RF: Reorgnaize the fitlins output naming structure to use node name a…

…s the base directory

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/psf/black
-    rev: 21.12b0
+    rev: 22.3.0
     hooks:
       - id: black
         exclude: ^(fitlins/_version.py|versioneer.py)
@@ -18,7 +18,7 @@ repos:
         name: Sort python imports (isort)
         args: ["--profile", "black", "--filter-files"]
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.0
+    rev: v2.31.1
     hooks:
       - id: pyupgrade
         exclude: ^(fitlins/_version.py|versioneer.py)

fitlins/data/fitlins.json

@@ -13,6 +13,10 @@
 
             "name": "name",
             "pattern": "[_/\\\\]name-([a-zA-Z0-9]+)"
+        },
+	{
+            "name": "node",
+            "pattern": "[_/\\\\]node-([a-zA-Z0-9]+)"
         }
     ]
 }

fitlins/interfaces/bids.py

@@ -2,28 +2,26 @@
 import os
 import re
 import shutil
-
-import numpy as np
-import nibabel as nb
-
+from gzip import GzipFile
 from itertools import chain
 from pathlib import Path
-from gzip import GzipFile
 
+import nibabel as nb
+import numpy as np
 from nipype import logging
-from nipype.utils.filemanip import copyfile
 from nipype.interfaces.base import (
     BaseInterfaceInputSpec,
-    TraitedSpec,
-    SimpleInterface,
+    Directory,
+    File,
     InputMultiPath,
     OutputMultiPath,
-    File,
-    Directory,
-    traits,
+    SimpleInterface,
+    TraitedSpec,
     isdefined,
+    traits,
 )
 from nipype.interfaces.io import IOBase
+from nipype.utils.filemanip import copyfile
 
 from ..utils import snake_to_camel, to_alphanum
 
@@ -238,8 +236,8 @@ class LoadBIDSModel(SimpleInterface):
     output_spec = LoadBIDSModelOutputSpec
 
     def _run_interface(self, runtime):
-        from bids.modeling import BIDSStatsModelsGraph
         from bids.layout import BIDSLayout
+        from bids.modeling import BIDSStatsModelsGraph
 
         layout = BIDSLayout.load(database_path=self.inputs.database_path)
         selectors = self.inputs.selectors
@@ -480,7 +478,7 @@ def _list_outputs(self):
             # format (eg: gain.Range, gain.EqualIndifference).
             # This prevents issues when creating/searching files for the report
             for k, v in ents.items():
-                if k in ("name", "contrast", "stat"):
+                if k in ("node", "name", "contrast", "stat"):
                     ents.update({k: to_alphanum(str(v))})
 
             out_fname = os.path.join(

fitlins/workflows/base.py

@@ -1,5 +1,4 @@
 import warnings
-
 from collections import OrderedDict
 from pathlib import Path
 
@@ -21,17 +20,23 @@ def init_fitlins_wf(
     base_dir=None,
     name='fitlins_wf',
 ):
-    from nipype.pipeline import engine as pe
     from nipype.interfaces import utility as niu
-    from ..interfaces.bids import ModelSpecLoader, LoadBIDSModel, BIDSSelect, BIDSDataSink
+    from nipype.pipeline import engine as pe
+
+    from ..interfaces.bids import (
+        BIDSDataSink,
+        BIDSSelect,
+        LoadBIDSModel,
+        ModelSpecLoader,
+    )
     from ..interfaces.nistats import DesignMatrix, SecondLevelModel
+    from ..interfaces.utils import CollateWithMetadata, MergeAll
     from ..interfaces.visualizations import (
-        DesignPlot,
-        DesignCorrelationPlot,
         ContrastMatrixPlot,
+        DesignCorrelationPlot,
+        DesignPlot,
         GlassBrainPlot,
     )
-    from ..interfaces.utils import MergeAll, CollateWithMetadata
     from ..utils import snake_to_camel
 
     if estimator == 'afni':
@@ -121,6 +126,7 @@ def init_fitlins_wf(
 
     def _deindex(tsv):
         from pathlib import Path
+
         import pandas as pd
 
         out_tsv = str(Path.cwd() / Path(tsv).name)
@@ -133,33 +139,33 @@ def _deindex(tsv):
 
