basic miss_hit code reformatting

NeuroJSON · Aug 5, 2022 · b89f80c · b89f80c
1 parent 4ce2cca
commit b89f80c
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diff --git a/.miss_hit b/.miss_hit
@@ -0,0 +1,9 @@
+project_root
+
+suppress_rule: "redundant_brackets"
+indent_function_file_body: false
+tab_width: 2
+copyright_location: "file_header"
+copyright_entity: "Qianqian Fang"
+line_length: 100
+octave: true
diff --git a/LICENSE_GPLv3.txt b/LICENSE_GPLv3.txt
@@ -1,26 +1,3 @@
-===============================================================================
-=                      Monte Carlo eXtreme (MCX) -- CUDA                      =
-===============================================================================
-
-Copyright (c) 2010-2019  Qianqian Fang <q.fang at neu.edu>
-
--------------------------------------------------------------------------------
-
-This program 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 3 of the License, or
-(at your option) any later version.
-
-This program 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 for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-------------------------------------------------------------------------
-
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 

diff --git a/loadnifti.m b/loadnifti.m
@@ -4,7 +4,7 @@
 %        or
 %    nii=loadnifti(filename,option)
 %
-%    Read a NIfTI-1/2 (*.nii/.nii.gz) or Analyze 7.5 (*.hdr/*.img/.hdr.gz/.img.gz) 
+%    Read a NIfTI-1/2 (*.nii/.nii.gz) or Analyze 7.5 (*.hdr/*.img/.hdr.gz/.img.gz)
 %    image file.
 %
 %    author: Qianqian Fang (q.fang <at> neu.edu)
@@ -18,4 +18,4 @@
 %    License: Apache 2.0, see https://github.com/fangq/jnifti for details
 %
 
-[varargout{1:nargout}]=nii2jnii(varargin{:});
+[varargout{1:nargout}] = nii2jnii(varargin{:});
diff --git a/memmapstream.m b/memmapstream.m
@@ -1,11 +1,11 @@
-function outstruct=memmapstream(bytes, format, varargin)
+function outstruct = memmapstream(bytes, format, varargin)
 %
 %    outstruct=memmapstream(bytes, format)
 %
 %    Map a byte-array (in char array or uint8/int8 array) into a structure
 %    using a dictionary (format is compatible with memmapfile in MATLAB)
 %
-%    This function is compatible with both MATLAB and GNU Octave. 
+%    This function is compatible with both MATLAB and GNU Octave.
 %
 %    author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -42,40 +42,40 @@
 %    License: Apache 2.0, see https://github.com/fangq/jnifti for details
 %
 
-if(nargin<2)
-   error('must provide bytes and format as inputs');
+if (nargin < 2)
+  error('must provide bytes and format as inputs');
 end
 
-if(~ischar(bytes) && ~isa(bytes,'int8') && ~isa(bytes,'uint8') || isempty(bytes))
-   error('first input, bytes, must be a char-array or uint8/int8 vector');
+if (~ischar(bytes) && ~isa(bytes, 'int8') && ~isa(bytes, 'uint8') || isempty(bytes))
+  error('first input, bytes, must be a char-array or uint8/int8 vector');
 end
 
-if(~iscell(format) || size(format,2)<3 || size(format,1)==0 || ~ischar(format{1,1}))
-   error('second input, format, must be a 3-column cell array, in a format described by the memmapfile Format field.');
+if (~iscell(format) || size(format, 2) < 3 || size(format, 1) == 0 || ~ischar(format{1, 1}))
+  error('second input, format, must be a 3-column cell array, in a format described by the memmapfile Format field.');
 end
 
-bytes=bytes(:)';
+bytes = bytes(:)';
 
-datatype=struct('int8',1,'int16',2,'int32',4,'int64',8,'uint8',1,'uint16',2,'uint32',4,'uint64',8,'single',4,'double',8);
+datatype = struct('int8', 1, 'int16', 2, 'int32', 4, 'int64', 8, 'uint8', 1, 'uint16', 2, 'uint32', 4, 'uint64', 8, 'single', 4, 'double', 8);
 
-opt=varargin2struct(varargin{:});
-opt.usemap=jsonopt('usemap',0,opt) && exist('containers.Map');
+opt = varargin2struct(varargin{:});
+opt.usemap = jsonopt('usemap', 0, opt) && exist('containers.Map');
 
