MAINT: Purge remaining pkg_resource uses

nipreps · Jan 29, 2024 · 42997bf · 42997bf
1 parent 7cbb35a
commit 42997bf
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Showing 4 changed files with 16 additions and 25 deletions.
diff --git a/nibabies/workflows/anatomical/brain_extraction.py b/nibabies/workflows/anatomical/brain_extraction.py
@@ -3,7 +3,6 @@
 """Baby brain extraction from T2w images."""
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
-from pkg_resources import resource_filename as pkgr_fn
 
 
 def init_infant_brain_extraction_wf(
@@ -79,16 +78,15 @@ def init_infant_brain_extraction_wf(
     from nipype.interfaces.ants import ImageMath, N4BiasFieldCorrection
     from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
     from niworkflows.interfaces.fixes import FixHeaderRegistration as Registration
-
-    # niworkflows
     from niworkflows.interfaces.nibabel import (
         ApplyMask,
         Binarize,
         BinaryDilation,
         IntensityClip,
     )
 
-    from ...utils.misc import cohort_by_months
+    from nibabies.data import load as load_data
+    from nibabies.utils.misc import cohort_by_months
 
     # handle template specifics
     template_specs = template_specs or {}
@@ -138,9 +136,7 @@ def init_infant_brain_extraction_wf(
     # Set up initial spatial normalization
     ants_params = "testing" if sloppy else "precise"
     norm = pe.Node(
-        Registration(
-            from_file=pkgr_fn("nibabies.data", f"antsBrainExtraction_{ants_params}.json")
-        ),
+        Registration(from_file=load_data(f"antsBrainExtraction_{ants_params}.json")),
         name="norm",
         n_procs=omp_nthreads,
         mem_gb=mem_gb,

diff --git a/nibabies/workflows/anatomical/segmentation.py b/nibabies/workflows/anatomical/segmentation.py
@@ -4,18 +4,17 @@
 from nipype.interfaces import utility as niu
 from nipype.interfaces.ants.segmentation import JointFusion
 from nipype.pipeline import engine as pe
+from niworkflows.data import load as load_nwf
 from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
 from niworkflows.interfaces.fixes import FixHeaderRegistration as Registration
-from niworkflows.interfaces.nibabel import MapLabels
-from pkg_resources import resource_filename as pkgr_fn
 from smriprep.utils.misc import apply_lut as _apply_bids_lut
 from smriprep.workflows.anatomical import (
     _aseg_to_three,
     _probseg_fast2bids,
     _split_segments,
 )
 
-from ...config import DEFAULT_MEMORY_MIN_GB
+from nibabies.config import DEFAULT_MEMORY_MIN_GB
 
 
 def init_anat_segmentations_wf(
@@ -104,9 +103,7 @@ def init_anat_segmentations_wf(
         ants_params = "testing" if sloppy else "precise"
         # Register to each subject space
         norm = pe.MapNode(
-            Registration(
-                from_file=pkgr_fn("niworkflows.data", f"antsBrainExtraction_{ants_params}.json")
-            ),
+            Registration(from_file=load_nwf(f"antsBrainExtraction_{ants_params}.json")),
             name="norm",
             iterfield=["moving_image"],
             n_procs=omp_nthreads,

diff --git a/nibabies/workflows/bold/alignment.py b/nibabies/workflows/bold/alignment.py
@@ -6,9 +6,9 @@
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
-from pkg_resources import resource_filename
 
-from ...interfaces.workbench import VolumeLabelImport
+from nibabies.data import load as load_data
+from nibabies.interfaces.workbench import VolumeLabelImport
 
 
 def init_subcortical_rois_wf(*, name="subcortical_rois_wf"):
@@ -70,17 +70,15 @@ def init_subcortical_rois_wf(*, name="subcortical_rois_wf"):
     # )
 
     map_labels = pe.Node(
-        MapLabels(
-            mappings_file=resource_filename("nibabies", "data/FreeSurferLabelRemappings.json")
-        ),
+        MapLabels(mappings_file=load_data("FreeSurferLabelRemappings.json")),
         name='map_labels',
     )
 
-    subcortical_labels = resource_filename(
-        "nibabies", "data/FreeSurferSubcorticalLabelTableLut.txt"
-    )
     refine_bold_rois = pe.Node(
-        VolumeLabelImport(label_list_file=subcortical_labels, discard_others=True),
+        VolumeLabelImport(
+            label_list_file=load_data("FreeSurferSubcorticalLabelTableLut.txt"),
+            discard_others=True,
+        ),
         name="refine_bold_rois",
     )
 

diff --git a/nibabies/workflows/bold/registration.py b/nibabies/workflows/bold/registration.py
@@ -13,12 +13,12 @@
 import logging
 import os
 
-import pkg_resources as pkgr
 from nipype.interfaces import c3, fsl
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 
-from ...config import DEFAULT_MEMORY_MIN_GB
+from nibabies.config import DEFAULT_MEMORY_MIN_GB
+from nibabies.data import load as load_data
 
 LOGGER = logging.getLogger("nipype.workflow")
 
@@ -793,7 +793,7 @@ def init_fsl_bbr_wf(use_bbr, bold2t1w_dof, bold2t1w_init, sloppy=False, name="fs
     else:
         # Should mostly be hit while building docs
         LOGGER.warning("FSLDIR unset - using packaged BBR schedule")
-        flt_bbr.inputs.schedule = pkgr.resource_filename("fmriprep", "data/flirtsch/bbr.sch")
+        flt_bbr.inputs.schedule = load_data("flirtsch/bbr.sch")
 
     # fmt: off
     workflow.connect([