niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/adjunct_tort_plot_dp_align.py

@@ -0,0 +1,248 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ADJUNCT_TORT_PLOT_DP_ALIGN_METADATA = Metadata(
+    id="85f0f975299d8bde02839f551146666cba69ff1f.boutiques",
+    name="adjunct_tort_plot_dp_align",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AdjunctTortPlotDpAlignParameters = typing.TypedDict('AdjunctTortPlotDpAlignParameters', {
+    "__STYX_TYPE__": typing.Literal["adjunct_tort_plot_dp_align"],
+    "input_file": InputPathType,
+    "output_prefix": str,
+    "enorm_max": typing.NotRequired[float | None],
+    "enorm_hline": typing.NotRequired[float | None],
+    "no_svg": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "adjunct_tort_plot_dp_align": adjunct_tort_plot_dp_align_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 {
+        "adjunct_tort_plot_dp_align": adjunct_tort_plot_dp_align_outputs,
+    }.get(t)
+
+
+class AdjunctTortPlotDpAlignOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `adjunct_tort_plot_dp_align(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    align_params: OutputPathType
+    """Text file containing 6 columns of data for the rigid-body alignment
+    parameters estimated by DIFFPREP."""
+    enorm_file: OutputPathType
+    """Text file with 1 column of data, the Euclidean norm of the differences of
+    the rigid body alignment parameters."""
+    plot_jpg: OutputPathType
+    """A plot of enorm and the alignment parameters in JPG format."""
+    plot_svg: OutputPathType
+    """A plot of enorm and the alignment parameters in SVG format."""
+
+
+def adjunct_tort_plot_dp_align_params(
+    input_file: InputPathType,
+    output_prefix: str,
+    enorm_max: float | None = None,
+    enorm_hline: float | None = None,
+    no_svg: bool = False,
+) -> AdjunctTortPlotDpAlignParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Name of DIFFPREP-produced file to parse, probably ending in\
+            '_transformations.txt'.
+        output_prefix: Base of output files; can contain path information.\
+            Should *not* include any extension.
+        enorm_max: Specify max value of y-axis of enorm plot in SVG image.\
+            Useful for having a constant value across a study.
+        enorm_hline: Specify value of a horizontal, dotted, bright cyan line\
+            for the enorm plot in SVG image. Can help with visualization.
+        no_svg: Opt to turn off even checking to plot an SVG version of the\
+            figure.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "adjunct_tort_plot_dp_align",
+        "input_file": input_file,
+        "output_prefix": output_prefix,
+        "no_svg": no_svg,
+    }
+    if enorm_max is not None:
+        params["enorm_max"] = enorm_max
+    if enorm_hline is not None:
+        params["enorm_hline"] = enorm_hline
+    return params
+
+
+def adjunct_tort_plot_dp_align_cargs(
+    params: AdjunctTortPlotDpAlignParameters,
+    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("adjunct_tort_plot_dp_align")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    if params.get("enorm_max") is not None:
+        cargs.extend([
+            "-enorm_max",
+            str(params.get("enorm_max"))
+        ])
+    if params.get("enorm_hline") is not None:
+        cargs.extend([
+            "-enorm_hline",
+            str(params.get("enorm_hline"))
+        ])
+    if params.get("no_svg"):
+        cargs.append("-no_svg")
+    return cargs
+
+
+def adjunct_tort_plot_dp_align_outputs(
+    params: AdjunctTortPlotDpAlignParameters,
+    execution: Execution,
+) -> AdjunctTortPlotDpAlignOutputs:
+    """
+    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 = AdjunctTortPlotDpAlignOutputs(
+        root=execution.output_file("."),
+        align_params=execution.output_file(params.get("output_prefix") + "_align.1D"),
+        enorm_file=execution.output_file(params.get("output_prefix") + "_enorm.1D"),
+        plot_jpg=execution.output_file(params.get("output_prefix") + ".jpg"),
+        plot_svg=execution.output_file(params.get("output_prefix") + ".svg"),
+    )
+    return ret
+
+
+def adjunct_tort_plot_dp_align_execute(
+    params: AdjunctTortPlotDpAlignParameters,
+    execution: Execution,
+) -> AdjunctTortPlotDpAlignOutputs:
+    """
+    Tool to display the rigid-body alignment parameters from TORTOISE's DIFFPREP,
+    useful for analyzing subject motion in DWI data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctTortPlotDpAlignOutputs`).
