niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_getrow.py

@@ -0,0 +1,243 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_GETROW_METADATA = Metadata(
+    id="d22ec4eb4bbd666f8edad727a5f0b3e13111b433.boutiques",
+    name="3dGetrow",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dGetrowParameters = typing.TypedDict('V3dGetrowParameters', {
+    "__STYX_TYPE__": typing.Literal["3dGetrow"],
+    "xrow": typing.NotRequired[list[int] | None],
+    "yrow": typing.NotRequired[list[int] | None],
+    "zrow": typing.NotRequired[list[int] | None],
+    "input_file": typing.NotRequired[InputPathType | None],
+    "output_file": 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 {
+        "3dGetrow": v_3d_getrow_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 {
+        "3dGetrow": v_3d_getrow_outputs,
+    }.get(t)
+
+
+class V3dGetrowOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_getrow(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Output .1D ASCII file"""
+
+
+def v_3d_getrow_params(
+    xrow: list[int] | None = None,
+    yrow: list[int] | None = None,
+    zrow: list[int] | None = None,
+    input_file: InputPathType | None = None,
+    output_file: str | None = None,
+) -> V3dGetrowParameters:
+    """
+    Build parameters.
+    
+    Args:
+        xrow: Extract row along the x-direction at fixed y-index of j and fixed\
+            z-index of k.
+        yrow: Extract row along the y-direction at fixed x-index of i and fixed\
+            z-index of k.
+        zrow: Extract row along the z-direction at fixed x-index of i and fixed\
+            y-index of j.
+        input_file: Read input from dataset 'ddd' (instead of putting dataset\
+            name at end of command line).
+        output_file: Filename for output .1D ASCII file will be 'ff' (if 'ff'\
+            is '-', then output is to stdout, the default).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dGetrow",
+    }
+    if xrow is not None:
+        params["xrow"] = xrow
+    if yrow is not None:
+        params["yrow"] = yrow
+    if zrow is not None:
+        params["zrow"] = zrow
+    if input_file is not None:
+        params["input_file"] = input_file
+    if output_file is not None:
+        params["output_file"] = output_file
+    return params
+
+
+def v_3d_getrow_cargs(
+    params: V3dGetrowParameters,
+    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("3dGetrow")
+    if params.get("xrow") is not None:
+        cargs.extend([
+            "-xrow",
+            *map(str, params.get("xrow"))
+        ])
+    if params.get("yrow") is not None:
+        cargs.extend([
+            "-yrow",
+            *map(str, params.get("yrow"))
+        ])
+    if params.get("zrow") is not None:
+        cargs.extend([
+            "-zrow",
+            *map(str, params.get("zrow"))
+        ])
+    if params.get("input_file") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input_file"))
+        ])
+    if params.get("output_file") is not None:
+        cargs.extend([
+            "-output",
+            params.get("output_file")
+        ])
+    return cargs
+
+
+def v_3d_getrow_outputs(
+    params: V3dGetrowParameters,
+    execution: Execution,
+) -> V3dGetrowOutputs:
+    """
+    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 = V3dGetrowOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("output_file") + ".1D") if (params.get("output_file") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_getrow_execute(
+    params: V3dGetrowParameters,
+    execution: Execution,
+) -> V3dGetrowOutputs:
+    """
+    Program to extract 1 row from a dataset and write it as 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 `V3dGetrowOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_getrow_cargs(params, execution)
+    ret = v_3d_getrow_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_getrow(
+    xrow: list[int] | None = None,
+    yrow: list[int] | None = None,
+    zrow: list[int] | None = None,
+    input_file: InputPathType | None = None,
+    output_file: str | None = None,
+    runner: Runner | None = None,
+) -> V3dGetrowOutputs:
+    """
+    Program to extract 1 row from a dataset and write it as a .1D file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        xrow: Extract row along the x-direction at fixed y-index of j and fixed\
+            z-index of k.
+        yrow: Extract row along the y-direction at fixed x-index of i and fixed\
+            z-index of k.
+        zrow: Extract row along the z-direction at fixed x-index of i and fixed\
+            y-index of j.
+        input_file: Read input from dataset 'ddd' (instead of putting dataset\
+            name at end of command line).
