niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_unifize.py

@@ -0,0 +1,403 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_UNIFIZE_METADATA = Metadata(
+    id="f384aca7310e07ceca93f58ec17ea0b68b11373d.boutiques",
+    name="3dUnifize",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dUnifizeParameters = typing.TypedDict('V3dUnifizeParameters', {
+    "__STYX_TYPE__": typing.Literal["3dUnifize"],
+    "cl_frac": typing.NotRequired[float | None],
+    "epi": bool,
+    "gm": bool,
+    "no_duplo": bool,
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "quiet": bool,
+    "rbt": typing.NotRequired[list[float] | None],
+    "prefix": typing.NotRequired[str | None],
+    "scale_file": typing.NotRequired[InputPathType | None],
+    "t2": bool,
+    "t2_up": typing.NotRequired[float | None],
+    "urad": typing.NotRequired[float | 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 {
+        "3dUnifize": v_3d_unifize_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 {
+        "3dUnifize": v_3d_unifize_outputs,
+    }.get(t)
+
+
+class V3dUnifizeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_unifize(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Output image file name."""
+    scale_file_outfile: OutputPathType | None
+    """Scale factor file."""
+
+
+def v_3d_unifize_params(
+    in_file: InputPathType,
+    cl_frac: float | None = None,
+    epi: bool = False,
+    gm: bool = False,
+    no_duplo: bool = False,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    quiet: bool = False,
+    rbt: list[float] | None = None,
+    prefix: str | None = None,
+    scale_file: InputPathType | None = None,
+    t2: bool = False,
+    t2_up: float | None = None,
+    urad: float | None = None,
+) -> V3dUnifizeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3dunifize.
+        cl_frac: Option for afni experts only.set the automask 'clip level\
+            fraction'. must be between 0.1 and 0.9. a small fraction means to make\
+            the initial threshold for clipping (a la 3dcliplevel) smaller, which\
+            will tend to make the mask larger. [default=0.1].
+        epi: Assume the input dataset is a t2 (or t2\\*) weighted epi time\
+            series. after computing the scaling, apply it to all volumes (trs) in\
+            the input dataset. that is, a given voxel will be scaled by the same\
+            factor at each tr. this option also implies '-noduplo' and '-t2'.this\
+            option turns off '-gm' if you turned it on.
+        gm: Also scale to unifize 'gray matter' = lower intensity voxels (to\
+            aid in registering images from different scanners).
+        no_duplo: Do not use the 'duplo down' step; this can be useful for\
+            lower resolution datasets.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        quiet: Don't print the progress messages.
+        rbt: (a float, a float, a float). Option for afni experts only.specify\
+            the 3 parameters for the algorithm:r = radius; same as given by option\
+            '-urad', [default=18.3]b = bottom percentile of normalizing data range,\
+            [default=70.0]r = top percentile of normalizing data range,\
+            [default=80.0].
+        prefix: Output image file name.
+        scale_file: Output file name to save the scale factor used at each\
+            voxel .
+        t2: Treat the input as if it were t2-weighted, rather than t1-weighted.\
+            this processing is done simply by inverting the image contrast,\
+            processing it as if that result were t1-weighted, and then re-inverting\
+            the results counts of voxel overlap, i.e., each voxel will contain the\
+            number of masks that it is set in.
+        t2_up: Option for afni experts only.set the upper percentile point used\
+            for t2-t1 inversion. allowed to be anything between 90 and 100\
+            (inclusive), with default to 98.5 (for no good reason).