-if(opt.usemap)
-    outstruct=containers.Map();
+if (opt.usemap)
+  outstruct = containers.Map();
 else
-    outstruct=struct();
+  outstruct = struct();
 end
-len=1;
-for i=1:size(format,1)
-    bytelen=datatype.(format{i,1})*prod(format{i,2});
-    if(opt.usemap)
-        outstruct(format{i,3})=reshape(typecast(uint8(bytes(len:bytelen+len-1)),format{i,1}),format{i,2});
-    else
-        outstruct.(format{i,3})=reshape(typecast(uint8(bytes(len:bytelen+len-1)),format{i,1}),format{i,2});
-    end
-    len=len+bytelen;
-    if(len>length(bytes))
-        break;
-    end
+len = 1;
+for i = 1:size(format, 1)
+  bytelen = datatype.(format{i, 1}) * prod(format{i, 2});
+  if (opt.usemap)
+    outstruct(format{i, 3}) = reshape(typecast(uint8(bytes(len:bytelen + len - 1)), format{i, 1}), format{i, 2});
+  else
+    outstruct.(format{i, 3}) = reshape(typecast(uint8(bytes(len:bytelen + len - 1)), format{i, 1}), format{i, 2});
+  end
+  len = len + bytelen;
+  if (len > length(bytes))
+    break
+  end
 end
diff --git a/nifticreate.m b/nifticreate.m
@@ -1,4 +1,4 @@
-function header=nifticreate(img,format)
+function header = nifticreate(img, format)
 %
 %    header=nifticreate(img)
 %       or
@@ -20,31 +20,31 @@
 %    License: Apache 2.0, see https://github.com/fangq/jnifti for details
 %
 
-if(nargin<2)
-    format='nifti1';
+if (nargin < 2)
+  format = 'nifti1';
 end
 
-datatype=struct('int8',256,'int16',4,'int32',8,'int64',1024,'uint8',2,'uint16',512,'uint32',768,'uint64',1280,'single',16,'double',64);
+datatype = struct('int8', 256, 'int16', 4, 'int32', 8, 'int64', 1024, 'uint8', 2, 'uint16', 512, 'uint32', 768, 'uint64', 1280, 'single', 16, 'double', 64);
 
-if(strcmp(format,'nifti1'))
-    headerlen=348;
+if (strcmp(format, 'nifti1'))
+  headerlen = 348;
 else
-    headerlen=540;
+  headerlen = 540;
 end
 
-header=memmapstream(uint8(zeros(1,headerlen+4)),niiformat(format));
-header.sizeof_hdr=cast(headerlen, class(header.sizeof_hdr));
-header.datatype=cast(datatype.(class(img)), class(header.datatype));
-header.dim(1:end)=cast(1,class(header.dim));
-header.dim(1:ndims(img)+1)=cast([ndims(img),size(img)], class(header.dim));
-header.pixdim(1:ndims(img)+1)=cast(1, class(header.pixdim));
-header.vox_offset=cast(headerlen+4, class(header.vox_offset));
-if(header.sizeof_hdr==540)
-    header.magic(1:3)=cast('ni2',class(header.magic));
+header = memmapstream(uint8(zeros(1, headerlen + 4)), niiformat(format));
+header.sizeof_hdr = cast(headerlen, class(header.sizeof_hdr));
+header.datatype = cast(datatype.(class(img)), class(header.datatype));
+header.dim(1:end) = cast(1, class(header.dim));
+header.dim(1:ndims(img) + 1) = cast([ndims(img), size(img)], class(header.dim));
+header.pixdim(1:ndims(img) + 1) = cast(1, class(header.pixdim));
+header.vox_offset = cast(headerlen + 4, class(header.vox_offset));
+if (header.sizeof_hdr == 540)
+  header.magic(1:3) = cast('ni2', class(header.magic));
 else
-    header.magic(1:3)=cast('ni1',class(header.magic));
+  header.magic(1:3) = cast('ni1', class(header.magic));
 end
-header.srow_x(1)=cast(1, class(header.srow_x));
-header.srow_y(2)=cast(1, class(header.srow_y));
-header.srow_z(3)=cast(1, class(header.srow_z));
-header.sform_code=cast(1, class(header.sform_code));
+header.srow_x(1) = cast(1, class(header.srow_x));
+header.srow_y(2) = cast(1, class(header.srow_y));
+header.srow_z(3) = cast(1, class(header.srow_z));
+header.sform_code = cast(1, class(header.sform_code));
diff --git a/niftiinfo.m b/niftiinfo.m
@@ -17,99 +17,98 @@
 %% @deftypefn  {Function File} {} niftiinfo (@var{filename})
 %% Read the metadata from a NIfTI-1/2 and Analyze7.5 formatted image file
 %%
-%% Parsing the metadata in a NIfTI-1/2 file or a two-part NIfTI 
-%% or Analyze7.5 header file specified by @var{filename}. The 
+%% Parsing the metadata in a NIfTI-1/2 file or a two-part NIfTI
+%% or Analyze7.5 header file specified by @var{filename}. The
 %% accepted file suffixes include .nii, .nii.gz, .hdr, and .hdr.gz.
 %%
 %% @seealso{niftiread, niftiwrite}
 %% @end deftypefn
 
 function nii = niftiinfo (filename, varargin)
 
