niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/un_warp_epi_py.py

@@ -0,0 +1,232 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+UN_WARP_EPI_PY_METADATA = Metadata(
+    id="e93607b1115d9db7a51efc4be5147b1c6e23ca56.boutiques",
+    name="unWarpEPI.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+UnWarpEpiPyParameters = typing.TypedDict('UnWarpEpiPyParameters', {
+    "__STYX_TYPE__": typing.Literal["unWarpEPI.py"],
+    "forward": InputPathType,
+    "reverse": InputPathType,
+    "anat4warp": InputPathType,
+    "data": str,
+    "subjID": str,
+    "giant_move": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "unWarpEPI.py": un_warp_epi_py_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class UnWarpEpiPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `un_warp_epi_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def un_warp_epi_py_params(
+    forward: InputPathType,
+    reverse: InputPathType,
+    anat4warp: InputPathType,
+    data: str,
+    subj_id: str,
+    giant_move: bool = False,
+) -> UnWarpEpiPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        forward: Calibration matching data to be corrected.
+        reverse: Calibration with opposing polarity to data to be corrected.
+        anat4warp: Reference anatomical dataset.
+        data: Data to be corrected (same polarity as forward calibration data).\
+            Separate with commas if specifying multiple datasets.
+        subj_id: ID of subject to be corrected.
+        giant_move: Set giant_move option for align_epi_anat if final align of\
+            anatomy to corrected EPI fails if datasets are far apart in space.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "unWarpEPI.py",
+        "forward": forward,
+        "reverse": reverse,
+        "anat4warp": anat4warp,
+        "data": data,
+        "subjID": subj_id,
+        "giant_move": giant_move,
+    }
+    return params
+
+
+def un_warp_epi_py_cargs(
+    params: UnWarpEpiPyParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("unWarpEPI.py")
+    cargs.extend([
+        "-f",
+        execution.input_file(params.get("forward"))
+    ])
+    cargs.extend([
+        "-r",
+        execution.input_file(params.get("reverse"))
+    ])
+    cargs.extend([
+        "-a",
+        execution.input_file(params.get("anat4warp"))
+    ])
+    cargs.extend([
+        "-d",
+        params.get("data")
+    ])
+    cargs.extend([
+        "-s",
+        params.get("subjID")
+    ])
+    if params.get("giant_move"):
+        cargs.append("-g")
+    return cargs
+
+
+def un_warp_epi_py_outputs(
+    params: UnWarpEpiPyParameters,
+    execution: Execution,
+) -> UnWarpEpiPyOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = UnWarpEpiPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def un_warp_epi_py_execute(
+    params: UnWarpEpiPyParameters,
+    execution: Execution,
+) -> UnWarpEpiPyOutputs:
+    """
+    Routine to unwarp EPI data set using another data set with opposite polarity.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `UnWarpEpiPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = un_warp_epi_py_cargs(params, execution)
+    ret = un_warp_epi_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def un_warp_epi_py(
+    forward: InputPathType,
+    reverse: InputPathType,
+    anat4warp: InputPathType,
+    data: str,
+    subj_id: str,
+    giant_move: bool = False,
+    runner: Runner | None = None,
+) -> UnWarpEpiPyOutputs:
+    """
+    Routine to unwarp EPI data set using another data set with opposite polarity.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        forward: Calibration matching data to be corrected.
+        reverse: Calibration with opposing polarity to data to be corrected.
+        anat4warp: Reference anatomical dataset.
+        data: Data to be corrected (same polarity as forward calibration data).\
+            Separate with commas if specifying multiple datasets.
+        subj_id: ID of subject to be corrected.
+        giant_move: Set giant_move option for align_epi_anat if final align of\
+            anatomy to corrected EPI fails if datasets are far apart in space.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `UnWarpEpiPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UN_WARP_EPI_PY_METADATA)
+    params = un_warp_epi_py_params(
+        forward=forward,
+        reverse=reverse,
+        anat4warp=anat4warp,
+        data=data,
+        subj_id=subj_id,
+        giant_move=giant_move,
+    )
+    return un_warp_epi_py_execute(params, execution)
+
+
+__all__ = [
+    "UN_WARP_EPI_PY_METADATA",
+    "UnWarpEpiPyOutputs",
+    "UnWarpEpiPyParameters",
+    "un_warp_epi_py",
+    "un_warp_epi_py_params",
+]

