niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_nwarp_apply.py

@@ -0,0 +1,349 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_NWARP_APPLY_METADATA = Metadata(
+    id="0a5385bf1fc9acdee0016adc133f63a8ec8a4e36.boutiques",
+    name="3dNwarpApply",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dNwarpApplyParameters = typing.TypedDict('V3dNwarpApplyParameters', {
+    "__STYX_TYPE__": typing.Literal["3dNwarpApply"],
+    "nwarp": str,
+    "iwarp": bool,
+    "source": str,
+    "master": typing.NotRequired[str | None],
+    "newgrid": typing.NotRequired[str | None],
+    "dxyz": typing.NotRequired[str | None],
+    "interp": typing.NotRequired[str | None],
+    "ainterp": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "suffix": typing.NotRequired[str | None],
+    "short": bool,
+    "wprefix": typing.NotRequired[str | None],
+    "quiet": bool,
+    "verb": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dNwarpApply": v_3d_nwarp_apply_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 {
+        "3dNwarpApply": v_3d_nwarp_apply_outputs,
+    }.get(t)
+
+
+class V3dNwarpApplyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_nwarp_apply(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    warped_output: OutputPathType | None
+    """Warped output dataset"""
+    generated_warp: OutputPathType | None
+    """Warp dataset generated during application"""
+
+
+def v_3d_nwarp_apply_params(
+    nwarp: str,
+    source: str,
+    iwarp: bool = False,
+    master: str | None = None,
+    newgrid: str | None = None,
+    dxyz: str | None = None,
+    interp: str | None = None,
+    ainterp: str | None = None,
+    prefix: str | None = None,
+    suffix: str | None = None,
+    short: bool = False,
+    wprefix: str | None = None,
+    quiet: bool = False,
+    verb: bool = False,
+) -> V3dNwarpApplyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        nwarp: The name of the 3D warp dataset. Multiple warps can be\
+            catenated.
+        source: The name of the source dataset to be warped. Multiple datasets\
+            can be supplied.
+        iwarp: Invert the warp specified in '-nwarp'.
+        master: The name of the master dataset which defines the output grid.
+        newgrid: The new grid spacing (cubical voxels, in mm).
+        dxyz: Specify a different grid spacing (cubical voxels, in mm).
+        interp: The interpolation mode ('NN', 'linear', 'cubic', 'quintic',\
+            'wsinc5').
+        ainterp: Specify a different interpolation mode for the data than the\
+            warp.
+        prefix: The name of the new output dataset. Multiple names can be\
+            supplied if more than one source dataset is input.
+        suffix: Change the default suffix '_Nwarp' to a user-defined suffix.
+        short: Write output dataset using 16-bit short integers rather than the\
+            usual 32-bit floats.
+        wprefix: Save every warp generated in the process to a separate\
+            dataset.
+        quiet: Don't be verbose.
+        verb: Be extra verbose.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dNwarpApply",
+        "nwarp": nwarp,
+        "iwarp": iwarp,
+        "source": source,
+        "short": short,
+        "quiet": quiet,
+        "verb": verb,
+    }
+    if master is not None:
+        params["master"] = master
+    if newgrid is not None:
+        params["newgrid"] = newgrid
+    if dxyz is not None:
+        params["dxyz"] = dxyz
+    if interp is not None:
+        params["interp"] = interp
+    if ainterp is not None:
+        params["ainterp"] = ainterp
+    if prefix is not None:
+        params["prefix"] = prefix
+    if suffix is not None:
+        params["suffix"] = suffix
+    if wprefix is not None:
+        params["wprefix"] = wprefix
+    return params
+
+
+def v_3d_nwarp_apply_cargs(
+    params: V3dNwarpApplyParameters,
+    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("3dNwarpApply")
+    cargs.extend([
+        "-nwarp",
+        params.get("nwarp")
+    ])
+    if params.get("iwarp"):
+        cargs.append("-iwarp")
+    cargs.extend([
+        "-source",
+        params.get("source")
+    ])
+    if params.get("master") is not None:
+        cargs.extend([
+            "-master",
+            params.get("master")
+        ])
+    if params.get("newgrid") is not None:
+        cargs.extend([
+            "-newgrid",
+            params.get("newgrid")
+        ])
+    if params.get("dxyz") is not None:
+        cargs.extend([
+            "-dxyz",
+            params.get("dxyz")
+        ])
+    if params.get("interp") is not None:
+        cargs.extend([
+            "-interp",
+            params.get("interp")
+        ])
+    if params.get("ainterp") is not None:
+        cargs.extend([
+            "-ainterp",
+            params.get("ainterp")
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("suffix") is not None:
+        cargs.extend([
+            "-suffix",
+            params.get("suffix")
+        ])
+    if params.get("short"):
+        cargs.append("-short")
+    if params.get("wprefix") is not None:
