SIMEXP · pbellec · Apr 30, 2016 · Apr 30, 2016 · Apr 30, 2016 · Apr 30, 2016
diff --git a/commands/read_write/niak_mkdir.m b/commands/read_write/niak_mkdir.m
@@ -5,7 +5,7 @@
 % existing directory. 
 %
 % SYNTAX:
-% [SUCCESS,MESSAGE,MESSAGEID] = MKDIR(PATH_NAME)
+% [SUCCESS,MESSAGE,MESSAGEID] = NIAK_MKDIR(PATH_NAME)
 %
 % _________________________________________________________________________
 % INPUTS:

diff --git a/commands/read_write/niak_read_data_minc.m b/commands/read_write/niak_read_data_minc.m
@@ -0,0 +1,89 @@
+function vol = niak_read_data_minc(hdr,precision_data)
+% Read data from a MINC file (.MNC or .MNC.GZ).
+%
+% SYNTAX: VOL = NIAK_READ_DATA_MINC(HDR)
+%
+% HDR (structure) a description of the data, generated from NIAK_READ_VOL.
+%   The name of the file that will be used to extract data is stored in 
+%   HDR.INFO.FILE_PARENT.
+% VOL (array) volume data from the minc file used to read HDR. 
+%
+% SEE ALSO: NIAK_READ_HDR_MINC, NIAK_WRITE_MINC, NIAK_READ_VOL, 
+%     NIAK_WRITE_VOL, NIAK_READ_MINC
+%
+% COMMENTS: the data is forced to float precision.
+%
+% EXAMPLE:
+%   % start by reading the header of an existing file
+%   hdr = niak_read_vol('my_file.mnc');
+%   % latter read the actual volume data 
+%   vol = niak_read_data_minc(hdr);
+%   % read a different file, with identical header structure
+%   hdr.info.file_parent = 'my_file2.mnc';
+%   vol2 = niak_read_data_minc(hdr);
+%
+% See license in the code. 
+
+% Copyright (c) Pierre Bellec, 2008-2016.
+% Montreal Neurological Institute, 2008-2010
+% Centre de recherche de l'institut de geriatrie de Montreal, 
+% Department of Computer Science and Operations Research
+% University of Montreal, Qubec, Canada, 2010-2016
+% Maintainer: [email protected]
+% See licensing information in the code.
+% Keywords: medical imaging, I/O, reader, nifti
+%
+% Permission is hereby granted, free of charge, to any person obtaining a copy
+% of this software and associated documentation files (the "Software"), to deal
+% in the Software without restriction, including without limitation the rights
+% to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+% copies of the Software, and to permit persons to whom the Software is
+% furnished to do so, subject to the following conditions:
+%
+% The above copyright notice and this permission notice shall be included in
+% all copies or substantial portions of the Software.
+%
+% THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+% IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+% FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+% AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+% LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+% OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+% THE SOFTWARE.
+
+if nargin < 2
+    precision_data = 'float';
+end
+
+%% Unzip file if necessary
+file_name = hdr.info.file_parent;
+[file_tmp_mnc,flag_zip] = niak_unzip(file_name);
+[path_tmp,name_tmp,ext_tmp] = fileparts(file_tmp_mnc);
+
+%% Generating a name for a temporary file
+file_tmp = niak_file_tmp([name_tmp '.dat']);
+
+%% extracting the data in float precision in the temporary file
+[flag,str_info] = system(cat(2,'minctoraw -',precision_data,' -normalize ',file_name,' > ',file_tmp));
+
+if flag>0
+    error(sprintf('niak:read : %s',str_info))
+end
+
+%% reading information
+hf = fopen(file_tmp,'r');
+try
+    vol = fread(hf,prod(hdr.info.dimensions),['*' precision_data]);
+catch
+    vol = fread(hf,prod(hdr.info.dimensions),precision_data);
+end
+
+%% Removing temporary stuff
+fclose(hf);
+if flag_zip
+  delete(file_tmp_mnc);
+end
+delete(file_tmp);
+
+%% Shapping vol as 3D+t array
+vol = reshape(vol,hdr.info.dimensions);
diff --git a/commands/read_write/niak_read_data_nifti.m b/commands/read_write/niak_read_data_nifti.m
@@ -0,0 +1,132 @@
+function vol = niak_read_data_nifti(hdr)
+% Read data from a NIFTI file (.NII or .IMG).
