Merge pull request #114 from HALFpipe/dev/fix-high-pass-filter-cutoff

Fix skipping the high pass filter for task-based feature extraction

Dockerfile

@@ -45,7 +45,7 @@ RUN pip install git+https://github.com/pydata/patsy.git
 
 # install dependencies and force reinstall of nipreps and nipype
 RUN cd /halfpipe && \
-    pip uninstall --yes fmriprep smriprep niworkflows nipype && \
+    pip uninstall --yes fmriprep smriprep niworkflows nipype pybids && \
     pip install -r requirements.txt
 
 # download all resources

halfpipe/model/feature.py

@@ -45,9 +45,19 @@ class TaskBasedFeatureSchema(BaseFeatureSchema):
     conditions = fields.List(fields.Str())
     contrasts = fields.List(fields.Nested(TContrastSchema))
 
-    high_pass_filter_cutoff = fields.Float(default=125.0, missing=125., validate=validate.Range(min=0.0))
+    high_pass_filter_cutoff = fields.Float(
+        default=125.0,
+        missing=125.,
+        allow_nan=True,
+        allow_none=True,
+        validate=validate.Range(min=0.0)
+    )
 
-    hrf = fields.Str(default="dgamma", missing="dgamma", validate=validate.OneOf(["dgamma", "dgamma_with_derivs", "flobs"]))
+    hrf = fields.Str(
+        default="dgamma",
+        missing="dgamma",
+        validate=validate.OneOf(["dgamma", "dgamma_with_derivs", "flobs"])
+    )
 
 
 class SeedBasedConnectivityFeatureSchema(BaseFeatureSchema):

halfpipe/ui/feature/task.py

@@ -170,7 +170,9 @@ def next(self, ctx):
             if isinstance(value, float):
                 ctx.spec.features[-1].high_pass_filter_cutoff = value
             elif value == "Skip":
-                pass
+                ctx.spec.features[-1].high_pass_filter_cutoff = None
+            else:
+                raise ValueError(f'Unknown high_pass_filter_cutoff value "{value}"')
 
         this_next_step_type = next_step_type
 

halfpipe/workflow/feature/taskbased.py

@@ -4,6 +4,7 @@
 
 import os
 from pathlib import Path
+from math import isfinite
 
 import numpy as np
 
@@ -152,10 +153,13 @@ def init_taskbased_wf(
 
     # first level model specification
     modelspec = pe.Node(model.SpecifyModel(), name="modelspec")
+
+    modelspec.inputs.high_pass_filter_cutoff = np.inf  # disable if missing
     if hasattr(feature, "high_pass_filter_cutoff"):
-        modelspec.inputs.high_pass_filter_cutoff = feature.high_pass_filter_cutoff
-    else:
-        modelspec.inputs.high_pass_filter_cutoff = np.inf
+        hpfc = feature.high_pass_filter_cutoff
+        if isinstance(hpfc, float) and isfinite(hpfc):
+            modelspec.inputs.high_pass_filter_cutoff = hpfc
+
     workflow.connect(inputnode, "bold", modelspec, "functional_runs")
     workflow.connect(inputnode, "condition_units", modelspec, "input_units")
     workflow.connect(inputnode, "repetition_time", modelspec, "time_repetition")

requirements.txt

@@ -20,7 +20,7 @@ sdcflows == 1.3.3
 mriqc @ git+https://github.com/poldracklab/mriqc@0.15.3
 niworkflows @ git+https://github.com/hippocampusgirl/niworkflows.git@1.3.3+halfpipe.1
 templateflow @ git+https://github.com/templateflow/python-client@0.7.1
-pybids >= 0.13.0
+pybids @ git+https://github.com/hippocampusgirl/pybids.git@0.13+halfpipe.1
 flufl.lock >= 5.0.3
 fasteners >= 0.15
 inflect
@@ -37,4 +37,4 @@ pympler >= 0.9
 stackprinter >= 0.2.5
 line_profiler
 more-itertools >= 8.7.0
-calamities ~= 0.0.13
+calamities >= 0.0.14

setup.cfg

@@ -43,7 +43,7 @@ install_requires =
     mriqc
     niworkflows
     templateflow
-    pybids >= 0.13.0
+    pybids
     flufl.lock >= 5.0.3
     fasteners >= 0.15
     inflect
@@ -60,7 +60,7 @@ install_requires =
     stackprinter >= 0.2.5
     line_profiler
     more-itertools >= 8.7.0
-    calamities ~= 0.0.13
+    calamities >= 0.0.14
 packages = find:
 
 [options.entry_points]