+        urad: Sets the radius (in voxels) of the ball used for the sneaky\
+            trick. default value is 18.3, and should be changed proportionally if\
+            the dataset voxel size differs significantly from 1 mm.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dUnifize",
+        "epi": epi,
+        "gm": gm,
+        "no_duplo": no_duplo,
+        "quiet": quiet,
+        "t2": t2,
+        "in_file": in_file,
+    }
+    if cl_frac is not None:
+        params["cl_frac"] = cl_frac
+    if num_threads is not None:
+        params["num_threads"] = num_threads
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    if rbt is not None:
+        params["rbt"] = rbt
+    if prefix is not None:
+        params["prefix"] = prefix
+    if scale_file is not None:
+        params["scale_file"] = scale_file
+    if t2_up is not None:
+        params["t2_up"] = t2_up
+    if urad is not None:
+        params["urad"] = urad
+    return params
+
+
+def v_3d_unifize_cargs(
+    params: V3dUnifizeParameters,
+    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("3dUnifize")
+    if params.get("cl_frac") is not None:
+        cargs.extend([
+            "-clfrac",
+            str(params.get("cl_frac"))
+        ])
+    if params.get("epi"):
+        cargs.append("-EPI")
+    if params.get("gm"):
+        cargs.append("-GM")
+    if params.get("no_duplo"):
+        cargs.append("-noduplo")
+    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("quiet"):
+        cargs.append("-quiet")
+    if params.get("rbt") is not None:
+        cargs.extend([
+            "-rbt",
+            *map(str, params.get("rbt"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("scale_file") is not None:
+        cargs.extend([
+            "-ssave",
+            execution.input_file(params.get("scale_file"))
+        ])
+    if params.get("t2"):
+        cargs.append("-T2")
+    if params.get("t2_up") is not None:
+        cargs.extend([
+            "-T2up",
+            str(params.get("t2_up"))
+        ])
+    if params.get("urad") is not None:
+        cargs.extend([
+            "-Urad",
+            str(params.get("urad"))
+        ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("in_file"))
+    ])
+    return cargs
+
+
+def v_3d_unifize_outputs(
+    params: V3dUnifizeParameters,
+    execution: Execution,
+) -> V3dUnifizeOutputs:
+    """
+    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 = V3dUnifizeOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        scale_file_outfile=execution.output_file(pathlib.Path(params.get("scale_file")).name) if (params.get("scale_file") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_unifize_execute(
+    params: V3dUnifizeParameters,
+    execution: Execution,
+) -> V3dUnifizeOutputs:
+    """
+    3dUnifize - for uniformizing image intensity
+    * The input dataset is supposed to be a T1-weighted volume, possibly already
+    skull-stripped (e.g., via 3dSkullStrip). However, this program can be a
+    useful step to take BEFORE 3dSkullStrip, since the latter program can fail
+    if the input volume is strongly shaded -- 3dUnifize will (mostly) remove
+    such shading artifacts.
+    * The output dataset has the white matter (WM) intensity approximately
+    uniformized across space, and scaled to peak at about 1000.
+    * The output dataset is always stored in float format!
+    * If the input dataset has more than 1 sub-brick, only sub-brick #0 will be
+    processed!
+    * Want to correct EPI datasets for nonuniformity? You can try the new and
+    experimental [Mar 2017] '-EPI' option.
+    * The principal motive for this program is for use in an image registration
+    script, and it may or may not be useful otherwise.
+    * This program replaces the older (and very different) 3dUniformize, which
+    is no longer maintained and may sublimate at any moment. (In other words, we
+    do not recommend the use of 3dUniformize.).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dUnifizeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_unifize_cargs(params, execution)
+    ret = v_3d_unifize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_unifize(
+    in_file: InputPathType,
+    cl_frac: float | None = None,
+    epi: bool = False,
+    gm: bool = False,
+    no_duplo: bool = False,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    quiet: bool = False,
+    rbt: list[float] | None = None,
+    prefix: str | None = None,
+    scale_file: InputPathType | None = None,
+    t2: bool = False,
+    t2_up: float | None = None,
+    urad: float | None = None,
+    runner: Runner | None = None,
+) -> V3dUnifizeOutputs:
+    """
+    3dUnifize - for uniformizing image intensity
+    * The input dataset is supposed to be a T1-weighted volume, possibly already
+    skull-stripped (e.g., via 3dSkullStrip). However, this program can be a
+    useful step to take BEFORE 3dSkullStrip, since the latter program can fail
+    if the input volume is strongly shaded -- 3dUnifize will (mostly) remove
+    such shading artifacts.
+    * The output dataset has the white matter (WM) intensity approximately
+    uniformized across space, and scaled to peak at about 1000.
+    * The output dataset is always stored in float format!
