fix(workflow): update suffices and replace with desc if required

oesteban · oesteban · commit 58ebda68b039 · 2019-05-01T09:08:10.000-07:00
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
@@ -436,12 +436,12 @@ def init_single_subject_wf(layout, subject_id, task_id, echo_idx, name, reportle
 
     ds_report_summary = pe.Node(
         DerivativesDataSink(base_directory=reportlets_dir,
-                            suffix='summary'),
+                            desc='summary', keep_dtype=True),
         name='ds_report_summary', run_without_submitting=True)
 
     ds_report_about = pe.Node(
         DerivativesDataSink(base_directory=reportlets_dir,
-                            suffix='about'),
+                            desc='about', keep_dtype=True),
         name='ds_report_about', run_without_submitting=True)
 
     # Preprocessing of T1w (includes registration to MNI)
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
@@ -636,11 +636,8 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
 
     if fmaps:
         from ..fieldmap.unwarp import init_fmap_unwarp_report_wf
-        sdc_type = fmaps[0]['suffix']
-
         # Report on BOLD correction
-        fmap_unwarp_report_wf = init_fmap_unwarp_report_wf(
-            suffix='sdc_%s' % sdc_type)
+        fmap_unwarp_report_wf = init_fmap_unwarp_report_wf()
         workflow.connect([
             (inputnode, fmap_unwarp_report_wf, [
                 ('t1_seg', 'inputnode.in_seg')]),
@@ -652,9 +649,9 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
                 ('outputnode.bold_ref', 'inputnode.in_post')]),
         ])
 
-        if force_syn and sdc_type != 'syn':
+        if force_syn and fmaps[0]['suffix'] != 'syn':
             syn_unwarp_report_wf = init_fmap_unwarp_report_wf(
-                suffix='forcedsyn', name='syn_unwarp_report_wf')
+                name='syn_unwarp_report_wf', forcedsyn=True)
             workflow.connect([
                 (inputnode, syn_unwarp_report_wf, [
                     ('t1_seg', 'inputnode.in_seg')]),
@@ -842,13 +839,13 @@ def init_func_preproc_wf(bold_file, ignore, freesurfer,
 
     # REPORTING ############################################################
     ds_report_summary = pe.Node(
-        DerivativesDataSink(suffix='summary'),
+        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,
-                            suffix='validation'),
+                            desc='validation', keep_dtype=True),
         name='ds_report_validation', run_without_submitting=True,
         mem_gb=DEFAULT_MEMORY_MIN_GB)
 
diff --git a/fmriprep/workflows/bold/confounds.py b/fmriprep/workflows/bold/confounds.py
@@ -219,7 +219,7 @@ def init_bold_confs_wf(mem_gb, metadata, name="bold_confs_wf"):
                         name='rois_plot', mem_gb=mem_gb)
 
     ds_report_bold_rois = pe.Node(
-        DerivativesDataSink(suffix='rois'),
+        DerivativesDataSink(desc='rois', keep_dtype=True),
         name='ds_report_bold_rois', run_without_submitting=True,
         mem_gb=DEFAULT_MEMORY_MIN_GB)
 
@@ -377,7 +377,7 @@ def init_carpetplot_wf(mem_gb, metadata, name="bold_carpet_wf"):
             ('framewise_displacement', 'mm', 'FD')]),
         name='conf_plot', mem_gb=mem_gb)
     ds_report_bold_conf = pe.Node(
-        DerivativesDataSink(suffix='carpetplot'),
+        DerivativesDataSink(desc='carpetplot', keep_dtype=True),
         name='ds_report_bold_conf', run_without_submitting=True,
         mem_gb=DEFAULT_MEMORY_MIN_GB)
 
@@ -579,7 +579,7 @@ def _getusans_func(image, thresh):
                                             name='ica_aroma_confound_extraction')
 
     ds_report_ica_aroma = pe.Node(
-        DerivativesDataSink(suffix='ica_aroma'),
+        DerivativesDataSink(desc='aroma', keep_dtype=True),
         name='ds_report_ica_aroma', run_without_submitting=True,
         mem_gb=DEFAULT_MEMORY_MIN_GB)
 
diff --git a/fmriprep/workflows/bold/resampling.py b/fmriprep/workflows/bold/resampling.py
@@ -589,20 +589,20 @@ def init_bold_preproc_report_wf(mem_gb, reportlets_dir, name='bold_preproc_repor
 
