niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dhistog.py

@@ -0,0 +1,365 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DHISTOG_METADATA = Metadata(
+    id="e7bd0d2e8a320bbb6bd63ecc03a72a5a7207b971.boutiques",
+    name="3dhistog",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dhistogParameters = typing.TypedDict('V3dhistogParameters', {
+    "__STYX_TYPE__": typing.Literal["3dhistog"],
+    "dataset": InputPathType,
+    "nbin": typing.NotRequired[float | None],
+    "dind": typing.NotRequired[float | None],
+    "omit": typing.NotRequired[list[float] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "roi_mask": typing.NotRequired[InputPathType | None],
+    "doall": bool,
+    "noempty": bool,
+    "notitle": bool,
+    "log10": bool,
+    "pdf": bool,
+    "min": typing.NotRequired[float | None],
+    "max": typing.NotRequired[float | None],
+    "igfac": bool,
+    "int": bool,
+    "float": bool,
+    "unq": typing.NotRequired[str | None],
+    "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 {
+        "3dhistog": v_3dhistog_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 {
+        "3dhistog": v_3dhistog_outputs,
+    }.get(t)
+
+
+class V3dhistogOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dhistog(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    histogram_output: OutputPathType
+    """Histogram output when -prefix option is used"""
+
+
+def v_3dhistog_params(
+    dataset: InputPathType,
+    nbin: float | None = None,
+    dind: float | None = None,
+    omit: list[float] | None = None,
+    mask: InputPathType | None = None,
+    roi_mask: InputPathType | None = None,
+    doall: bool = False,
+    noempty: bool = False,
+    notitle: bool = False,
+    log10: bool = False,
+    pdf: bool = False,
+    min_: float | None = None,
+    max_: float | None = None,
+    igfac: bool = False,
+    int_: bool = False,
+    float_: bool = False,
+    unq: str | None = None,
+    prefix: str | None = None,
+) -> V3dhistogParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset.
+        nbin: Use specified number of bins.
+        dind: Use data from specified sub-brick index.
+        omit: Omit specified value from the count.
+        mask: Use mask dataset to determine which voxels to use.
+        roi_mask: Create histogram for each non-zero value in 'r' dataset.
+        doall: Include all sub-bricks in the calculation.
+        noempty: Only output bins that are not empty.
+        notitle: Leave the title line off the output.
+        log10: Output log10() of the counts.
+        pdf: Output the counts divided by the number of samples.
+        min_: Specify minimum (inclusive) of histogram.
+        max_: Specify maximum (inclusive) of histogram.
+        igfac: Ignore sub-brick scale factors and histogram-ize the 'raw' data.
+        int_: Treat data and output as integers.
+        float_: Treat data and output as floats.
+        unq: Writes out the sorted unique values to file.
+        prefix: Write a copy of the histogram into specified file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dhistog",
+        "dataset": dataset,
+        "doall": doall,
+        "noempty": noempty,
+        "notitle": notitle,
+        "log10": log10,
+        "pdf": pdf,
+        "igfac": igfac,
+        "int": int_,
+        "float": float_,
+    }
+    if nbin is not None:
+        params["nbin"] = nbin
+    if dind is not None:
+        params["dind"] = dind
+    if omit is not None:
+        params["omit"] = omit
+    if mask is not None:
+        params["mask"] = mask
+    if roi_mask is not None:
+        params["roi_mask"] = roi_mask
+    if min_ is not None:
+        params["min"] = min_
+    if max_ is not None:
+        params["max"] = max_
+    if unq is not None:
+        params["unq"] = unq
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3dhistog_cargs(
+    params: V3dhistogParameters,
+    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("3dhistog")
+    cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("nbin") is not None:
+        cargs.extend([
+            "-nbin",
+            str(params.get("nbin"))
+        ])
+    if params.get("dind") is not None:
+        cargs.extend([
+            "-dind",
+            str(params.get("dind"))
+        ])
+    if params.get("omit") is not None:
+        cargs.extend([
+            "-omit",
+            *map(str, params.get("omit"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("roi_mask") is not None:
+        cargs.extend([
+            "-roi_mask",
+            execution.input_file(params.get("roi_mask"))
+        ])
+    if params.get("doall"):
+        cargs.append("-doall")
+    if params.get("noempty"):
+        cargs.append("-noempty")
+    if params.get("notitle"):
+        cargs.append("-notitle")
+    if params.get("log10"):
+        cargs.append("-log10")
+    if params.get("pdf"):
+        cargs.append("-pdf")
+    if params.get("min") is not None:
+        cargs.extend([
+            "-min",
+            str(params.get("min"))
+        ])
+    if params.get("max") is not None:
+        cargs.extend([
+            "-max",
+            str(params.get("max"))
+        ])
+    if params.get("igfac"):
