niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_auto_tcorrelate.py

@@ -0,0 +1,314 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_AUTO_TCORRELATE_METADATA = Metadata(
+    id="54f323538871e62136cb28afd7fdc9c55ace001b.boutiques",
+    name="3dAutoTcorrelate",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAutoTcorrelateParameters = typing.TypedDict('V3dAutoTcorrelateParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAutoTcorrelate"],
+    "input_dataset": InputPathType,
+    "pearson": bool,
+    "eta2": bool,
+    "polort": typing.NotRequired[int | None],
+    "autoclip": bool,
+    "automask": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_only_targets": bool,
+    "mask_source": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "out1d": typing.NotRequired[str | None],
+    "time": bool,
+    "mmap": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAutoTcorrelate": v_3d_auto_tcorrelate_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 {
+        "3dAutoTcorrelate": v_3d_auto_tcorrelate_outputs,
+    }.get(t)
+
+
+class V3dAutoTcorrelateOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_auto_tcorrelate(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_brick: OutputPathType | None
+    """Main output dataset"""
+    output_head: OutputPathType | None
+    """Header information for main output dataset"""
+    out1d_file: OutputPathType | None
+    """Output in 1D text format"""
+
+
+def v_3d_auto_tcorrelate_params(
+    input_dataset: InputPathType,
+    pearson: bool = False,
+    eta2: bool = False,
+    polort: int | None = None,
+    autoclip: bool = False,
+    automask: bool = False,
+    mask: InputPathType | None = None,
+    mask_only_targets: bool = False,
+    mask_source: InputPathType | None = None,
+    prefix: str | None = None,
+    out1d: str | None = None,
+    time_: bool = False,
+    mmap_: bool = False,
+) -> V3dAutoTcorrelateParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset.
+        pearson: Correlation is the normal Pearson (product moment) correlation\
+            coefficient [default].
+        eta2: Output is eta^2 measure from Cohen et al., NeuroImage, 2008.
+        polort: Remove polynomial trend of order 'm', for m=-1..3.
+        autoclip: Clip off low-intensity regions in the dataset.
+        automask: Apply automask to the dataset.
+        mask: Mask of both 'source' and 'target' voxels.
+        mask_only_targets: Provide output for all voxels.
+        mask_source: Provide output for voxels only in specified mask.
+        prefix: Save output into dataset with specified prefix.
+        out1d: Save output in a text file in 1D format.
+        time_: Mark output as a 3D+time dataset.
+        mmap_: Write .BRIK results to disk directly using Unix mmap().
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAutoTcorrelate",
+        "input_dataset": input_dataset,
+        "pearson": pearson,
+        "eta2": eta2,
+        "autoclip": autoclip,
+        "automask": automask,
+        "mask_only_targets": mask_only_targets,
+        "time": time_,
+        "mmap": mmap_,
+    }
+    if polort is not None:
+        params["polort"] = polort
+    if mask is not None:
+        params["mask"] = mask
+    if mask_source is not None:
+        params["mask_source"] = mask_source
+    if prefix is not None:
+        params["prefix"] = prefix
+    if out1d is not None:
+        params["out1d"] = out1d
+    return params
+
+
+def v_3d_auto_tcorrelate_cargs(
+    params: V3dAutoTcorrelateParameters,
+    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("3dAutoTcorrelate")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    if params.get("pearson"):
+        cargs.append("-pearson")
+    if params.get("eta2"):
+        cargs.append("-eta2")
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    if params.get("autoclip"):
+        cargs.append("-autoclip")
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("mask_only_targets"):
+        cargs.append("-mask_only_targets")
+    if params.get("mask_source") is not None:
+        cargs.extend([
+            "-mask_source",
+            execution.input_file(params.get("mask_source"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("out1d") is not None:
+        cargs.extend([
+            "-out1D",
+            params.get("out1d")
+        ])
+    if params.get("time"):
+        cargs.append("-time")
+    if params.get("mmap"):
+        cargs.append("-mmap")
+    return cargs
+
+
+def v_3d_auto_tcorrelate_outputs(
+    params: V3dAutoTcorrelateParameters,
+    execution: Execution,
+) -> V3dAutoTcorrelateOutputs:
+    """
+    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 = V3dAutoTcorrelateOutputs(
+        root=execution.output_file("."),
+        output_brick=execution.output_file(params.get("prefix") + ".BRIK") if (params.get("prefix") is not None) else None,