+    """
+    params = execution.params(params)
+    cargs = adjunct_tort_plot_dp_align_cargs(params, execution)
+    ret = adjunct_tort_plot_dp_align_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def adjunct_tort_plot_dp_align(
+    input_file: InputPathType,
+    output_prefix: str,
+    enorm_max: float | None = None,
+    enorm_hline: float | None = None,
+    no_svg: bool = False,
+    runner: Runner | None = None,
+) -> AdjunctTortPlotDpAlignOutputs:
+    """
+    Tool to display the rigid-body alignment parameters from TORTOISE's DIFFPREP,
+    useful for analyzing subject motion in DWI data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Name of DIFFPREP-produced file to parse, probably ending in\
+            '_transformations.txt'.
+        output_prefix: Base of output files; can contain path information.\
+            Should *not* include any extension.
+        enorm_max: Specify max value of y-axis of enorm plot in SVG image.\
+            Useful for having a constant value across a study.
+        enorm_hline: Specify value of a horizontal, dotted, bright cyan line\
+            for the enorm plot in SVG image. Can help with visualization.
+        no_svg: Opt to turn off even checking to plot an SVG version of the\
+            figure.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctTortPlotDpAlignOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADJUNCT_TORT_PLOT_DP_ALIGN_METADATA)
+    params = adjunct_tort_plot_dp_align_params(
+        input_file=input_file,
+        output_prefix=output_prefix,
+        enorm_max=enorm_max,
+        enorm_hline=enorm_hline,
+        no_svg=no_svg,
+    )
+    return adjunct_tort_plot_dp_align_execute(params, execution)
+
+
+__all__ = [
+    "ADJUNCT_TORT_PLOT_DP_ALIGN_METADATA",
+    "AdjunctTortPlotDpAlignOutputs",
+    "AdjunctTortPlotDpAlignParameters",
+    "adjunct_tort_plot_dp_align",
+    "adjunct_tort_plot_dp_align_params",
+]

niwrap_afni/afni/adwarp.py

@@ -0,0 +1,296 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ADWARP_METADATA = Metadata(
+    id="22410e65c1361d9cb6b13a0fd56cc72bae69129b.boutiques",
+    name="adwarp",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AdwarpParameters = typing.TypedDict('AdwarpParameters', {
+    "__STYX_TYPE__": typing.Literal["adwarp"],
+    "apar": InputPathType,
+    "dpar": str,
+    "prefix": typing.NotRequired[str | None],
+    "dxyz": typing.NotRequired[float | None],
+    "verbose": bool,
+    "force": bool,
+    "resam": typing.NotRequired[str | None],
+    "thr": typing.NotRequired[str | None],
+    "func": 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 {
+        "adwarp": adwarp_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 {
+        "adwarp": adwarp_outputs,
+    }.get(t)
+
+
+class AdwarpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `adwarp(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    header_output: OutputPathType | None
+    """Output dataset header file"""
+    brick_output: OutputPathType | None
+    """Output dataset brick file"""
+
+
+def adwarp_params(
+    apar: InputPathType,
+    dpar: str,
+    prefix: str | None = None,
+    dxyz: float | None = None,
+    verbose: bool = False,
+    force: bool = False,
+    resam: str | None = None,
+    thr: str | None = None,
+    func: str | None = None,
+) -> AdwarpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        apar: Set the anat parent dataset (nonoptional).
+        dpar: Set the data parent dataset (nonoptional). dset may contain a\
+            sub-brick selector, e.g., -dpar 'dset+orig[2,5,7]'.
+        prefix: Set the prefix for the output dataset. Default is the prefix of\
+            'dset'.
+        dxyz: Set the grid spacing in the output dataset. Default is 1 mm.
+        verbose: Print out progress reports.
+        force: Write out result even if it means deleting an existing dataset.\
+            Default is not to overwrite.
+        resam: Set resampling mode for all sub-bricks. Modes: NN (Nearest\
+            Neighbor), Li (Linear Interpolation), Cu (Cubic Interpolation), Bk\
+            (Blocky Interpolation). Default is Li for all sub-bricks.
+        thr: Set resampling mode for threshold sub-bricks. Modes: NN (Nearest\
+            Neighbor), Li (Linear Interpolation), Cu (Cubic Interpolation), Bk\
+            (Blocky Interpolation).