+    * If the input dataset has more than 1 sub-brick, only sub-brick #0 will be
+    processed!
+    * Want to correct EPI datasets for nonuniformity? You can try the new and
+    experimental [Mar 2017] '-EPI' option.
+    * The principal motive for this program is for use in an image registration
+    script, and it may or may not be useful otherwise.
+    * This program replaces the older (and very different) 3dUniformize, which
+    is no longer maintained and may sublimate at any moment. (In other words, we
+    do not recommend the use of 3dUniformize.).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3dunifize.
+        cl_frac: Option for afni experts only.set the automask 'clip level\
+            fraction'. must be between 0.1 and 0.9. a small fraction means to make\
+            the initial threshold for clipping (a la 3dcliplevel) smaller, which\
+            will tend to make the mask larger. [default=0.1].
+        epi: Assume the input dataset is a t2 (or t2\\*) weighted epi time\
+            series. after computing the scaling, apply it to all volumes (trs) in\
+            the input dataset. that is, a given voxel will be scaled by the same\
+            factor at each tr. this option also implies '-noduplo' and '-t2'.this\
+            option turns off '-gm' if you turned it on.
+        gm: Also scale to unifize 'gray matter' = lower intensity voxels (to\
+            aid in registering images from different scanners).
+        no_duplo: Do not use the 'duplo down' step; this can be useful for\
+            lower resolution datasets.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        quiet: Don't print the progress messages.
+        rbt: (a float, a float, a float). Option for afni experts only.specify\
+            the 3 parameters for the algorithm:r = radius; same as given by option\
+            '-urad', [default=18.3]b = bottom percentile of normalizing data range,\
+            [default=70.0]r = top percentile of normalizing data range,\
+            [default=80.0].
+        prefix: Output image file name.
+        scale_file: Output file name to save the scale factor used at each\
+            voxel .
+        t2: Treat the input as if it were t2-weighted, rather than t1-weighted.\
+            this processing is done simply by inverting the image contrast,\
+            processing it as if that result were t1-weighted, and then re-inverting\
+            the results counts of voxel overlap, i.e., each voxel will contain the\
+            number of masks that it is set in.
+        t2_up: Option for afni experts only.set the upper percentile point used\
+            for t2-t1 inversion. allowed to be anything between 90 and 100\
+            (inclusive), with default to 98.5 (for no good reason).
+        urad: Sets the radius (in voxels) of the ball used for the sneaky\
+            trick. default value is 18.3, and should be changed proportionally if\
+            the dataset voxel size differs significantly from 1 mm.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dUnifizeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_UNIFIZE_METADATA)
+    params = v_3d_unifize_params(
+        cl_frac=cl_frac,
+        epi=epi,
+        gm=gm,
+        no_duplo=no_duplo,
+        num_threads=num_threads,
+        outputtype=outputtype,
+        quiet=quiet,
+        rbt=rbt,
+        prefix=prefix,
+        scale_file=scale_file,
+        t2=t2,
+        t2_up=t2_up,
+        urad=urad,
+        in_file=in_file,
+    )
+    return v_3d_unifize_execute(params, execution)
+
+
+__all__ = [
+    "V3dUnifizeOutputs",
+    "V3dUnifizeParameters",
+    "V_3D_UNIFIZE_METADATA",
+    "v_3d_unifize",
+    "v_3d_unifize_params",
+]

niwrap_afni/afni/v_3d_upsample.py

@@ -0,0 +1,245 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_UPSAMPLE_METADATA = Metadata(
+    id="e4750d1cff9a9b319ed4f1652bde0087af37e6dc.boutiques",
+    name="3dUpsample",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dUpsampleParameters = typing.TypedDict('V3dUpsampleParameters', {
+    "__STYX_TYPE__": typing.Literal["3dUpsample"],
+    "upsample_factor": int,
+    "input_dataset": str,
+    "linear_interpolation": bool,
+    "output_prefix": typing.NotRequired[str | None],
+    "verbose_flag": bool,
+    "datatype": 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 {
+        "3dUpsample": v_3d_upsample_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 {
+        "3dUpsample": v_3d_upsample_outputs,
+    }.get(t)
+
+
+class V3dUpsampleOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_upsample(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_brik: OutputPathType | None
+    """Upsampled dataset in BRIK format."""
