niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_hist.py

@@ -0,0 +1,406 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_HIST_METADATA = Metadata(
+    id="5dff8f7ac913ce4a3781c6d59d7827316323eded.boutiques",
+    name="3dHist",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dHistParameters = typing.TypedDict('V3dHistParameters', {
+    "__STYX_TYPE__": typing.Literal["3dHist"],
+    "input": InputPathType,
+    "mask_dset": typing.NotRequired[InputPathType | None],
+    "mask_range": typing.NotRequired[list[float] | None],
+    "cmask": typing.NotRequired[str | None],
+    "hist_file": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "equalized": typing.NotRequired[str | None],
+    "nbin": typing.NotRequired[float | None],
+    "min": typing.NotRequired[float | None],
+    "max": typing.NotRequired[float | None],
+    "binwidth": typing.NotRequired[float | None],
+    "ignore_out": bool,
+    "range_hist": typing.NotRequired[InputPathType | None],
+    "showhist": bool,
+    "at_val": typing.NotRequired[float | None],
+    "get_params": typing.NotRequired[str | None],
+    "voxvol": typing.NotRequired[float | None],
+    "val_at": typing.NotRequired[str | None],
+    "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 {
+        "3dHist": v_3d_hist_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 V3dHistOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_hist(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_hist_params(
+    input_: InputPathType,
+    mask_dset: InputPathType | None = None,
+    mask_range: list[float] | None = None,
+    cmask: str | None = None,
+    hist_file: InputPathType | None = None,
+    prefix: str | None = None,
+    equalized: str | None = None,
+    nbin: float | None = None,
+    min_: float | None = None,
+    max_: float | None = None,
+    binwidth: float | None = None,
+    ignore_out: bool = False,
+    range_hist: InputPathType | None = None,
+    showhist: bool = False,
+    at_val: float | None = None,
+    get_params: str | None = None,
+    voxvol: float | None = None,
+    val_at: str | None = None,
+    quiet: bool = False,
+) -> V3dHistParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Dataset providing values for histogram.
+        mask_dset: Provide mask dataset to select subset of input.
+        mask_range: Specify the range of values to consider from MSET. Default\
+            is anything non-zero.
+        cmask: Provide cmask expression. Voxels where expression is 0 are\
+            excluded from computations.
+        hist_file: Read this previously created histogram instead of forming\
+            one from DSET.
+        prefix: Write histogram to niml file called PREF.niml.hist.
+        equalized: Write a histogram equalized version of the input dataset.
+        nbin: Use K bins.
+        min_: Minimum intensity.
+        max_: Maximum intensity.
+        binwidth: Bin width.
+        ignore_out: Do not count samples outside the user specified range.
+        range_hist: Use previously created histogram to set range and binwidth\
+            parameters.
+        showhist: Display histogram to stdout.
+        at_val: Set the value at which you want histogram values.
+        get_params: Return the desired properties at a given value. You can\
+            select multiple properties.
+        voxvol: Specify voxel volume in mm^3. To be used with upvol.
+        val_at: Return the value where histogram property PAR is equal to\
+            PARVAL. PAR can be: cdf, rcdf, ncdf, nrcdf, upvol.
