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ENH: Drop FSL prefix from utils (#58)
* WIP: Drop FSL prefix from utils Improves consistency with Nipype. Compatibility aliases will be maintained in 0.0.x. * WIP: selectvols and roi * WIP: orient and reorient2std * WIP: merge + fixes * WIP: info and interleave * WIP: chfiletype and fft
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‎README.md

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@@ -26,17 +26,17 @@ for FMRI, MRI and DTI brain imaging data.
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## Available tasks
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| Module | Tasks |
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|----------|-----------------------------------------------------------------------------------------------------------------------------------------------------------|
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| bet | BET, RobustFOV |
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| eddy | Eddy, ApplyTopup, Topup |
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| fast | FAST |
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| flirt | FLIRT, ApplyXFM, ConcatXFM, ConvertXFM, InvertXFM, FixScaleSkew, Img2ImgCoord, Img2StdCoord, Std2ImgCoord |
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| fnirt | FNIRT, FNIRTFileUtils, ApplyWarp, ConvertWarp, InvWarp |
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| fugue | FUGUE, FSLPrepareFieldmap, Prelude, SigLoss |
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| fslmaths | (**experimental**) FSLMaths, Mul |
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| susan | SUSAN |
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| utils | FSLFFT, FSLROI, FSLChFileType, FSLInfo, FSLInterleave, FSLMerge, FSLOrient, FSLReorient2Std, FSLSelectVols, FSLSlice, FSLSmoothFill, FSLSplit, FSLSwapDim |
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| Module | Tasks |
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|----------|--------------------------------------------------------------------------------------------------------------------|
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| bet | BET, RobustFOV |
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| eddy | Eddy, ApplyTopup, Topup |
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| fast | FAST |
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| flirt | FLIRT, ApplyXFM, ConcatXFM, ConvertXFM, InvertXFM, FixScaleSkew, Img2ImgCoord, Img2StdCoord, Std2ImgCoord |
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| fnirt | FNIRT, FNIRTFileUtils, ApplyWarp, ConvertWarp, InvWarp |
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| fugue | FUGUE, FSLPrepareFieldmap, Prelude, SigLoss |
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| fslmaths | (**experimental**) FSLMaths, Mul |
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| susan | SUSAN |
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| utils | ChFileType, FFT, Info, Interleave, Merge, Orient, Reorient2Std, ROI, SelectVols, Slice, SmoothFill, Split, SwapDim |
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## Installation
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‎src/pydra/tasks/fsl/__init__.py

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from .fugue import FUGUE, FSLPrepareFieldmap, Prelude, SigLoss
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from .susan import SUSAN
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from .utils import (
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FSLFFT,
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FSLROI,
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FSLChFileType,
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FSLInfo,
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FSLInterleave,
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FSLMerge,
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FSLOrient,
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FSLReorient2Std,
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FSLSelectVols,
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FSLSlice,
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FSLSmoothFill,
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FSLSplit,
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FSLSwapDim,
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FFT,
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ROI,
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ChFileType,
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Info,
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Interleave,
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Merge,
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Orient,
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Reorient2Std,
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SelectVols,
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Slice,
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SmoothFill,
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Split,
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SwapDim,
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)
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# TODO: Drop compatibility aliases when 0.x is released.
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FSLFFT = FFT
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FSLROI = ROI
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FSLChFileType = ChFileType
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FSLInfo = Info
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FSLInterleave = Interleave
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FSLMerge = Merge
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FSLOrient = Orient
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FSLReorient2Std = Reorient2Std
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FSLSelectVols = SelectVols
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FSLSlice = Slice
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FSLSmoothFill = SmoothFill
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FSLSplit = Split
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FSLSwapDim = SwapDim

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

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Utils
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=====
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.. automodule:: pydra.tasks.fsl.utils.fslchfiletype
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.. automodule:: pydra.tasks.fsl.utils.fslfft
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.. automodule:: pydra.tasks.fsl.utils.fslinfo
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.. automodule:: pydra.tasks.fsl.utils.fslinterleave
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.. automodule:: pydra.tasks.fsl.utils.fslmerge
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.. automodule:: pydra.tasks.fsl.utils.fslorient
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.. automodule:: pydra.tasks.fsl.utils.fslreorient2std
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.. automodule:: pydra.tasks.fsl.utils.fslroi
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.. automodule:: pydra.tasks.fsl.utils.fslselectvols
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.. automodule:: pydra.tasks.fsl.utils.fslsmoothfill
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.. automodule:: pydra.tasks.fsl.utils.fslsplit
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.. automodule:: pydra.tasks.fsl.utils.fslswapdim
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.. automodule:: pydra.tasks.fsl.utils.chfiletype
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.. automodule:: pydra.tasks.fsl.utils.fft
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.. automodule:: pydra.tasks.fsl.utils.info
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.. automodule:: pydra.tasks.fsl.utils.interleave
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.. automodule:: pydra.tasks.fsl.utils.merge
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.. automodule:: pydra.tasks.fsl.utils.orient
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.. automodule:: pydra.tasks.fsl.utils.reorient2std
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.. automodule:: pydra.tasks.fsl.utils.roi
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.. automodule:: pydra.tasks.fsl.utils.selectvols
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.. automodule:: pydra.tasks.fsl.utils.smoothfill
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.. automodule:: pydra.tasks.fsl.utils.split
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.. automodule:: pydra.tasks.fsl.utils.swapdim
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"""
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from .fslchfiletype import FSLChFileType
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from .fslfft import FSLFFT
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from .fslinfo import FSLInfo
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from .fslinterleave import FSLInterleave
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from .fslmerge import FSLMerge
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from .fslorient import FSLOrient
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from .fslreorient2std import FSLReorient2Std
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from .fslroi import FSLROI
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from .fslselectvols import FSLSelectVols
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from .fslsmoothfill import FSLSmoothFill
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from .fslsplit import FSLSlice, FSLSplit
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from .fslswapdim import FSLSwapDim
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from .chfiletype import ChFileType
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from .fft import FFT
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from .info import Info
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from .interleave import Interleave
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from .merge import Merge
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from .orient import Orient
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from .reorient2std import Reorient2Std
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from .roi import ROI
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from .selectvols import SelectVols
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from .smoothfill import SmoothFill
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from .split import Slice, Split
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from .swapdim import SwapDim