-if(nargin<1)
-    error('must provide the file name');
+if (nargin < 1)
+  error('must provide the file name');
 end
 
 try
-    header=nii2jnii(filename,'niiheader');
+  header = nii2jnii(filename, 'niiheader');
 
-    fileinfo=dir(filename);
-    nii=struct('Filename',which(filename),...
-               'Filemoddate',fileinfo.date,...
-               'Filesize',fileinfo.bytes,...
-               'Version','NIfTI1',...
-               'Description',deblank(char(header.hdr.descrip)),...
-               'ImageSize',header.hdr.dim(2:header.hdr.dim(1)+1),...
-               'PixelDimensions',header.hdr.pixdim(2:header.hdr.dim(1)+1),...
-               'Datatype',header.datatype,...
-               'BitsPerPixel',header.hdr.bitpix,...
-               'SpaceUnits',niicodemap('unit',bitand(header.hdr.xyzt_units, 7)),...
-               'TimeUnits',niicodemap('unit',bitand(header.hdr.xyzt_units, 56)),...
-               'AdditiveOffset',header.hdr.scl_inter,...
-               'MultiplicativeScaling',header.hdr.scl_slope,...
-               'TimeOffset',header.hdr.toffset,...
-               'SliceCode',niicodemap('slicetype',header.hdr.slice_code),...
-               'FrequencyDimension',bitand(header.hdr.dim_info,7),...
-               'PhaseDimension',bitand(bitshift(header.hdr.dim_info,-3),7),...
-               'SpatialDimension',0,...
-               'DisplayIntensityRange',[header.hdr.cal_min,header.hdr.cal_max],...
-               'TransformName',0,...
-               'Transform',0,...
-               'Qfactor',header.hdr.pixdim(1),...
-               'raw',header.hdr ...
-               );
-    if(header.hdr.sizeof_hdr==540)
-        nii.Version='NIfTI2';
-    end
-    if(header.hdr.sform_code>0)
-        nii.TransformName='Sform';
-        Aaffine=[header.hdr.srow_x;header.hdr.srow_y;header.hdr.srow_z]';
-        Aaffine(4,4)=1;
-    elseif(header.hdr.qform_code>0)
-        nii.TransformName='Qform';
-        b=header.hdr.quatern_b;
-        c=header.hdr.quatern_c;
-        d=header.hdr.quatern_d;
-        a=sqrt(1.0-(b*b+c*c+d*d));
-        R=[a*a+b*b-c*c-d*d   2*b*c-2*a*d       2*b*d+2*a*c     
-           2*b*c+2*a*d       a*a+c*c-b*b-d*d   2*c*d-2*a*b     
-           2*b*d-2*a*c       2*c*d+2*a*b       a*a+d*d-c*c-b*b ];
-        if(det(R)==0)
-            Aaffine=[R [nii0.hdr.qoffset_x,nii0.hdr.qoffset_y,nii0.hdr.qoffset_z]']';
-        else
-            Aaffine=[R*diag([header.hdr.pixdim(2:3),header.hdr.pixdim(1)*header.hdr.pixdim(4)]) ...
-                  [nii0.hdr.qoffset_x,nii0.hdr.qoffset_y,nii0.hdr.qoffset_z]']';
-        end
-        Aaffine(4,4)=1;
+  fileinfo = dir(filename);
+  nii = struct('Filename', which(filename), ...
+               'Filemoddate', fileinfo.date, ...
+               'Filesize', fileinfo.bytes, ...
+               'Version', 'NIfTI1', ...
+               'Description', deblank(char(header.hdr.descrip)), ...
+               'ImageSize', header.hdr.dim(2:header.hdr.dim(1) + 1), ...
+               'PixelDimensions', header.hdr.pixdim(2:header.hdr.dim(1) + 1), ...
+               'Datatype', header.datatype, ...
+               'BitsPerPixel', header.hdr.bitpix, ...
+               'SpaceUnits', niicodemap('unit', bitand(header.hdr.xyzt_units, 7)), ...
+               'TimeUnits', niicodemap('unit', bitand(header.hdr.xyzt_units, 56)), ...
