update code

Author: Remi-Gau

init_env.m renamed to init_spm_2_bids.m

@@ -1,4 +1,4 @@
-function init_env
+function init_spm_2_bids
     %
     % 1 - Check if version requirements
     % are satisfied and the packages are
@@ -18,7 +18,7 @@
     OCTAVE_VER = '4.0.3';
     MATLAB_VER = '8.6.0';
 
-    INSTALL_LIST = {'io', 'statistics', 'image'};
+    INSTALL_LIST = {};
 
     if is_octave
 

miss_hit.cfg

@@ -6,7 +6,9 @@ line_length: 100
 regex_function_name: "[a-z]+(_[a-z0-9]+)*"
 regex_class_name: "[A-Z]{1}[a-z]+"
 regex_script_name: "[a-z]+(_[a-z]+)*"
-regex_parameter_name: "[a-z]+(_[a-z0-9]+)*"
+
+# suppress_rule: "naming_parameters" 
+# regex_parameter_name: "[a-z]+(_[a-z0-9]+)*"
 
 exclude_dir: "lib"
 

requirements.txt

@@ -1,4 +1,4 @@
-miss_hit==0.9.26
+miss_hit==0.9.27
 pre-commit
 jupyterlab
 octave_kernel

src/defaults/Mapping.m

@@ -3,28 +3,28 @@
     % Creates a mapping object that will contain the list how an spm file will be renamed
     % into a bids derivatives.
     %
-    % Has the following attributes::
+    % Has the following attributes:
     %
-    %   - mapping : (n X 1) structure with the following fiels
+    %   - mapping, (n X 1) structure with the following fields:
     %
-    %         - prefix
-    %         - suffix
-    %         - entities
-    %         - ext
-    %         - name_spec: structure that must resemble the output of bids.internal.parse_filename
+    %         - ``prefix``
+    %         - ``suffix``
+    %         - ``entities``
+    %         - ``ext``
+    %         - ``name_spec``: structure that must resemble the output of bids.File
     %
-    %   - cfg : describes the common properties to be used for several names in the output.
-    %           See ``check_cfg``
+    %   - cfg describes the common properties to be used for several names in the output.
+    %     (See ``check_cfg()``)
     %
-    %   - list of SPM prefixes from ``get_spm_prefix_list()``
+    %   - list of SPM prefixes from ``get_spm_prefix_list()``:
     %
-    %    - stc = ''
-    %    - realign = ''
-    %    - unwarp = ''
-    %    - coreg = ''
-    %    - bias_cor = ''
-    %    - norm = ''
-    %    - smooth = ''
+    %           - ``stc = ''``
+    %           - ``realign = ''``
+    %           - ``unwarp = ''``
+    %           - ``coreg = ''``
+    %           - ``bias_cor = ''``
+    %           - ``norm = ''``
+    %           - ``smooth = ''``
     %
     % (C) Copyright 2021 spm_2_bids developers
 
@@ -91,7 +91,7 @@
             %  map = add_mapping('prefix', prefix, 'suffix', 'entities', 'ext', 'name_spec')
             %
 
-            % TODO add possibility to pass "filter" arugment that is a structure
+            % TODO add possibility to pass "filter" argument that is a structure
             % with shape (allows to chain the output from bids parsing)
             %
             % filter.prefix

src/defaults/check_cfg.m

@@ -5,7 +5,7 @@
     %
     % USAGE::
     %
-    % cfg = check_cfg(cfg)
+    %   cfg = check_cfg(cfg)
     %
     % :param cfg: structure or json filename containing the spm_2_bids.anat.
     % :type cfg: structure

src/defaults/get_spm_prefix_list.m

@@ -5,7 +5,18 @@
     %
     % (C) Copyright 2021 spm_2_bids developers
 
-    spm_defaults = spm_get_defaults();
+    try
+        spm_defaults = spm_get_defaults();
+    catch
+        spm_defaults.slicetiming.prefix = 's';
+        spm_defaults.realign.write.prefix = 'r';
+        spm_defaults.unwarp.write.prefix = 'u';
+        spm_defaults.coreg.write.prefix = 'r';
+        spm_defaults.deformations.modulate.prefix = 'm';
+        spm_defaults.normalise.write.prefix = 'w';
+        spm_defaults.smooth.prefix = 's';
+    end
+
     prefix_list.stc = spm_defaults.slicetiming.prefix;
     prefix_list.realign = spm_defaults.realign.write.prefix;
     prefix_list.unwarp = spm_defaults.unwarp.write.prefix;

src/spm_2_bids.m

@@ -39,18 +39,18 @@
     % deal with suffixes modified by SPM
     % turns them into prefixes that can be handled by the default mapping
     if strfind(file, '_uw.mat') %#ok<*STRIFCND>
-        file = spm_file(file, 'prefix', 'unwarpparam_');
+        file = bids.internal.file_utils(file, 'prefix', 'unwarpparam_');
         file = strrep(file, '_uw.mat', '.mat');
         use_suffix_as_label = true;
     end
     if strfind(file, '_seg8.mat') %#ok<*STRIFCND>
-        file = spm_file(file, 'prefix', 'segparam_');
+        file = bids.internal.file_utils(file, 'prefix', 'segparam_');
         file = strrep(file, '_seg8.mat', '.mat');
         use_suffix_as_label = true;
     end
 
-    pth = spm_fileparts(file);
-    new_filename = spm_file(file, 'filename');
+    pth = fileparts(file);
+    new_filename = bids.internal.file_utils(file, 'filename');
     json = [];
 
     p = bids.internal.parse_filename(file);

tests/test_spm_2_bids.m

@@ -11,8 +11,9 @@
 function test_spm_2_bids_suffix()
 
     input_output = {
-                    'sub-01_T1w_seg8.mat', 'sub-01_label-T1w_segparam.mat'
-                    'sub-01_task-auditory_bold_uw.mat', 'sub-01_task-auditory_label-bold_unwarpparam.mat'};
+                    'sub-01_T1w_seg8.mat', 'sub-01_label-T1w_segparam.mat'; ...
+                    'sub-01_task-auditory_bold_uw.mat', ...
+                    'sub-01_task-auditory_label-bold_unwarpparam.mat'};
 
     for i = 1:numel(size(input_output, 1))