ENH: Drop FSL prefix from prepare_fieldmap (#59)

Author: ghisvail

src/pydra/tasks/fsl/__init__.py

@@ -33,7 +33,7 @@
     Std2ImgCoord,
 )
 from .fnirt import FNIRT, ApplyWarp, ConvertWarp, FNIRTFileUtils, InvWarp
-from .fugue import FUGUE, FSLPrepareFieldmap, Prelude, SigLoss
+from .fugue import FUGUE, Prelude, PrepareFieldmap, SigLoss
 from .susan import SUSAN
 from .utils import (
     FFT,
@@ -59,6 +59,7 @@
 FSLInterleave = Interleave
 FSLMerge = Merge
 FSLOrient = Orient
+FSLPrepareFieldmap = PrepareFieldmap
 FSLReorient2Std = Reorient2Std
 FSLSelectVols = SelectVols
 FSLSlice = Slice

src/pydra/tasks/fsl/fugue/__init__.py

@@ -3,12 +3,12 @@
 =====
 
 .. automodule:: pydra.tasks.fsl.fugue.fugue
-.. automodule:: pydra.tasks.fsl.fugue.fsl_prepare_fieldmap
+.. automodule:: pydra.tasks.fsl.fugue.prepare_fieldmap
 .. automodule:: pydra.tasks.fsl.fugue.prelude
 .. automodule:: pydra.tasks.fsl.fugue.sigloss
 """
 
-from .fsl_prepare_fieldmap import FSLPrepareFieldmap
 from .fugue import FUGUE
 from .prelude import Prelude
+from .prepare_fieldmap import PrepareFieldmap
 from .sigloss import SigLoss

src/pydra/tasks/fsl/fugue/fsl_prepare_fieldmap.py

@@ -0,0 +1,60 @@
+"""
+PrepareFieldmap
+===============
+
+EPI fieldmap preprocessing.
+
+Examples
+========
+
+>>> task = PrepareFieldmap(phase_image="gre_phase.nii", magnitude_image="gre_mag.nii", output_image="fmap.nii")
+>>> task.cmdline
+'fsl_prepare_fieldmap SIEMENS gre_phase.nii gre_mag.nii fmap.nii 2.46'
+"""
+
+__all__ = ["PrepareFieldmap"]
+
+from os import PathLike
+
+from attrs import define, field
+from pydra.engine.specs import ShellSpec, SpecInfo
+from pydra.engine.task import ShellCommandTask
+
+
+@define(kw_only=True)
+class PrepareFieldmapSpec(ShellSpec):
+    """Specifications for fsl_prepare_fieldmap."""
+
+    scanner: str = field(default="SIEMENS", metadata={"help_string": "scanner (usually SIEMENS)", "argstr": ""})
+
+    phase_image: PathLike = field(metadata={"help_string": "phase image", "mandatory": True, "argstr": ""})
+
+    magnitude_image: PathLike = field(
+        metadata={"help_string": "magnitude (brain extracted) image", "mandatory": True, "argstr": ""}
+    )
+
+    output_image: str = field(
+        metadata={
+            "help_string": "output fieldmap image in rad/s",
+            "argstr": "",
+            "output_file_template": "{phase_image}_fmap",
+        }
+    )
+
+    delta_te: float = field(
+        default=2.46,
+        metadata={
+            "help_string": "echo time difference of the fieldmap sequence in milliseconds (usually 2.46 on SIEMENS)",
+            "argstr": "",
+        },
+    )
+
+    no_check: bool = field(metadata={"help_string": "disable sanity checks for images", "argstr": "--nocheck"})
+
+
+class PrepareFieldmap(ShellCommandTask):
+    """Task definition for fsl_prepare_fieldmap."""
+
+    executable = "fsl_prepare_fieldmap"
+
+    input_spec = SpecInfo(name="Input", bases=(PrepareFieldmapSpec,))