niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dvolreg.py

@@ -0,0 +1,360 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DVOLREG_METADATA = Metadata(
+    id="c46b5b6b0476664b007efa7fc17a0ef89b83a78a.boutiques",
+    name="3dvolreg",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dvolregParameters = typing.TypedDict('V3dvolregParameters', {
+    "__STYX_TYPE__": typing.Literal["3dvolreg"],
+    "copyorigin": bool,
+    "twopass": bool,
+    "Fourier": bool,
+    "in_weight_volume": typing.NotRequired[list[str] | None],
+    "in_weight_volume_2": typing.NotRequired[InputPathType | None],
+    "interp": typing.NotRequired[typing.Literal["fourier", "cubic", "heptic", "quintic", "linear"] | None],
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "timeshift": bool,
+    "verbose": bool,
+    "basefile": typing.NotRequired[InputPathType | None],
+    "zpad": typing.NotRequired[int | None],
+    "prefix": str,
+    "Maxdisp1d": typing.NotRequired[str | None],
+    "in_file": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dvolreg": v_3dvolreg_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 {
+        "3dvolreg": v_3dvolreg_outputs,
+    }.get(t)
+
+
+class V3dvolregOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dvolreg(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    md1d_file: OutputPathType
+    """Max displacement output file."""
+    oned_file: OutputPathType
+    """1d movement parameters output file."""
+    oned_matrix_save: OutputPathType
+    """Save the matrix transformation."""
+    md1d_file_: OutputPathType
+    """Max displacement info file."""
+    oned_file_: OutputPathType
+    """Movement parameters info file."""
+    oned_matrix_save_: OutputPathType
+    """Matrix transformation from base to input."""
+    out_file: OutputPathType
+    """Registered file."""
+
+
+def v_3dvolreg_params(
+    prefix: str,
+    in_file: InputPathType,
+    copyorigin: bool = False,
+    twopass: bool = False,
+    fourier: bool = False,
+    in_weight_volume: list[str] | None = None,
+    in_weight_volume_2: InputPathType | None = None,
+    interp: typing.Literal["fourier", "cubic", "heptic", "quintic", "linear"] | None = None,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    timeshift: bool = False,
+    verbose: bool = False,
+    basefile: InputPathType | None = None,
+    zpad: int | None = None,
+    maxdisp1d: str | None = None,
+) -> V3dvolregParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix.
+        in_file: Input file to 3dvolreg.
+        copyorigin: Copy base file origin coords to output.
+        twopass: Do two passes of the registration algorithm.
+        fourier: Perform the alignments using Fourier interpolation.
+        in_weight_volume: (file or string, an integer) or file or string.\
+            Weights for each voxel specified by a file with an optional volume\
+            number (defaults to 0).
+        in_weight_volume_2: (file or string, an integer) or file or string.\
+            Weights for each voxel specified by a file with an optional volume\
+            number (defaults to 0).
+        interp: 'fourier' or 'cubic' or 'heptic' or 'quintic' or 'linear'.\
+            Spatial interpolation methods [default = heptic].
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        timeshift: Time shift to mean slice time offset.
+        verbose: More detailed description of the process.
+        basefile: Base file for registration.
+        zpad: Zeropad around the edges by 'n' voxels during rotations.
+        maxdisp1d: Do '-maxdisp' and also write the max displacement for each\
+            sub-brick into file 'mm' in 1D (columnar) format.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dvolreg",
+        "copyorigin": copyorigin,
+        "twopass": twopass,
+        "Fourier": fourier,
+        "timeshift": timeshift,
+        "verbose": verbose,
+        "prefix": prefix,
+        "in_file": in_file,
+    }
+    if in_weight_volume is not None:
+        params["in_weight_volume"] = in_weight_volume
+    if in_weight_volume_2 is not None:
+        params["in_weight_volume_2"] = in_weight_volume_2
+    if interp is not None:
+        params["interp"] = interp
+    if num_threads is not None:
+        params["num_threads"] = num_threads
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    if basefile is not None:
+        params["basefile"] = basefile
+    if zpad is not None:
+        params["zpad"] = zpad
+    if maxdisp1d is not None:
+        params["Maxdisp1d"] = maxdisp1d
+    return params
+
+
+def v_3dvolreg_cargs(
+    params: V3dvolregParameters,
+    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("3dvolreg")
+    if params.get("copyorigin"):
+        cargs.append("-twodup")
+    if params.get("twopass"):
+        cargs.append("-twopass")
+    if params.get("Fourier"):
+        cargs.append("-Fourier")
+    if params.get("in_weight_volume") is not None:
+        cargs.extend([
+            "-weight '",
+            *params.get("in_weight_volume")
+        ])
