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source: trunk/src/get_file_info.m @ 1164

Last change on this file since 1164 was 1164, checked in by sommeria, 2 months ago
civ3D updated
File size: 13.1 KB

Rev	Line
[784]	1	%'get_file_info': determine info about a file (image, multimage, civdata,...) .
	2	%------------------------------------------------------------------------
	3	% [FileInfo,VideoObject]=get_file_info(fileinput)
	4	%
	5	% OUTPUT:
	6	% FileInfo: structure containing info on the file (case of images or video), in particular
	7	% .FileType: type of file, needed as input of read_field.m
[1033]	8	% ='figure': Matlab figure
[1089]	9	% ='mat': Matlab data file
[1033]	10	% ='xml': xml file
	11	% ='xls': Excel file
	12	% ='dat': text file for data,
	13	% ='image': image format recognised by Matlab
	14	% ='multimage': image format recognised by Matlab with multiple frames
	15	% ='video': video movie file
	16	% ='mmreader': video from old versions of Matlab (<2009)
	17	% ='rdvision': images in binary format from company rdvision
	18	% ='image_DaVis': images from softwar DaVis (company LaVision)
	19	% ='cine_phantom': images from fast camera Phantom
	20	% ='bin': binary file without specific organisation
	21	% ='netcdf': netcdf file
	22	% ='civdata': netcdf files provided by civ_series
	23	% ='civx': netcdf files provided by the obsolete program civx (in fortran)
	24	% ='pivdata_fluidimage': PIV data from software 'fluidimage'
[1040]	25	% .FieldType='image' for all kinds of images and movies, =FileType else
	26	% .FileIndexing='on'/'off', for data files (when series of indexed files are expected)
[784]	27	% .Height: image height in pixels
	28	% .Width: image width in pixels
	29	% .BitDepth: nbre of bits per pixel (8 of 16)
	30	% .ColorType: 'greyscale' or 'color'
[1040]	31	% .NumberOfFrames: defined for images or movies
[784]	32	% .FrameRate: nbre of frames per second, =[] for images
	33	% VideoObject: in case of video
	34	%
	35	% INPUT:
	36	% fileinput: name, including path, of the file to analyse
[809]	37
	38	%=======================================================================
[1126]	39	% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
[809]	40	% http://www.legi.grenoble-inp.fr
[1127]	41	% Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
[809]	42	%
	43	% This file is part of the toolbox UVMAT.
	44	%
	45	% UVMAT is free software; you can redistribute it and/or modify
	46	% it under the terms of the GNU General Public License as published
	47	% by the Free Software Foundation; either version 2 of the license,
	48	% or (at your option) any later version.
	49	%
	50	% UVMAT is distributed in the hope that it will be useful,
	51	% but WITHOUT ANY WARRANTY; without even the implied warranty of
	52	% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	53	% GNU General Public License (see LICENSE.txt) for more details.
	54	%=======================================================================
	55
[784]	56	function [FileInfo,VideoObject]=get_file_info(fileinput)
[1162]	57
[784]	58	VideoObject=[];
[1041]	59	FileInfo.FileType='';% input file does not exist
	60	FileInfo.FieldType=''; %default output
[1122]	61	if ~ischar(fileinput)
	62	return
	63	end
[1041]	64	% check the existence (not possible for OpenDAP data)
[1134]	65	if ~isempty(regexp(fileinput,'^http://','once'))\|\| exist(fileinput,'file')
[784]	66	FileInfo.FileName=fileinput;
	67	FileInfo.FileType='txt'; %default
[1162]	68	else
	69	return %input file does not exist.
