niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_local_bistat.py

@@ -0,0 +1,325 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_LOCAL_BISTAT_METADATA = Metadata(
+    id="e90dc29ecfbe470e814874e0a612f6a2f98a8350.boutiques",
+    name="3dLocalBistat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dLocalBistatParameters = typing.TypedDict('V3dLocalBistatParameters', {
+    "__STYX_TYPE__": typing.Literal["3dLocalBistat"],
+    "nbhd": str,
+    "stats": list[str],
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "weight": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "histpow": typing.NotRequired[float | None],
+    "histbin": typing.NotRequired[float | None],
+    "hclip1": typing.NotRequired[list[str] | None],
+    "hclip2": typing.NotRequired[list[str] | None],
+    "dataset1": InputPathType,
+    "dataset2": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dLocalBistat": v_3d_local_bistat_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 {
+        "3dLocalBistat": v_3d_local_bistat_outputs,
+    }.get(t)
+
+
+class V3dLocalBistatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_local_bistat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_head: OutputPathType
+    """Output dataset header for AFNI format"""
+    output_brik: OutputPathType
+    """Output dataset BRIK for AFNI format"""
+
+
+def v_3d_local_bistat_params(
+    nbhd: str,
+    stats: list[str],
+    prefix: str,
+    dataset1: InputPathType,
+    dataset2: InputPathType,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    weight: InputPathType | None = None,
+    histpow: float | None = None,
+    histbin: float | None = None,
+    hclip1: list[str] | None = None,
+    hclip2: list[str] | None = None,
+) -> V3dLocalBistatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        nbhd: Specifies the neighborhood around each voxel for statistics\
+            calculation. Types include: SPHERE(r), RECT(a,b,c), RHDD(r), TOHD(r).
+        stats: Statistic to compute in the region around each voxel. Multiple\
+            options allowed. Includes: pearson, spearman, quadrant, mutinfo,\
+            normuti, jointent, hellinger, crU, crM, crA, L2slope, L1slope, num,\
+            ALL.
+        prefix: Prefix of the output dataset.
+        dataset1: The first input dataset (e.g. data1.nii).
+        dataset2: The second input dataset (e.g. data2.nii).
+        mask: Read in a dataset to use as a mask. Non-zero voxels define the\
+            mask region.
+        automask: Compute the mask as in program 3dAutomask. Mutually exclusive\
+            with -mask.
+        weight: Use dataset as a weight (applies to pearson).
+        histpow: Sets the exponent for the number of bins in the histogram used\
+            for Hellinger, Mutual Information, and Correlation Ratio statistics.
+        histbin: Sets the number of bins directly in the histogram used for\
+            Hellinger, Mutual Information, and Correlation Ratio statistics.
+        hclip1: Clip dataset1 to lie between specified values.
+        hclip2: Clip dataset2 to lie between specified values.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dLocalBistat",
+        "nbhd": nbhd,
+        "stats": stats,
+        "automask": automask,
+        "prefix": prefix,
+        "dataset1": dataset1,
+        "dataset2": dataset2,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if weight is not None:
+        params["weight"] = weight
+    if histpow is not None:
+        params["histpow"] = histpow
+    if histbin is not None:
+        params["histbin"] = histbin
+    if hclip1 is not None:
+        params["hclip1"] = hclip1
+    if hclip2 is not None:
+        params["hclip2"] = hclip2
+    return params
+
+
+def v_3d_local_bistat_cargs(
+    params: V3dLocalBistatParameters,
+    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("3dLocalBistat")
+    cargs.extend([
+        "-nbhd",
+        params.get("nbhd")
+    ])
+    cargs.extend([
+        "-stat",
+        *params.get("stats")
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("weight") is not None:
+        cargs.extend([
+            "-weight",
+            execution.input_file(params.get("weight"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("histpow") is not None:
+        cargs.extend([
+            "-histpow",
+            str(params.get("histpow"))
+        ])
+    if params.get("histbin") is not None:
+        cargs.extend([
+            "-histbin",
+            str(params.get("histbin"))
+        ])
+    if params.get("hclip1") is not None:
+        cargs.extend([
+            "-hclip1",
+            *params.get("hclip1")
+        ])
+    if params.get("hclip2") is not None:
+        cargs.extend([
+            "-hclip2",
+            *params.get("hclip2")
+        ])
+    cargs.append(execution.input_file(params.get("dataset1")))
+    cargs.append(execution.input_file(params.get("dataset2")))
+    return cargs
+
+
+def v_3d_local_bistat_outputs(
+    params: V3dLocalBistatParameters,
+    execution: Execution,
+) -> V3dLocalBistatOutputs:
+    """
+    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 = V3dLocalBistatOutputs(
+        root=execution.output_file("."),
+        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
+        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+    )
+    return ret
+
+
+def v_3d_local_bistat_execute(
+    params: V3dLocalBistatParameters,
+    execution: Execution,
+) -> V3dLocalBistatOutputs:
+    """
+    Compute statistics between 2 datasets at each voxel based on a local
+    neighborhood.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dLocalBistatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_local_bistat_cargs(params, execution)
+    ret = v_3d_local_bistat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_local_bistat(
+    nbhd: str,
+    stats: list[str],
+    prefix: str,
+    dataset1: InputPathType,
+    dataset2: InputPathType,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    weight: InputPathType | None = None,
+    histpow: float | None = None,
+    histbin: float | None = None,
+    hclip1: list[str] | None = None,
+    hclip2: list[str] | None = None,
+    runner: Runner | None = None,
+) -> V3dLocalBistatOutputs:
+    """
+    Compute statistics between 2 datasets at each voxel based on a local
+    neighborhood.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        nbhd: Specifies the neighborhood around each voxel for statistics\
+            calculation. Types include: SPHERE(r), RECT(a,b,c), RHDD(r), TOHD(r).
