Merge pull request #45 from ghisvail/new/fslsmoothfill

NEW: Add task definition for fslsmoothfill
aramis-lab · May 4, 2023 · d1d0a8f · d1d0a8f
2 parents 94e2e9e + 58e75a5
commit d1d0a8f
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Showing 4 changed files with 58 additions and 10 deletions.
diff --git a/README.md b/README.md
@@ -25,16 +25,16 @@ for FMRI, MRI and DTI brain imaging data.
 
 ## Available tasks
 
-| Module | Tasks                                                                                                                                     |
-|--------|-------------------------------------------------------------------------------------------------------------------------------------------|
-| bet    | BET, RobustFOV                                                                                                                            |
-| eddy   | Eddy                                                                                                                                      |
-| fast   | FAST                                                                                                                                      |
-| flirt  | FLIRT, ApplyXFM, ConcatXFM, ConvertXFM, InvertXFM, Img2ImgCoord, Img2StdCoord, Std2ImgCoord                                               |
-| fnirt  | FNIRT, FNIRTFileUtils, ApplyWarp, ConvertWarp, InvWarp                                                                                    |
-| fugue  | FUGUE                                                                                                                                     |
-| susan  | SUSAN                                                                                                                                     |
-| utils  | fslmaths, FSLFFT, FSLROI, FSLChFileType, FSLInfo, FSLInterleave, FSLMerge, FSLReorient2Std, FSLSelectVols, FSLSlice, FSLSplit, FSLSwapDim |
+| Module | Tasks                                                                                                                                                    |
+|--------|----------------------------------------------------------------------------------------------------------------------------------------------------------|
+| bet    | BET, RobustFOV                                                                                                                                           |
+| eddy   | Eddy                                                                                                                                                     |
+| fast   | FAST                                                                                                                                                     |
+| flirt  | FLIRT, ApplyXFM, ConcatXFM, ConvertXFM, InvertXFM, Img2ImgCoord, Img2StdCoord, Std2ImgCoord                                                              |
+| fnirt  | FNIRT, FNIRTFileUtils, ApplyWarp, ConvertWarp, InvWarp                                                                                                   |
+| fugue  | FUGUE                                                                                                                                                    |
+| susan  | SUSAN                                                                                                                                                    |
+| utils  | fslmaths, FSLFFT, FSLROI, FSLChFileType, FSLInfo, FSLInterleave, FSLMerge, FSLReorient2Std, FSLSelectVols, FSLSlice, FSLSmoothFill, FSLSplit, FSLSwapDim |
 
 ## Installation
 

diff --git a/src/pydra/tasks/fsl/__init__.py b/src/pydra/tasks/fsl/__init__.py
@@ -29,6 +29,7 @@
     FSLReorient2Std,
     FSLSelectVols,
     FSLSlice,
+    FSLSmoothFill,
     FSLSplit,
     FSLSwapDim,
     fslmaths,

diff --git a/src/pydra/tasks/fsl/utils/__init__.py b/src/pydra/tasks/fsl/utils/__init__.py
@@ -7,5 +7,6 @@
 from .fslreorient2std import FSLReorient2Std
 from .fslroi import FSLROI
 from .fslselectvols import FSLSelectVols
+from .fslsmoothfill import FSLSmoothFill
 from .fslsplit import FSLSlice, FSLSplit
 from .fslswapdim import FSLSwapDim
diff --git a/src/pydra/tasks/fsl/utils/fslsmoothfill.py b/src/pydra/tasks/fsl/utils/fslsmoothfill.py
@@ -0,0 +1,46 @@
+"""
+FSLSmoothFill
+=============
+
+Examples
+--------
+
+>>> task = FSLSmoothFill(input_image="input.nii", output_image="smoothed.nii", input_mask="mask.nii")
+>>> task.cmdline
+'fslsmoothfill --in input.nii --out smoothed.nii --mask mask.nii'
+"""
+
+__all__ = ["FSLSmoothFill"]
+
+import os
+
+import attrs
+
+import pydra
+
+
+@attrs.define(slots=False, kw_only=True)
+class FSLSmoothFillSpec(pydra.specs.ShellSpec):
+    """Specifications for fslsmoothfill."""
+
+    input_image: os.PathLike = attrs.field(metadata={"help_string": "input image", "mandatory": True, "argstr": "--in"})
+
+    output_image: str = attrs.field(
+        metadata={
+            "help_string": "output image",
+            "argstr": "--out",
+            "output_file_template": "{input_image}_smoothed",
+        }
+    )
+
+    input_mask: os.PathLike = attrs.field(metadata={"help_string": "input mask", "argstr": "--mask"})
+
+    num_iterations: int = attrs.field(metadata={"help_string": "number of iterations", "argstr": "--niter"})
+
+
+class FSLSmoothFill(pydra.engine.ShellCommandTask):
+    """Task definition for fslsmoothfill."""
+
+    executable = "fslsmoothfill"
+
+    input_spec = pydra.specs.SpecInfo(name="Inputs", bases=(FSLSmoothFillSpec,))