+    if params.get("in_weight_volume_2") is not None:
+        cargs.extend([
+            "-weight '",
+            execution.input_file(params.get("in_weight_volume_2"))
+        ])
+    if params.get("interp") is not None:
+        cargs.extend([
+            "-",
+            params.get("interp")
+        ])
+    if params.get("num_threads") is not None:
+        cargs.append(str(params.get("num_threads")))
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    if params.get("timeshift"):
+        cargs.append("-tshift 0")
+    if params.get("verbose"):
+        cargs.append("-verbose")
+    if params.get("basefile") is not None:
+        cargs.extend([
+            "-base",
+            execution.input_file(params.get("basefile"))
+        ])
+    if params.get("zpad") is not None:
+        cargs.extend([
+            "-zpad",
+            str(params.get("zpad"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("Maxdisp1d") is not None:
+        cargs.extend([
+            "-maxdisp1d",
+            params.get("Maxdisp1d")
+        ])
+    cargs.append(execution.input_file(params.get("in_file")))
+    return cargs
+
+
+def v_3dvolreg_outputs(
+    params: V3dvolregParameters,
+    execution: Execution,
+) -> V3dvolregOutputs:
+    """
+    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 = V3dvolregOutputs(
+        root=execution.output_file("."),
+        md1d_file=execution.output_file(params.get("prefix") + "_md.1D"),
+        oned_file=execution.output_file(params.get("prefix") + ".1D"),
+        oned_matrix_save=execution.output_file(params.get("prefix") + ".aff12.1D"),
+        md1d_file_=execution.output_file("md1d_file"),
+        oned_file_=execution.output_file("oned_file"),
+        oned_matrix_save_=execution.output_file("oned_matrix_save"),
+        out_file=execution.output_file(params.get("prefix")),
+    )
+    return ret
+
+
+def v_3dvolreg_execute(
+    params: V3dvolregParameters,
+    execution: Execution,
+) -> V3dvolregOutputs:
+    """
+    Register input volumes to a base volume using AFNI 3dvolreg command.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dvolregOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dvolreg_cargs(params, execution)
+    ret = v_3dvolreg_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dvolreg(
+    prefix: str,
+    in_file: InputPathType,
+    copyorigin: bool = False,
+    twopass: bool = False,
+    fourier: bool = False,
+    in_weight_volume: list[str] | None = None,
+    in_weight_volume_2: InputPathType | None = None,
+    interp: typing.Literal["fourier", "cubic", "heptic", "quintic", "linear"] | None = None,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    timeshift: bool = False,
+    verbose: bool = False,
+    basefile: InputPathType | None = None,
+    zpad: int | None = None,
+    maxdisp1d: str | None = None,
+    runner: Runner | None = None,
+) -> V3dvolregOutputs:
+    """
+    Register input volumes to a base volume using AFNI 3dvolreg command.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix.
+        in_file: Input file to 3dvolreg.
+        copyorigin: Copy base file origin coords to output.
+        twopass: Do two passes of the registration algorithm.
+        fourier: Perform the alignments using Fourier interpolation.
+        in_weight_volume: (file or string, an integer) or file or string.\
+            Weights for each voxel specified by a file with an optional volume\
+            number (defaults to 0).
+        in_weight_volume_2: (file or string, an integer) or file or string.\
+            Weights for each voxel specified by a file with an optional volume\
+            number (defaults to 0).
+        interp: 'fourier' or 'cubic' or 'heptic' or 'quintic' or 'linear'.\
+            Spatial interpolation methods [default = heptic].
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        timeshift: Time shift to mean slice time offset.
+        verbose: More detailed description of the process.
+        basefile: Base file for registration.
+        zpad: Zeropad around the edges by 'n' voxels during rotations.
+        maxdisp1d: Do '-maxdisp' and also write the max displacement for each\
+            sub-brick into file 'mm' in 1D (columnar) format.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dvolregOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DVOLREG_METADATA)
+    params = v_3dvolreg_params(
+        copyorigin=copyorigin,
+        twopass=twopass,
+        fourier=fourier,
+        in_weight_volume=in_weight_volume,
+        in_weight_volume_2=in_weight_volume_2,
+        interp=interp,
+        num_threads=num_threads,
+        outputtype=outputtype,
+        timeshift=timeshift,
+        verbose=verbose,
+        basefile=basefile,
+        zpad=zpad,
+        prefix=prefix,
+        maxdisp1d=maxdisp1d,
+        in_file=in_file,
+    )
+    return v_3dvolreg_execute(params, execution)
+
+
+__all__ = [
+    "V3dvolregOutputs",
+    "V3dvolregParameters",
+    "V_3DVOLREG_METADATA",
+    "v_3dvolreg",
+    "v_3dvolreg_params",
+]