+        cargs.append("-igfac")
+    if params.get("int"):
+        cargs.append("-int")
+    if params.get("float"):
+        cargs.append("-float")
+    if params.get("unq") is not None:
+        cargs.extend([
+            "-unq",
+            params.get("unq")
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    return cargs
+
+
+def v_3dhistog_outputs(
+    params: V3dhistogParameters,
+    execution: Execution,
+) -> V3dhistogOutputs:
+    """
+    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 = V3dhistogOutputs(
+        root=execution.output_file("."),
+        histogram_output=execution.output_file("HOUT.1D"),
+    )
+    return ret
+
+
+def v_3dhistog_execute(
+    params: V3dhistogParameters,
+    execution: Execution,
+) -> V3dhistogOutputs:
+    """
+    Compute histogram of a 3D dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dhistogOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dhistog_cargs(params, execution)
+    ret = v_3dhistog_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dhistog(
+    dataset: InputPathType,
+    nbin: float | None = None,
+    dind: float | None = None,
+    omit: list[float] | None = None,
+    mask: InputPathType | None = None,
+    roi_mask: InputPathType | None = None,
+    doall: bool = False,
+    noempty: bool = False,
+    notitle: bool = False,
+    log10: bool = False,
+    pdf: bool = False,
+    min_: float | None = None,
+    max_: float | None = None,
+    igfac: bool = False,
+    int_: bool = False,
+    float_: bool = False,
+    unq: str | None = None,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dhistogOutputs:
+    """
+    Compute histogram of a 3D dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset.
+        nbin: Use specified number of bins.
+        dind: Use data from specified sub-brick index.
+        omit: Omit specified value from the count.
+        mask: Use mask dataset to determine which voxels to use.
+        roi_mask: Create histogram for each non-zero value in 'r' dataset.
+        doall: Include all sub-bricks in the calculation.
+        noempty: Only output bins that are not empty.
+        notitle: Leave the title line off the output.
+        log10: Output log10() of the counts.
+        pdf: Output the counts divided by the number of samples.
+        min_: Specify minimum (inclusive) of histogram.
+        max_: Specify maximum (inclusive) of histogram.
+        igfac: Ignore sub-brick scale factors and histogram-ize the 'raw' data.
+        int_: Treat data and output as integers.
+        float_: Treat data and output as floats.
+        unq: Writes out the sorted unique values to file.
+        prefix: Write a copy of the histogram into specified file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dhistogOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DHISTOG_METADATA)
+    params = v_3dhistog_params(
+        dataset=dataset,
+        nbin=nbin,
+        dind=dind,
+        omit=omit,
+        mask=mask,
+        roi_mask=roi_mask,
+        doall=doall,
+        noempty=noempty,
+        notitle=notitle,
+        log10=log10,
+        pdf=pdf,
+        min_=min_,
+        max_=max_,
+        igfac=igfac,
+        int_=int_,
+        float_=float_,
+        unq=unq,
+        prefix=prefix,
+    )
+    return v_3dhistog_execute(params, execution)
+
+
+__all__ = [
+    "V3dhistogOutputs",
+    "V3dhistogParameters",
+    "V_3DHISTOG_METADATA",
+    "v_3dhistog",
+    "v_3dhistog_params",
+]

niwrap_afni/afni/v_3dinfill.py

@@ -0,0 +1,302 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DINFILL_METADATA = Metadata(
+    id="263217e116d12496939583b1c3c4001f87f5e06c.boutiques",
+    name="3dinfill",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dinfillParameters = typing.TypedDict('V3dinfillParameters', {
+    "__STYX_TYPE__": typing.Literal["3dinfill"],
+    "input": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "niter": typing.NotRequired[float | None],
+    "blend": typing.NotRequired[typing.Literal["MODE", "AVG", "AUTO", "SOLID", "SOLID_CLEAN"] | None],
+    "minhits": typing.NotRequired[float | None],
+    "ed": typing.NotRequired[list[float] | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_range": typing.NotRequired[list[float] | None],
+    "mrange": typing.NotRequired[list[float] | None],
+    "cmask": 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 {
+        "3dinfill": v_3dinfill_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 {
+        "3dinfill": v_3dinfill_outputs,
+    }.get(t)
+
+
+class V3dinfillOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dinfill(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_filled: OutputPathType | None
+    """Filled volume output"""
+
+
+def v_3dinfill_params(
+    input_: InputPathType,
+    prefix: str | None = None,
+    niter: float | None = None,
+    blend: typing.Literal["MODE", "AVG", "AUTO", "SOLID", "SOLID_CLEAN"] | None = None,
+    minhits: float | None = None,
+    ed: list[float] | None = None,
+    mask: InputPathType | None = None,
+    mask_range: list[float] | None = None,
+    mrange: list[float] | None = None,
+    cmask: str | None = None,
+) -> V3dinfillParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Fill volume dataset.