+        output_head=execution.output_file(params.get("prefix") + ".HEAD") if (params.get("prefix") is not None) else None,
+        out1d_file=execution.output_file(params.get("out1d")) if (params.get("out1d") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_auto_tcorrelate_execute(
+    params: V3dAutoTcorrelateParameters,
+    execution: Execution,
+) -> V3dAutoTcorrelateOutputs:
+    """
+    Computes the correlation coefficient between the time series of each pair of
+    voxels in the input dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAutoTcorrelateOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_auto_tcorrelate_cargs(params, execution)
+    ret = v_3d_auto_tcorrelate_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_auto_tcorrelate(
+    input_dataset: InputPathType,
+    pearson: bool = False,
+    eta2: bool = False,
+    polort: int | None = None,
+    autoclip: bool = False,
+    automask: bool = False,
+    mask: InputPathType | None = None,
+    mask_only_targets: bool = False,
+    mask_source: InputPathType | None = None,
+    prefix: str | None = None,
+    out1d: str | None = None,
+    time_: bool = False,
+    mmap_: bool = False,
+    runner: Runner | None = None,
+) -> V3dAutoTcorrelateOutputs:
+    """
+    Computes the correlation coefficient between the time series of each pair of
+    voxels in the input dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset.
+        pearson: Correlation is the normal Pearson (product moment) correlation\
+            coefficient [default].
+        eta2: Output is eta^2 measure from Cohen et al., NeuroImage, 2008.
+        polort: Remove polynomial trend of order 'm', for m=-1..3.
+        autoclip: Clip off low-intensity regions in the dataset.
+        automask: Apply automask to the dataset.
+        mask: Mask of both 'source' and 'target' voxels.
+        mask_only_targets: Provide output for all voxels.
+        mask_source: Provide output for voxels only in specified mask.
+        prefix: Save output into dataset with specified prefix.
+        out1d: Save output in a text file in 1D format.
+        time_: Mark output as a 3D+time dataset.
+        mmap_: Write .BRIK results to disk directly using Unix mmap().
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAutoTcorrelateOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AUTO_TCORRELATE_METADATA)
+    params = v_3d_auto_tcorrelate_params(
+        input_dataset=input_dataset,
+        pearson=pearson,
+        eta2=eta2,
+        polort=polort,
+        autoclip=autoclip,
+        automask=automask,
+        mask=mask,
+        mask_only_targets=mask_only_targets,
+        mask_source=mask_source,
+        prefix=prefix,
+        out1d=out1d,
+        time_=time_,
+        mmap_=mmap_,
+    )
+    return v_3d_auto_tcorrelate_execute(params, execution)
+
+
+__all__ = [
+    "V3dAutoTcorrelateOutputs",
+    "V3dAutoTcorrelateParameters",
+    "V_3D_AUTO_TCORRELATE_METADATA",
+    "v_3d_auto_tcorrelate",
+    "v_3d_auto_tcorrelate_params",
+]

niwrap_afni/afni/v_3d_autobox.py

@@ -0,0 +1,335 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_AUTOBOX_METADATA = Metadata(
+    id="614b8e391ea136b04b4fe49d62f798c0eada766e.boutiques",
+    name="3dAutobox",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dAutoboxParameters = typing.TypedDict('V3dAutoboxParameters', {
+    "__STYX_TYPE__": typing.Literal["3dAutobox"],
+    "input": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "alt_input": typing.NotRequired[InputPathType | None],
+    "noclust": bool,
+    "extent": bool,
+    "extent_ijk": bool,
+    "extent_ijk_to_file": typing.NotRequired[str | None],
+    "extent_ijk_midslice": bool,
+    "extent_ijkord": bool,
+    "extent_ijkord_to_file": typing.NotRequired[str | None],
+    "extent_xyz_to_file": typing.NotRequired[str | None],
+    "extent_xyz_midslice": bool,
+    "npad": typing.NotRequired[float | None],
+    "npad_safety_on": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dAutobox": v_3d_autobox_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 V3dAutoboxOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_autobox(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_autobox_params(
+    input_: InputPathType,
+    prefix: str | None = None,
+    alt_input: InputPathType | None = None,
+    noclust: bool = False,
+    extent: bool = False,
+    extent_ijk: bool = False,
+    extent_ijk_to_file: str | None = None,
+    extent_ijk_midslice: bool = False,
+    extent_ijkord: bool = False,
+    extent_ijkord_to_file: str | None = None,
+    extent_xyz_to_file: str | None = None,
+    extent_xyz_midslice: bool = False,
+    npad: float | None = None,
+    npad_safety_on: bool = False,
+) -> V3dAutoboxParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Input dataset.
