Add missing entities to outputs (#114)

Author: tsalo

src/fmripost_aroma/data/io_spec.json

@@ -173,13 +173,14 @@
         }
       ],
     "patterns": [
-        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_desc-{desc}]_{suffix<bold|boldref|dseg|mask>}.{extension<nii|nii.gz|json>|nii.gz}",
-        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<nii|nii.gz|json>|nii.gz}",
-        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<tsv|json>|tsv}",
-        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_part-{part}][_desc-{desc}]_{suffix<metrics>}.{extension<tsv|json>|tsv}",
-        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_part-{part}][_desc-{desc}]_{suffix<timeseries>}.{extension<tsv|json>}",
-        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_hemi-{hemi}][_space-{space}][_res-{res}][_den-{density}][_label-{label}][_desc-{desc}]_{suffix<|boldref|dseg|mask>}.{extension<dtseries.nii|dtseries.json>}",
-        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
-        "sub-{subject}[/ses-{session}]/{datatype<func|figures>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing|bold>}.{extension<svg|html>|svg}"
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_chunk-{chunk}][_space-{space}][_res-{res}][_desc-{desc}]_{suffix<bold|boldref|dseg|mask>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_chunk-{chunk}][_space-{space}][_cohort-{cohort}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<mixing>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_chunk-{chunk}][_space-{space}][_cohort-{cohort}][_res-{res}][_stat-{statistic}][_thresh-{threshold}][_desc-{desc}]_{suffix<components>}.{extension<nii|nii.gz|json>|nii.gz}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_chunk-{chunk}][_space-{space}][_cohort-{cohort}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing>}.{extension<tsv|json>|tsv}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_chunk-{chunk}][_desc-{desc}]_{suffix<metrics>}.{extension<tsv|json>|tsv}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_chunk-{chunk}][_desc-{desc}]_{suffix<timeseries>}.{extension<tsv|json>}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_chunk-{chunk}][_hemi-{hemi}][_space-{space}][_cohort-{cohort}][_res-{res}][_den-{density}][_label-{label}][_desc-{desc}]_{suffix<|boldref|dseg|mask>}.{extension<dtseries.nii|dtseries.json>}",
+        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_chunk-{chunk}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}.{extension<txt|h5>}",
+        "sub-{subject}[/ses-{session}]/{datatype<func|figures>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_chunk-{chunk}][_space-{space}][_cohort-{cohort}][_res-{res}][_stat-{statistic}][_desc-{desc}]_{suffix<components|mixing|bold>}.{extension<svg|html>|svg}"
     ]
 }

src/fmripost_aroma/tests/data/test_ds005115_deriv_and_raw_outputs.txt

@@ -6,8 +6,8 @@ sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.json
 sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.tsv
 sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_timeseries.tsv
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-aggrDenoised_bold.nii.gz
-sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_components.nii.gz
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_mixing.tsv
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-orthaggrDenoised_bold.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_thresh-0p5_desc-melodic_components.nii.gz
 sub-01.html

src/fmripost_aroma/tests/data/test_ds005115_deriv_only_outputs.txt

@@ -6,8 +6,8 @@ sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.json
 sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.tsv
 sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_timeseries.tsv
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-aggrDenoised_bold.nii.gz
-sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_components.nii.gz
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_mixing.tsv
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-orthaggrDenoised_bold.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_thresh-0p5_desc-melodic_components.nii.gz
 sub-01.html

src/fmripost_aroma/tests/data/test_ds005115_resampling_and_raw_outputs.txt

@@ -6,8 +6,8 @@ sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.json
 sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_metrics.tsv
 sub-01/ses-01/func/sub-01_ses-01_task-rest_desc-aroma_timeseries.tsv
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-aggrDenoised_bold.nii.gz
-sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_components.nii.gz
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-melodic_mixing.tsv
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-nonaggrDenoised_bold.nii.gz
 sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_desc-orthaggrDenoised_bold.nii.gz
+sub-01/ses-01/func/sub-01_ses-01_task-rest_space-MNI152NLin6Asym_res-2_thresh-0p5_desc-melodic_components.nii.gz
 sub-01.html

src/fmripost_aroma/workflows/aroma.py

@@ -296,6 +296,7 @@ def init_ica_aroma_wf(
             source_file=bold_file,
             compress=True,
             datatype='func',
+            threshold='0p5',
             desc='melodic',
             suffix='components',
         ),