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[DOC] Improve doc example out stats (#1014)
* improve doc example out stats * [DATALAD] Recorded changes * parametrize tests
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‎docs/source/output_files.md‎

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@@ -124,3 +124,160 @@ bidspm-stats
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│   └── sub-blnd01_task-taskName_run-*_onsets.tsv --------------------------
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...
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```
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```
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outputs/derivatives/bidspm-stats
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├── CHANGES
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├── dataset_description.json
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├── derivatives
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│   └── bidspm-groupStats
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│   ├── CHANGES
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│   ├── dataset_description.json
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│   ├── jobs
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│   │   └── <taskLabel>
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│   │   └── group
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│   │   ├── batch_contrasts_rfx_2023-05-06T12-49.json
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│   │   ├── batch_contrasts_rfx_2023_05_06T12_49.m
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│   │   ├── batch_group_level_model_specification_estimation_2023-05-06T12-49.json
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│   │   └── batch_group_level_model_specification_estimation_2023_05_06T12_49.m
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│   ├── LICENSE
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│   ├── README.md
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│   ├── sub-ALL_task-<taskLabel>_space-<spaceLabel>_FWHM-6_conFWHM-0_node-dataset_contrast-<taskLabel>
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│   │   ├── beta_0001.nii
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│   │   ├── con_0001.nii
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│   │   ├── mask.nii
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│   │   ├── ResMS.nii
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│   │   ├── RPV.nii
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│   │   ├── SPM.mat
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│   │   ├── spmT_0001.nii
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│   │   ├── task-<taskLabel>_space-<spaceLabel>_desc-afterEstimation_designmatrix.png
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│   │   └── task-<taskLabel>_space-<spaceLabel>_desc-beforeEstimation_designmatrix.png
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│   └── sub-ALL_task-<taskLabel>_space-<spaceLabel>_FWHM-6_conFWHM-6_node-dataset_contrast-<taskLabel>
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│   ├── beta_0001.nii
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│   ├── con_0001.nii
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│   ├── mask.nii
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│   ├── ResMS.nii
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│   ├── RPV.nii
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│   ├── SPM.mat
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│   ├── spmT_0001.nii
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│   ├── task-<taskLabel>_space-<spaceLabel>_desc-afterEstimation_designmatrix.png
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│   └── task-<taskLabel>_space-<spaceLabel>_desc-beforeEstimation_designmatrix.png
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├── jobs
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│   └── <taskLabel>
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│   ├── group
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│   │   ├── batch_smooth_con_FWHM-6_task-<taskLabel>_2023-05-06T12-49.json
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│   │   └── batch_smooth_con_FWHM_6_task_<taskLabel>_2023_05_06T12_49.m
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│   ├── sub-292
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│   │   ├── batch_contrasts_ffx_task-<taskLabel>_space-<spaceLabel>_FWHM-6_2023-05-06T12-43.json
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│   │   ├── batch_contrasts_ffx_task_<taskLabel>_space_<spaceLabel>_FWHM_6_2023_05_06T12_43.m
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│   │   ├── batch_specifyAndEstimate_ffx_task-<taskLabel>_space-<spaceLabel>_FWHM-6_2023-05-06T12-35.json
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│   │   └── batch_specifyAndEstimate_ffx_task_<taskLabel>_space_<spaceLabel>_FWHM_6_2023_05_06T12_35.m
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│   ├── sub-302
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│   └── sub-307
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├── LICENSE
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├── README.md
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├── reports
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│   ├── bidspm.bib
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│   └── stats_model-default_es_model_citation.md
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├── sub-292
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│   └── task-<taskLabel>_space-<spaceLabel>_FWHM-6
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│   ├── beta_0001.nii
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│   ├── beta_0002.nii
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│   ├── ...
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│   ├── beta_0060.nii
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│   ├── con_0001.nii
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│   ├── con_0002.nii
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│   ├── con_0003.nii
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│   ├── con_0004.nii
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│   ├── con_0005.nii
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│   ├── con_0006.nii
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│   ├── mask.nii
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│   ├── ResMS.nii
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│   ├── RPV.nii
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│   ├── s6con_0001.nii
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│   ├── s6con_0002.nii
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│   ├── s6con_0003.nii
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│   ├── s6con_0004.nii
