Mercurial > hg > octave-image
annotate inst/analyze75write.m @ 892:a2140b980079
iptcheckconn: implement in C++ as static method for connectivity.
* iptcheckconn.m: file removed; help text and tests reused for C++.
* conndef.cc: implement two new connectivity::validate() methods and
the iptcheckconn function for Octave as caller to those methods.
* conndef.h: define the connectivity::validate() static methods.
* COPYING
| author | Carnë Draug <carandraug@octave.org> |
|---|---|
| date | Wed, 01 Oct 2014 20:22:37 +0100 |
| parents | df3accfcddb8 |
| children |
| rev | line source |
|---|---|
| 641 | 1 %% Copyright (C) 2012 Adam H Aitkenhead <adamaitkenhead@hotmail.com> |
| 2 %% | |
| 3 %% This program is free software; you can redistribute it and/or modify | |
| 4 %% it under the terms of the GNU General Public License as published by | |
| 5 %% the Free Software Foundation; either version 3 of the License, or | |
| 6 %% (at your option) any later version. | |
| 7 %% | |
| 8 %% This program is distributed in the hope that it will be useful, | |
| 9 %% but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 10 %% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| 11 %% GNU General Public License for more details. | |
| 12 %% | |
| 13 %% You should have received a copy of the GNU General Public License | |
| 14 %% along with this program; If not, see <http://www.gnu.org/licenses/>. | |
| 15 | |
| 16 %% -*- texinfo -*- | |
| 17 %% @deftypefn {Function File} analyze75write (@var{filename}, @var{data}, @var{header}) | |
| 18 %% @deftypefnx {Function File} analyze75write (@var{filename}, @var{data}, @var{x}, @var{y}, @var{z}) | |
| 19 %% @deftypefnx {Function File} analyze75write (@var{filename}, @var{data}, @var{header}, @var{x}, @var{y}, @var{z}) | |
| 20 %% Write image data to an Analyze 7.5 file. | |
| 21 %% | |
| 22 %% @var{filename} is the path to write the Analyze 7.5 file; @var{data} is | |
| 23 %% the 3D image data; @var{header} is a structure containing the file | |
| 24 %% information; @var{x}, @var{y}, @var{z} are lists of the x,y,z coordinates | |
| 25 %% (in cm) of the data grid. | |
| 26 %% | |
| 27 %% @seealso{analyze75info, analyze75read} | |
| 28 %% @end deftypefn | |
| 29 | |
| 30 %% Author: Adam H. Aitkenhead <adamaitkenhead@hotmail.com> | |
| 31 | |
| 32 function analyze75write (varargin); | |
| 33 | |
| 34 if (nargin ~= 3 && nargin ~= 5 && nargin ~= 6) | |
| 35 print_usage; | |
| 36 else | |
| 37 filename = varargin{1}; | |
| 38 data = varargin{2}; | |
| 39 if (nargin ==3) | |
| 40 header = varargin{3}; | |
| 41 x = ( (0:header.Dimensions(2)-1) - (header.Dimensions(2)-1)/2 ) * header.PixelDimensions(2); | |
| 42 y = ( (0:header.Dimensions(1)-1) - (header.Dimensions(1)-1)/2 ) * header.PixelDimensions(1); | |
| 43 z = ( (0:header.Dimensions(3)-1) - (header.Dimensions(3)-1)/2 ) * header.PixelDimensions(3); | |
| 44 % Convert mm to cm | |
| 45 if strncmpi(header.VoxelUnits,'mm',2)==1 | |
| 46 x = x / 10; | |
| 47 y = y / 10; | |
| 48 z = z / 10; | |
| 49 end | |
| 50 elseif (nargin ==5) | |
| 51 header = struct; | |
| 52 x = varargin{3}; | |
| 53 y = varargin{4}; | |
| 54 z = varargin{5}; | |
| 55 elseif (nargin ==6) | |
| 56 header = varargin{3}; | |
| 57 x = varargin{4}; | |
| 58 y = varargin{5}; | |
| 59 z = varargin{6}; | |
| 60 end | |