+        output_file: Filename for output .1D ASCII file will be 'ff' (if 'ff'\
+            is '-', then output is to stdout, the default).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dGetrowOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_GETROW_METADATA)
+    params = v_3d_getrow_params(
+        xrow=xrow,
+        yrow=yrow,
+        zrow=zrow,
+        input_file=input_file,
+        output_file=output_file,
+    )
+    return v_3d_getrow_execute(params, execution)
+
+
+__all__ = [
+    "V3dGetrowOutputs",
+    "V3dGetrowParameters",
+    "V_3D_GETROW_METADATA",
+    "v_3d_getrow",
+    "v_3d_getrow_params",
+]

niwrap_afni/afni/v_3d_grayplot.py

@@ -0,0 +1,343 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_GRAYPLOT_METADATA = Metadata(
+    id="6d17ab08ae2c6bafb3bb5a4bc0dd707aa3956213.boutiques",
+    name="3dGrayplot",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dGrayplotParameters = typing.TypedDict('V3dGrayplotParameters', {
+    "__STYX_TYPE__": typing.Literal["3dGrayplot"],
+    "input": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "dimensions": typing.NotRequired[list[float] | None],
+    "resample_old": bool,
+    "polort": typing.NotRequired[float | None],
+    "fwhm": typing.NotRequired[float | None],
+    "pvorder": bool,
+    "LJorder": bool,
+    "peelorder": bool,
+    "ijkorder": bool,
+    "range": typing.NotRequired[float | None],
+    "percent": bool,
+    "raw_with_bounds": typing.NotRequired[list[float] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dGrayplot": v_3d_grayplot_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 {
+        "3dGrayplot": v_3d_grayplot_outputs,
+    }.get(t)
+
+
+class V3dGrayplotOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_grayplot(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    grayplot_img: OutputPathType | None
+    """Grayplot image file"""
+
+
+def v_3d_grayplot_params(
+    input_: InputPathType,
+    mask: InputPathType | None = None,
+    prefix: str | None = None,
+    dimensions: list[float] | None = None,
+    resample_old: bool = False,
+    polort: float | None = None,
+    fwhm: float | None = None,
+    pvorder: bool = False,
+    ljorder: bool = False,
+    peelorder: bool = False,
+    ijkorder: bool = False,
+    range_: float | None = None,
+    percent: bool = False,
+    raw_with_bounds: list[float] | None = None,
+) -> V3dGrayplotParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Input dataset.
+        mask: Name of mask dataset. Voxels that are 0 in the mask will not be\
+            processed.
+        prefix: Name for the output file. Default is Grayplot.png.
+        dimensions: Output size of image in pixels: [width height]. Defaults\
+            are width=1024 and height=512.
+        resample_old: Original resampling method for processed dataset.
+        polort: Order of polynomials for detrending. Default is 2. Use '-1' if\
+            data is already detrended and de-meaned.
+        fwhm: FWHM of blurring radius to use in the dataset before making the\
+            image. Default is 0 mm.
+        pvorder: Order the voxels by how well they match the two leading\
+            principal components of their partition.
+        ljorder: Order the voxels by their Ljung-Box statistics, a measure of\
+            temporal correlation.
+        peelorder: Order the voxels by how many 'peel' steps are needed to get\
+            from the partition boundary to the voxel.
+        ijkorder: Default intra-partition ordering by dataset 3D index ('ijk').
+        range_: Set the range of the data to be plotted. Value of 0 is\
+            middle-gray, +X is white, -X is black.
+        percent: Scale values to percent differences from the mean of each\
+            voxel timeseries. Suitable for raw time series datasets.