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│   ├── s6con_0005.nii
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│   ├── s6con_0006.nii
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│   ├── SPM.mat
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│   ├── spmT_0001.nii
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│   ├── spmT_0002.nii
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│   ├── spmT_0003.nii
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│   ├── spmT_0004.nii
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│   ├── spmT_0005.nii
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│   ├── spmT_0006.nii
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│   ├── sub-292_ses-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.mat
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│   ├── sub-292_ses-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.tsv
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│   ├── sub-292_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.mat
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│   ├── sub-292_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.tsv
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│   ├── sub-292_task-<taskLabel>_space-<spaceLabel>_desc-afterEstimation_designmatrix.png
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│   └── sub-292_task-<taskLabel>_space-<spaceLabel>_desc-beforeEstimation_designmatrix.png
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├── sub-302
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│   └── task-<taskLabel>_space-<spaceLabel>_FWHM-6
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│   ├── beta_0001.nii
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│   ├── beta_0002.nii
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│   ├── ...
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│   ├── beta_0154.nii
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│   ├── con_0001.nii
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│   ├── con_0002.nii
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│   ├── con_0003.nii
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│   ├── mask.nii
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│   ├── ResMS.nii
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│   ├── RPV.nii
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│   ├── s6con_0001.nii
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│   ├── s6con_0002.nii
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│   ├── s6con_0003.nii
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│   ├── SPM.mat
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│   ├── spmT_0001.nii
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│   ├── spmT_0002.nii
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│   ├── spmT_0003.nii
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│   ├── sub-302_ses-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.mat
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│   ├── sub-302_ses-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.tsv
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│   ├── sub-302_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.mat
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│   ├── sub-302_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.tsv
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│   ├── sub-302_task-<taskLabel>_space-<spaceLabel>_desc-afterEstimation_designmatrix.png
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│   └── sub-302_task-<taskLabel>_space-<spaceLabel>_desc-beforeEstimation_designmatrix.png
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└── sub-307
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└── task-<taskLabel>_space-<spaceLabel>_FWHM-6
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├── beta_0001.nii
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├── beta_0002.nii
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├── ...
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├── beta_0237.nii
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├── con_0001.nii
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├── con_0002.nii
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├── con_0003.nii
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├── con_0004.nii
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├── con_0005.nii
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├── con_0006.nii
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├── con_0007.nii
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├── con_0008.nii
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├── mask.nii
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├── ResMS.nii
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├── RPV.nii
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├── s6con_0001.nii
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├── s6con_0002.nii
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├── s6con_0003.nii
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├── s6con_0004.nii
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├── s6con_0005.nii
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├── s6con_0006.nii
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├── s6con_0007.nii
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├── s6con_0008.nii
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├── SPM.mat
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├── spmT_0001.nii
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├── spmT_0002.nii
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├── spmT_0003.nii
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├── spmT_0004.nii
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├── spmT_0005.nii
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├── spmT_0006.nii
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├── spmT_0007.nii
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├── spmT_0008.nii
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├── sub-307_ses-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.mat
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├── sub-307_ses-<sesLabel>_task-<taskLabel>_run-01_desc-confounds_regressors.tsv
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├── sub-307_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.mat
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├── sub-307_ses-<sesLabel>_task-<taskLabel>_run-01_onsets.tsv
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├── sub-307_task-<taskLabel>_space-<spaceLabel>_desc-afterEstimation_designmatrix.png
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└── sub-307_task-<taskLabel>_space-<spaceLabel>_desc-beforeEstimation_designmatrix.png
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```