| 61 end | |
| 62 | |
| 63 if (~ischar (filename)) | |
| 64 error ('analyze75write: `filename'' must be a string.'); | |
| 65 end | |
| 66 | |
| 67 %% Strip the filename of the extension | |
| 68 fileextH = strfind (filename, '.hdr'); | |
| 69 fileextI = strfind (filename, '.img'); | |
| 70 if (~isempty (fileextH)) | |
| 71 fileprefix = filename(1:fileextH(end)-1); | |
| 72 elseif (~isempty (fileextI)) | |
| 73 fileprefix = filename(1:fileextI(end)-1); | |
| 74 else | |
| 75 fileprefix = filename; | |
| 76 end | |
| 77 | |
| 78 % Check the byteorder | |
| 79 if (nargin == 6) | |
| 80 if (isfield (header, 'ByteOrder')) && (any (strcmpi (header.ByteOrder, {'ieee-be', 'b'}))) | |
| 81 warning ('analyze75write: No support for big-endian. Please consider submitting a patch. Attempting to write as little-endian'); | |
| 82 end | |
| 83 end | |
| 84 header.ByteOrder = 'ieee-le'; | |
| 85 | |
| 86 %% Rearrange the data | |
| 87 data = permute(data,[2,1,3]); | |
| 88 | |
| 89 % Force uniform slice spacing | |
| 90 if (max(unique(diff(z))) - min(unique(diff(z))) > 1e-4) | |
| 91 warning ('analyze75write: Data slices must be equally spaced. Attempting to interpolate the data onto equally spaced slices.') | |
| 92 [data,z] = interpslices(data,x,y,z); | |
| 93 end | |
| 94 | |
| 95 % Check certain header fields | |
| 96 header.PixelDimensions = single(10 * [x(2)-x(1),y(2)-y(1),z(2)-z(1)]); | |
| 97 header.Dimensions = int16([size(data),1]); | |
| 98 header.HdrFileSize = int32(348); | |
| 99 header.VoxelUnits = 'mm '; | |
| 100 header.GlobalMin = int32(min(data(:))); | |
| 101 header.GlobalMax = int32(max(data(:))); | |
| 102 header.FileName = [fileprefix,'.hdr']; | |
| 103 | |
|
739
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
104 % Descriptor: Generate a string containing the coordinates of the first voxel (stored in the header for information only) |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
105 origintext = ['Coordinates of first voxel: ',num2str( 10* [x(1),y(1),z(1)] ,' %07.2f' )]; |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
106 header.Descriptor = sprintf('%-80s',origintext); |
| 641 | 107 |
| 108 % Determine the type of data | |
|
645
cc81e4acc53c
analyze75write: Now write int16 and int32 datasets correctly.
adam78a
parents:
643
diff
changeset
|
109 if (isa(data,'int16')) |
| 641 | 110 header.ImgDataType = 'DT_SIGNED_SHORT'; |
| 111 header.BitDepth = int16(16); | |
|
645
cc81e4acc53c
analyze75write: Now write int16 and int32 datasets correctly.
adam78a
parents:
643
diff
changeset
|
112 DataTypeLabel = int16(4); |
|
cc81e4acc53c
analyze75write: Now write int16 and int32 datasets correctly.
adam78a
parents:
643
diff
changeset
|
113 DataTypeString = 'int16'; |
| 647 | 114 elseif (isa(data,'int32')) |
|
645
cc81e4acc53c
analyze75write: Now write int16 and int32 datasets correctly.
adam78a
parents:
643
diff
changeset
|
115 header.ImgDataType = 'DT_SIGNED_INT'; |
|
cc81e4acc53c
analyze75write: Now write int16 and int32 datasets correctly.
adam78a
parents:
643
diff
changeset
|
116 header.BitDepth = int16(32); |
|
cc81e4acc53c
analyze75write: Now write int16 and int32 datasets correctly.
adam78a
parents:
643
diff
changeset
|
117 DataTypeLabel = int16(8); |
|
cc81e4acc53c
analyze75write: Now write int16 and int32 datasets correctly.
