niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__xyz_to_ijk.py

@@ -0,0 +1,221 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__XYZ_TO_IJK_METADATA = Metadata(
+    id="0cb41267f9ba92100e532b1ea585dcb9d2d9ce27.boutiques",
+    name="@xyz_to_ijk",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VXyzToIjkParameters = typing.TypedDict('VXyzToIjkParameters', {
+    "__STYX_TYPE__": typing.Literal["@xyz_to_ijk"],
+    "inset": InputPathType,
+    "x_coord": float,
+    "y_coord": float,
+    "z_coord": float,
+    "prefix": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@xyz_to_ijk": v__xyz_to_ijk_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 {
+        "@xyz_to_ijk": v__xyz_to_ijk_outputs,
+    }.get(t)
+
+
+class VXyzToIjkOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__xyz_to_ijk(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Output file containing the translated indices"""
+
+
+def v__xyz_to_ijk_params(
+    inset: InputPathType,
+    x_coord: float,
+    y_coord: float,
+    z_coord: float,
+    prefix: str | None = None,
+) -> VXyzToIjkParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inset: Volumetric file name (e.g. FILE.nii.gz).
+        x_coord: Three coordinates (in units of the dataset, like mm).
+        y_coord: Three coordinates (in units of the dataset, like mm).
+        z_coord: Three coordinates (in units of the dataset, like mm).
+        prefix: File name (including path) to output the three indices.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@xyz_to_ijk",
+        "inset": inset,
+        "x_coord": x_coord,
+        "y_coord": y_coord,
+        "z_coord": z_coord,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v__xyz_to_ijk_cargs(
+    params: VXyzToIjkParameters,
+    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("@xyz_to_ijk")
+    cargs.extend([
+        "-inset",
+        execution.input_file(params.get("inset"))
+    ])
+    cargs.extend([
+        "-xyz",
+        str(params.get("x_coord"))
+    ])
+    cargs.append(str(params.get("y_coord")))
+    cargs.append(str(params.get("z_coord")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    return cargs
+
+
+def v__xyz_to_ijk_outputs(
+    params: VXyzToIjkParameters,
+    execution: Execution,
+) -> VXyzToIjkOutputs:
+    """
+    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 = VXyzToIjkOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__xyz_to_ijk_execute(
+    params: VXyzToIjkParameters,
+    execution: Execution,
+) -> VXyzToIjkOutputs:
+    """
+    Helper script to convert (x, y, z) coordinates to (i, j, k) indices for a
+    volumetric dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VXyzToIjkOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__xyz_to_ijk_cargs(params, execution)
+    ret = v__xyz_to_ijk_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__xyz_to_ijk(
+    inset: InputPathType,
+    x_coord: float,
+    y_coord: float,
+    z_coord: float,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> VXyzToIjkOutputs:
+    """
+    Helper script to convert (x, y, z) coordinates to (i, j, k) indices for a
+    volumetric dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        inset: Volumetric file name (e.g. FILE.nii.gz).
+        x_coord: Three coordinates (in units of the dataset, like mm).
+        y_coord: Three coordinates (in units of the dataset, like mm).
+        z_coord: Three coordinates (in units of the dataset, like mm).
+        prefix: File name (including path) to output the three indices.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VXyzToIjkOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__XYZ_TO_IJK_METADATA)
+    params = v__xyz_to_ijk_params(
+        inset=inset,
+        x_coord=x_coord,
+        y_coord=y_coord,
+        z_coord=z_coord,
+        prefix=prefix,
+    )
+    return v__xyz_to_ijk_execute(params, execution)
+
+
+__all__ = [
+    "VXyzToIjkOutputs",
+    "VXyzToIjkParameters",
+    "V__XYZ_TO_IJK_METADATA",
+    "v__xyz_to_ijk",
+    "v__xyz_to_ijk_params",
+]