+        quiet: Return a concise output to simplify parsing.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dHist",
+        "input": input_,
+        "ignore_out": ignore_out,
+        "showhist": showhist,
+        "quiet": quiet,
+    }
+    if mask_dset is not None:
+        params["mask_dset"] = mask_dset
+    if mask_range is not None:
+        params["mask_range"] = mask_range
+    if cmask is not None:
+        params["cmask"] = cmask
+    if hist_file is not None:
+        params["hist_file"] = hist_file
+    if prefix is not None:
+        params["prefix"] = prefix
+    if equalized is not None:
+        params["equalized"] = equalized
+    if nbin is not None:
+        params["nbin"] = nbin
+    if min_ is not None:
+        params["min"] = min_
+    if max_ is not None:
+        params["max"] = max_
+    if binwidth is not None:
+        params["binwidth"] = binwidth
+    if range_hist is not None:
+        params["range_hist"] = range_hist
+    if at_val is not None:
+        params["at_val"] = at_val
+    if get_params is not None:
+        params["get_params"] = get_params
+    if voxvol is not None:
+        params["voxvol"] = voxvol
+    if val_at is not None:
+        params["val_at"] = val_at
+    return params
+
+
+def v_3d_hist_cargs(
+    params: V3dHistParameters,
+    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("3dHist")
+    cargs.append(execution.input_file(params.get("input")))
+    if params.get("mask_dset") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_dset"))
+        ])
+    if params.get("mask_range") is not None:
+        cargs.extend([
+            "-mask_range",
+            *map(str, params.get("mask_range"))
+        ])
+    if params.get("cmask") is not None:
+        cargs.extend([
+            "-cmask",
+            params.get("cmask")
+        ])
+    if params.get("hist_file") is not None:
+        cargs.extend([
+            "-thishist",
+            execution.input_file(params.get("hist_file"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("equalized") is not None:
+        cargs.extend([
+            "-equalized",
+            params.get("equalized")
+        ])
+    if params.get("nbin") is not None:
+        cargs.extend([
+            "-nbin",
+            str(params.get("nbin"))
+        ])
+    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("binwidth") is not None:
+        cargs.extend([
+            "-binwidth",
+            str(params.get("binwidth"))
+        ])
+    if params.get("ignore_out"):
+        cargs.append("-ignore_out")
+    if params.get("range_hist") is not None:
+        cargs.extend([
+            "-rhist",
+            execution.input_file(params.get("range_hist"))
+        ])
+    if params.get("showhist"):
+        cargs.append("-showhist")
+    if params.get("at_val") is not None:
+        cargs.extend([
+            "-at",
+            str(params.get("at_val"))
+        ])
+    if params.get("get_params") is not None:
+        cargs.extend([
+            "-get",
+            params.get("get_params")
+        ])
+    if params.get("voxvol") is not None:
+        cargs.extend([
+            "-voxvol",
+            str(params.get("voxvol"))
+        ])
+    if params.get("val_at") is not None:
+        cargs.extend([
+            "-val_at",
+            params.get("val_at")
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3d_hist_outputs(
+    params: V3dHistParameters,
+    execution: Execution,
+) -> V3dHistOutputs:
+    """
+    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 = V3dHistOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_hist_execute(
+    params: V3dHistParameters,
+    execution: Execution,
+) -> V3dHistOutputs:
+    """
+    Computes histograms using functions for generating priors.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dHistOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_hist_cargs(params, execution)
+    ret = v_3d_hist_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_hist(
+    input_: InputPathType,
+    mask_dset: InputPathType | None = None,
+    mask_range: list[float] | None = None,
+    cmask: str | None = None,
+    hist_file: InputPathType | None = None,
+    prefix: str | None = None,
+    equalized: str | None = None,
+    nbin: float | None = None,
+    min_: float | None = None,
+    max_: float | None = None,
+    binwidth: float | None = None,
+    ignore_out: bool = False,
+    range_hist: InputPathType | None = None,
+    showhist: bool = False,
+    at_val: float | None = None,
+    get_params: str | None = None,
+    voxvol: float | None = None,
+    val_at: str | None = None,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> V3dHistOutputs:
+    """
+    Computes histograms using functions for generating priors.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Dataset providing values for histogram.
+        mask_dset: Provide mask dataset to select subset of input.
+        mask_range: Specify the range of values to consider from MSET. Default\
+            is anything non-zero.
+        cmask: Provide cmask expression. Voxels where expression is 0 are\
+            excluded from computations.
+        hist_file: Read this previously created histogram instead of forming\
+            one from DSET.
+        prefix: Write histogram to niml file called PREF.niml.hist.
+        equalized: Write a histogram equalized version of the input dataset.
+        nbin: Use K bins.
+        min_: Minimum intensity.
+        max_: Maximum intensity.
+        binwidth: Bin width.
+        ignore_out: Do not count samples outside the user specified range.
+        range_hist: Use previously created histogram to set range and binwidth\
+            parameters.
+        showhist: Display histogram to stdout.
+        at_val: Set the value at which you want histogram values.
+        get_params: Return the desired properties at a given value. You can\
+            select multiple properties.
+        voxvol: Specify voxel volume in mm^3. To be used with upvol.
+        val_at: Return the value where histogram property PAR is equal to\
+            PARVAL. PAR can be: cdf, rcdf, ncdf, nrcdf, upvol.