‎src/reports/boilerplate_stats.mustache‎

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@@ -43,8 +43,7 @@ to censor any time points flagged as outlier,
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{{/confounds}}.
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{{#smoothing}}
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Contrast images were computed for the following condition and spatially smoothed
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using a 3D gaussian kernel (FWHM = {{fwhm.contrast}} mm).
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Contrast images were spatially smoothed using a 3D gaussian kernel (FWHM = {{fwhm.contrast}} mm).
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{{/smoothing}}
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{{! TODO Table of conditions with duration of each event}}
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‎tests/tests_reports/test_boilerplate.m‎

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function test_boilerplate_spatial_preproc()
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% GIVEN
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useUnwarp = {true, false};
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space = { {'individual'}, ...
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{'individual', 'IXI549Space'} };
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19-
opt = setOptions('MoAE-preproc');
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for iUseUnwarp = 1:2
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for iSpace = 1:numel(space)
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for fwhm = [0, 6]
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for dummy_scans = [0, 4]
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21-
filter = opt.bidsFilterFile.bold;
22-
filter.task = opt.taskName;
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printTestParameters(mfilename(), ...
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dummy_scans, ...
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space{iSpace}, ...
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useUnwarp{iUseUnwarp}, ...
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fwhm);
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24-
opt.stc.referenceSlice = 32;
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outputPath = tempName();
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opt.dummy_scans = 4;
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opt = setOptions('MoAE-preproc');
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% opt.space = {'individual'};
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opt.stc.referenceSlice = 32;
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30-
% opt.realign.useUnwarp = false;
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opt.dummy_scans = dummy_scans;
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opt.space = space{iSpace};
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opt.realign.useUnwarp = useUnwarp{iUseUnwarp};
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opt.fwhm.func = fwhm;
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% opt.fwhm.func = 0;
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outputFile = boilerplate(opt, ...
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'outputPath', outputPath, ...
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'pipelineType', 'preproc', ...
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'partialsPath', partialsPath(), ...
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'verbosity', 0);
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34-
outputFile = boilerplate(opt, ...
35-
'outputPath', pwd, ...
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'pipelineType', 'preproc', ...
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'partialsPath', partialsPapth(), ...
38-
'verbosity', 0);
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assertEqual(exist(outputFile, 'file'), 2);
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40-
assertEqual(exist(outputFile, 'file'), 2);
41-
delete(outputFile);
42-
delete('bidspm.bib');
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end
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end
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end
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end
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4459
end
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function test_boilerplate_spatial_subject_glm()
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48-
% GIVEN
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desginTypes = {'block', 'event'};
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for fwhm = [0, 6]
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for i = 1:numel(desginTypes)
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50-
opt = setOptions('facerep');
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outputPath = tempName();
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opt.fwhm.contrast = 0;
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opt = setOptions('facerep');
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opt.designType = 'block';
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opt.fwhm.contrast = fwhm;
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outputFile = boilerplate(opt, ...
57-
'outputPath', pwd, ...
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'pipelineType', 'stats', ...
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'partialsPath', partialsPapth(), ...
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'verbosity', 0);
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opt.designType = desginTypes{i};
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62-
assertEqual(exist(outputFile, 'file'), 2);
63-
delete(outputFile);
64-
delete('bidspm.bib');
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outputFile = boilerplate(opt, ...
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'outputPath', outputPath, ...
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'pipelineType', 'stats', ...
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'partialsPath', partialsPath(), ...
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'verbosity', 0);
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82+
assertEqual(exist(outputFile, 'file'), 2);
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end
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end
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6687
end
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function value = partialsPapth()
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function value = partialsPath()
6990
value = fullfile(returnRootDir(), 'src', 'reports', 'partials');
7091
end
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function pth = tempName()
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pth = tempname();
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mkdir(pth);
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end

‎tests/utils/printTestParameters.m‎

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function printTestParameters(varargin)
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%
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% prints the parameters used for a test
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%
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% USAGE::
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%
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% printTestParameters('test_boilerplate', 0, {'individual'}, true, 0)
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%
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10+
% (C) Copyright 2023 bidspm developers
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args = sanitize(varargin{:});
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pattern = ['\t%s: ', ...
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strjoin(repmat({'%s'}, 1, numel(args) - 1), ' / '), ...
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'\n'];
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fprintf(1, pattern, args{:});
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end
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function args = sanitize(varargin)
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% turn all inputs into a cellstr
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args = {};
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for i = 1:numel(varargin)
25+
if iscell(varargin{i})
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tmp = sanitize(varargin{i}{:});
27+
tmp = ['{' strjoin(tmp, ', ') '}'];
28+
args{end + 1} = tmp; %#ok<*AGROW>
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else
30+
args{end + 1} = stringify(varargin{i});
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end
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end
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end
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function out = stringify(in)
36+
if ischar(in)
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out = in;
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return
39+
end
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if isnumeric(in)
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out = num2str(in);
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return
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end
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if islogical(in)
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if in
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out = 'true';
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else
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out = 'false';
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end
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return
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end
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out = in;
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end

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