‎src/pydra/tasks/fsl/utils/chfiletype.py

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"""
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ChFileType
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==========
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Convert image to a different NIfTI file format.
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Examples
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--------
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>>> task = ChFileType(filetype="NIFTI2_GZ", input_image="input.nii", output_basename="output")
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>>> task.cmdline
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'fslchfiletype NIFTI2_GZ input.nii output'
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"""
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__all__ = ["ChFileType"]
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from os import PathLike
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from pathlib import Path
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from attrs import define, field
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from pydra.engine.specs import File, ShellOutSpec, ShellSpec, SpecInfo
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from pydra.engine.task import ShellCommandTask
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ALLOWED_FILETYPES = {
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"ANALYZE",
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"ANALYZE_GZ",
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"NIFTI",
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"NIFTI_GZ",
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"NIFTI_STD::PAIR",
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"NIFTI_STD::PAIR_GZ",
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"NIFTI2",
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"NIFTI2_GZ",
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"NIFTI2_STD::PAIR",
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"NIFTI2_STD::PAIR_GZ",
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}
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def _get_output_basename(output_basename, input_image):
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return output_basename or Path(input_image).name.split(".", 1)[0]
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def _get_output_image(output_basename, input_image, filetype):
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output_basename = _get_output_basename(output_basename, input_image)
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extension = "img" if any(pat in filetype for pat in ["ANALYZE", "PAIR"]) else "nii"
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if "GZ" in filetype:
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extension += ".gz"
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return Path.cwd() / f"{output_basename}.{extension}"
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def _get_output_header(output_basename, input_image, filetype):
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output_basename = _get_output_basename(output_basename, input_image)
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if any(pat in filetype for pat in ["ANALYZE", "PAIR"]):
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extension = "hdr.gz" if "GZ" in filetype else "hdr"
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return Path.cwd() / f"{output_basename}.{extension}"
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else:
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return None
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@define(kw_only=True)
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class ChFileTypeSpec(ShellSpec):
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"""Specifications for fslchfiletype."""
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filetype: str = field(
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metadata={
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"help_string": "change to this file type",
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"mandatory": True,
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"argstr": "",
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"allowed_values": ALLOWED_FILETYPES,
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}
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)
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input_image: PathLike = field(metadata={"help_string": "input image", "mandatory": True, "argstr": ""})
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output_basename: str = field(metadata={"help_string": "output basename", "formatter": _get_output_basename})
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@define(slots=False, kw_only=True)
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class ChFileTypeOutSpec(ShellOutSpec):
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"""Output specifications for fslchfiletype."""
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output_image: File = field(metadata={"help_string": "output image", "callable": _get_output_image})
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output_header: File = field(
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metadata={"help_string": "output header for filetypes which support it", "callable": _get_output_header}
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)
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class ChFileType(ShellCommandTask):
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"""Task definition for fslchfiletype."""
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executable = "fslchfiletype"
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input_spec = SpecInfo(name="Input", bases=(ChFileTypeSpec,))
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output_spec = SpecInfo(name="Output", bases=(ChFileTypeOutSpec,))

‎src/pydra/tasks/fsl/utils/fft.py

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"""
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FFT (Fast Fourier Transform)
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============================
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Compute the forward or inverse Fast Fourier Transform of a NIfTI image.
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Examples
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--------
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Compute the forward FFT:
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>>> task = FFT(input_image="input.nii")
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>>> task.cmdline # doctest: +ELLIPSIS
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'fslfft input.nii .../input_fft.nii'
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Compute the inverse FFT:
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>>> task = FFT(input_image="input.nii", output_image="output.nii", inverse=True)
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>>> task.cmdline
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'fslfft input.nii output.nii -inv'
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"""
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__all__ = ["FFT"]
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from os import PathLike
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from attrs import define, field
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from pydra.engine.specs import ShellSpec, SpecInfo
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from pydra.engine.task import ShellCommandTask
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@define(kw_only=True)
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class FFTSpec(ShellSpec):
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"""Specifications for fslfft."""
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input_image: PathLike = field(metadata={"help_string": "input image", "mandatory": True, "argstr": ""})
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output_image: str = field(
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metadata={"help_string": "output image", "argstr": "", "output_file_template": "{input_image}_fft"}
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)
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inverse: bool = field(metadata={"help_string": "compute the inverse FFT", "argstr": "-inv"})
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class FFT(ShellCommandTask):
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"""Task definition for fslfft."""
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executable = "fslfft"
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input_spec = SpecInfo(name="Input", bases=(FFTSpec,))

‎src/pydra/tasks/fsl/utils/fslchfiletype.py

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