adam78a
parents:
643
diff
changeset
|
118 DataTypeString = 'int32'; |
| 641 | 119 elseif (isa(data,'single')) |
| 120 header.ImgDataType = 'DT_FLOAT'; | |
| 121 header.BitDepth = int16(32); | |
| 122 DataTypeLabel = int16(16); | |
| 123 DataTypeString = 'single'; | |
| 124 elseif (isa(data,'double')) | |
| 125 header.ImgDataType = 'DT_DOUBLE'; | |
| 126 header.BitDepth = int16(64); | |
| 127 DataTypeLabel = int16(64); | |
| 128 DataTypeString = 'double'; | |
| 129 end | |
| 130 | |
| 131 % Write the .hdr file | |
| 132 fidH = fopen([fileprefix,'.hdr'],'w'); | |
| 133 | |
| 134 fwrite(fidH,header.HdrFileSize,'int32',header.ByteOrder); % HdrFileSize | |
| 135 fwrite(fidH,repmat(' ',1,10),'char',header.ByteOrder); % HdrDataType | |
| 136 fwrite(fidH,repmat(' ',1,18),'char',header.ByteOrder); % DatabaseName | |
| 137 fwrite(fidH,zeros(1,1,'int32'),'int32',header.ByteOrder); % Extents | |
| 138 fwrite(fidH,zeros(1,1,'int16'),'int16',header.ByteOrder); % SessionError | |
| 139 fwrite(fidH,'r','char',header.ByteOrder); % Regular | |
| 140 fwrite(fidH,repmat(' ',1,1),'char',header.ByteOrder); % unused | |
| 141 fwrite(fidH,zeros(1,1,'int16'),'int16',header.ByteOrder); % unused | |
| 142 fwrite(fidH,header.Dimensions(1),'int16',header.ByteOrder); % Dimensions(1) | |
| 143 fwrite(fidH,header.Dimensions(2),'int16',header.ByteOrder); % Dimensions(2) | |
| 144 fwrite(fidH,header.Dimensions(3),'int16',header.ByteOrder); % Dimensions(3) | |
| 145 fwrite(fidH,header.Dimensions(4),'int16',header.ByteOrder); % Dimensions(4) | |
| 146 fwrite(fidH,zeros(1,3,'int16'),'int16',header.ByteOrder); % unused | |
| 147 fwrite(fidH,header.VoxelUnits,'char',header.ByteOrder); % VoxelUnits | |
|
739
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
148 |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
149 if (isfield(header,'CalibrationUnits')) % CalibrationUnits |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
150 fwrite(fidH,sprintf('%-8s',header.CalibrationUnits(1:min([8,numel(header.CalibrationUnits)]))),'char',header.ByteOrder); |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
151 else |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
152 fwrite(fidH,repmat(' ',1,8),'char',header.ByteOrder); |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
153 end |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
154 |
| 641 | 155 fwrite(fidH,zeros(1,1,'int16'),'int16',header.ByteOrder); % unused |
| 156 fwrite(fidH,DataTypeLabel,'int16',header.ByteOrder); % ImgDataType | |
| 157 fwrite(fidH,header.BitDepth,'int16',header.ByteOrder); % BitDepth | |
| 158 fwrite(fidH,zeros(1,1,'int16'),'int16',header.ByteOrder); % unused | |
| 159 fwrite(fidH,zeros(1,1,'single'),'float',header.ByteOrder); % unused | |
| 160 fwrite(fidH,header.PixelDimensions(1),'float',header.ByteOrder); % PixelDimensions(1) | |
| 161 fwrite(fidH,header.PixelDimensions(2),'float',header.ByteOrder); % PixelDimensions(2) | |
| 162 fwrite(fidH,header.PixelDimensions(3),'float',header.ByteOrder); % PixelDimensions(3) | |
| 163 fwrite(fidH,zeros(1,4,'single'),'float',header.ByteOrder); % unused | |
| 164 fwrite(fidH,zeros(1,1,'single'),'float',header.ByteOrder); % VoxelOffset | |
| 165 fwrite(fidH,zeros(1,3,'single'),'float',header.ByteOrder); % unused | |
| 166 fwrite(fidH,zeros(1,1,'single'),'float',header.ByteOrder); % CalibrationMax | |
| 167 fwrite(fidH,zeros(1,1,'single'),'float',header.ByteOrder); % CalibrationMin | |
| 168 fwrite(fidH,zeros(1,1,'single'),'float',header.ByteOrder); % Compressed | |
| 169 fwrite(fidH,zeros(1,1,'single'),'float',header.ByteOrder); % Verified | |
| 170 fwrite(fidH,header.GlobalMax,'int32',header.ByteOrder); % GlobalMax | |