+        func: Set resampling mode for functional sub-bricks. Modes: NN (Nearest\
+            Neighbor), Li (Linear Interpolation), Cu (Cubic Interpolation), Bk\
+            (Blocky Interpolation).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "adwarp",
+        "apar": apar,
+        "dpar": dpar,
+        "verbose": verbose,
+        "force": force,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if dxyz is not None:
+        params["dxyz"] = dxyz
+    if resam is not None:
+        params["resam"] = resam
+    if thr is not None:
+        params["thr"] = thr
+    if func is not None:
+        params["func"] = func
+    return params
+
+
+def adwarp_cargs(
+    params: AdwarpParameters,
+    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("adwarp")
+    cargs.extend([
+        "-apar",
+        execution.input_file(params.get("apar"))
+    ])
+    cargs.extend([
+        "-dpar",
+        params.get("dpar")
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("dxyz") is not None:
+        cargs.extend([
+            "-dxyz",
+            str(params.get("dxyz"))
+        ])
+    if params.get("verbose"):
+        cargs.append("-verbose")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("resam") is not None:
+        cargs.extend([
+            "-resam",
+            params.get("resam")
+        ])
+    if params.get("thr") is not None:
+        cargs.extend([
+            "-thr",
+            params.get("thr")
+        ])
+    if params.get("func") is not None:
+        cargs.extend([
+            "-func",
+            params.get("func")
+        ])
+    return cargs
+
+
+def adwarp_outputs(
+    params: AdwarpParameters,
+    execution: Execution,
+) -> AdwarpOutputs:
+    """
+    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 = AdwarpOutputs(
+        root=execution.output_file("."),
+        header_output=execution.output_file(params.get("prefix") + ".HEAD") if (params.get("prefix") is not None) else None,
+        brick_output=execution.output_file(params.get("prefix") + ".BRIK") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def adwarp_execute(
+    params: AdwarpParameters,
+    execution: Execution,
+) -> AdwarpOutputs:
+    """
+    Resamples a 'data parent' dataset to the grid defined by an 'anat parent'
+    dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AdwarpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = adwarp_cargs(params, execution)
+    ret = adwarp_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def adwarp(
+    apar: InputPathType,
+    dpar: str,
+    prefix: str | None = None,
+    dxyz: float | None = None,
+    verbose: bool = False,
+    force: bool = False,
+    resam: str | None = None,
+    thr: str | None = None,
+    func: str | None = None,
+    runner: Runner | None = None,
+) -> AdwarpOutputs:
+    """
+    Resamples a 'data parent' dataset to the grid defined by an 'anat parent'
+    dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        apar: Set the anat parent dataset (nonoptional).
+        dpar: Set the data parent dataset (nonoptional). dset may contain a\
+            sub-brick selector, e.g., -dpar 'dset+orig[2,5,7]'.
+        prefix: Set the prefix for the output dataset. Default is the prefix of\
+            'dset'.
+        dxyz: Set the grid spacing in the output dataset. Default is 1 mm.
+        verbose: Print out progress reports.
+        force: Write out result even if it means deleting an existing dataset.\
+            Default is not to overwrite.
+        resam: Set resampling mode for all sub-bricks. Modes: NN (Nearest\
+            Neighbor), Li (Linear Interpolation), Cu (Cubic Interpolation), Bk\
+            (Blocky Interpolation). Default is Li for all sub-bricks.
+        thr: Set resampling mode for threshold sub-bricks. Modes: NN (Nearest\
+            Neighbor), Li (Linear Interpolation), Cu (Cubic Interpolation), Bk\
+            (Blocky Interpolation).
+        func: Set resampling mode for functional sub-bricks. Modes: NN (Nearest\
+            Neighbor), Li (Linear Interpolation), Cu (Cubic Interpolation), Bk\
+            (Blocky Interpolation).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AdwarpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADWARP_METADATA)
+    params = adwarp_params(
+        apar=apar,
+        dpar=dpar,
+        prefix=prefix,
+        dxyz=dxyz,
+        verbose=verbose,
+        force=force,
+        resam=resam,
+        thr=thr,
+        func=func,
+    )
+    return adwarp_execute(params, execution)
+
+
+__all__ = [
+    "ADWARP_METADATA",
+    "AdwarpOutputs",
+    "AdwarpParameters",
+    "adwarp",
+    "adwarp_params",
+]