+        raw_with_bounds: Map values <= A to black, values >= B to white, and\
+            intermediate values to grays.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dGrayplot",
+        "input": input_,
+        "resample_old": resample_old,
+        "pvorder": pvorder,
+        "LJorder": ljorder,
+        "peelorder": peelorder,
+        "ijkorder": ijkorder,
+        "percent": percent,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if prefix is not None:
+        params["prefix"] = prefix
+    if dimensions is not None:
+        params["dimensions"] = dimensions
+    if polort is not None:
+        params["polort"] = polort
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if range_ is not None:
+        params["range"] = range_
+    if raw_with_bounds is not None:
+        params["raw_with_bounds"] = raw_with_bounds
+    return params
+
+
+def v_3d_grayplot_cargs(
+    params: V3dGrayplotParameters,
+    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("3dGrayplot")
+    cargs.append(execution.input_file(params.get("input")))
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("dimensions") is not None:
+        cargs.extend([
+            "-dimen",
+            *map(str, params.get("dimensions"))
+        ])
+    if params.get("resample_old"):
+        cargs.append("-oldresam")
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "-fwhm",
+            str(params.get("fwhm"))
+        ])
+    if params.get("pvorder"):
+        cargs.append("-pvorder")
+    if params.get("LJorder"):
+        cargs.append("-LJorder")
+    if params.get("peelorder"):
+        cargs.append("-peelorder")
+    if params.get("ijkorder"):
+        cargs.append("-ijkorder")
+    if params.get("range") is not None:
+        cargs.extend([
+            "-range",
+            str(params.get("range"))
+        ])
+    if params.get("percent"):
+        cargs.append("-percent")
+    if params.get("raw_with_bounds") is not None:
+        cargs.extend([
+            "-raw_with_bounds",
+            *map(str, params.get("raw_with_bounds"))
+        ])
+    return cargs
+
+
+def v_3d_grayplot_outputs(
+    params: V3dGrayplotParameters,
+    execution: Execution,
+) -> V3dGrayplotOutputs:
+    """
+    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 = V3dGrayplotOutputs(
+        root=execution.output_file("."),
+        grayplot_img=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_grayplot_execute(
+    params: V3dGrayplotParameters,
+    execution: Execution,
+) -> V3dGrayplotOutputs:
+    """
+    Make a grayplot from a 3D+time dataset, like a carpet plot. Result is saved to a
+    PNG image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dGrayplotOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_grayplot_cargs(params, execution)
+    ret = v_3d_grayplot_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_grayplot(
+    input_: InputPathType,
+    mask: InputPathType | None = None,
+    prefix: str | None = None,
+    dimensions: list[float] | None = None,
+    resample_old: bool = False,
+    polort: float | None = None,
+    fwhm: float | None = None,
+    pvorder: bool = False,
+    ljorder: bool = False,
+    peelorder: bool = False,
+    ijkorder: bool = False,
+    range_: float | None = None,
+    percent: bool = False,
+    raw_with_bounds: list[float] | None = None,
+    runner: Runner | None = None,
+) -> V3dGrayplotOutputs:
+    """
+    Make a grayplot from a 3D+time dataset, like a carpet plot. Result is saved to a
+    PNG image.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Input dataset.
+        mask: Name of mask dataset. Voxels that are 0 in the mask will not be\
+            processed.
+        prefix: Name for the output file. Default is Grayplot.png.
+        dimensions: Output size of image in pixels: [width height]. Defaults\
+            are width=1024 and height=512.
+        resample_old: Original resampling method for processed dataset.
+        polort: Order of polynomials for detrending. Default is 2. Use '-1' if\
+            data is already detrended and de-meaned.
+        fwhm: FWHM of blurring radius to use in the dataset before making the\
+            image. Default is 0 mm.
+        pvorder: Order the voxels by how well they match the two leading\
+            principal components of their partition.
+        ljorder: Order the voxels by their Ljung-Box statistics, a measure of\
+            temporal correlation.
+        peelorder: Order the voxels by how many 'peel' steps are needed to get\
+            from the partition boundary to the voxel.
+        ijkorder: Default intra-partition ordering by dataset 3D index ('ijk').
+        range_: Set the range of the data to be plotted. Value of 0 is\
+            middle-gray, +X is white, -X is black.
+        percent: Scale values to percent differences from the mean of each\
+            voxel timeseries. Suitable for raw time series datasets.
+        raw_with_bounds: Map values <= A to black, values >= B to white, and\
+            intermediate values to grays.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dGrayplotOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_GRAYPLOT_METADATA)
+    params = v_3d_grayplot_params(
+        input_=input_,
+        mask=mask,
+        prefix=prefix,
+        dimensions=dimensions,
+        resample_old=resample_old,
+        polort=polort,
+        fwhm=fwhm,
+        pvorder=pvorder,
+        ljorder=ljorder,
+        peelorder=peelorder,
+        ijkorder=ijkorder,
+        range_=range_,
+        percent=percent,
+        raw_with_bounds=raw_with_bounds,
+    )
+    return v_3d_grayplot_execute(params, execution)
+
+
+__all__ = [
+    "V3dGrayplotOutputs",
+    "V3dGrayplotParameters",
+    "V_3D_GRAYPLOT_METADATA",
+    "v_3d_grayplot",
+    "v_3d_grayplot_params",
+]