+        stats: Statistic to compute in the region around each voxel. Multiple\
+            options allowed. Includes: pearson, spearman, quadrant, mutinfo,\
+            normuti, jointent, hellinger, crU, crM, crA, L2slope, L1slope, num,\
+            ALL.
+        prefix: Prefix of the output dataset.
+        dataset1: The first input dataset (e.g. data1.nii).
+        dataset2: The second input dataset (e.g. data2.nii).
+        mask: Read in a dataset to use as a mask. Non-zero voxels define the\
+            mask region.
+        automask: Compute the mask as in program 3dAutomask. Mutually exclusive\
+            with -mask.
+        weight: Use dataset as a weight (applies to pearson).
+        histpow: Sets the exponent for the number of bins in the histogram used\
+            for Hellinger, Mutual Information, and Correlation Ratio statistics.
+        histbin: Sets the number of bins directly in the histogram used for\
+            Hellinger, Mutual Information, and Correlation Ratio statistics.
+        hclip1: Clip dataset1 to lie between specified values.
+        hclip2: Clip dataset2 to lie between specified values.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dLocalBistatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCAL_BISTAT_METADATA)
+    params = v_3d_local_bistat_params(
+        nbhd=nbhd,
+        stats=stats,
+        mask=mask,
+        automask=automask,
+        weight=weight,
+        prefix=prefix,
+        histpow=histpow,
+        histbin=histbin,
+        hclip1=hclip1,
+        hclip2=hclip2,
+        dataset1=dataset1,
+        dataset2=dataset2,
+    )
+    return v_3d_local_bistat_execute(params, execution)
+
+
+__all__ = [
+    "V3dLocalBistatOutputs",
+    "V3dLocalBistatParameters",
+    "V_3D_LOCAL_BISTAT_METADATA",
+    "v_3d_local_bistat",
+    "v_3d_local_bistat_params",
+]

niwrap_afni/afni/v_3d_local_histog.py

@@ -0,0 +1,268 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_LOCAL_HISTOG_METADATA = Metadata(
+    id="de01f1dbbd5bfe5031e2c7c493ec364d82e32012.boutiques",
+    name="3dLocalHistog",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dLocalHistogParameters = typing.TypedDict('V3dLocalHistogParameters', {
+    "__STYX_TYPE__": typing.Literal["3dLocalHistog"],
+    "nbhd_option": typing.NotRequired[str | None],
+    "prefix": str,
+    "hsave": typing.NotRequired[str | None],
+    "lab_file": typing.NotRequired[InputPathType | None],
+    "exclude": typing.NotRequired[list[str] | None],
+    "mincount": typing.NotRequired[float | None],
+    "input_datasets": 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 {
+        "3dLocalHistog": v_3d_local_histog_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 {
+        "3dLocalHistog": v_3d_local_histog_outputs,
+    }.get(t)
+
+
+class V3dLocalHistogOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_local_histog(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset_head: OutputPathType
+    """The output dataset with the specified prefix"""
+    output_dataset_brik: OutputPathType
+    """The output dataset with the specified prefix"""
+    histogram_file: OutputPathType | None
+    """The overall histogram saved into the specified file"""
+
+
+def v_3d_local_histog_params(
+    prefix: str,
+    input_datasets: list[InputPathType],
+    nbhd_option: str | None = None,
+    hsave: str | None = None,
+    lab_file: InputPathType | None = None,
+    exclude: list[str] | None = None,
+    mincount: float | None = None,
+) -> V3dLocalHistogParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Use string 'ppp' as the prefix for the output dataset.
