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[MAINT] lint with miss hit #30

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[MAINT] lint with miss hit #30

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439524a
lint
Remi-Gau Nov 8, 2023
be2f7fd
set line length to 110
Remi-Gau Nov 8, 2023
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26 changes: 26 additions & 0 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,32 @@ repos:
- id: check-merge-conflict


- repo: local

hooks:
- id: mh_style
name: mh_style
entry: mh_style
args: [--process-slx, --fix]
files: ^(.*\.(m|slx))$
language: python
additional_dependencies: [miss_hit_core]

- id: mh_metric
name: mh_metric
entry: mh_metric
args: [--ci]
files: ^(.*\.(m|slx))$
language: python
additional_dependencies: [miss_hit_core]

- id: mh_lint
name: mh_lint
entry: mh_lint
files: ^(.*\.(m|slx))$
language: python
additional_dependencies: [miss_hit]

- repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
rev: 0.2.3
hooks:
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20 changes: 20 additions & 0 deletions miss_hit.cfg
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@@ -0,0 +1,20 @@
project_root

octave: true

# style guide (https://florianschanda.github.io/miss_hit/style_checker.html)
line_length: 110

# camelCase
regex_script_name: "[a-zA-Z0-9]+(_[a-zA-Z0-9]*)*"

suppress_rule: "naming_parameters"
suppress_rule: "copyright_notice"

tab_width: 4

# metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
metric "cnest": limit 4
metric "file_length": limit 500
metric "cyc": limit 47
metric "parameters": limit 5
28 changes: 15 additions & 13 deletions pipeline_group.m
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Original file line number Diff line number Diff line change
@@ -1,16 +1,18 @@
%==========================================================================
% ==========================================================================
% C O N F I G U R A T I O N F I L E : G R O U P
%==========================================================================
% ==========================================================================

% Available variables: BIDS and BIDS_App

%==========================================================================
%-Structural mean image
%==========================================================================
a = spm_select('FPListRec',BIDS_App.outdir,'wm.*_T1w.nii');
if isempty(a), error('Cannot find preprocessed T1-weighted images.'); end
% ==========================================================================
% -Structural mean image
% ==========================================================================
a = spm_select('FPListRec', BIDS_App.outdir, 'wm.*_T1w.nii');
if isempty(a)
error('Cannot find preprocessed T1-weighted images.');
end

clear matlabbatch
clear matlabbatch;

matlabbatch{1}.spm.util.imcalc.input = cellstr(a);
matlabbatch{1}.spm.util.imcalc.output = 'meanT1w.nii';
Expand All @@ -19,9 +21,9 @@
matlabbatch{1}.spm.util.imcalc.options.dmtx = 1;
matlabbatch{1}.spm.util.imcalc.options.dtype = 4;

[~,prov] = spm_jobman('run',matlabbatch);
[~, prov] = spm_jobman('run', matlabbatch);

%==========================================================================
%-Second Level fMRI
%==========================================================================
%fprintf('Nothing to do at fMRI second level.\n');
% ==========================================================================
% -Second Level fMRI
% ==========================================================================
% fprintf('Nothing to do at fMRI second level.\n');
57 changes: 30 additions & 27 deletions pipeline_participant.m
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
%==========================================================================
% ==========================================================================
% C O N F I G U R A T I O N F I L E : P A R T I C I P A N T
%==========================================================================
% ==========================================================================

% Available variables: BIDS and BIDS_App

%==========================================================================
%-fMRI Preprocessing
%==========================================================================
% ==========================================================================
% -fMRI Preprocessing
% ==========================================================================
% ask for: slice timing correction (before or after realign)
% ask for: fieldmap
% ask for: realign and unwarp
Expand All @@ -18,48 +18,51 @@
vox_func = [3 3 3];
FWHM = [12 12 12];

f = spm_BIDS(BIDS,'data', 'modality','func', 'type','bold');
if isempty(f), error('Cannot find BOLD time series.'); end
a = spm_BIDS(BIDS,'data', 'modality','anat', 'type','T1w');
if isempty(a), error('Cannot find T1-weighted image.'); end
f = spm_BIDS(BIDS, 'data', 'modality', 'func', 'type', 'bold');
if isempty(f)
error('Cannot find BOLD time series.');
end
a = spm_BIDS(BIDS, 'data', 'modality', 'anat', 'type', 'T1w');
if isempty(a)
error('Cannot find T1-weighted image.');
end

clear matlabbatch
clear matlabbatch;

% Realign
%------------------------------------------------------------------
matlabbatch{1}.spm.spatial.realign.estwrite.data = cellfun(@(x) {{x}},f)';
% ------------------------------------------------------------------
matlabbatch{1}.spm.spatial.realign.estwrite.data = cellfun(@(x) {{x}}, f)';
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.which = [0 1];

% Coregister
%------------------------------------------------------------------
matlabbatch{2}.spm.spatial.coreg.estimate.ref = cellstr(spm_file(f{1},'prefix','mean','number',1));
% ------------------------------------------------------------------
matlabbatch{2}.spm.spatial.coreg.estimate.ref = cellstr(spm_file(f{1}, 'prefix', 'mean', 'number', 1));
matlabbatch{2}.spm.spatial.coreg.estimate.source = cellstr(a);

% Segment
%------------------------------------------------------------------
% ------------------------------------------------------------------
matlabbatch{3}.spm.spatial.preproc.channel.vols = cellstr(a);
matlabbatch{3}.spm.spatial.preproc.channel.write = [0 1];
matlabbatch{3}.spm.spatial.preproc.warp.write = [0 1];

% Normalise: Write
%------------------------------------------------------------------
matlabbatch{4}.spm.spatial.normalise.write.subj.def = cellstr(spm_file(a,'prefix','y_','ext','nii'));
% ------------------------------------------------------------------
matlabbatch{4}.spm.spatial.normalise.write.subj.def = cellstr(spm_file(a, 'prefix', 'y_', 'ext', 'nii'));
matlabbatch{4}.spm.spatial.normalise.write.subj.resample = cellstr(f);
matlabbatch{4}.spm.spatial.normalise.write.woptions.vox = vox_func;

matlabbatch{5}.spm.spatial.normalise.write.subj.def = cellstr(spm_file(a,'prefix','y_','ext','nii'));
matlabbatch{5}.spm.spatial.normalise.write.subj.resample = cellstr(spm_file(a,'prefix','m','ext','nii'));
matlabbatch{5}.spm.spatial.normalise.write.subj.def = cellstr(spm_file(a, 'prefix', 'y_', 'ext', 'nii'));
matlabbatch{5}.spm.spatial.normalise.write.subj.resample = cellstr(spm_file(a, 'prefix', 'm', 'ext', 'nii'));
matlabbatch{5}.spm.spatial.normalise.write.woptions.vox = vox_anat;

% Smooth
%------------------------------------------------------------------
matlabbatch{6}.spm.spatial.smooth.data = cellstr(spm_file(f,'prefix','w'));
% ------------------------------------------------------------------
matlabbatch{6}.spm.spatial.smooth.data = cellstr(spm_file(f, 'prefix', 'w'));
matlabbatch{6}.spm.spatial.smooth.fwhm = FWHM;

[~,prov] = spm_jobman('run',matlabbatch);
[~, prov] = spm_jobman('run', matlabbatch);


%==========================================================================
%-First Level fMRI
%==========================================================================
%fprintf('Nothing to do at fMRI first level.\n');
% ==========================================================================
% -First Level fMRI
% ==========================================================================
% fprintf('Nothing to do at fMRI first level.\n');
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