+%
+% SYNTAX: VOL = NIAK_READ_DATA_NIFTI(HDR)
+%
+% HDR (structure) a description of the data, generated from NIAK_READ_VOL.
+%   The name of the file that will be used to extract data is stored in 
+%   HDR.INFO.FILE_PARENT.
+% VOL (array) volume data from the nifti file used to read HDR. 
+%
+% SEE ALSO: NIAK_READ_HDR_NIFTI, NIAK_WRITE_NIFTI, NIAK_READ_VOL, 
+%     NIAK_WRITE_VOL, NIAK_READ_NIFI
+%
+% COMMENTS: the data is forced to single precision.
+%
+% EXAMPLE:
+%   % start by reading the header of an existing file
+%   hdr = niak_read_vol('my_file.nii.gz');
+%   % latter read the actual volume data 
+%   vol = niak_read_data_nifti(hdr);
+%   % read a different file, with identical header structure
+%   hdr.info.file_parent = 'my_file2.nii.gz';
+%   vol2 = niak_read_data_nifti(hdr);
+%
+% See license in the code. 
+
+% Copyright (c) Pierre Bellec, 2008-2016.
+% Montreal Neurological Institute, 2008-2010
+% Centre de recherche de l'institut de geriatrie de Montreal, 
+% Department of Computer Science and Operations Research
+% University of Montreal, Qubec, Canada, 2010-2016
+% Maintainer: [email protected]
+% See licensing information in the code.
+% Keywords: medical imaging, I/O, reader, nifti
+%
+% Permission is hereby granted, free of charge, to any person obtaining a copy
+% of this software and associated documentation files (the "Software"), to deal
+% in the Software without restriction, including without limitation the rights
+% to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+% copies of the Software, and to permit persons to whom the Software is
+% furnished to do so, subject to the following conditions:
+%
+% The above copyright notice and this permission notice shall be included in
+% all copies or substantial portions of the Software.
+%
+% THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+% IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+% FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+% AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+% LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+% OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+% THE SOFTWARE.
+
+%% Unzip file if necessary
+file_name = hdr.info.file_parent;
+[file_tmp,flag_zip] = niak_unzip(file_name);
+
+%% Opening the data file
+fid = fopen(file_tmp,'r',hdr.info.machine);
+
+if fid < 0,
+    msg = sprintf('Cannot open file %s.',file_name);
+    error(msg);
+end
+
+if hdr.details.dim(5) < 1
+    hdr.details.dim(5) = 1;
+end
+
+%  move pointer to the start of image block
+%
+switch hdr.type
+    case {'vol', 'analyze'}
+        fseek(fid, 0, 'bof');
+    case 'nii'
+        fseek(fid, hdr.details.vox_offset, 'bof');
+end
+
+
+%  For each frame, precision of value will be read
+%  in vol_siz times, where vol_siz is only the
+%  dimension size of an image, not the byte storage
+%  size of an image.