| 171 fwrite(fidH,header.GlobalMin,'int32',header.ByteOrder); % GlobalMin | |
| 172 fwrite(fidH,header.Descriptor,'char',header.ByteOrder); % Descriptor | |
| 173 fwrite(fidH,'none ','char',header.ByteOrder); % AuxFile | |
| 174 fwrite(fidH,repmat(' ',1,1),'char',header.ByteOrder); % Orientation | |
| 175 fwrite(fidH,repmat(' ',1,10),'char',header.ByteOrder); % Originator | |
| 176 fwrite(fidH,repmat(' ',1,10),'char',header.ByteOrder); % Generated | |
| 177 fwrite(fidH,repmat(' ',1,10),'char',header.ByteOrder); % Scannumber | |
| 178 | |
| 643 | 179 if (isfield(header,'PatientID')) % PatientID |
|
739
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
180 fwrite(fidH,sprintf('%-10s',header.PatientID(1:min([10,numel(header.PatientID)]))),'char',header.ByteOrder); |
| 641 | 181 else |
| 182 fwrite(fidH,repmat(' ',1,10),'char',header.ByteOrder); | |
| 183 end | |
| 184 | |
| 643 | 185 if (isfield(header,'ExposureDate')) % ExposureDate |
|
739
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
186 fwrite(fidH,sprintf('%-10s',header.ExposureDate(1:min([10,numel(header.ExposureDate)]))),'char',header.ByteOrder); |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
187 elseif (isfield(header,'StudyDate')) |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
188 fwrite(fidH,sprintf('%-10s',header.StudyDate(1:min([10,numel(header.StudyDate)]))),'char',header.ByteOrder); |
| 641 | 189 else |
| 190 fwrite(fidH,repmat(' ',1,10),'char',header.ByteOrder); | |
| 191 end | |
| 192 | |
| 643 | 193 if (isfield(header,'ExposureTime')) % ExposureTime |
|
739
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
194 fwrite(fidH,sprintf('%-10s',header.ExposureTime(1:min([10,numel(header.ExposureTime)]))),'char',header.ByteOrder); |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
195 elseif (isfield(header,'StudyTime')) |
|
df3accfcddb8
analyze75write: Write CalibrationUnits to header if that information is provided in the input. Also, ensure all char entries in the header are left justified.
adam78a
parents:
647
diff
changeset
|
196 fwrite(fidH,sprintf('%-10s',header.StudyTime(1:min([10,numel(header.StudyTime)]))),'char',header.ByteOrder); |
| 641 | 197 else |
| 198 fwrite(fidH,repmat(' ',1,10),'char',header.ByteOrder); | |
| 199 end | |
| 200 | |
| 201 fwrite(fidH,repmat(' ',1,3),'char',header.ByteOrder); % unused | |
| 202 fwrite(fidH,zeros(1,1,'int32'),'int32',header.ByteOrder); % Views | |
| 203 fwrite(fidH,zeros(1,1,'int32'),'int32',header.ByteOrder); % VolumesAdded | |
| 204 fwrite(fidH,zeros(1,1,'int32'),'int32',header.ByteOrder); % StartField | |
| 205 fwrite(fidH,zeros(1,1,'int32'),'int32',header.ByteOrder); % FieldSkip | |
| 206 fwrite(fidH,zeros(1,1,'int32'),'int32',header.ByteOrder); % OMax | |
| 207 fwrite(fidH,zeros(1,1,'int32'),'int32',header.ByteOrder); % OMin | |
| 208 fwrite(fidH,zeros(1,1,'int32'),'int32',header.ByteOrder); % SMax | |
| 209 fwrite(fidH,zeros(1,1,'int32'),'int32',header.ByteOrder); % SMin | |
| 210 | |
| 211 fclose(fidH); | |
| 212 | |
| 213 % Write the .img file | |
| 214 fidI = fopen([fileprefix,'.img'],'w'); | |
| 215 fwrite(fidI,data,DataTypeString,header.ByteOrder); | |
| 216 fclose(fidI); | |
| 217 | |
| 218 end | |
| 219 | |
| 220 | |
| 221 function [datanew,znew] = interpslices(data,x,y,z) | |
| 222 znew = z(1):min(diff(z)):z(end); | |
|
645
cc81e4acc53c
analyze75write: Now write int16 and int32 datasets correctly.
adam78a
parents:
643
diff
changeset
|
223 datanew = zeros(numel(x),numel(y),numel(znew),class(data)); |
| 641 | 224 for loopN = 1:numel(znew) |
| 225 datanew(:,:,loopN) = interpn(x,y,z,data,x,y,znew(loopN)); | |
| 226 end | |
| 227 end |