Merge pull request #102 from oesteban/enh/new-datasinks

ENH: Use new ``DerivativesDataSink`` from NiWorkflows 1.2.0

Author: oesteban

docs/requirements.txt

@@ -3,7 +3,7 @@ git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398
 nbsphinx
 niflow-nipype1-workflows ~= 0.0.1
 nipype>=1.3.1
-niworkflows >=1.2.0rc4,<1.4
+git+https://github.com/nipreps/niworkflows.git@master
 packaging
 pydot>=1.2.3
 pydotplus

sdcflows/workflows/fmap.py

@@ -242,7 +242,7 @@ def init_fmap2field_wf(omp_nthreads, debug, name='fmap2field_wf',
             reference_label='EPI Reference',
             moving_label='Magnitude', show='both'), name='fmap_rpt')
         ds_report_sdc = pe.Node(
-            DerivativesDataSink(desc='fieldmap', suffix='bold'),
+            DerivativesDataSink(desc='fieldmap', suffix='bold', datatype='figures'),
             name='ds_report_fmap', mem_gb=0.01, run_without_submitting=True
         )
 

sdcflows/workflows/outputs.py

@@ -63,8 +63,8 @@ def init_sdc_unwarp_report_wf(name='sdc_unwarp_report_wf', forcedsyn=False):
     bold_rpt = pe.Node(SimpleBeforeAfter(), name='bold_rpt',
                        mem_gb=0.1)
     ds_report_sdc = pe.Node(
-        DerivativesDataSink(desc='sdc' if not forcedsyn else 'forcedsyn',
-                            suffix='bold'), name='ds_report_sdc',
+        DerivativesDataSink(desc=('sdc', 'forcedsyn')[forcedsyn], suffix='bold',
+                            datatype='figures'), name='ds_report_sdc',
         mem_gb=DEFAULT_MEMORY_MIN_GB, run_without_submitting=True
     )
 

sdcflows/workflows/tests/test_pepolar.py

@@ -160,9 +160,8 @@ def test_pepolar_wf1(bids_layouts, output_path, dataset, workdir):
         rep = pe.Node(FieldmapReportlet(reference_label='EPI Reference'), 'simple_report')
         rep.interface._always_run = True
         dsink = pe.Node(DerivativesDataSink(
-            base_directory=str(output_path), keep_dtype=True,
-            desc='pepolar'), name='dsink')
-        dsink.interface.out_path_base = 'sdcflows'
+            base_directory=str(output_path), out_path_base='sdcflows', datatype="figures",
+            suffix='fieldmap', desc='pepolar', dismiss_entities='fmap'), name='dsink')
         dsink.inputs.source_file = epidata[0].path
 
         boiler.connect([

sdcflows/workflows/tests/test_phdiff.py

@@ -40,13 +40,14 @@ def test_phdiff(bids_layouts, tmpdir, output_path, dataset, workdir):
         rep = pe.Node(FieldmapReportlet(reference_label='Magnitude'), 'simple_report')
         rep.interface._always_run = True
 
-        dsink = pe.Node(DerivativesDataSink(
-            base_directory=str(output_path), keep_dtype=True), name='dsink')
-        dsink.interface.out_path_base = 'sdcflows'
-        dsink.inputs.source_file = phdiff_files[0].path
+        ds_report = pe.Node(DerivativesDataSink(
+            base_directory=str(output_path), out_path_base='sdcflows', datatype='figures',
+            suffix='fieldmap', desc='phasediff', dismiss_entities='fmap'), name='ds_report')
+        ds_report.inputs.source_file = phdiff_files[0].path
 
         dsink_fmap = pe.Node(DerivativesDataSink(
-            base_directory=str(output_path), keep_dtype=True), name='dsink_fmap')
+            base_directory=str(output_path), dismiss_entities='fmap',
+            desc='phasediff', suffix='fieldmap'), name='dsink_fmap')
         dsink_fmap.interface.out_path_base = 'sdcflows'
         dsink_fmap.inputs.source_file = phdiff_files[0].path
 
@@ -55,7 +56,7 @@ def test_phdiff(bids_layouts, tmpdir, output_path, dataset, workdir):
                 ('outputnode.fmap', 'fieldmap'),
                 ('outputnode.fmap_ref', 'reference'),
                 ('outputnode.fmap_mask', 'mask')]),
-            (rep, dsink, [('out_report', 'in_file')]),
+            (rep, ds_report, [('out_report', 'in_file')]),
             (phdiff_wf, dsink_fmap, [('outputnode.fmap', 'in_file')]),
         ])
     else:
@@ -91,13 +92,14 @@ def test_phases(bids_layouts, tmpdir, output_path, workdir):
         rep = pe.Node(FieldmapReportlet(reference_label='Magnitude'), 'simple_report')
         rep.interface._always_run = True
 
-        dsink = pe.Node(DerivativesDataSink(
-            base_directory=str(output_path), keep_dtype=True), name='dsink')
-        dsink.interface.out_path_base = 'sdcflows'
-        dsink.inputs.source_file = phdiff_files[0].path
+        ds_report = pe.Node(DerivativesDataSink(
+            base_directory=str(output_path), out_path_base='sdcflows', datatype='figures',
+            suffix='fieldmap', desc='twophases', dismiss_entities='fmap'), name='ds_report')
+        ds_report.inputs.source_file = phdiff_files[0].path
 
         dsink_fmap = pe.Node(DerivativesDataSink(
-            base_directory=str(output_path), keep_dtype=True), name='dsink_fmap')
+            base_directory=str(output_path), suffix='fieldmap', desc='twophases',
+            dismiss_entities='fmap'), name='dsink_fmap')
         dsink_fmap.interface.out_path_base = 'sdcflows'
         dsink_fmap.inputs.source_file = phdiff_files[0].path
 
@@ -106,7 +108,7 @@ def test_phases(bids_layouts, tmpdir, output_path, workdir):
                 ('outputnode.fmap', 'fieldmap'),
                 ('outputnode.fmap_ref', 'reference'),
                 ('outputnode.fmap_mask', 'mask')]),
-            (rep, dsink, [('out_report', 'in_file')]),
+            (rep, ds_report, [('out_report', 'in_file')]),
             (phdiff_wf, dsink_fmap, [('outputnode.fmap', 'in_file')]),
         ])
     else:

setup.cfg

@@ -29,9 +29,9 @@ install_requires =
     nibabel >=3.0.1
     niflow-nipype1-workflows ~= 0.0.1
     nipype >=1.3.1,<2.0
-    niworkflows >=1.2.0rc4,<1.4
+    niworkflows @ git+https://github.com/nipreps/niworkflows.git@master
     numpy
-    pybids >= 0.9.2
+    pybids >= 0.10.2
     templateflow >=0.4
 test_requires =
     codecov