+        cargs.extend([
+            "-wprefix",
+            params.get("wprefix")
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("verb"):
+        cargs.append("-verb")
+    return cargs
+
+
+def v_3d_nwarp_apply_outputs(
+    params: V3dNwarpApplyParameters,
+    execution: Execution,
+) -> V3dNwarpApplyOutputs:
+    """
+    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 = V3dNwarpApplyOutputs(
+        root=execution.output_file("."),
+        warped_output=execution.output_file(params.get("prefix") + "_" + params.get("source") + "_warped.nii.gz") if (params.get("prefix") is not None) else None,
+        generated_warp=execution.output_file(params.get("wprefix") + "_warp_????.nii.gz") if (params.get("wprefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_nwarp_apply_execute(
+    params: V3dNwarpApplyParameters,
+    execution: Execution,
+) -> V3dNwarpApplyOutputs:
+    """
+    Program to apply a nonlinear 3D warp saved from 3dQwarp (or 3dNwarpCat, etc.) to
+    a 3D dataset, to produce a warped version of the source dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dNwarpApplyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_nwarp_apply_cargs(params, execution)
+    ret = v_3d_nwarp_apply_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_nwarp_apply(
+    nwarp: str,
+    source: str,
+    iwarp: bool = False,
+    master: str | None = None,
+    newgrid: str | None = None,
+    dxyz: str | None = None,
+    interp: str | None = None,
+    ainterp: str | None = None,
+    prefix: str | None = None,
+    suffix: str | None = None,
+    short: bool = False,
+    wprefix: str | None = None,
+    quiet: bool = False,
+    verb: bool = False,
+    runner: Runner | None = None,
+) -> V3dNwarpApplyOutputs:
+    """
+    Program to apply a nonlinear 3D warp saved from 3dQwarp (or 3dNwarpCat, etc.) to
+    a 3D dataset, to produce a warped version of the source dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        nwarp: The name of the 3D warp dataset. Multiple warps can be\
+            catenated.
+        source: The name of the source dataset to be warped. Multiple datasets\
+            can be supplied.
+        iwarp: Invert the warp specified in '-nwarp'.
+        master: The name of the master dataset which defines the output grid.
+        newgrid: The new grid spacing (cubical voxels, in mm).
+        dxyz: Specify a different grid spacing (cubical voxels, in mm).
+        interp: The interpolation mode ('NN', 'linear', 'cubic', 'quintic',\
+            'wsinc5').
+        ainterp: Specify a different interpolation mode for the data than the\
+            warp.
+        prefix: The name of the new output dataset. Multiple names can be\
+            supplied if more than one source dataset is input.
+        suffix: Change the default suffix '_Nwarp' to a user-defined suffix.
+        short: Write output dataset using 16-bit short integers rather than the\
+            usual 32-bit floats.
+        wprefix: Save every warp generated in the process to a separate\
+            dataset.
+        quiet: Don't be verbose.
+        verb: Be extra verbose.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dNwarpApplyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NWARP_APPLY_METADATA)
+    params = v_3d_nwarp_apply_params(
+        nwarp=nwarp,
+        iwarp=iwarp,
+        source=source,
+        master=master,
+        newgrid=newgrid,
+        dxyz=dxyz,
+        interp=interp,
+        ainterp=ainterp,
+        prefix=prefix,
+        suffix=suffix,
+        short=short,
+        wprefix=wprefix,
+        quiet=quiet,
+        verb=verb,
+    )
+    return v_3d_nwarp_apply_execute(params, execution)
+
+
+__all__ = [
+    "V3dNwarpApplyOutputs",
+    "V3dNwarpApplyParameters",
+    "V_3D_NWARP_APPLY_METADATA",
+    "v_3d_nwarp_apply",
+    "v_3d_nwarp_apply_params",
+]

niwrap_afni/afni/v_3d_nwarp_cat.py

@@ -0,0 +1,277 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_NWARP_CAT_METADATA = Metadata(
+    id="50ffd879ac4756b7a539af68c646c32f78b68146.boutiques",
+    name="3dNwarpCat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dNwarpCatParameters = typing.TypedDict('V3dNwarpCatParameters', {
+    "__STYX_TYPE__": typing.Literal["3dNwarpCat"],
+    "interpolation": typing.NotRequired[str | None],
+    "verbosity": bool,
+    "output_prefix": str,
+    "space_marker": typing.NotRequired[str | None],
+    "warp1": InputPathType,
+    "warp2": InputPathType,
+    "additional_warps": typing.NotRequired[list[InputPathType] | None],
+    "invert_final_warp": bool,
+    "extra_padding": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dNwarpCat": v_3d_nwarp_cat_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 {
+        "3dNwarpCat": v_3d_nwarp_cat_outputs,
+    }.get(t)
+
+
+class V3dNwarpCatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_nwarp_cat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_matrix: OutputPathType
+    """Output matrix file when only matrix warps are provided."""
+    output_dataset: OutputPathType
+    """Output dataset when warp files are provided."""