     # Set up common patterns
     image_pattern = (
-        "reports/[sub-{subject}/][ses-{session}/]figures/[run-{run}/]"
+        "reports/[node-{node}/][sub-{subject}/][ses-{session}/]figures/[run-{run}/]"
         "[level-{level}_][name-{name}_][sub-{subject}_][ses-{session}_][task-{task}_]"
         "[acq-{acquisition}_][rec-{reconstruction}_][run-{run}_][echo-{echo}_]"
         "{suffix<design|corr|contrasts>}{extension<.svg>|.svg}"
     )
 
     contrast_plot_pattern = (
-        "reports/[sub-{subject}/][ses-{session}/]figures/[run-{run}/]"
+        "reports/[node-{node}/][sub-{subject}/][ses-{session}/]figures/[run-{run}/]"
         "[level-{level}_][name-{name}_][sub-{subject}_][ses-{session}_][task-{task}_]"
         "[acq-{acquisition}_][rec-{reconstruction}_][run-{run}_][echo-{echo}_][space-{space}_]"
         "contrast-{contrast}_stat-{stat<effect|variance|z|p|t|F|Meta>}_ortho{extension<.png>|.png}"
     )
     design_matrix_pattern = (
-        "[sub-{subject}/][ses-{session}/]"
+        "[node-{node}/][sub-{subject}/][ses-{session}/]"
         "[level-{level}_][name-{name}_][sub-{subject}_][ses-{session}_][task-{task}_]"
         "[acq-{acquisition}_][rec-{reconstruction}_][run-{run}_][echo-{echo}_]"
         "{suffix<design>}{extension<.tsv>|.tsv}"
     )
     contrast_pattern = (
-        "[sub-{subject}/][ses-{session}/]"
+        "[node-{node}/][sub-{subject}/][ses-{session}/]"
         "[level-{level}_][name-{name}_][sub-{subject}_][ses-{session}_][task-{task}_]"
         "[acq-{acquisition}_][rec-{reconstruction}_][run-{run}_][echo-{echo}_][space-{space}_]"
         "contrast-{contrast}_stat-{stat<effect|variance|z|p|t|F|Meta>}_"
         "statmap{extension<.nii.gz|.dscalar.nii>}"
     )
     model_map_pattern = (
-        "[sub-{subject}/][ses-{session}/]"
+        "[node-{node}/][sub-{subject}/][ses-{session}/]"
         "[level-{level}_][name-{name}_][sub-{subject}_][ses-{session}_][task-{task}_]"
         "[acq-{acquisition}_][rec-{reconstruction}_][run-{run}_][echo-{echo}_][space-{space}_]"
         "stat-{stat<rSquare|logLikelihood|tsnr|errorts|a|b|lam|LjungBox|residtsnr|"
@@ -171,14 +177,20 @@ def _deindex(tsv):
     # saved as individual derivative files
     #
 