[784]	70	end
	71	[tild,tild,FileExt]=fileparts(fileinput);%get the file extension FileExt
	72
	73	switch FileExt
	74	case '.fig'
	75	FileInfo.FileType='figure';
[1088]	76	case '.mat'
	77	FileInfo.FileType='mat';
[784]	78	case {'.xml','.xls','.dat','.bin'}
	79	FileInfo.FileType=regexprep(FileExt,'^.','');% eliminate the dot of the extension;
[790]	80	case {'.seq','.sqb'}
[1157]	81	[~,FileInfo,timestamps,errormsg]=read_rdvision(fileinput,[]);
[1007]	82	case '.im7'
	83	try
[1162]	84	Input=readimx(fileinput);
	85	Image=Input.Frames{1}.Components{1}.Planes{1};
	86	FileInfo.FileType='image_DaVis';
	87	FileInfo.NumberOfFrames=numel(Input.Frames);
	88	FileInfo.Height=size(Image,2);
	89	FileInfo.Width=size(Image,1);
	90	FileInfo.TimeName='timestamp';
	91	for ilist=1:numel(Input.Attributes)
	92	% if strcmp(Input.Attributes{ilist}.Name,'_Date')
	93	% DateString=Input.Attributes{ilist}.Value;
	94	% end
	95	% if strcmp(Input.Attributes{ilist}.Name,'_Time')
	96	% TimeString=Input.Attributes{ilist}.Value;
	97	% end
	98	end
[1007]	99	catch ME
[1033]	100	msgbox_uvmat('ERROR',{ME.message;'reading image from DaVis is possible only with Matlab version 2013 or earlier'})
[1007]	101	return
	102	end
[946]	103	case '.h5'
[1134]	104	hinfo=h5info(fileinput);
	105	FileInfo.CivStage=0;
	106	for igroup=1:numel(hinfo.Groups)
	107	if strcmp(hinfo.Groups(igroup).Name,'/piv0')
	108	FileInfo.CivStage=3;
	109	end
	110	if strcmp(hinfo.Groups(igroup).Name,'/piv1')
	111	FileInfo.CivStage=6;
	112	break
	113	end
	114	end
	115	if FileInfo.CivStage~=0
[946]	116	FileInfo.FileType='pivdata_fluidimage';
[1134]	117	else
	118	FileInfo.FileType='h5';
[946]	119	end
[979]	120	case '.cine'
	121	[FileInfo,BitmapInfoHeader, CameraSetup]=readCineHeader(fileinput);
	122	FileInfo.FileType='cine_phantom';
	123	FileInfo.NumberOfFrames=FileInfo.ImageCount;
	124	FileInfo.FrameRate=CameraSetup.FrameRate;
	125	FileInfo.Height=BitmapInfoHeader.biHeight;
	126	FileInfo.Width=BitmapInfoHeader.biWidth;
[1162]	127	FileInfo.BitDepth=BitmapInfoHeader.biBitCount;
	128	FileInfo.TimeName='video';
[784]	129	otherwise
	130	if ~isempty(FileExt)% exclude empty extension
	131	FileExt=regexprep(FileExt,'^.','');% eliminate the dot of the extension
	132	if ~isempty(FileExt)
	133	if ~isempty(imformats(FileExt))%case of images
[1120]	134	FileInfo.FileType='image';
[784]	135	try
	136	imainfo=imfinfo(fileinput);
[1162]	137	if length(imainfo) >1 %case of image with multiple frames
[784]	138	FileInfo=imainfo(1);%take info from the first frame
	139	FileInfo.NumberOfFrames=length(imainfo);
	140	FileInfo.FileType='multimage';
	141	else
	142	FileInfo=imainfo;
	143	FileInfo.NumberOfFrames=1;
	144	FileInfo.FileType='image';
	145	end
	146	FileInfo.FileName=FileInfo.Filename; %correct the info given by imfinfo
	147	nbfield=numel(fieldnames(FileInfo));
	148	FileInfo=orderfields(FileInfo,[nbfield nbfield-1 nbfield-2 (1:nbfield-3)]); %reorder the fields of fileInfo for clarity
	149	end
	150	else
	151	error_nc=0;
[1162]	152	try %try netcdf file
	153	[Data,tild,tild,errormsg]=nc2struct(fileinput,[]);
	154	if isempty(errormsg)
[1164]	155	% if isfield(Data,'absolut_time_T0') && isfield(Data,'hart') && ~isempty(Data.absolut_time_T0) && ~isempty(Data.hart)
	156	% FileInfo.FileType='civx';%old civ data from the Fortran program
	157	% if isfield(Data,'patch2') && isequal(Data.patch2,1)
	158	% FileInfo.CivStage=6;
	159	% elseif isfield(Data,'fix2') && isequal(Data.fix2,1)
	160	% FileInfo.CivStage=5;
	161	% elseif isfield(Data,'civ2')&& isequal(Data.civ2,1)