niwrap_afni/afni/v_4swap.py

@@ -0,0 +1,181 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_4SWAP_METADATA = Metadata(
+    id="b931a726528adf5a726f46c604f9851351673fb9.boutiques",
+    name="4swap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V4swapParameters = typing.TypedDict('V4swapParameters', {
+    "__STYX_TYPE__": typing.Literal["4swap"],
+    "files": list[InputPathType],
+    "quiet": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "4swap": v_4swap_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 V4swapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_4swap(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_4swap_params(
+    files: list[InputPathType],
+    quiet: bool = False,
+) -> V4swapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        files: List of files to process.
+        quiet: Work quietly; suppress output messages.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "4swap",
+        "files": files,
+        "quiet": quiet,
+    }
+    return params
+
+
+def v_4swap_cargs(
+    params: V4swapParameters,
+    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("4swap")
+    cargs.extend([execution.input_file(f) for f in params.get("files")])
+    if params.get("quiet"):
+        cargs.append("-q")
+    return cargs
+
+
+def v_4swap_outputs(
+    params: V4swapParameters,
+    execution: Execution,
+) -> V4swapOutputs:
+    """
+    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 = V4swapOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_4swap_execute(
+    params: V4swapParameters,
+    execution: Execution,
+) -> V4swapOutputs:
+    """
+    Swaps byte quadruples on the listed files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V4swapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_4swap_cargs(params, execution)
+    ret = v_4swap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_4swap(
+    files: list[InputPathType],
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> V4swapOutputs:
+    """
+    Swaps byte quadruples on the listed files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        files: List of files to process.
+        quiet: Work quietly; suppress output messages.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V4swapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_4SWAP_METADATA)
+    params = v_4swap_params(
+        files=files,
+        quiet=quiet,
+    )
+    return v_4swap_execute(params, execution)
+
+
+__all__ = [
+    "V4swapOutputs",
+    "V4swapParameters",
+    "V_4SWAP_METADATA",
+    "v_4swap",
+    "v_4swap_params",
+]

niwrap_afni/afni/v__1d_diff_mag.py

@@ -0,0 +1,178 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__1D_DIFF_MAG_METADATA = Metadata(
+    id="3cc44230d870dce2798531d9f3285fb0f32f1bda.boutiques",
+    name="@1dDiffMag",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dDiffMagParameters = typing.TypedDict('V1dDiffMagParameters', {
+    "__STYX_TYPE__": typing.Literal["@1dDiffMag"],
+    "infile": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@1dDiffMag": v__1d_diff_mag_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 {
+        "@1dDiffMag": v__1d_diff_mag_outputs,
+    }.get(t)
+
+
+class V1dDiffMagOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__1d_diff_mag(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    result_stdout: OutputPathType
+    """The result as a single number displayed on stdout"""
+
+
+def v__1d_diff_mag_params(
+    infile: InputPathType,
+) -> V1dDiffMagParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: 1D input file to compute the magnitude estimate of the first\
+            differences.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@1dDiffMag",
+        "infile": infile,
+    }
+    return params
+
+
+def v__1d_diff_mag_cargs(
+    params: V1dDiffMagParameters,
+    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("@1dDiffMag")
+    cargs.append(execution.input_file(params.get("infile")))
+    return cargs
+
+
+def v__1d_diff_mag_outputs(
+    params: V1dDiffMagParameters,
+    execution: Execution,
+) -> V1dDiffMagOutputs:
+    """
+    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 = V1dDiffMagOutputs(
+        root=execution.output_file("."),
+        result_stdout=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def v__1d_diff_mag_execute(
+    params: V1dDiffMagParameters,
+    execution: Execution,
+) -> V1dDiffMagOutputs:
+    """
+    Computes a magnitude estimate of the first differences of a 1D file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dDiffMagOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__1d_diff_mag_cargs(params, execution)
+    ret = v__1d_diff_mag_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__1d_diff_mag(
+    infile: InputPathType,
+    runner: Runner | None = None,
+) -> V1dDiffMagOutputs:
+    """
+    Computes a magnitude estimate of the first differences of a 1D file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: 1D input file to compute the magnitude estimate of the first\
+            differences.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dDiffMagOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__1D_DIFF_MAG_METADATA)
+    params = v__1d_diff_mag_params(
+        infile=infile,
+    )
+    return v__1d_diff_mag_execute(params, execution)
+
+
+__all__ = [
+    "V1dDiffMagOutputs",
+    "V1dDiffMagParameters",
+    "V__1D_DIFF_MAG_METADATA",
+    "v__1d_diff_mag",
+    "v__1d_diff_mag_params",
+]