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Established convention for docstrings #145

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Established convention for docstrings #145

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74ece3b
Drafted prototype for header convention
jcohenadad Jun 20, 2020
0eb3323
Minor refactoring
jcohenadad Jun 20, 2020
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51 changes: 39 additions & 12 deletions +imutils/dicom_to_nifti.m
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Original file line number Diff line number Diff line change
@@ -1,14 +1,41 @@
function dicom_to_nifti( unsortedDicomDir, niftiPath )
%DICOM_TO_NIFTI converts dicoms into niftis with dcm2bids output
function dicom_to_nifti(unsortedDicomDir, niftiPath)
%% DICOM_TO_NIFTI converts DICOM data to organized NIfTI files.
%
% This function uses <https://github.com/cbedetti/Dcm2Bids dcm2bids> to
% convert all DICOM files within a directory, into NIfTI
%
% SYNTAX:
%
% dicom_to_nifti(unsortedDicomDir, niftiPath)
%
% dicom_to_nifti( unsortedDicomDir, niftiPath )
% INPUTS:
%
% The input `unsortedDicomDir` is a path to a folder containing either be
% ".dcm" or ".IMA". The input `iftiPath`is a folder for the output.
% unsortedDicomDir (str):
% Path to a folder containing either be ".dcm" or ".IMA".
%
% niftiPath (str):
% Output folder that will enclose the converted NIfTI files.
%
% The output will be niftis in seperate folders according to their
% acquisition names that are in `niftiPath`.

% OUTPUTS:
%
% None
%
% EXAMPLE:
%
% dicom_to_nifti('/home/bob/data_dicom', '/home/bob/data_nii_bids')
%
% DEPENDENCIES:
%
% <https://github.com/cbedetti/Dcm2Bids dcm2bids>
%
% <https://github.com/rordenlab/dcm2niix dcm2niix>
%
% AUTHORS:
%
% Ryan Topfer <[email protected]>
%
% Alexandre D'Astous <[email protected]>
%%
mkdir(niftiPath);
disp(unsortedDicomDir);
disp(niftiPath);
Expand Down Expand Up @@ -109,11 +136,11 @@ function dicom_to_nifti( unsortedDicomDir, niftiPath )
end

end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Local functions
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


function filePath = createConfig(outputDir, acquisitionNumber, acquisitionName, modality)

% Create config for blablabla (to be continued...)

% Create names
name = [acquisitionNumber '_' acquisitionName];
ext = '.json';
Expand Down
14 changes: 8 additions & 6 deletions external/genToolboxHelp.m
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Original file line number Diff line number Diff line change
Expand Up @@ -57,15 +57,16 @@
% August 2015; Last revision: 31-Aug-2015
% Copyright 2014-2015 Johannes Milvich
%------------- BEGIN CODE --------------%

global MAKECONTENTSFILES; MAKECONTENTSFILES = false; % Create Contents.m file within each folder.
global FOLDERHTML; FOLDERHTML = 'html'; % Folder name for output html files.
global PUBLISHSHOWCODE; PUBLISHSHOWCODE = false; % show code in published html

%% 1) Initialisation
% Check inputs - if no ignored folders are specified, only the default ones
% (.git and the Help folder itself) are ignored. By default, the code is not
% evaluated for the published .m files and a searchable database is
% created. Also check if the specified ToolBoxpath exists.
global MAKECONTENTSFILES
MAKECONTENTSFILES = false; % Create Contents.m file within each folder.
global FOLDERHTML
FOLDERHTML = 'html'; % Folder name for output html files.

if nargin<3
IgnoredFolders = {};
Expand Down Expand Up @@ -637,12 +638,13 @@
% email address: [email protected]
% August 2015; Last revision: 31-Aug-2015
% Copyright 2014-2015 Johannes Milvich
global PUBLISHSHOWCODE
help_file_name = strrep(strrep(m_file_name,rootDir,''),'.m','.html');
help_file_name_fp = fullfile(help_folder_name,help_file_name);
if ~exist(help_file_name_fp,'file')
% If a helpfile of that name does not exist yet, directly
% publish it to the right folder
publish(m_file_name, 'format','html','outputDir',help_folder_name,'evalCode',false);
publish(m_file_name, 'format','html','outputDir',help_folder_name,'evalCode',false, 'showCode', PUBLISHSHOWCODE);
status = 1;
else
% If a helpfile of that name already exists, publish to a
Expand All @@ -652,7 +654,7 @@
% keep the old one
tmp_folder = fullfile(help_folder_name,'tmp');
mkdir(tmp_folder);
tmp_help_file_name_fp = publish(m_file_name, 'format','html','outputDir',tmp_folder,'evalCode',false);
tmp_help_file_name_fp = publish(m_file_name, 'format','html','outputDir',tmp_folder,'evalCode',false, 'showCode', PUBLISHSHOWCODE);

[status,~] = system(['fc ' tmp_help_file_name_fp ' ' help_file_name_fp]);
if status
Expand Down