niwrap_afni/afni/uniq_images.py

@@ -0,0 +1,180 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+UNIQ_IMAGES_METADATA = Metadata(
+    id="78da67a816d6d0b1ae55b072a61c7cc76bbe87da.boutiques",
+    name="uniq_images",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+UniqImagesParameters = typing.TypedDict('UniqImagesParameters', {
+    "__STYX_TYPE__": typing.Literal["uniq_images"],
+    "input_files": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "uniq_images": uniq_images_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "uniq_images": uniq_images_outputs,
+    }.get(t)
+
+
+class UniqImagesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `uniq_images(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    unique_files_list: OutputPathType
+    """Generated list of filenames with unique images"""
+
+
+def uniq_images_params(
+    input_files: list[InputPathType],
+) -> UniqImagesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: List of image filenames to be processed.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "uniq_images",
+        "input_files": input_files,
+    }
+    return params
+
+
+def uniq_images_cargs(
+    params: UniqImagesParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("uniq_images")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    return cargs
+
+
+def uniq_images_outputs(
+    params: UniqImagesParameters,
+    execution: Execution,
+) -> UniqImagesOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = UniqImagesOutputs(
+        root=execution.output_file("."),
+        unique_files_list=execution.output_file("unique_images_list.txt"),
+    )
+    return ret
+
+
+def uniq_images_execute(
+    params: UniqImagesParameters,
+    execution: Execution,
+) -> UniqImagesOutputs:
+    """
+    Simple program to read in a list of image filenames, determine which files have
+    unique images inside, and echo out only a list of the filenames with unique
+    images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `UniqImagesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = uniq_images_cargs(params, execution)
+    ret = uniq_images_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def uniq_images(
+    input_files: list[InputPathType],
+    runner: Runner | None = None,
+) -> UniqImagesOutputs:
+    """
+    Simple program to read in a list of image filenames, determine which files have
+    unique images inside, and echo out only a list of the filenames with unique
+    images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: List of image filenames to be processed.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `UniqImagesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(UNIQ_IMAGES_METADATA)
+    params = uniq_images_params(
+        input_files=input_files,
+    )
+    return uniq_images_execute(params, execution)
+
+
+__all__ = [
+    "UNIQ_IMAGES_METADATA",
+    "UniqImagesOutputs",
+    "UniqImagesParameters",
+    "uniq_images",
+    "uniq_images_params",
+]

