+    diff_time=max(max(diff(time)));
+    if diff_time>0
+        msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
+    end   
+end
+if size(time,2) < i2_series{1}(end) || size(time,3) < j2_series{1}(end)% time array absent or too short in ImaDoc xml file' 
+    time=[];
+end
+
+%% coordinate transform or other user defined transform
+transform_fct='';%default
+if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'TransformHandle')
+    transform_fct=Param.FieldTransform.TransformHandle;
+end
+%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
+ % EDIT FROM HERE
+
+%% check the validity of  input file types
+if CheckImage{1}
+    FileExtOut='.png'; % write result as .png images for image inputs
+elseif CheckNc{1}
+    FileExtOut='.nc';% write result as .nc files for netcdf inputs
+else 
+    msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
+    return
+end
+if nbview==2 && ~isequal(CheckImage{1},CheckImage{2})
+        msgbox_uvmat('ERROR','input must be two image series or two netcdf file series')
+    return
+end
+NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series
+if NbSlice~=nbfield_j
+    answer=msgbox_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]);
+    if ~strcmp(answer,'Yes')
+        return
+    end
+end
+
+%% Set field names and velocity types
+InputFields{1}=[];%default (case of images)
+if isfield(Param,'InputFields')
+    InputFields{1}=Param.InputFields;
+end
+if nbview==2
+    InputFields{2}=[];%default (case of images)
+    if isfield(Param,'InputFields')
+        InputFields{2}=Param.InputFields{1};%default
+        if isfield(Param.InputFields,'FieldName_1')
+            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
+            if isfield(Param.InputFields,'VelType_1')
+                InputFields{2}.VelType=Param.InputFields.VelType_1;
+            end
+        end
+    end
+end
+
+%% Initiate output fields
+%initiate the output structure as a copy of the first input one (reproduce fields)
+[DataOut,ParamOut,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1);
+if ~isempty(errormsg)
+    msgbox_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg])
+    return
+end
+time_1=[];
+if isfield(DataOut,'Time')
+    time_1=DataOut.Time(1);
+end
+if CheckNc{iview}
+    if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute))
+        DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute];
+    end
+    DataOut.Conventions='uvmat';
+    DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}];
+    ActionKey='Action';
+    while isfield(DataOut,ActionKey)
+        ActionKey=[ActionKey '_1'];
+    end
+    DataOut.(ActionKey)=Param.Action;
+    DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}];
+    if isfield(DataOut,'Time')
+        DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}];
+    end
+end
+
+%% MAIN LOOP ON SLICES
+%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
+for i_slice=1:NbSlice
+    index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
+    nbfiles=0;
+    nbmissing=0;
+    
+   %initiate result fields
+   for ivar=1:length(DataOut.ListVarName)
+       DataOut.(DataOut.ListVarName{ivar})=0; % initialise all fields to zero
+   end
+
+    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
+    for index=index_slice
+        if checkrun
+            update_waitbar(hseries.waitbar_frame,WaitbarPos,index/(nbfield))
+            stopstate=get(hseries.RUN,'BusyAction');
+        else
+            stopstate='queue';
+        end
 %OUTPUT
 % GUI_input=list of options in the GUI series.fig needed for the function
@@ -15 +297 @@
 %  or name of the xml file containing these parameters (BATCH case)
 %
-function GUI_input=merge_proj(Param)
-
-%requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
-if ~exist('Param','var')
-    GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
-        'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
-        'RootFile';'on';... %root input file name ('on' by default)
-        'FileExt';'on';... %input file extension ('on' by default)
-        'NomType';'on';...%type of file indexing ('on' by default)
-        'NbSlice';'on'; ...%nbre of slices ('off' by default)
-        'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default)
-        'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
-        'CoordType';'on';...%can use a transform function 'off' by default
-        'GetObject';'on';...%can use projection object ,'off' by default
-        'OutputDirExt';'.proj';...
-        %'GetMask';'on'...%can use mask option   ,'off' by default
-        %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter 
-               ''};
-    return %exit the function 
-end
-
-%% input parameters: 
-% read the xml file for batch case
-if ischar(Param) && ~isempty(find(regexp('Param','.xml$')))
-    Param=xml2struct(Param);
-else % RUN case : parameters introduced as the input structure Param
-    hseries=guidata(Param.hseries);%handles of the GUI series
-    WaitbarPos=get(hseries.waitbar_frame,'Position');% info for the waitbar
-end
-[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
-
-%% coordinate transform or other user defined transform
-transform_fct='';%default
-if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'fct_handle')
-    transform_fct=Param.FieldTransform.fct_handle;
-end
+
 
 %% projection object