Changeset 783 for trunk/src/find_file_series.m

Timestamp:

Jun 5, 2014, 10:39:28 PM (10 years ago)

Author:

sommeria

Message:

-pb of mulitple tiff reading solved
-modif of output parma in get-file_type and find_file_series

• introduction of transform/ima_noise_rms

File:

• trunk/src/find_file_series.m (modified) (5 diffs)

trunk/src/find_file_series.m

@@ -1 +1 @@
 %'find_file_series': check the content of an input file and find the corresponding file series
 %--------------------------------------------------------------------------
-% function [RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object,i1_input,i2_input,j1_input,j2_input]=find_file_series(fileinput)
+% function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,Object,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput,checkxml)
 %
 % OUTPUT:
+% RootPath: path to the dir containing the input file
+% SubDir: data dir containing the input file series
 % RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file)
 % i1_series(pair,ref_j+1, ref_i+1),i2_series,j1_series,j2_series: set of indices (i1,i2,j1,j2) sorted by ref index ref_i, ref_j, and pairindex in case of multiple pairs with the same ref
 %  (ref_i+1 is used to deal with the image index zero sometimes used)
 % NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string)
-% FileType: type of file, =
-%       = 'image', usual image as recognised by Matlab
-%       = 'multimage', image series stored in a single file
-%       = 'civx', netcdf file with civx convention
-%       = 'civdata', civ data with new convention
-%       = 'netcdf' other netcdf files
-%       = 'video': movie recognised by VideoReader (e;g. avi)
-% MovieObject: video object (=[] otherwise)
+% FileInfo: structure containing info on the input files (assumed identical on the whole series)
+    % FileInfo.FileType: type of file, =
+    %       = 'image', usual image as recognised by Matlab
+    %       = 'multimage', image series stored in a single file
+    %       = 'civx', netcdf file with civx convention
+    %       = 'civdata', civ data with new convention
+    %       = 'netcdf' other netcdf files
+    %       = 'video': movie recognised by VideoReader (e;g. avi)
+% MovieObject: video object (=[] otherwise
+% i1_input,i2_input,j1_input,j2_input: indices of the input file, or of the first file in the series if the input file does not exist
 %
 %INPUT
-% RootPath: path to the directory to be scanned
+% FilePath: path to the directory to be scanned
 % fileinput: name (without path) of the input file sample 
 % checkxml: =1(default) take into account xml file existence to possibly include indexes in RootFile
@@ -39 +43 @@
 %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
 
-function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,FileInfo,MovieObject,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput,checkxml)
+function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput,checkxml)
 %------------------------------------------------------------------------
 
@@ -52 +56 @@
 j1_series=zeros(1,1,1);
 j2_series=zeros(1,1,1);
-[FileType,FileInfo,MovieObject]=get_file_type(fullfileinput);
+[FileInfo,MovieObject]=get_file_type(fullfileinput);
 if ~exist(FilePath,'dir')
     return % don't go further if the dir path does not exist
@@ -233 +237 @@
         NomType=regexprep(NomType,['^' NomTypePref],'');
         %% update the file type if the input file does not exist (pb of 0001)
-        if isempty(FileType)
-            [FileType,FileInfo,MovieObject]=get_file_type(fullfile(FilePath,dirpair(ifile_min).name));
+        if isempty(FileInfo.FileType)
+            [FileInfo,MovieObject]=get_file_type(fullfile(FilePath,dirpair(ifile_min).name));
         end
     end
@@ -247 +251 @@
 %% introduce the frame index in case of movies or multimage type
 if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1
-    if isempty(i1_series)
+    if isempty(i1_series)% if there is no file index, i denotes the frame index
         i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
         i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
         i1_input=1;
         NomType='*';
-    else
-        i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);
-        i1_series=[zeros(size(i1_series,1),1) i1_series];
-        j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);
-        j1_series=[zeros(size(i1_series,1),1) j1_series];
-        %  include the first index in the root name
-        r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType
-        if ~isempty(r)
-            fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
-            if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
-                rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
-            else% if a separator '_' is  detected
-                rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
-            end
-            if ~isempty(rr)
-%                 RootFile=[RootFile rr.i1];% new root file
-%                 NomTypePref=r.tiretnum;
-%                 NomType=regexprep(NomType,['^'  NomTypePref],'');
-              %  i1_input=j1_input;
-              %  i2_input=j2_input;
-                j1_input=1;
-                j2_input=[];
+    else  % if there is a file index, j denotes the frame index while i denotes the file index
+        if strcmp(NomType(end-1:end),'ab')% recognized as a pair
+            RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices       
+            i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0
+            i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1
+            j1_series=[];
+            i1_input=1;
+            NomType='*';
+        else
+            i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);%
+            i1_series=[zeros(size(i1_series,1),1) i1_series];
+            j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);%
+            j1_series=[zeros(size(i1_series,1),1) j1_series];
+            %  include the first index in the root name
+            r=regexp(NomType,'^(?<tiretnum>_?\d+)','names');%look for a number or _1 at the beginning of NomType
+            if ~isempty(r)
+                fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput
+                if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not  detected
+                    rr=regexp(fileinput_end,'^(?<i1>\d+)','names');
+                else% if a separator '_' is  detected
+                    rr=regexp(fileinput_end,'^(?<i1>_\d+)','names');
+                end
+                if ~isempty(rr)
+                    j1_input=1;
+                    j2_input=[];
+                end
             end
         end