%'read_field': read the fields from files in different formats (netcdf files, images, video) %-------------------------------------------------------------------------- % function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) % % OUTPUT: % Field: matlab structure representing the field % ParamOut: structure representing parameters: % .FieldName; field name % .VelType % .CivStage: stage of civx processing (=0, not Civx, =1 (civ1), =2 (fix1).... % .Npx,.Npy: for images, nbre of pixels in x and y % errormsg: error message, ='' by default % %INPUT % FileName: name of the input file % FileType: type of file, as determined by the function get_file_info.m % ParamIn: movie object or Matlab structure of input parameters % .FieldName: name (char string) of the input field (for Civx data) % .VelType: char string giving the type of velocity data ('civ1', 'filter1', 'civ2'...) % .ColorVar: variable used for vector color % .Npx, .Npy: nbre of pixels along x and y (used for .vol input files) % .TimeDimName: name of the dimension considered as 'time', selected index value then set by input 'num' % num: frame number for movies % % see also read_image.m,read_civxdata.m,read_civdata.m, %======================================================================= % Copyright 2008-2018, 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 [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num) %% default output and check input Field=[]; if ~exist('num','var') num=1; end if isempty(num) num=1; end if ~exist('ParamIn','var') ParamIn=[]; end ParamOut=ParamIn;%default errormsg=''; if isempty(regexp(FileName,'^http://'))&& ~exist(FileName,'file') errormsg=['input file ' FileName ' does not exist']; return end A=[]; InputField={}; check_colorvar=0; if isstruct(ParamIn) if isfield(ParamIn,'FieldName') if ischar(ParamIn.FieldName) InputField={ParamIn.FieldName}; else InputField= ParamIn.FieldName; end end check_colorvar=zeros(size(InputField)); if isfield(ParamIn,'ColorVar')&&~isempty(ParamIn.ColorVar) InputField=[ParamIn.FieldName {ParamIn.ColorVar}]; check_colorvar(numel(InputField))=1; end end %% distingush different input file types switch FileType case 'civdata'% new format for civ results [Field,ParamOut.VelType,errormsg]=read_civdata(FileName,InputField,ParamIn.VelType); if ~isempty(errormsg),errormsg=['read_civdata / ' errormsg];return,end ParamOut.CivStage=Field.CivStage; case 'pivdata_fluidimage' [Field,ParamOut.VelType,errormsg]=read_pivdata_fluidimage(FileName,InputField,ParamIn.VelType); ParamOut.CivStage=Field.CivStage; case 'civx'% old (obsolete) format for civ results ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default [Field,ParamOut.VelType,errormsg]=read_civxdata(FileName,InputField,ParamIn.VelType); if ~isempty(errormsg),errormsg=['read_civxdata / ' errormsg];return,end ParamOut.CivStage=Field.CivStage; case 'netcdf'% general netcdf file (not recognized as civ) ListVarName={}; Role={}; ProjModeRequest={}; %ListInputField={}; %checkU=0; %checkV=0; % scan the list InputField Operator=cell(1,numel(InputField)); InputVar=cell(1,numel(InputField)); for ilist=1:numel(InputField) % look for input variables to read r=regexp(InputField{ilist},'(?(^vec|^norm))\((?.+),(?.