+vol_siz = prod(hdr.details.dim(2:5));
+
+%%  For complex float32 or complex float64, voxel values
+%%  include [real, imag]
+if (hdr.details.datatype == 32) || (hdr.details.datatype == 1792)
+    vol_siz = vol_siz * 2;
+end
+
+%% MPH: For RGB24, voxel values include 3 separate color planes
+if (hdr.details.datatype == 128) || (hdr.details.datatype == 511)
+    vol_siz = vol_siz * 3;
+end
+
+vol = fread(fid, vol_siz, sprintf('*%s',hdr.info.precision));
+
+%%  For complex float32 or complex float64, voxel values
+%%  include [real, imag]
+if (hdr.details.datatype == 32) || (hdr.details.datatype == 1792)
+    vol = reshape(vol, [2, length(vol)/2]);
+    vol = complex(vol(1,:)', vol(2,:)');
+end
+fclose(fid);
+
+%% Reshape the volume to correct dimensions
+vol_idx = 1:hdr.details.dim(5);
+
+if (hdr.details.datatype == 128) && (hdr.details.bitpix == 24)
+    vol = squeeze(reshape(vol, [3 hdr.details.dim(2:4) length(vol_idx)]));
+    vol = permute(vol, [2 3 4 1 5]);
+elseif (hdr.details.datatype == 511) && (hdr.details.bitpix == 96)
+    vol = single(vol);
+    vol = (vol - min(vol))/(max(vol) - min(vol));
+    vol = squeeze(reshape(vol, [3 hdr.details.dim(2:4) length(vol_idx)]));
+    vol = permute(vol, [2 3 4 1 5]);
+else
+    vol = squeeze(reshape(vol, [hdr.details.dim(2:4) length(vol_idx)]));
+end
+
+if ((hdr.details.scl_slope~=0)&&(hdr.details.scl_slope~=1))||(hdr.details.scl_inter~=0)
+    vol = hdr.details.scl_slope * single(vol) + hdr.details.scl_inter;
+end  
+
+%% Hack: force to single precision
+vol = single(vol);
+
+%% remove temporary file
+if flag_zip
+    delete(file_tmp);
+end    
diff --git a/commands/read_write/niak_read_hdr_nifti.m b/commands/read_write/niak_read_hdr_nifti.m
@@ -4,47 +4,32 @@
 % affine transformation information will be included.
 % http://nifti.nimh.nih.gov/nifti-1
 % 
-% SYNTAX:
-% HDR = NIAK_READ_HDR_NIFTI(FILE_NAME)
+% SYNTAX: HDR = NIAK_READ_HDR_NIFTI(FILE_NAME)
 %
-% _________________________________________________________________________
-% INPUT:
+% FILE_NAME (string) name of a single 3D+t nifti file or a 3D nifti file.
+%   Compressed files (.nii.gz) are not supported.
+% HDR (structure) contain a description of the data. For a list of fields 
+%   common to all data types, see NIAK_READ_VOL.
+% HDR.DETAILS (structure) contains the standard fields of a nifti file. 
+%   See http://nifti.nimh.nih.gov/nifti-1.
 %
-% FILE_NAME     
-%    (string) name of a single 3D+t minc file or a 3D minc file.
+% EXAMPLE:
+%   hdr = niak_read_hdr_nifti('my_vol.nii');
 %
-% _________________________________________________________________________
-% OUTPUT:
-%
-% HDR           
-%    (structure) contain a description of the data. For a list of fields 
-%    common to all data types, see NIAK_READ_VOL.
-%
-%    HDR.DETAILS 
-%        (structure) contains the standard fields of a nifti file. 
-%        See http://nifti.nimh.nih.gov/nifti-1.
-%
-% _________________________________________________________________________
 % SEE ALSO:
+%   NIAK_READ_NIFTI, NIAK_WRITE_NIFTI, NIAK_READ_VOL, NIAK_WRITE_VOL
 %
-% NIAK_READ_NIFTI, NIAK_WRITE_NIFTI, NIAK_READ_VOL, NIAK_WRITE_VOL
-%
-% _________________________________________________________________________
-% COMMENTS:
-%
-% Part of this file is copied and modified under GNU license from
-% MRI_TOOLBOX developed by CNSP in Flinders University, Australia
-%
-% Important parts of this code are copied and modified from a matlab
-% toolbox by Jimmy Shen ([email protected]). Unfortunately, this
-% toolbox did not include a copyright notice.
-% http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=8797&objectType=file
-%
-% Copyright (c) Pierre Bellec, Montreal Neurological Institute, 2008.
-% Maintainer : [email protected]
+% See license in the code. 
+
+% Copyright (c) Pierre Bellec, Jimmy Shen, 2008-2016.
+% Montreal Neurological Institute, 2008-2010
+% Centre de recherche de l'institut de geriatrie de Montreal, 
+% Department of Computer Science and Operations Research
+% University of Montreal, Qubec, Canada, 2010-2016
+% Maintainer: [email protected]
 % See licensing information in the code.
-% Keywords : medical imaging, I/O, reader, nifti
-
+% Keywords: medical imaging, I/O, reader, nifti
+%
 % Permission is hereby granted, free of charge, to any person obtaining a copy
 % of this software and associated documentation files (the "Software"), to deal
 % in the Software without restriction, including without limitation the rights