     bold_rpt = pe.Node(SimpleBeforeAfter(), name='bold_rpt',
                        mem_gb=0.1)
-    bold_rpt_ds = pe.Node(
-        DerivativesDataSink(base_directory=reportlets_dir,
-                            suffix='variant-preproc'), name='bold_rpt_ds',
+    ds_report_bold = pe.Node(
+        DerivativesDataSink(base_directory=reportlets_dir, desc='preproc',
+                            keep_dtype=True), name='ds_report_bold',
         mem_gb=DEFAULT_MEMORY_MIN_GB,
         run_without_submitting=True
     )
 
     workflow.connect([
-        (inputnode, bold_rpt_ds, [('name_source', 'source_file')]),
+        (inputnode, ds_report_bold, [('name_source', 'source_file')]),
         (inputnode, pre_tsnr, [('in_pre', 'in_file')]),
         (inputnode, pos_tsnr, [('in_post', 'in_file')]),
         (pre_tsnr, bold_rpt, [('stddev_file', 'before')]),
         (pos_tsnr, bold_rpt, [('stddev_file', 'after')]),
-        (bold_rpt, bold_rpt_ds, [('out_report', 'in_file')]),
+        (bold_rpt, ds_report_bold, [('out_report', 'in_file')]),
     ])
 
     return workflow
diff --git a/fmriprep/workflows/fieldmap/fmap.py b/fmriprep/workflows/fieldmap/fmap.py
@@ -64,8 +64,9 @@ def init_fmap_wf(omp_nthreads, fmap_bspline, name='fmap_wf'):
                          name='n4_correct', n_procs=omp_nthreads)
     bet = pe.Node(BETRPT(generate_report=True, frac=0.6, mask=True),
                   name='bet')
-    ds_fmap_mask = pe.Node(DerivativesDataSink(suffix='fmap_mask'),
-                           name='ds_report_fmap_mask', run_without_submitting=True)
+    ds_report_fmap_mask = pe.Node(DerivativesDataSink(
+        desc='brain', suffix='mask'), name='ds_report_fmap_mask',
+        run_without_submitting=True)
 
     workflow.connect([
         (inputnode, magmrg, [('magnitude', 'in_files')]),
@@ -74,8 +75,8 @@ def init_fmap_wf(omp_nthreads, fmap_bspline, name='fmap_wf'):
         (n4_correct, bet, [('output_image', 'in_file')]),
         (bet, outputnode, [('mask_file', 'fmap_mask'),
                            ('out_file', 'fmap_ref')]),
-        (inputnode, ds_fmap_mask, [('fieldmap', 'source_file')]),
-        (bet, ds_fmap_mask, [('out_report', 'in_file')]),
+        (inputnode, ds_report_fmap_mask, [('fieldmap', 'source_file')]),
+        (bet, ds_report_fmap_mask, [('out_report', 'in_file')]),
     ])
 
     if fmap_bspline:
diff --git a/fmriprep/workflows/fieldmap/phdiff.py b/fmriprep/workflows/fieldmap/phdiff.py
@@ -83,8 +83,9 @@ def _pick1st(inlist):
                  name='n4', n_procs=omp_nthreads)
     bet = pe.Node(BETRPT(generate_report=True, frac=0.6, mask=True),
                   name='bet')
-    ds_fmap_mask = pe.Node(DerivativesDataSink(suffix='fmap_mask'), name='ds_report_fmap_mask',
-                           mem_gb=0.01, run_without_submitting=True)
+    ds_report_fmap_mask = pe.Node(DerivativesDataSink(
+        desc='brain', suffix='mask'), name='ds_report_fmap_mask',
+        mem_gb=0.01, run_without_submitting=True)
     # uses mask from bet; outputs a mask
     # dilate = pe.Node(fsl.maths.MathsCommand(
     #     nan2zeros=True, args='-kernel sphere 5 -dilM'), name='MskDilate')
@@ -127,8 +128,8 @@ def _pick1st(inlist):
         (compfmap, outputnode, [('out_file', 'fmap')]),
         (bet, outputnode, [('mask_file', 'fmap_mask'),
                            ('out_file', 'fmap_ref')]),
-        (inputnode, ds_fmap_mask, [('phasediff', 'source_file')]),
-        (bet, ds_fmap_mask, [('out_report', 'in_file')]),
+        (inputnode, ds_report_fmap_mask, [('phasediff', 'source_file')]),
+        (bet, ds_report_fmap_mask, [('out_report', 'in_file')]),
     ])
 
     return workflow
diff --git a/fmriprep/workflows/fieldmap/unwarp.py b/fmriprep/workflows/fieldmap/unwarp.py
@@ -105,8 +105,9 @@ def init_sdc_unwarp_wf(omp_nthreads, fmap_demean, debug, name='sdc_unwarp_wf'):
                             output_inverse_warped_image=True, output_warped_image=True),
         name='fmap2ref_reg', n_procs=omp_nthreads)
 