+)\)$','names'); if isempty(r)% no operator used ListVarName=[ListVarName InputField(ilist)];%append the variable name %InputVar{ilist}=InputField(ilist); %ListInputField=[ListInputField InputField(ilist)]; if check_colorvar(ilist)% case of field used for vector color Role{numel(ListVarName)}='ancillary';% not projected with interpolation ProjModeRequest{numel(ListVarName)}=''; else Role{numel(ListVarName)}='scalar'; ProjModeRequest{numel(ListVarName)}='interp_lin';%scalar field (requires interpolation for plot) end Operator{numel(ListVarName)}=''; else % an operator 'vec' or 'norm' is used ListVarName=[ListVarName {r.UName}]; % append the variable in the list if not previously listed if strcmp(r.Operator,'norm') if check_colorvar(ilist) Role=[Role {'ancillary'}]; else Role=[Role {'scalar'}]; end else Role=[Role {'vector_x'}]; end %ListInputField=[ListInputField InputField(ilist)]; ListVarName=[ListVarName {r.VName}];% append the variable in the list if not previously listed Role=[Role {'vector_y'}]; %ListInputField=[ListInputField InputField(ilist)]; Operator{numel(ListVarName)-1}=r.Operator; Operator{numel(ListVarName)}=''; if ~check_colorvar(ilist) && strcmp(r.Operator,'norm') ProjModeRequest{numel(ListVarName)}='interp_lin';%scalar field (requires interpolation for plot) ProjModeRequest{numel(ListVarName)-1}='interp_lin';%scalar field (requires interpolation for plot) else ProjModeRequest{numel(ListVarName)}=''; ProjModeRequest{numel(ListVarName)-1}=''; end end end if ~isfield(ParamIn,'Coord_z') ParamIn.Coord_z=[]; end NbCoord=~isempty(ParamIn.Coord_x)+~isempty(ParamIn.Coord_y)+~isempty(ParamIn.Coord_z); if isfield(ParamIn,'TimeDimName')% case of reading of a single time index in a multidimensional array [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeDimName',ParamIn.TimeDimName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVarName]); elseif isfield(ParamIn,'TimeVarName')% case of reading of a single time in a multidimensional array [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeVarName',ParamIn.TimeVarName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVarName]); if numel(num)~=1 NbCoord=NbCoord+1;% adds time coordinate, except if a single time has been selected end else [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVarName]); end if ~isempty(errormsg) return end CheckStructured=1; %scan all the variables NbCoord=0; if ~isempty(ParamIn.Coord_x) index_Coord_x=find(strcmp(ParamIn.Coord_x,Field.ListVarName)); Field.VarAttribute{index_Coord_x}.Role='coord_x';% NbCoord=NbCoord+1; end if ~isempty(ParamIn.Coord_y) if ischar(ParamIn.Coord_y) index_Coord_y=find(strcmp(ParamIn.Coord_y,Field.ListVarName)); Field.VarAttribute{index_Coord_y}.Role='coord_y';% NbCoord=NbCoord+1; else for icoord_y=1:numel(ParamIn.Coord_y) index_Coord_y=find(strcmp(ParamIn.Coord_y{icoord_y},Field.ListVarName)); Field.VarAttribute{index_Coord_y}.Role='coord_y';% NbCoord=NbCoord+1; end end end NbDim=1; if ~isempty(ParamIn.Coord_z) index_Coord_z=find(strcmp(ParamIn.Coord_z,Field.ListVarName)); Field.VarAttribute{index_Coord_z}.Role='coord_z';% NbCoord=NbCoord+1; NbDim=3; elseif ~isempty(ParamIn.FieldName) NbDim=2; end NormName=''; UName=''; VName=''; if numel(Field.ListVarName)>NbCoord % if there are variables beyond coord (exclude 1 D plots) VarAttribute=cell(1,numel(ListVarName)); for ilist=1:numel(ListVarName) index_var=find(strcmp(ListVarName{ilist},Field.ListVarName),1); VarDimName{ilist}=Field.VarDimName{index_var}; DimOrder=[]; if NbDim ==2 DimOrder=[find(strcmp(ParamIn.Coord_y,VarDimName{ilist})) find(strcmp(ParamIn.Coord_x,VarDimName{ilist}))]; elseif NbDim ==3 DimOrder=[find(strcmp(ParamIn.Coord_z,VarDimName{ilist}))... find(strcmp(ParamIn.Coord_y,VarDimName{ilist}))... find(strcmp(ParamIn.Coord_x,VarDimName{ilist}))]; end if ~isempty(DimOrder) Field.(ListVarName{ilist})=permute(Field.