+    n_run = [
+        snake_to_camel(node.name.replace('-', '_'))
+        for node in graph.nodes.values()
+        if node.level == 'run'
+    ][0]
     reportlet_dir = Path(base_dir) / 'reportlets' / 'fitlins'
     reportlet_dir.mkdir(parents=True, exist_ok=True)
     snippet_pattern = (
-        '[sub-{subject}/][ses-{session}/][level-{level}_][sub-{subject}_]'
+        '[node-{node}/][sub-{subject}/][ses-{session}/][level-{level}_][sub-{subject}_]'
         '[ses-{session}_][task-{task}_][run-{run}_]snippet.html'
     )
     ds_model_warnings = pe.MapNode(
         BIDSDataSink(base_directory=str(reportlet_dir), path_patterns=snippet_pattern),
+        fixed_entities={'node': n_run},
         iterfield=['entities', 'in_file'],
         run_without_submitting=True,
         name='ds_model_warning',
@@ -201,7 +213,7 @@ def _deindex(tsv):
     ds_design = pe.MapNode(
         BIDSDataSink(
             base_directory=out_dir,
-            fixed_entities={"level": "run", 'suffix': 'design'},
+            fixed_entities={"level": "run", 'suffix': 'design', 'node': n_run},
             path_patterns=image_pattern,
         ),
         iterfield=['entities', 'in_file'],
@@ -212,7 +224,7 @@ def _deindex(tsv):
     ds_design_matrix = pe.MapNode(
         BIDSDataSink(
             base_directory=out_dir,
-            fixed_entities={"level": "run", 'suffix': 'design'},
+            fixed_entities={"level": "run", 'suffix': 'design', 'node': n_run},
             path_patterns=design_matrix_pattern,
         ),
         iterfield=['entities', 'in_file'],
@@ -223,7 +235,7 @@ def _deindex(tsv):
     ds_corr = pe.MapNode(
         BIDSDataSink(
             base_directory=out_dir,
-            fixed_entities={"level": "run", 'suffix': 'corr'},
+            fixed_entities={"level": "run", 'suffix': 'corr', 'node': n_run},
             path_patterns=image_pattern,
         ),
         iterfield=['entities', 'in_file'],
@@ -234,7 +246,7 @@ def _deindex(tsv):
     ds_run_contrasts = pe.MapNode(
         BIDSDataSink(
             base_directory=out_dir,
-            fixed_entities={"level": "run", 'suffix': 'contrasts'},
+            fixed_entities={"level": "run", 'suffix': 'contrasts', 'node': n_run},
             path_patterns=image_pattern,
         ),
         iterfield=['entities', 'in_file'],
@@ -333,20 +345,32 @@ def _select_specs(all_specs, name):
         )
 
         ds_contrast_maps = pe.Node(
-            BIDSDataSink(base_directory=out_dir, path_patterns=contrast_pattern),
+            BIDSDataSink(
+                base_directory=out_dir,
+                fixed_entities={'node': name},
+                path_patterns=contrast_pattern,
+            ),
             run_without_submitting=True,
             name=f'ds_{name}_contrast_maps',
         )
 
         ds_contrast_plots = pe.Node(
-            BIDSDataSink(base_directory=out_dir, path_patterns=contrast_plot_pattern),
+            BIDSDataSink(
+                base_directory=out_dir,
+                fixed_entities={'node': name},
+                path_patterns=contrast_plot_pattern,
+            ),
             run_without_submitting=True,
             name=f'ds_{name}_contrast_plots',
         )
 
         if level == 'run':
             ds_model_maps = pe.Node(
-                BIDSDataSink(base_directory=out_dir, path_patterns=model_map_pattern),
+                BIDSDataSink(
+                    base_directory=out_dir,
+                    fixed_entities={'node': name},
+                    path_patterns=model_map_pattern,
+                ),
                 run_without_submitting=True,
                 name=f'ds_{name}_model_maps',
             )
@@ -408,9 +432,13 @@ def _select_specs(all_specs, name):
                 model.inputs.smoothing_type = smoothing_type
             else:
                 if smoothing_type == "isoblurto":
-                    from nipype.interfaces.afni.preprocess import BlurToFWHM as smooth_interface
+                    from nipype.interfaces.afni.preprocess import (
+                        BlurToFWHM as smooth_interface,
+                    )
                 elif smoothing_type == "iso":
-                    from nipype.interfaces.afni.preprocess import BlurInMask as smooth_interface
+                    from nipype.interfaces.afni.preprocess import (
+                        BlurInMask as smooth_interface,
+                    )
                 smooth = pe.MapNode(
                     smooth_interface(), iterfield=["in_file", "mask"], name="smooth"
                 )