niwrap_afni/afni/vecwarp.py

@@ -0,0 +1,265 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+VECWARP_METADATA = Metadata(
+    id="b6a386dcbdfb7b07edd1e2d0325362df44cdb19e.boutiques",
+    name="Vecwarp",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VecwarpParameters = typing.TypedDict('VecwarpParameters', {
+    "__STYX_TYPE__": typing.Literal["Vecwarp"],
+    "apar": typing.NotRequired[InputPathType | None],
+    "matvec": typing.NotRequired[InputPathType | None],
+    "forward": bool,
+    "backward": bool,
+    "input": typing.NotRequired[InputPathType | None],
+    "output": typing.NotRequired[str | None],
+    "force": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "Vecwarp": vecwarp_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 {
+        "Vecwarp": vecwarp_outputs,
+    }.get(t)
+
+
+class VecwarpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `vecwarp(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """The output file containing the transformed 3-vectors."""
+
+
+def vecwarp_params(
+    apar: InputPathType | None = None,
+    matvec: InputPathType | None = None,
+    forward: bool = False,
+    backward: bool = False,
+    input_: InputPathType | None = None,
+    output: str | None = None,
+    force: bool = False,
+) -> VecwarpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        apar: Use the AFNI dataset 'aaa' as the source of the transformation;\
+            this dataset must be in +acpc or +tlrc coordinates, and must contain\
+            the attributes WARP_TYPE and WARP_DATA which describe the forward\
+            transformation from +orig coordinates to the 'aaa' coordinate system.
+        matvec: Read an affine transformation matrix-vector from file 'mmm',\
+            which must be in the specified format.
+        forward: To apply the forward transformation. If neither -forward nor\
+            -backward is given, -forward is the default.
+        backward: To apply the backward transformation.
+        input_: Read input 3-vectors from the file 'iii' (from stdin if 'iii'\
+            is '-' or the -input option is missing).
+        output: Write the output to file 'ooo' (to stdout if 'ooo' is '-', or\
+            if the -output option is missing).
+        force: If the output file already exists, use -force to overwrite it.\
+            If -force is used, it must come before -output on the command line.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "Vecwarp",
+        "forward": forward,
+        "backward": backward,
+        "force": force,
+    }
+    if apar is not None:
+        params["apar"] = apar
+    if matvec is not None:
+        params["matvec"] = matvec
+    if input_ is not None:
+        params["input"] = input_
+    if output is not None:
+        params["output"] = output
+    return params
+
+
+def vecwarp_cargs(
+    params: VecwarpParameters,
+    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("Vecwarp")
+    if params.get("apar") is not None:
+        cargs.extend([
+            "-apar",
+            execution.input_file(params.get("apar"))
+        ])
+    if params.get("matvec") is not None:
+        cargs.extend([
+            "-matvec",
+            execution.input_file(params.get("matvec"))
+        ])
+    if params.get("forward"):
+        cargs.append("-forward")
+    if params.get("backward"):
+        cargs.append("-backward")
+    if params.get("input") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input"))
+        ])
+    if params.get("output") is not None:
+        cargs.extend([
+            "-output",
+            params.get("output")
+        ])
+    if params.get("force"):
+        cargs.append("-force")
+    return cargs
+
+
+def vecwarp_outputs(
+    params: VecwarpParameters,
+    execution: Execution,
+) -> VecwarpOutputs:
+    """
+    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 = VecwarpOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output")) if (params.get("output") is not None) else None,
+    )
+    return ret
+
+
+def vecwarp_execute(
+    params: VecwarpParameters,
+    execution: Execution,
+) -> VecwarpOutputs:
+    """
+    Transforms (warps) a list of 3-vectors into another list of 3-vectors according
+    to the specified options.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VecwarpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = vecwarp_cargs(params, execution)
+    ret = vecwarp_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def vecwarp(
+    apar: InputPathType | None = None,
+    matvec: InputPathType | None = None,
+    forward: bool = False,
+    backward: bool = False,
+    input_: InputPathType | None = None,
+    output: str | None = None,
+    force: bool = False,
+    runner: Runner | None = None,
+) -> VecwarpOutputs:
+    """
+    Transforms (warps) a list of 3-vectors into another list of 3-vectors according
+    to the specified options.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        apar: Use the AFNI dataset 'aaa' as the source of the transformation;\
+            this dataset must be in +acpc or +tlrc coordinates, and must contain\
+            the attributes WARP_TYPE and WARP_DATA which describe the forward\
+            transformation from +orig coordinates to the 'aaa' coordinate system.
+        matvec: Read an affine transformation matrix-vector from file 'mmm',\
+            which must be in the specified format.
+        forward: To apply the forward transformation. If neither -forward nor\
+            -backward is given, -forward is the default.
+        backward: To apply the backward transformation.
+        input_: Read input 3-vectors from the file 'iii' (from stdin if 'iii'\
+            is '-' or the -input option is missing).
+        output: Write the output to file 'ooo' (to stdout if 'ooo' is '-', or\
+            if the -output option is missing).
+        force: If the output file already exists, use -force to overwrite it.\
+            If -force is used, it must come before -output on the command line.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VecwarpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(VECWARP_METADATA)
+    params = vecwarp_params(
+        apar=apar,
+        matvec=matvec,
+        forward=forward,
+        backward=backward,
+        input_=input_,
+        output=output,
+        force=force,
+    )
+    return vecwarp_execute(params, execution)
+
+
+__all__ = [
+    "VECWARP_METADATA",
+    "VecwarpOutputs",
+    "VecwarpParameters",
+    "vecwarp",
+    "vecwarp_params",
+]