-    ds_reg = pe.Node(DerivativesDataSink(suffix='fmap_reg'), name='ds_report_reg',
-                     mem_gb=0.01, run_without_submitting=True)
+    ds_report_reg = pe.Node(DerivativesDataSink(
+        desc='magnitude', suffix='bold'), name='ds_report_reg',
+        mem_gb=0.01, run_without_submitting=True)
 
     # Map the VSM into the EPI space
     fmap2ref_apply = pe.Node(ANTSApplyTransformsRPT(
@@ -118,8 +119,9 @@ def init_sdc_unwarp_wf(omp_nthreads, fmap_demean, debug, name='sdc_unwarp_wf'):
         float=True),
         name='fmap_mask2ref_apply')
 
-    ds_reg_vsm = pe.Node(DerivativesDataSink(suffix='fmap_reg_vsm'), name='ds_report_vsm',
-                         mem_gb=0.01, run_without_submitting=True)
+    ds_report_vsm = pe.Node(DerivativesDataSink(
+        desc='fieldmap', suffix='bold'), name='ds_report_vsm',
+        mem_gb=0.01, run_without_submitting=True)
 
     # Fieldmap to rads and then to voxels (VSM - voxel shift map)
     torads = pe.Node(FieldToRadS(fmap_range=0.5), name='torads')
@@ -159,9 +161,9 @@ def init_sdc_unwarp_wf(omp_nthreads, fmap_demean, debug, name='sdc_unwarp_wf'):
         (inputnode, fmap_mask2ref_apply, [('in_reference', 'reference_image')]),
         (fmap2ref_reg, fmap_mask2ref_apply, [
             ('composite_transform', 'transforms')]),
-        (fmap2ref_apply, ds_reg_vsm, [('out_report', 'in_file')]),
+        (fmap2ref_apply, ds_report_vsm, [('out_report', 'in_file')]),
         (inputnode, fmap2ref_reg, [('in_reference_brain', 'fixed_image')]),
-        (fmap2ref_reg, ds_reg, [('out_report', 'in_file')]),
+        (fmap2ref_reg, ds_report_reg, [('out_report', 'in_file')]),
         (inputnode, fmap2ref_apply, [('fmap', 'input_image')]),
         (inputnode, fmap_mask2ref_apply, [('fmap_mask', 'input_image')]),
         (fmap2ref_apply, torads, [('output_image', 'in_file')]),
@@ -211,7 +213,7 @@ def init_sdc_unwarp_wf(omp_nthreads, fmap_demean, debug, name='sdc_unwarp_wf'):
     return workflow
 
 
-def init_fmap_unwarp_report_wf(name='fmap_unwarp_report_wf', suffix='variant-hmcsdc_preproc'):
+def init_fmap_unwarp_report_wf(name='fmap_unwarp_report_wf', forcedsyn=False):
     """
     This workflow generates and saves a reportlet showing the effect of fieldmap
     unwarping a BOLD image.
@@ -227,8 +229,8 @@ def init_fmap_unwarp_report_wf(name='fmap_unwarp_report_wf', suffix='variant-hmc
 
         name : str, optional
             Workflow name (default: fmap_unwarp_report_wf)
-        suffix : str, optional
-            Suffix to be appended to this reportlet
+        forcedsyn : bool, optional
+            Whether SyN-SDC was forced.
 
     **Inputs**
 
@@ -264,7 +266,8 @@ def init_fmap_unwarp_report_wf(name='fmap_unwarp_report_wf', suffix='variant-hmc
     bold_rpt = pe.Node(SimpleBeforeAfter(), name='bold_rpt',
                        mem_gb=0.1)
     ds_report_sdc = pe.Node(
-        DerivativesDataSink(suffix=suffix), name='ds_report_sdc',
+        DerivativesDataSink(desc='sdc' if not forcedsyn else 'forcedsyn',
+                            suffix='bold'), name='ds_report_sdc',
         mem_gb=DEFAULT_MEMORY_MIN_GB, run_without_submitting=True
     )
 