niwrap_afni/afni/v_1d_apar2mat.py

@@ -0,0 +1,262 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_APAR2MAT_METADATA = Metadata(
+    id="ca46e845c2aeb2bfc0d1ca66f53ca7adef2d7e64.boutiques",
+    name="1dApar2mat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dApar2matParameters = typing.TypedDict('V1dApar2matParameters', {
+    "__STYX_TYPE__": typing.Literal["1dApar2mat"],
+    "x_shift": float,
+    "y_shift": float,
+    "z_shift": float,
+    "z_angle": float,
+    "x_angle": float,
+    "y_angle": float,
+    "x_scale": float,
+    "y_scale": float,
+    "z_scale": float,
+    "y_x_shear": float,
+    "z_x_shear": float,
+    "z_y_shear": float,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dApar2mat": v_1d_apar2mat_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class V1dApar2matOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_apar2mat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_1d_apar2mat_params(
+    x_shift: float,
+    y_shift: float,
+    z_shift: float,
+    z_angle: float,
+    x_angle: float,
+    y_angle: float,
+    x_scale: float,
+    y_scale: float,
+    z_scale: float,
+    y_x_shear: float,
+    z_x_shear: float,
+    z_y_shear: float,
+) -> V1dApar2matParameters:
+    """
+    Build parameters.
+    
+    Args:
+        x_shift: x-shift in mm.
+        y_shift: y-shift in mm.
+        z_shift: z-shift in mm.
+        z_angle: z-angle (roll) in degrees.
+        x_angle: x-angle (pitch) in degrees.
+        y_angle: y-angle (yaw) in degrees.
+        x_scale: x-scale factor in [0.10,10.0].
+        y_scale: y-scale factor in [0.10,10.0].
+        z_scale: z-scale factor in [0.10,10.0].
+        y_x_shear: y/x-shear factor in [-0.3333,0.3333].
+        z_x_shear: z/x-shear factor in [-0.3333,0.3333].
+        z_y_shear: z/y-shear factor in [-0.3333,0.3333].
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dApar2mat",
+        "x_shift": x_shift,
+        "y_shift": y_shift,
+        "z_shift": z_shift,
+        "z_angle": z_angle,
+        "x_angle": x_angle,
+        "y_angle": y_angle,
+        "x_scale": x_scale,
+        "y_scale": y_scale,
+        "z_scale": z_scale,
+        "y_x_shear": y_x_shear,
+        "z_x_shear": z_x_shear,
+        "z_y_shear": z_y_shear,
+    }
+    return params
+
+
+def v_1d_apar2mat_cargs(
+    params: V1dApar2matParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("1dApar2mat")
+    cargs.append(str(params.get("x_shift")))
+    cargs.append(str(params.get("y_shift")))
+    cargs.append(str(params.get("z_shift")))
+    cargs.append(str(params.get("z_angle")))
+    cargs.append(str(params.get("x_angle")))
+    cargs.append(str(params.get("y_angle")))
+    cargs.append(str(params.get("x_scale")))
+    cargs.append(str(params.get("y_scale")))
+    cargs.append(str(params.get("z_scale")))
+    cargs.append(str(params.get("y_x_shear")))
+    cargs.append(str(params.get("z_x_shear")))
+    cargs.append(str(params.get("z_y_shear")))
+    return cargs
+
+
+def v_1d_apar2mat_outputs(
+    params: V1dApar2matParameters,
+    execution: Execution,
+) -> V1dApar2matOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = V1dApar2matOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_1d_apar2mat_execute(
+    params: V1dApar2matParameters,
+    execution: Execution,
+) -> V1dApar2matOutputs:
+    """
+    Computes the affine transformation matrix from the set of 3dAllineate
+    parameters.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dApar2matOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_apar2mat_cargs(params, execution)
+    ret = v_1d_apar2mat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_apar2mat(
+    x_shift: float,
+    y_shift: float,
+    z_shift: float,
+    z_angle: float,
+    x_angle: float,
+    y_angle: float,
+    x_scale: float,
+    y_scale: float,
+    z_scale: float,
+    y_x_shear: float,
+    z_x_shear: float,
+    z_y_shear: float,
+    runner: Runner | None = None,
+) -> V1dApar2matOutputs:
+    """
+    Computes the affine transformation matrix from the set of 3dAllineate
+    parameters.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        x_shift: x-shift in mm.
+        y_shift: y-shift in mm.
+        z_shift: z-shift in mm.
+        z_angle: z-angle (roll) in degrees.
+        x_angle: x-angle (pitch) in degrees.
+        y_angle: y-angle (yaw) in degrees.
+        x_scale: x-scale factor in [0.10,10.0].
+        y_scale: y-scale factor in [0.10,10.0].
+        z_scale: z-scale factor in [0.10,10.0].
+        y_x_shear: y/x-shear factor in [-0.3333,0.3333].
+        z_x_shear: z/x-shear factor in [-0.3333,0.3333].
+        z_y_shear: z/y-shear factor in [-0.3333,0.3333].
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dApar2matOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_APAR2MAT_METADATA)
+    params = v_1d_apar2mat_params(
+        x_shift=x_shift,
+        y_shift=y_shift,
+        z_shift=z_shift,
+        z_angle=z_angle,
+        x_angle=x_angle,
+        y_angle=y_angle,
+        x_scale=x_scale,
+        y_scale=y_scale,
+        z_scale=z_scale,
+        y_x_shear=y_x_shear,
+        z_x_shear=z_x_shear,
+        z_y_shear=z_y_shear,
+    )
+    return v_1d_apar2mat_execute(params, execution)
+
+
+__all__ = [
+    "V1dApar2matOutputs",
+    "V1dApar2matParameters",
+    "V_1D_APAR2MAT_METADATA",
+    "v_1d_apar2mat",
+    "v_1d_apar2mat_params",
+]