[ENH] Compress recon derivatives (#787)

PennLINC · Jul 18, 2024 · 83dd70f · 83dd70f
1 parent 6a00f6c
commit 83dd70f
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Showing 5 changed files with 36 additions and 18 deletions.
diff --git a/qsiprep/interfaces/recon_scalars.py b/qsiprep/interfaces/recon_scalars.py
@@ -106,6 +106,7 @@ class _ReconScalarsDataSinkInputSpec(BaseInterfaceInputSpec):
     base_directory = File()
     resampled_files = InputMultiObject(File(exists=True))
     recon_scalars = InputMultiObject(traits.Any())
+    compress = traits.Bool(True, usedefault=True)
 
 
 class ReconScalarsDataSink(SimpleInterface):
@@ -114,6 +115,14 @@ class ReconScalarsDataSink(SimpleInterface):
 
     def _run_interface(self, runtime):
 
+        force_compress = False
+        force_decompress = False
+        if isdefined(self.inputs.compress):
+            if self.inputs.compress:
+                force_compress = True
+            else:
+                force_decompress = True
+
         for recon_scalar in self.inputs.recon_scalars:
             output_filename = get_recon_output_name(
                 base_dir=self.inputs.base_directory,
@@ -123,6 +132,13 @@ def _run_interface(self, runtime):
                 output_bids_entities=recon_scalar["bids"],
                 use_ext=True,
             )
+
+            if force_decompress and output_filename.endswith(".gz"):
+                output_filename = output_filename.rstrip(".gz")
+
+            if force_compress and not output_filename.endswith(".gz"):
+                output_filename += ".gz"
+
             output_dir = op.dirname(output_filename)
             os.makedirs(output_dir, exist_ok=True)
             _copy_any(recon_scalar["path"], output_filename)

diff --git a/qsiprep/tests/data/autotrack_outputs.txt b/qsiprep/tests/data/autotrack_outputs.txt
@@ -12,8 +12,8 @@ qsirecon
 qsirecon-DSIStudio
 qsirecon-DSIStudio/sub-ABCD
 qsirecon-DSIStudio/sub-ABCD/dwi
-qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundle-Association_ArcuateFasciculusL_streamlines.tck
-qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundle-Association_ArcuateFasciculusR_streamlines.tck
+qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundle-Association_ArcuateFasciculusL_streamlines.tck.gz
+qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundle-Association_ArcuateFasciculusR_streamlines.tck.gz
 qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundlestats.csv
 qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_dwimap.fib.gz
 qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_mapping.map.gz

diff --git a/qsiprep/tests/data/scalar_mapper_outputs.txt b/qsiprep/tests/data/scalar_mapper_outputs.txt
@@ -50,8 +50,8 @@ qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-MNI152NLin2009cAsym_
 qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-MNI152NLin2009cAsym_desc-preproc_model-tensor_mfp-tyy_dwimap.nii.gz
 qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-MNI152NLin2009cAsym_desc-preproc_model-tensor_mfp-tyz_dwimap.nii.gz
 qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-MNI152NLin2009cAsym_desc-preproc_model-tensor_mfp-tzz_dwimap.nii.gz
-qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundle-Association_ArcuateFasciculusL_streamlines.tck
-qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundle-Association_ArcuateFasciculusR_streamlines.tck
+qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundle-Association_ArcuateFasciculusL_streamlines.tck.gz
+qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundle-Association_ArcuateFasciculusR_streamlines.tck.gz
 qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundles-DSIStudio_scalarstats.tsv
 qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundles-DSIStudio_tdistats.tsv
 qsirecon-DSIStudio/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_bundlestats.csv

diff --git a/qsiprep/tests/data/tortoise_recon_outputs.txt b/qsiprep/tests/data/tortoise_recon_outputs.txt
@@ -12,17 +12,17 @@ qsirecon
 qsirecon-TORTOISE
 qsirecon-TORTOISE/sub-ABCD
 qsirecon-TORTOISE/sub-ABCD/dwi
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-NG_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-NGpar_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-NGperp_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-PA_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-PAth_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-RTAP_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-RTOP_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-RTPP_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-tensor_mdp-ad_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-tensor_mdp-fa_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-tensor_mdp-li_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-tensor_mdp-rd_dwimap.nii
-qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-tensor_mfp-AM_dwimap.nii
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-NG_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-NGpar_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-NGperp_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-PA_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-PAth_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-RTAP_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-RTOP_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-mapmri_mdp-RTPP_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-tensor_mdp-ad_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-tensor_mdp-fa_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-tensor_mdp-li_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-tensor_mdp-rd_dwimap.nii.gz
+qsirecon-TORTOISE/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_desc-preproc_model-tensor_mfp-AM_dwimap.nii.gz
 qsirecon/sub-ABCD
diff --git a/qsiprep/workflows/recon/dsi_studio.py b/qsiprep/workflows/recon/dsi_studio.py
@@ -331,7 +331,9 @@ def init_dsi_studio_autotrack_wf(
 
     # Save tck files of the bundles into the outputs
     ds_tckfiles = pe.MapNode(
-        ReconDerivativesDataSink(suffix="streamlines", qsirecon_suffix=qsirecon_suffix),
+        ReconDerivativesDataSink(
+            suffix="streamlines", qsirecon_suffix=qsirecon_suffix, compress=True
+        ),
         iterfield=["in_file", "bundle"],
         name="ds_tckfiles",
     )