fix: remove diffusionsummary

Author: oesteban

dmriprep/config/reports-spec.yml

@@ -29,7 +29,6 @@ sections:
 - name: Diffusion
   ordering: session,acquisition,run
   reportlets:
-  - bids: {datatype: dwi, desc: summary, suffix: dwi}
   - bids: {datatype: dwi, desc: validation, suffix: dwi}
 - name: About
   reportlets:

dmriprep/interfaces/reports.py

@@ -23,13 +23,6 @@
 \t</ul>
 """
 
-DWI_TEMPLATE = """\t\t<h3 class="elem-title">Summary</h3>
-\t\t<ul class="elem-desc">
-\t\t\t<li>Susceptibility distortion correction: {sdc}</li>
-\t\t\t<li>Registration: {registration}</li>
-\t\t</ul>
-"""
-
 ABOUT_TEMPLATE = """\t<ul>
 \t\t<li>dMRIPrep version: {version}</li>
 \t\t<li>dMRIPrep command: <code>{command}</code></li>
@@ -128,39 +121,3 @@ def _generate_segment(self):
         return ABOUT_TEMPLATE.format(version=self.inputs.version,
                                      command=self.inputs.command,
                                      date=time.strftime("%Y-%m-%d %H:%M:%S %z"))
-
-
-class DiffusionSummaryInputSpec(BaseInterfaceInputSpec):
-    distortion_correction = traits.Str(desc='Susceptibility distortion correction method',
-                                       mandatory=True)
-    pe_direction = traits.Enum(None, 'i', 'i-', 'j', 'j-', mandatory=True,
-                               desc='Phase-encoding direction detected')
-    registration = traits.Enum('FSL', 'FreeSurfer', mandatory=True,
-                               desc='Diffusion/anatomical registration method')
-    fallback = traits.Bool(desc='Boundary-based registration rejected')
-    registration_dof = traits.Enum(6, 9, 12, desc='Registration degrees of freedom',
-                                   mandatory=True)
-
-
-class DiffusionSummary(SummaryInterface):
-    input_spec = DiffusionSummaryInputSpec
-
-    def _generate_segment(self):
-        dof = self.inputs.registration_dof
-        reg = {
-            'FSL': [
-                'FSL <code>flirt</code> with boundary-based registration'
-                ' (BBR) metric - %d dof' % dof,
-                'FSL <code>flirt</code> rigid registration - 6 dof'],
-            'FreeSurfer': [
-                'FreeSurfer <code>bbregister</code> '
-                '(boundary-based registration, BBR) - %d dof' % dof,
-                'FreeSurfer <code>mri_coreg</code> - %d dof' % dof],
-        }[self.inputs.registration][self.inputs.fallback]
-        if self.inputs.pe_direction is None:
-            pedir = 'MISSING - Assuming Anterior-Posterior'
-        else:
-            pedir = {'i': 'Left-Right', 'j': 'Anterior-Posterior'}[self.inputs.pe_direction[0]]
-
-        return DWI_TEMPLATE.format(
-            pedir=pedir, sdc=self.inputs.distortion_correction, registration=reg)

dmriprep/workflows/dwi/base.py

@@ -10,7 +10,6 @@
 from ...config import DEFAULT_MEMORY_MIN_GB
 
 from ...interfaces import DerivativesDataSink
-from ...interfaces.reports import DiffusionSummary
 from ...interfaces.vectors import CheckGradientTable
 
 
@@ -125,13 +124,9 @@ def init_dwi_preproc_wf(
         LOGGER.log(25, 'No valid layout: building empty workflow.')
         bvec_file = '/completely/made/up/path/sub-01_dwi.bvec'
         bval_file = '/completely/made/up/path/sub-01_dwi.bval'
-        metadata = {
-            'PhaseEncodingDirection': 'j',
-        }
     else:
         bvec_file = layout.get_bvec(dwi_file)
         bval_file = layout.get_bval(dwi_file)
-        metadata = layout.get_metadata(dwi_file)
 
     inputnode = pe.Node(niu.IdentityInterface(
         fields=['dwi_file', 'bvec_file', 'bval_file',
@@ -150,12 +145,6 @@ def init_dwi_preproc_wf(
                 'out_dwi_mask']),
         name='outputnode')
 
-    summary = pe.Node(
-        DiffusionSummary(
-            distortion_correction='Not implemented',
-            pe_direction=metadata.get("PhaseEncodingDirection")),
-        name='summary', mem_gb=DEFAULT_MEMORY_MIN_GB, run_without_submitting=True)
-
     gradient_table = pe.Node(CheckGradientTable(), name='gradient_table')
 
     dwi_reference_wf = init_dwi_reference_wf(omp_nthreads=1, gen_report=True)
@@ -178,21 +167,14 @@ def init_dwi_preproc_wf(
     ])
 
     # REPORTING
-    ds_report_summary = pe.Node(
-        DerivativesDataSink(desc='summary', keep_dtype=True),
-        name='ds_report_summary', run_without_submitting=True,
-        mem_gb=DEFAULT_MEMORY_MIN_GB
-    )
-
     ds_report_validation = pe.Node(
         DerivativesDataSink(base_directory=reportlets_dir,
                             desc='validation', keep_dtype=True),
         name='ds_report_validation', run_without_submitting=True,
         mem_gb=DEFAULT_MEMORY_MIN_GB)
 
     workflow.connect([
-        (inputnode, ds_report_summary, [('dwi_file', 'source_file')]),
-        (summary, ds_report_summary, [('out_report', 'in_file')]),
+        (inputnode, ds_report_validation, [('dwi', 'source_file')]),
         (dwi_reference_wf, ds_report_validation, [
             ('outputnode.validation_report', 'in_file')]),
     ])