Merge pull request #156 from nipreps/fix/update-niworkflows-1.4.0rc4

FIX: Update to new *NiWorkflows* API

Author: oesteban

dmriprep/workflows/dwi/base.py

@@ -68,8 +68,10 @@ def init_dwi_preproc_wf(dwi_file, has_fieldmap=False):
     * :py:func:`~dmriprep.workflows.dwi.outputs.init_reportlets_wf`
 
     """
+    from niworkflows.interfaces.reportlets.registration import (
+        SimpleBeforeAfterRPT as SimpleBeforeAfter,
+    )
     from ...interfaces.vectors import CheckGradientTable
-    from niworkflows.interfaces import SimpleBeforeAfter
     from .util import init_dwi_reference_wf
     from .outputs import init_reportlets_wf
     from .eddy import init_eddy_wf
@@ -219,7 +221,10 @@ def _bold_reg_suffix(fallback):
         )
 
         eddy_report = pe.Node(
-            SimpleBeforeAfter(before_label="Distorted", after_label="Eddy Corrected",),
+            SimpleBeforeAfter(
+                before_label="Distorted",
+                after_label="Eddy Corrected",
+            ),
             name="eddy_report",
             mem_gb=0.1,
         )
@@ -268,7 +273,6 @@ def _bold_reg_suffix(fallback):
         # fmt: on
         return workflow
 
-    from niworkflows.interfaces import SimpleBeforeAfter
     from niworkflows.interfaces.utility import KeySelect
     from sdcflows.workflows.apply.registration import init_coeff2epi_wf
     from sdcflows.workflows.apply.correction import init_unwarp_wf
@@ -279,8 +283,7 @@ def _bold_reg_suffix(fallback):
         write_coeff=True,
     )
     unwarp_wf = init_unwarp_wf(
-        debug=config.execution.debug,
-        omp_nthreads=config.nipype.omp_nthreads
+        debug=config.execution.debug, omp_nthreads=config.nipype.omp_nthreads
     )
     unwarp_wf.inputs.inputnode.metadata = layout.get_metadata(str(dwi_file))
 
@@ -297,7 +300,10 @@ def _bold_reg_suffix(fallback):
         )
 
     sdc_report = pe.Node(
-        SimpleBeforeAfter(before_label="Distorted", after_label="Corrected",),
+        SimpleBeforeAfter(
+            before_label="Distorted",
+            after_label="Corrected",
+        ),
         name="sdc_report",
         mem_gb=0.1,
     )

dmriprep/workflows/dwi/outputs.py

@@ -7,13 +7,19 @@
 
 def init_reportlets_wf(output_dir, sdc_report=False, name="reportlets_wf"):
     """Set up a battery of datasinks to store reports in the right location."""
-    from niworkflows.interfaces.masks import SimpleShowMaskRPT
+    from niworkflows.interfaces.reportlets.masks import SimpleShowMaskRPT
 
     workflow = Workflow(name=name)
 
     inputnode = pe.Node(
         niu.IdentityInterface(
-            fields=["source_file", "dwi_ref", "dwi_mask", "validation_report", "sdc_report"]
+            fields=[
+                "source_file",
+                "dwi_ref",
+                "dwi_mask",
+                "validation_report",
+                "sdc_report",
+            ]
         ),
         name="inputnode",
     )

dmriprep/workflows/dwi/util.py

@@ -1,17 +1,7 @@
 """Utility workflows for :abbr:`DWI (diffusion weighted imaging)` data."""
-
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu, fsl, afni
-
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
-from niworkflows.interfaces.images import ValidateImage
-from niworkflows.interfaces.fixes import (
-    FixN4BiasFieldCorrection as N4BiasFieldCorrection,
-)
-from niworkflows.interfaces.nibabel import ApplyMask
-from niworkflows.interfaces.utils import CopyXForm
-
-from ...interfaces.images import ExtractB0, RescaleB0
 
 
 def init_dwi_reference_wf(mem_gb, omp_nthreads, name="dwi_reference_wf"):
@@ -68,6 +58,10 @@ def init_dwi_reference_wf(mem_gb, omp_nthreads, name="dwi_reference_wf"):
     * :py:func:`~dmriprep.workflows.dwi.util.init_enhance_and_skullstrip_wf`
 
     """
+    from niworkflows.interfaces.header import ValidateImage
+
+    from ...interfaces.images import ExtractB0, RescaleB0
+
     workflow = Workflow(name=name)
 
     inputnode = pe.Node(
@@ -185,6 +179,12 @@ def init_enhance_and_skullstrip_dwi_wf(
         reportlet for the skull-stripping
 
     """
+    from niworkflows.interfaces.header import CopyXForm
+    from niworkflows.interfaces.fixes import (
+        FixN4BiasFieldCorrection as N4BiasFieldCorrection,
+    )
+    from niworkflows.interfaces.nibabel import ApplyMask
+
     workflow = Workflow(name=name)
     inputnode = pe.Node(
         niu.IdentityInterface(fields=["in_file", "pre_mask"]), name="inputnode"

docs/requirements.txt

@@ -2,12 +2,12 @@ git+https://github.com/AleksandarPetrov/napoleon.git@0dc3f28a309ad602be5f44a9049
 git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398feff05344051bbce0f63#egg=sphinxcontrib-versioning
 nbsphinx
 nipype ~= 1.5.1
-niworkflows >=1.4.0rc0,<1.5
+niworkflows >=1.4.0rc5,<1.5
 packaging
 pydot>=1.2.3
 pydotplus
 sdcflows ~= 2.0.0
-smriprep >= 0.8.0rc0
+smriprep >= 0.8.0rc2
 sphinx >=2.1.2,<3.0
 sphinx-argparse
 sphinx_rtd_theme

setup.cfg

@@ -25,12 +25,12 @@ install_requires =
     indexed_gzip >=0.8.8
     nibabel ~= 3.0
     nipype >= 1.5.1, < 2.0
-    niworkflows >= 1.4.0rc0, <1.5
+    niworkflows >= 1.4.0rc5, <1.5
     numpy
     pybids >= 0.11.1
     pyyaml
     sdcflows ~= 2.0.0
-    smriprep >= 0.8.0rc0
+    smriprep >= 0.8.0rc2
     svgutils != 0.3.2
     templateflow ~= 0.6
     toml