	162	% FileInfo.CivStage=4;
	163	% elseif isfield(Data,'patch')&&isequal(Data.patch,1)
	164	% FileInfo.CivStage=3;
	165	% elseif isfield(Data,'fix')&&isequal(Data.fix,1)
	166	% FileInfo.CivStage=2;
	167	% else
	168	% FileInfo.CivStage=1;
	169	% end
	170	% else
	171	if isfield(Data,'Conventions') && strcmp(Data.Conventions,'uvmat/civdata')
[1161]	172	FileInfo.FileType='civdata'; % test for civ velocity fields
[784]	173	FileInfo.CivStage=Data.CivStage;
[1164]	174	MaskFile='';
	175	if isfield(Data,'Civ2_Mask')
	176	MaskFile=Data.Civ2_Mask;
	177	if isfield(Data,'Civ2_NbSlice')
	178	FileInfo.MaskNbSlice=Data.Civ2_NbSlice;
	179	end
	180	elseif isfield(Data,'Civ1_Mask')
	181	MaskFile=Data.Civ1_Mask;
	182	if isfield(Data,'Civ1_NbSlice')
	183	FileInfo.MaskNbSlice=Data.Civ1_NbSlice;
	184	end
	185	end
	186	if isfield(Data,'VolumeScan')
	187	FileInfo.VolumeScan=Data.VolumeScan;
	188	end
	189	if ~isempty(MaskFile)
	190	[RootPath,SubDir,RootFile,~,~,~,~,FileExt,NomType]=fileparts_uvmat(MaskFile);
	191	if strcmp(NomType,'_1')&& isfield(FileInfo,'MaskNbSlice')
	192	FileInfo.MaskFile=fullfile(RootPath,SubDir,RootFile);
	193	else
	194	FileInfo.MaskFile=MaskFile;% single mask for the series (no indexing)
	195	end
	196	FileInfo.MaskExt=FileExt;
	197	end
[1161]	198	elseif isfield(Data,'Conventions') && strcmp(Data.Conventions,'uvmat/civdata_3D')
	199	FileInfo.FileType='civdata_3D'; % test for 3D volume civ velocity fields
	200	FileInfo.CivStage=Data.CivStage;
[1162]	201	z_dim_index=find(strcmp(Data.ListDimName,'npz'));
	202	FileInfo.NumberOfFrames=Data.DimValue(z_dim_index);
[784]	203	else
	204	FileInfo.FileType='netcdf';
	205	FileInfo.ListVarName=Data.ListVarName;
[1162]	206	FileInfo.VarAttribute={};
	207	if isfield(Data,'VarAttribute')
	208	FileInfo.VarAttribute=Data.VarAttribute;
	209	end
	210	FileInfo.ListDimName=Data.ListDimName;
	211	FileInfo.NumberOfFrames=Data.DimValue;
[784]	212	end
[1162]	213	else
	214	error_nc=1;
[784]	215	end
	216	catch ME
	217	error_nc=1;
	218	end
	219	if error_nc
	220	try
[1162]	221	if exist('mmreader.m','file')% Matlab 2009a
	222	INFO=mmfileinfo (fileinput);
	223	if ~isempty(INFO.Video.Format)
	224
	225	VideoObject=mmreader(fileinput);
	226	FileInfo=get(VideoObject);
	227	FileInfo.FileType='mmreader';
	228	end
[784]	229	end
	230	FileInfo.BitDepth=FileInfo.BitsPerPixel/3;
	231	FileInfo.ColorType='truecolor';
[1032]	232	FileInfo.TimeName='video';
[784]	233	FileInfo.FileName=fileinput;
	234	nbfield=numel(fieldnames(FileInfo));
[1032]	235	FileInfo=orderfields(FileInfo,[nbfield nbfield-4 nbfield-3 nbfield-1 nbfield-2 (1:nbfield-5)]); %reorder the fields of fileInfo for clarity
[1025]	236	if ~isfield(FileInfo,'NumberOfFrames')
	237	FileInfo.NumberOfFrames=floor(FileInfo.Duration*FileInfo.FrameRate);
	238	end
[784]	239	end
	240	end
	241	end
	242	end
	243	end
[790]	244	end
[1041]	245
[1089]	246	if ismember (FileInfo.FileType,{'mat','image','image_DaVis','multimage','mmreader','cine_phantom','video','netcdf','civdata'})
[1162]	247	FileInfo.FileIndexing='on'; % allow to detect file index for scanning series
[1041]	248	else
	249	FileInfo.FileIndexing='off';
[809]	250	end
[1033]	251	FileInfo.FieldType=FileInfo.FileType;%default
	252	switch FileInfo.FileType
	253	case {'image','multimage','video','mmreader','rdvision','image_DaVis','cine_phantom'}
[1162]	254	FileInfo.FieldType='image';
[1041]	255	case {'civx','civdata','pivdata_fluidimage'}
	256	FileInfo.FieldType='civdata';
[1033]	257	end
	258

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