+        prefix: Crop the input dataset to the size of the box, and write an\
+            output dataset with PREFIX for the name. If not used, no new volume is\
+            written out.
+        alt_input: An alternate way to specify the input dataset.
+        noclust: Don't do any clustering to find the box. Any non-zero voxel\
+            will be preserved in the cropped volume.
+        extent: Write to standard out the spatial extent of the box.
+        extent_ijk: Write out the 6 auto bbox ijk slice numbers to screen: imin\
+            imax jmin jmax kmin kmax.
+        extent_ijk_to_file: Write out the 6 auto bbox ijk slice numbers to a\
+            simple-formatted text file FF: imin imax jmin jmax kmin kmax.
+        extent_ijk_midslice: Write out the 3 ijk midslices of the autobox to\
+            the screen: imid jmid kmid.
+        extent_ijkord: Write out the 6 auto bbox ijk slice numbers to screen in\
+            a particular order and format. Useful for scripting.
+        extent_ijkord_to_file: Write out the 6 auto bbox ijk slice numbers to a\
+            file in a particular order and format. Useful for 3dcalc expressions.
+        extent_xyz_to_file: Write out the 6 auto bbox xyz coordinates to a\
+            simple-formatted text file GG: xmin xmax ymin ymax zmin zmax.
+        extent_xyz_midslice: Write out the 3 xyz midslices of the autobox to\
+            the screen: xmid ymid zmid.
+        npad: Number of extra voxels to pad on each side of box.
+        npad_safety_on: Constrain npad-ded extents to be within dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dAutobox",
+        "input": input_,
+        "noclust": noclust,
+        "extent": extent,
+        "extent_ijk": extent_ijk,
+        "extent_ijk_midslice": extent_ijk_midslice,
+        "extent_ijkord": extent_ijkord,
+        "extent_xyz_midslice": extent_xyz_midslice,
+        "npad_safety_on": npad_safety_on,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if alt_input is not None:
+        params["alt_input"] = alt_input
+    if extent_ijk_to_file is not None:
+        params["extent_ijk_to_file"] = extent_ijk_to_file
+    if extent_ijkord_to_file is not None:
+        params["extent_ijkord_to_file"] = extent_ijkord_to_file
+    if extent_xyz_to_file is not None:
+        params["extent_xyz_to_file"] = extent_xyz_to_file
+    if npad is not None:
+        params["npad"] = npad
+    return params
+
+
+def v_3d_autobox_cargs(
+    params: V3dAutoboxParameters,
+    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("3dAutobox")
+    cargs.append(execution.input_file(params.get("input")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("alt_input") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("alt_input"))
+        ])
+    if params.get("noclust"):
+        cargs.append("-noclust")
+    if params.get("extent"):
+        cargs.append("-extent")
+    if params.get("extent_ijk"):
+        cargs.append("-extent_ijk")
+    if params.get("extent_ijk_to_file") is not None:
+        cargs.extend([
+            "-extent_ijk_to_file",
+            params.get("extent_ijk_to_file")
+        ])
+    if params.get("extent_ijk_midslice"):
+        cargs.append("-extent_ijk_midslice")
+    if params.get("extent_ijkord"):
+        cargs.append("-extent_ijkord")
+    if params.get("extent_ijkord_to_file") is not None:
+        cargs.extend([
+            "-extent_ijkord_to_file",
+            params.get("extent_ijkord_to_file")
+        ])
+    if params.get("extent_xyz_to_file") is not None:
+        cargs.extend([
+            "-extent_xyz_to_file",
+            params.get("extent_xyz_to_file")
+        ])
+    if params.get("extent_xyz_midslice"):
+        cargs.append("-extent_xyz_midslice")
+    if params.get("npad") is not None:
+        cargs.extend([
+            "-npad",
+            str(params.get("npad"))
+        ])
+    if params.get("npad_safety_on"):
+        cargs.append("-npad_safety_on")