+
+
+def v_3d_nwarp_cat_params(
+    output_prefix: str,
+    warp1: InputPathType,
+    warp2: InputPathType,
+    interpolation: str | None = None,
+    verbosity: bool = False,
+    space_marker: str | None = None,
+    additional_warps: list[InputPathType] | None = None,
+    invert_final_warp: bool = False,
+    extra_padding: float | None = None,
+) -> V3dNwarpCatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        output_prefix: Prefix name for the output dataset that holds the warp.
+        warp1: Specify the first warp.
+        warp2: Specify the second warp.
+        interpolation: Interpolation mode: linear, quintic, or wsinc5\
+            (default).
+        verbosity: Print various fun messages during execution.
+        space_marker: Attach string 'sss' to the output dataset as its atlas\
+            space marker.
+        additional_warps: Additional warp files.
+        invert_final_warp: Invert the final warp before output.
+        extra_padding: Pad the nonlinear warps by 'PP' voxels in all\
+            directions.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dNwarpCat",
+        "verbosity": verbosity,
+        "output_prefix": output_prefix,
+        "warp1": warp1,
+        "warp2": warp2,
+        "invert_final_warp": invert_final_warp,
+    }
+    if interpolation is not None:
+        params["interpolation"] = interpolation
+    if space_marker is not None:
+        params["space_marker"] = space_marker
+    if additional_warps is not None:
+        params["additional_warps"] = additional_warps
+    if extra_padding is not None:
+        params["extra_padding"] = extra_padding
+    return params
+
+
+def v_3d_nwarp_cat_cargs(
+    params: V3dNwarpCatParameters,
+    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("3dNwarpCat")
+    if params.get("interpolation") is not None:
+        cargs.extend([
+            "-interp",
+            params.get("interpolation")
+        ])
+    if params.get("verbosity"):
+        cargs.append("-verb")
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    if params.get("space_marker") is not None:
+        cargs.extend([
+            "-space",
+            params.get("space_marker")
+        ])
+    cargs.extend([
+        "-warp1",
+        execution.input_file(params.get("warp1"))
+    ])
+    cargs.extend([
+        "-warp2",
+        execution.input_file(params.get("warp2"))
+    ])
+    if params.get("additional_warps") is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("additional_warps")])
+    if params.get("invert_final_warp"):
+        cargs.append("-iwarp")
+    if params.get("extra_padding") is not None:
+        cargs.extend([
+            "-expad",
+            str(params.get("extra_padding"))
+        ])
+    return cargs
+
+
+def v_3d_nwarp_cat_outputs(
+    params: V3dNwarpCatParameters,
+    execution: Execution,
+) -> V3dNwarpCatOutputs:
+    """
+    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 = V3dNwarpCatOutputs(
+        root=execution.output_file("."),
+        output_matrix=execution.output_file(params.get("output_prefix") + ".aff12.1D"),
+        output_dataset=execution.output_file(params.get("output_prefix") + "+tlrc.HEAD"),
+    )
+    return ret
+
+
+def v_3d_nwarp_cat_execute(
+    params: V3dNwarpCatParameters,
+    execution: Execution,
+) -> V3dNwarpCatOutputs:
+    """
+    Catenates (composes) 3D warps defined on a grid or via a matrix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dNwarpCatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_nwarp_cat_cargs(params, execution)
+    ret = v_3d_nwarp_cat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_nwarp_cat(
+    output_prefix: str,
+    warp1: InputPathType,
+    warp2: InputPathType,
+    interpolation: str | None = None,
+    verbosity: bool = False,
+    space_marker: str | None = None,
+    additional_warps: list[InputPathType] | None = None,
+    invert_final_warp: bool = False,
+    extra_padding: float | None = None,
+    runner: Runner | None = None,
+) -> V3dNwarpCatOutputs:
+    """
+    Catenates (composes) 3D warps defined on a grid or via a matrix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        output_prefix: Prefix name for the output dataset that holds the warp.
+        warp1: Specify the first warp.
+        warp2: Specify the second warp.
+        interpolation: Interpolation mode: linear, quintic, or wsinc5\
+            (default).
+        verbosity: Print various fun messages during execution.
+        space_marker: Attach string 'sss' to the output dataset as its atlas\
+            space marker.
+        additional_warps: Additional warp files.
+        invert_final_warp: Invert the final warp before output.
+        extra_padding: Pad the nonlinear warps by 'PP' voxels in all\
+            directions.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dNwarpCatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NWARP_CAT_METADATA)
+    params = v_3d_nwarp_cat_params(
+        interpolation=interpolation,
+        verbosity=verbosity,
+        output_prefix=output_prefix,
+        space_marker=space_marker,
+        warp1=warp1,
+        warp2=warp2,
+        additional_warps=additional_warps,
+        invert_final_warp=invert_final_warp,
+        extra_padding=extra_padding,
+    )
+    return v_3d_nwarp_cat_execute(params, execution)
+
+
+__all__ = [
+    "V3dNwarpCatOutputs",
+    "V3dNwarpCatParameters",
+    "V_3D_NWARP_CAT_METADATA",
+    "v_3d_nwarp_cat",
+    "v_3d_nwarp_cat_params",
+]