+    output_head: OutputPathType | None
+    """Header information for the upsampled dataset."""
+
+
+def v_3d_upsample_params(
+    upsample_factor: int,
+    input_dataset: str,
+    linear_interpolation: bool = False,
+    output_prefix: str | None = None,
+    verbose_flag: bool = False,
+    datatype: str | None = None,
+) -> V3dUpsampleParameters:
+    """
+    Build parameters.
+    
+    Args:
+        upsample_factor: Upsampling factor; must be between 2 and 320\
+            (inclusive).
+        input_dataset: Input dataset.
+        linear_interpolation: Use linear interpolation instead of 7th order\
+            polynomial interpolation.
+        output_prefix: Define the prefix name of the output dataset; default is\
+            'Upsam'.
+        verbose_flag: Print verbose output.
+        datatype: Specify the datatype for the output dataset (float, short,\
+            byte); default is float.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dUpsample",
+        "upsample_factor": upsample_factor,
+        "input_dataset": input_dataset,
+        "linear_interpolation": linear_interpolation,
+        "verbose_flag": verbose_flag,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if datatype is not None:
+        params["datatype"] = datatype
+    return params
+
+
+def v_3d_upsample_cargs(
+    params: V3dUpsampleParameters,
+    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("3dUpsample")
+    cargs.extend([
+        "-n",
+        str(params.get("upsample_factor"))
+    ])
+    cargs.extend([
+        "-input",
+        params.get("input_dataset")
+    ])
+    if params.get("linear_interpolation"):
+        cargs.append("-1")
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("verbose_flag"):
+        cargs.append("-verb")
+    if params.get("datatype") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datatype")
+        ])
+    return cargs
+
+
+def v_3d_upsample_outputs(
+    params: V3dUpsampleParameters,
+    execution: Execution,
+) -> V3dUpsampleOutputs:
+    """
+    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 = V3dUpsampleOutputs(
+        root=execution.output_file("."),
+        output_brik=execution.output_file(params.get("output_prefix") + "+orig.BRIK") if (params.get("output_prefix") is not None) else None,
+        output_head=execution.output_file(params.get("output_prefix") + "+orig.HEAD") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_upsample_execute(
+    params: V3dUpsampleParameters,
+    execution: Execution,
+) -> V3dUpsampleOutputs:
+    """
+    Upsamples a 3D+time dataset in the time direction by a specified factor.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dUpsampleOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_upsample_cargs(params, execution)
+    ret = v_3d_upsample_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_upsample(
+    upsample_factor: int,
+    input_dataset: str,
+    linear_interpolation: bool = False,
+    output_prefix: str | None = None,
+    verbose_flag: bool = False,
+    datatype: str | None = None,
+    runner: Runner | None = None,
+) -> V3dUpsampleOutputs:
+    """
+    Upsamples a 3D+time dataset in the time direction by a specified factor.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        upsample_factor: Upsampling factor; must be between 2 and 320\
+            (inclusive).
+        input_dataset: Input dataset.
+        linear_interpolation: Use linear interpolation instead of 7th order\
+            polynomial interpolation.
+        output_prefix: Define the prefix name of the output dataset; default is\
+            'Upsam'.
+        verbose_flag: Print verbose output.
+        datatype: Specify the datatype for the output dataset (float, short,\
+            byte); default is float.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dUpsampleOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_UPSAMPLE_METADATA)
+    params = v_3d_upsample_params(
+        upsample_factor=upsample_factor,
+        input_dataset=input_dataset,
+        linear_interpolation=linear_interpolation,
+        output_prefix=output_prefix,
+        verbose_flag=verbose_flag,
+        datatype=datatype,
+    )
+    return v_3d_upsample_execute(params, execution)
+
+
+__all__ = [
+    "V3dUpsampleOutputs",
+    "V3dUpsampleParameters",
+    "V_3D_UPSAMPLE_METADATA",
+    "v_3d_upsample",
+    "v_3d_upsample_params",
+]