+    return cargs
+
+
+def v_3d_autobox_outputs(
+    params: V3dAutoboxParameters,
+    execution: Execution,
+) -> V3dAutoboxOutputs:
+    """
+    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 = V3dAutoboxOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_autobox_execute(
+    params: V3dAutoboxParameters,
+    execution: Execution,
+) -> V3dAutoboxOutputs:
+    """
+    Computes size of a box that fits around the volume. Can also be used to crop the
+    volume to that box.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dAutoboxOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_autobox_cargs(params, execution)
+    ret = v_3d_autobox_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_autobox(
+    input_: InputPathType,
+    prefix: str | None = None,
+    alt_input: InputPathType | None = None,
+    noclust: bool = False,
+    extent: bool = False,
+    extent_ijk: bool = False,
+    extent_ijk_to_file: str | None = None,
+    extent_ijk_midslice: bool = False,
+    extent_ijkord: bool = False,
+    extent_ijkord_to_file: str | None = None,
+    extent_xyz_to_file: str | None = None,
+    extent_xyz_midslice: bool = False,
+    npad: float | None = None,
+    npad_safety_on: bool = False,
+    runner: Runner | None = None,
+) -> V3dAutoboxOutputs:
+    """
+    Computes size of a box that fits around the volume. Can also be used to crop the
+    volume to that box.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Input dataset.
+        prefix: Crop the input dataset to the size of the box, and write an\
+            output dataset with PREFIX for the name. If not used, no new volume is\
+            written out.
+        alt_input: An alternate way to specify the input dataset.
+        noclust: Don't do any clustering to find the box. Any non-zero voxel\
+            will be preserved in the cropped volume.
+        extent: Write to standard out the spatial extent of the box.
+        extent_ijk: Write out the 6 auto bbox ijk slice numbers to screen: imin\
+            imax jmin jmax kmin kmax.
+        extent_ijk_to_file: Write out the 6 auto bbox ijk slice numbers to a\
+            simple-formatted text file FF: imin imax jmin jmax kmin kmax.
+        extent_ijk_midslice: Write out the 3 ijk midslices of the autobox to\
+            the screen: imid jmid kmid.
+        extent_ijkord: Write out the 6 auto bbox ijk slice numbers to screen in\
+            a particular order and format. Useful for scripting.
+        extent_ijkord_to_file: Write out the 6 auto bbox ijk slice numbers to a\
+            file in a particular order and format. Useful for 3dcalc expressions.
+        extent_xyz_to_file: Write out the 6 auto bbox xyz coordinates to a\
+            simple-formatted text file GG: xmin xmax ymin ymax zmin zmax.
+        extent_xyz_midslice: Write out the 3 xyz midslices of the autobox to\
+            the screen: xmid ymid zmid.
+        npad: Number of extra voxels to pad on each side of box.
+        npad_safety_on: Constrain npad-ded extents to be within dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dAutoboxOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AUTOBOX_METADATA)
+    params = v_3d_autobox_params(
+        input_=input_,
+        prefix=prefix,
+        alt_input=alt_input,
+        noclust=noclust,
+        extent=extent,
+        extent_ijk=extent_ijk,
+        extent_ijk_to_file=extent_ijk_to_file,
+        extent_ijk_midslice=extent_ijk_midslice,
+        extent_ijkord=extent_ijkord,
+        extent_ijkord_to_file=extent_ijkord_to_file,
+        extent_xyz_to_file=extent_xyz_to_file,
+        extent_xyz_midslice=extent_xyz_midslice,
+        npad=npad,
+        npad_safety_on=npad_safety_on,
+    )
+    return v_3d_autobox_execute(params, execution)
+
+
+__all__ = [
+    "V3dAutoboxOutputs",
+    "V3dAutoboxParameters",
+    "V_3D_AUTOBOX_METADATA",
+    "v_3d_autobox",
+    "v_3d_autobox_params",
+]