Drop old stuff.

sdcflows/conftest.py

@@ -72,7 +72,6 @@ def doctest_fixture(doctest_namespace, request):
             dsA_dir=data_dir / "dsA",
             dsB_dir=data_dir / "dsB",
             dsC_dir=data_dir / "dsC",
-            dsD_dir=data_dir / "dsD",
         )
         doctest_namespace.update((key, Path(val.root)) for key, val in layouts.items())
 

sdcflows/interfaces/fmap.py

@@ -52,7 +52,7 @@ class _PhaseMap2radsOutputSpec(TraitedSpec):
 
 
 class PhaseMap2rads(SimpleInterface):
-    """Convert a phase map given in a.u. (e.g., 0-4096) to radians."""
+    """Convert a phase map given in a.u. (e.g., 0-4096) to radians (0 to 2pi)."""
 
     input_spec = _PhaseMap2radsInputSpec
     output_spec = _PhaseMap2radsOutputSpec
@@ -73,7 +73,10 @@ class _PhaseMap2rads2OutputSpec(TraitedSpec):
 
 
 class PhaseMap2rads2(SimpleInterface):
-    """Convert a phase map given in a.u. (e.g., 0-4096) to radians."""
+    """Convert a phase map given in a.u. (e.g., 0-4096) to radians (-pi to pi).
+
+    This differs from PhaseMap2rads, which scales the phase to [0, 2*pi].
+    """
 
     input_spec = _PhaseMap2rads2InputSpec
     output_spec = _PhaseMap2rads2OutputSpec

sdcflows/utils/phasemanip.py

@@ -24,7 +24,7 @@
 
 
 def au2rads(in_file, newpath=None):
-    """Convert the input phase map in arbitrary units (a.u.) to rads."""
+    """Convert the input phase map in arbitrary units (a.u.) to rads (0 to 2pi)."""
     import numpy as np
     import nibabel as nb
     from nipype.utils.filemanip import fname_presuffix
@@ -47,7 +47,10 @@ def au2rads(in_file, newpath=None):
 
 
 def au2rads2(in_file, newpath=None):
-    """Convert the input phase map in arbitrary units (a.u.) to rads (-pi to pi)."""
+    """Convert the input phase map in arbitrary units (a.u.) to rads (-pi to pi).
+
+    This differs from au2rads, which scales the phase to [0, 2*pi].
+    """
     import numpy as np
     import nibabel as nb
     from nipype.utils.filemanip import fname_presuffix
@@ -58,6 +61,7 @@ def au2rads2(in_file, newpath=None):
 
     # Rescale to [0, 2*pi]
     data = (data - data.min()) * (2 * np.pi / (data.max() - data.min()))
+    # Rescale to [-pi, pi]
     data = data - np.pi
 
     # Round to float32 and clip

sdcflows/utils/wrangler.py

@@ -321,15 +321,6 @@ def find_estimators(
     FieldmapEstimation(sources=<2 files>, method=<EstimatorType.ANAT: 5>,
                        bids_id='auto_...')]
 
-    It should find MEDIC-style files too:
-
-    >>> find_estimators(
-    ...     layout=layouts['dsD'],
-    ...     subject="01",
-    ... )  # doctest: +ELLIPSIS
-    [FieldmapEstimation(sources=<10 files>, method=<EstimatorType.MEDIC: 10>,
-                        bids_id='medic')]
-
     """
     from .misc import create_logger
     from bids.layout import Query