+        quiet: Return a concise output to simplify parsing.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dHistOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_HIST_METADATA)
+    params = v_3d_hist_params(
+        input_=input_,
+        mask_dset=mask_dset,
+        mask_range=mask_range,
+        cmask=cmask,
+        hist_file=hist_file,
+        prefix=prefix,
+        equalized=equalized,
+        nbin=nbin,
+        min_=min_,
+        max_=max_,
+        binwidth=binwidth,
+        ignore_out=ignore_out,
+        range_hist=range_hist,
+        showhist=showhist,
+        at_val=at_val,
+        get_params=get_params,
+        voxvol=voxvol,
+        val_at=val_at,
+        quiet=quiet,
+    )
+    return v_3d_hist_execute(params, execution)
+
+
+__all__ = [
+    "V3dHistOutputs",
+    "V3dHistParameters",
+    "V_3D_HIST_METADATA",
+    "v_3d_hist",
+    "v_3d_hist_params",
+]

niwrap_afni/afni/v_3d_icc.py

@@ -0,0 +1,228 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ICC_METADATA = Metadata(
+    id="6b7ec5c6de013c42d47420ebf12a564c200ff8a3.boutiques",
+    name="3dICC",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dIccParameters = typing.TypedDict('V3dIccParameters', {
+    "__STYX_TYPE__": typing.Literal["3dICC"],
+    "model": str,
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "data_table": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dICC": v_3d_icc_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 {
+        "3dICC": v_3d_icc_outputs,
+    }.get(t)
+
+
+class V3dIccOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_icc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Name of the output file"""
+
+
+def v_3d_icc_params(
+    model: str,
+    prefix: str,
+    data_table: str,
+    mask: InputPathType | None = None,
+) -> V3dIccParameters:
+    """
+    Build parameters.
+    
+    Args:
+        model: Model structure for all the variables. The expression FORMULA\
+            with more than one variable has to be surrounded within quotes.\
+            Variable names should be consistent with the ones used in the header of\
+            -dataTable.
+        prefix: Name of output file. For AFNI format, provide prefix only, with\
+            no view+suffix needed. Filename for NIfTI format should have .nii\
+            attached, while file name for surface data is expected to end with\
+            .niml.dset.
+        data_table: List the data structure with a header as the first line.\
+            The first column is reserved with label 'Subj', and the last is\
+            reserved for 'InputFile'.
+        mask: Path to mask file. Only process voxels inside this mask.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dICC",
+        "model": model,
+        "prefix": prefix,
+        "data_table": data_table,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3d_icc_cargs(
+    params: V3dIccParameters,
+    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("3dICC")
+    cargs.append(params.get("model"))
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    cargs.extend([
+        "-dataTable",
+        params.get("data_table")
+    ])
+    cargs.append("[OPTIONS]")
+    return cargs
+
+
+def v_3d_icc_outputs(
+    params: V3dIccParameters,
+    execution: Execution,
+) -> V3dIccOutputs:
+    """
+    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 = V3dIccOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix")),
+    )
+    return ret
+
+
+def v_3d_icc_execute(
+    params: V3dIccParameters,
+    execution: Execution,
+) -> V3dIccOutputs:
+    """
+    AFNI Program for IntraClass Correlatin (ICC) Analysis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dIccOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_icc_cargs(params, execution)
+    ret = v_3d_icc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_icc(
+    model: str,
+    prefix: str,
+    data_table: str,
+    mask: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> V3dIccOutputs:
+    """
+    AFNI Program for IntraClass Correlatin (ICC) Analysis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        model: Model structure for all the variables. The expression FORMULA\
+            with more than one variable has to be surrounded within quotes.\
+            Variable names should be consistent with the ones used in the header of\
+            -dataTable.
+        prefix: Name of output file. For AFNI format, provide prefix only, with\
+            no view+suffix needed. Filename for NIfTI format should have .nii\
+            attached, while file name for surface data is expected to end with\
+            .niml.dset.
+        data_table: List the data structure with a header as the first line.\
+            The first column is reserved with label 'Subj', and the last is\
+            reserved for 'InputFile'.
+        mask: Path to mask file. Only process voxels inside this mask.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dIccOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ICC_METADATA)
+    params = v_3d_icc_params(
+        model=model,
+        prefix=prefix,
+        mask=mask,
+        data_table=data_table,
+    )
+    return v_3d_icc_execute(params, execution)
+
+
+__all__ = [
+    "V3dIccOutputs",
+    "V3dIccParameters",
+    "V_3D_ICC_METADATA",
+    "v_3d_icc",
+    "v_3d_icc_params",
+]