(ListVarName{ilist}),DimOrder); VarDimName{ilist}=VarDimName{ilist}(DimOrder); end if numel(Field.VarAttribute)>=index_var VarAttribute{ilist}=Field.VarAttribute{index_var};% read var attributes from input if exist end end check_remove=false(1,numel(Field.ListVarName)); for ilist=1:numel(ListVarName) VarAttribute{ilist}.Role=Role{ilist}; VarAttribute{ilist}.ProjModeRequest=ProjModeRequest{ilist}; if isfield(ParamIn,'FieldName') VarAttribute{ilist}.Operator=Operator{ilist}; end if strcmp(Operator{ilist},'norm') UName=ListVarName{ilist}; VName=ListVarName{ilist+1}; ListVarName{ilist}='norm'; Field.norm=Field.(UName).*Field.(UName)+Field.(VName).*Field.(VName); Field.norm=sqrt(Field.norm); check_remove(ilist+1)=true; VarAttribute{ilist}.Operator=''; end end ListVarName(check_remove)=[]; VarDimName(check_remove)=[]; VarAttribute(check_remove)=[]; Field.ListVarName=[Field.ListVarName(1:NbCoord) ListVarName];% complement the list of vqriables, which may be listed twice Field.VarDimName=[Field.VarDimName(1:NbCoord) VarDimName]; Field.VarAttribute=[Field.VarAttribute(1:NbCoord) VarAttribute]; end case 'video' if strcmp(class(ParamIn),'VideoReader') A=read(ParamIn,num); else ParamOut=VideoReader(FileName); A=read(ParamOut,num); end case 'mmreader' if strcmp(class(ParamIn),'mmreader') A=read(ParamIn,num); else ParamOut=mmreader(FileName); A=read(ParamOut,num); end case 'vol' A=imread(FileName); Npz=size(A,1)/ParamIn.Npy; A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz); A=permute(A,[3 2 1]); case 'multimage' % warning 'off' A=imread(FileName,num); case 'image' A=imread(FileName); case 'rdvision' [A,FileInfo,timestamps,errormsg]=read_rdvision(FileName,num); case 'image_DaVis' Input=readimx(FileName); if numel(Input.Frames)==1 num=1; end A=Input.Frames{num}.Components{1}.Planes{1}'; for ilist=1:numel(Input.Frames{1}.Attributes) if strcmp(Input.Frames{1}.Attributes{ilist}.Name,'AcqTimeSeries') timestamps=str2num(Input.Frames{1}.Attributes{ilist}.Value(1:end-3))/1000000; break end end case 'cine_phantom' [A,FileInfo] = read_cine_phantom(FileName,num ); otherwise errormsg=[ FileType ': invalid input file type for uvmat']; end %% case of image if ~isempty(A) if strcmp(FileType,'rdvision')||strcmp(FileType,'image_DaVis') Field.Time=timestamps; end if isstruct(ParamOut) ParamOut.FieldName='image'; end Npz=1;%default npxy=size(A); Field.NbDim=2;%default Field.AName='image'; Field.ListVarName={'Coord_y','Coord_x','A'}; % Field.VarAttribute{1}.Unit='pixel'; Field.VarAttribute{2}.Unit='pixel'; Field.VarAttribute{1}.Role='coord_y'; Field.VarAttribute{2}.Role='coord_x'; Field.VarAttribute{3}.Role='scalar'; if ndims(A)==3 if Npz==1;%color Field.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x','rgb'}}; % Field.Coord_y=[npxy(1)-0.5 0.5]; Field.Coord_x=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers if isstruct(ParamOut) ParamOut.Npx=npxy(2);% display image size on the interface ParamOut.Npy=npxy(1); end else Field.NbDim=3; Field.ListVarName=['AZ' Field.ListVarName]; Field.VarDimName={'AZ','Coord_y','Coord_x',{'AZ','Coord_y','Coord_x'}}; Field.AZ=[npxy(1)-0.5 0.5]; Field.Coord_y=[npxy(2)-0.5 0.5]; Field.Coord_x=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers if isstruct(ParamOut) ParamOut.Npx=npxy(3);% display image size on the interface ParamOut.Npy=npxy(2); end end else Field.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x'}}; % Field.Coord_y=[npxy(1)-0.5 0.5]; Field.Coord_x=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers end Field.A=A; Field.CoordUnit='pixel'; %used for mouse_motion end