+        input_datasets: Input dataset(s) for the 3dLocalHistog tool.
+        nbhd_option: Defines the region around each voxel to be used for the\
+            statistics calculation. Available formats: 'SPHERE(r)', 'RECT(a,b,c)',\
+            'RHDD(a)', 'TOHD(a)'.
+        hsave: Save the overall histogram into file 'sss'. This file will have\
+            2 columns: value and count.
+        lab_file: Use file 'LL' as a label file.
+        exclude: Exclude values from 'a' to 'b' from the counting. This option\
+            can be used more than once.
+        mincount: Exclude values which appear in the overall histogram fewer\
+            than 'mm' times.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dLocalHistog",
+        "prefix": prefix,
+        "input_datasets": input_datasets,
+    }
+    if nbhd_option is not None:
+        params["nbhd_option"] = nbhd_option
+    if hsave is not None:
+        params["hsave"] = hsave
+    if lab_file is not None:
+        params["lab_file"] = lab_file
+    if exclude is not None:
+        params["exclude"] = exclude
+    if mincount is not None:
+        params["mincount"] = mincount
+    return params
+
+
+def v_3d_local_histog_cargs(
+    params: V3dLocalHistogParameters,
+    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("3dLocalHistog")
+    if params.get("nbhd_option") is not None:
+        cargs.extend([
+            "-nbhd",
+            params.get("nbhd_option")
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("hsave") is not None:
+        cargs.extend([
+            "-hsave",
+            params.get("hsave")
+        ])
+    if params.get("lab_file") is not None:
+        cargs.extend([
+            "-lab_file",
+            execution.input_file(params.get("lab_file"))
+        ])
+    if params.get("exclude") is not None:
+        cargs.extend([
+            "-exclude",
+            *params.get("exclude")
+        ])
+    if params.get("mincount") is not None:
+        cargs.extend([
+            "-mincount",
+            str(params.get("mincount"))
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("input_datasets")])
+    return cargs
+
+
+def v_3d_local_histog_outputs(
+    params: V3dLocalHistogParameters,
+    execution: Execution,
+) -> V3dLocalHistogOutputs:
+    """
+    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 = V3dLocalHistogOutputs(
+        root=execution.output_file("."),
+        output_dataset_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
+        output_dataset_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+        histogram_file=execution.output_file(params.get("hsave")) if (params.get("hsave") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_local_histog_execute(
+    params: V3dLocalHistogParameters,
+    execution: Execution,
+) -> V3dLocalHistogOutputs:
+    """
+    This program computes a local histogram at each voxel in the input datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dLocalHistogOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_local_histog_cargs(params, execution)
+    ret = v_3d_local_histog_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_local_histog(
+    prefix: str,
+    input_datasets: list[InputPathType],
+    nbhd_option: str | None = None,
+    hsave: str | None = None,
+    lab_file: InputPathType | None = None,
+    exclude: list[str] | None = None,
+    mincount: float | None = None,
+    runner: Runner | None = None,
+) -> V3dLocalHistogOutputs:
+    """
+    This program computes a local histogram at each voxel in the input datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Use string 'ppp' as the prefix for the output dataset.
+        input_datasets: Input dataset(s) for the 3dLocalHistog tool.
+        nbhd_option: Defines the region around each voxel to be used for the\
+            statistics calculation. Available formats: 'SPHERE(r)', 'RECT(a,b,c)',\
+            'RHDD(a)', 'TOHD(a)'.
+        hsave: Save the overall histogram into file 'sss'. This file will have\
+            2 columns: value and count.
+        lab_file: Use file 'LL' as a label file.
+        exclude: Exclude values from 'a' to 'b' from the counting. This option\
+            can be used more than once.
+        mincount: Exclude values which appear in the overall histogram fewer\
+            than 'mm' times.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dLocalHistogOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOCAL_HISTOG_METADATA)
+    params = v_3d_local_histog_params(
+        nbhd_option=nbhd_option,
+        prefix=prefix,
+        hsave=hsave,
+        lab_file=lab_file,
+        exclude=exclude,
+        mincount=mincount,
+        input_datasets=input_datasets,
+    )
+    return v_3d_local_histog_execute(params, execution)
+
+
+__all__ = [
+    "V3dLocalHistogOutputs",
+    "V3dLocalHistogParameters",
+    "V_3D_LOCAL_HISTOG_METADATA",
+    "v_3d_local_histog",
+    "v_3d_local_histog_params",
+]