+               'AdditiveOffset', header.hdr.scl_inter, ...
+               'MultiplicativeScaling', header.hdr.scl_slope, ...
+               'TimeOffset', header.hdr.toffset, ...
+               'SliceCode', niicodemap('slicetype', header.hdr.slice_code), ...
+               'FrequencyDimension', bitand(header.hdr.dim_info, 7), ...
+               'PhaseDimension', bitand(bitshift(header.hdr.dim_info, -3), 7), ...
+               'SpatialDimension', 0, ...
+               'DisplayIntensityRange', [header.hdr.cal_min, header.hdr.cal_max], ...
+               'TransformName', 0, ...
+               'Transform', 0, ...
+               'Qfactor', header.hdr.pixdim(1), ...
+               'raw', header.hdr ...
+              );
+  if (header.hdr.sizeof_hdr == 540)
+    nii.Version = 'NIfTI2';
+  end
+  if (header.hdr.sform_code > 0)
+    nii.TransformName = 'Sform';
+    Aaffine = [header.hdr.srow_x; header.hdr.srow_y; header.hdr.srow_z]';
+    Aaffine(4, 4) = 1;
+  elseif (header.hdr.qform_code > 0)
+    nii.TransformName = 'Qform';
+    b = header.hdr.quatern_b;
+    c = header.hdr.quatern_c;
+    d = header.hdr.quatern_d;
+    a = sqrt(1.0 - (b * b + c * c + d * d));
+    R = [a * a + b * b - c * c - d * d   2 * b * c - 2 * a * d       2 * b * d + 2 * a * c
+         2 * b * c + 2 * a * d       a * a + c * c - b * b - d * d   2 * c * d - 2 * a * b
+         2 * b * d - 2 * a * c       2 * c * d + 2 * a * b       a * a + d * d - c * c - b * b];
+    if (det(R) == 0)
+      Aaffine = [R [nii0.hdr.qoffset_x, nii0.hdr.qoffset_y, nii0.hdr.qoffset_z]']';
     else
-        nii.TransformName='Old';
-        Aaffine=diag(header.hdr.pixdim(2:4));
-        Aaffine(4,4)=1;
+      Aaffine = [R * diag([header.hdr.pixdim(2:3), header.hdr.pixdim(1) * header.hdr.pixdim(4)]) ...
+                 [nii0.hdr.qoffset_x, nii0.hdr.qoffset_y, nii0.hdr.qoffset_z]']';
     end
-    if(exist('Aaffine','var'))
-        if(exist('affine3d'))
-            nii.Transform=affine3d(Aaffine);
-        else
-            nii.Transform=Aaffine;
-        end
+    Aaffine(4, 4) = 1;
+  else
+    nii.TransformName = 'Old';
+    Aaffine = diag(header.hdr.pixdim(2:4));
+    Aaffine(4, 4) = 1;
+  end
+  if (exist('Aaffine', 'var'))
+    if (exist('affine3d'))
+      nii.Transform = affine3d(Aaffine);
     else
-        nii.Transform=diag([1,1,1,1]);
+      nii.Transform = Aaffine;
     end
+  else
+    nii.Transform = diag([1, 1, 1, 1]);
+  end
 catch ME
-    rethrow(ME);
+  rethrow(ME);
 end
 
-endfunction
-
+endfunction;
 
-%!demo
-%! %% Reading a
-%! urlwrite('https://nifti.nimh.nih.gov/nifti-1/data/minimal.nii.gz','minimal.nii.gz')
-%! gunzip ('minimal.nii.gz');
-%! header=niftiinfo('minimal.nii');
+% !demo
+% ! %% Reading a
+% ! urlwrite('https://nifti.nimh.nih.gov/nifti-1/data/minimal.nii.gz','minimal.nii.gz')
+% ! gunzip ('minimal.nii.gz');
+% ! header=niftiinfo('minimal.nii');
 
-%!test
-%! urlwrite('https://nifti.nimh.nih.gov/nifti-1/data/minimal.nii.gz','minimal.nii.gz')
-%! gunzip ('minimal.nii.gz');
-%! header=niftiinfo('minimal.nii');
-%! assert (header.ImageSize,[64 64 10]);
+% !test
+% ! urlwrite('https://nifti.nimh.nih.gov/nifti-1/data/minimal.nii.gz','minimal.nii.gz')
+% ! gunzip ('minimal.nii.gz');
+% ! header=niftiinfo('minimal.nii');
+% ! assert (header.ImageSize,[64 64 10]);