+        prefix: Use PREF for output prefix.
+        niter: Do not allow the fill function to do more than NITER passes.
+        blend: Method for assigning a value to a hole.
+        minhits: Criterion for considering a zero voxel to be a hole. Can only\
+            be used with -blend SOLID.
+        ed: Erode N times then dilate N times to get rid of hanging chunks.\
+            Values filled in by this process get value V.
+        mask: Provide mask dataset to select subset of input.
+        mask_range: Specify the range of values to consider from mask dataset.
+        mrange: Alias for -mask_range option.
+        cmask: Provide cmask expression. Voxels where expression is 0 are\
+            excluded from computations.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dinfill",
+        "input": input_,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if niter is not None:
+        params["niter"] = niter
+    if blend is not None:
+        params["blend"] = blend
+    if minhits is not None:
+        params["minhits"] = minhits
+    if ed is not None:
+        params["ed"] = ed
+    if mask is not None:
+        params["mask"] = mask
+    if mask_range is not None:
+        params["mask_range"] = mask_range
+    if mrange is not None:
+        params["mrange"] = mrange
+    if cmask is not None:
+        params["cmask"] = cmask
+    return params
+
+
+def v_3dinfill_cargs(
+    params: V3dinfillParameters,
+    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("3dinfill")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input"))
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("niter") is not None:
+        cargs.extend([
+            "-Niter",
+            str(params.get("niter"))
+        ])
+    if params.get("blend") is not None:
+        cargs.extend([
+            "-blend",
+            params.get("blend")
+        ])
+    if params.get("minhits") is not None:
+        cargs.extend([
+            "-minhits",
+            str(params.get("minhits"))
+        ])
+    if params.get("ed") is not None:
+        cargs.extend([
+            "-ed",
+            *map(str, params.get("ed"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("mask_range") is not None:
+        cargs.extend([
+            "-mask_range",
+            *map(str, params.get("mask_range"))
+        ])
+    if params.get("mrange") is not None:
+        cargs.extend([
+            "-mrange",
+            *map(str, params.get("mrange"))
+        ])
+    if params.get("cmask") is not None:
+        cargs.extend([
+            "-cmask",
+            params.get("cmask")
+        ])
+    return cargs
+
+
+def v_3dinfill_outputs(
+    params: V3dinfillParameters,
+    execution: Execution,
+) -> V3dinfillOutputs:
+    """
+    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 = V3dinfillOutputs(
+        root=execution.output_file("."),
+        output_filled=execution.output_file(params.get("prefix") + "_filled.nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3dinfill_execute(
+    params: V3dinfillParameters,
+    execution: Execution,
+) -> V3dinfillOutputs:
+    """
+    A program to fill holes in volumes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dinfillOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dinfill_cargs(params, execution)
+    ret = v_3dinfill_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dinfill(
+    input_: InputPathType,
+    prefix: str | None = None,
+    niter: float | None = None,
+    blend: typing.Literal["MODE", "AVG", "AUTO", "SOLID", "SOLID_CLEAN"] | None = None,
+    minhits: float | None = None,
+    ed: list[float] | None = None,
+    mask: InputPathType | None = None,
+    mask_range: list[float] | None = None,
+    mrange: list[float] | None = None,
+    cmask: str | None = None,
+    runner: Runner | None = None,
+) -> V3dinfillOutputs:
+    """
+    A program to fill holes in volumes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Fill volume dataset.
+        prefix: Use PREF for output prefix.
+        niter: Do not allow the fill function to do more than NITER passes.
+        blend: Method for assigning a value to a hole.
+        minhits: Criterion for considering a zero voxel to be a hole. Can only\
+            be used with -blend SOLID.
+        ed: Erode N times then dilate N times to get rid of hanging chunks.\
+            Values filled in by this process get value V.
+        mask: Provide mask dataset to select subset of input.
+        mask_range: Specify the range of values to consider from mask dataset.
+        mrange: Alias for -mask_range option.
+        cmask: Provide cmask expression. Voxels where expression is 0 are\
+            excluded from computations.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dinfillOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DINFILL_METADATA)
+    params = v_3dinfill_params(
+        input_=input_,
+        prefix=prefix,
+        niter=niter,
+        blend=blend,
+        minhits=minhits,
+        ed=ed,
+        mask=mask,
+        mask_range=mask_range,
+        mrange=mrange,
+        cmask=cmask,
+    )
+    return v_3dinfill_execute(params, execution)
+
+
+__all__ = [
+    "V3dinfillOutputs",
+    "V3dinfillParameters",
+    "V_3DINFILL_METADATA",
+    "v_3dinfill",
+    "v_3dinfill_params",
+]