niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_sharpen.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_SHARPEN_METADATA = Metadata(
+    id="44eead3d035544b0d1ef18d1ea40f5df1b442bcb.boutiques",
+    name="3dSharpen",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSharpenParameters = typing.TypedDict('V3dSharpenParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSharpen"],
+    "sharpening_factor": typing.NotRequired[float | None],
+    "input_dataset": InputPathType,
+    "output_prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dSharpen": v_3d_sharpen_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 {
+        "3dSharpen": v_3d_sharpen_outputs,
+    }.get(t)
+
+
+class V3dSharpenOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_sharpen(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType
+    """Sharpened output dataset."""
+
+
+def v_3d_sharpen_params(
+    input_dataset: InputPathType,
+    output_prefix: str,
+    sharpening_factor: float | None = None,
+) -> V3dSharpenParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset (e.g., input.nii.gz).
+        output_prefix: Name of the output dataset (e.g., output.nii.gz) which\
+            will be in floating point format.
+        sharpening_factor: Sharpening factor, between 0.1 and 0.9 (inclusive).\
+            Larger values mean more sharpening.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSharpen",
+        "input_dataset": input_dataset,
+        "output_prefix": output_prefix,
+    }
+    if sharpening_factor is not None:
+        params["sharpening_factor"] = sharpening_factor
+    return params
+
+
+def v_3d_sharpen_cargs(
+    params: V3dSharpenParameters,
+    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("3dSharpen")
+    if params.get("sharpening_factor") is not None:
+        cargs.extend([
+            "-phi",
+            str(params.get("sharpening_factor"))
+        ])
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    return cargs
+
+
+def v_3d_sharpen_outputs(
+    params: V3dSharpenParameters,
+    execution: Execution,
+) -> V3dSharpenOutputs:
+    """
+    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 = V3dSharpenOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("output_prefix") + ".nii.gz"),
+    )
+    return ret
+
+
+def v_3d_sharpen_execute(
+    params: V3dSharpenParameters,
+    execution: Execution,
+) -> V3dSharpenOutputs:
+    """
+    Applies a simple 3D sharpening filter to the positive values in the #0 volume of
+    the input dataset, and writes out a new dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSharpenOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_sharpen_cargs(params, execution)
+    ret = v_3d_sharpen_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_sharpen(
+    input_dataset: InputPathType,
+    output_prefix: str,
+    sharpening_factor: float | None = None,
+    runner: Runner | None = None,
+) -> V3dSharpenOutputs:
+    """
+    Applies a simple 3D sharpening filter to the positive values in the #0 volume of
+    the input dataset, and writes out a new dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset (e.g., input.nii.gz).
+        output_prefix: Name of the output dataset (e.g., output.nii.gz) which\
+            will be in floating point format.
+        sharpening_factor: Sharpening factor, between 0.1 and 0.9 (inclusive).\
+            Larger values mean more sharpening.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSharpenOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SHARPEN_METADATA)
+    params = v_3d_sharpen_params(
+        sharpening_factor=sharpening_factor,
+        input_dataset=input_dataset,
+        output_prefix=output_prefix,
+    )
+    return v_3d_sharpen_execute(params, execution)
+
+
+__all__ = [
+    "V3dSharpenOutputs",
+    "V3dSharpenParameters",
+    "V_3D_SHARPEN_METADATA",
+    "v_3d_sharpen",
+    "v_3d_sharpen_params",
+]

niwrap_afni/afni/v_3d_signatures.py

@@ -0,0 +1,230 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_SIGNATURES_METADATA = Metadata(
+    id="6f7958fe91c1d63deab2f5ca691371fc161ee645.boutiques",
+    name="3dSignatures",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSignaturesParameters = typing.TypedDict('V3dSignaturesParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSignatures"],
+    "infile": InputPathType,
+    "outfile": str,
+    "segmentation": bool,
+    "filter": bool,
+    "threshold": typing.NotRequired[float | None],
+    "smoothing": typing.NotRequired[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 {
+        "3dSignatures": v_3d_signatures_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 {
+        "3dSignatures": v_3d_signatures_outputs,
+    }.get(t)
+
+
+class V3dSignaturesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_signatures(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    results_file: OutputPathType
+    """Main analysis results file"""
+
+
+def v_3d_signatures_params(
+    infile: InputPathType,
+    outfile: str,
+    segmentation: bool = False,
+    filter_: bool = False,
+    threshold: float | None = None,
+    smoothing: float | None = None,
+) -> V3dSignaturesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input file containing 3D genome data (e.g. genome_data.txt).
+        outfile: Output file to store analysis results (e.g.\
+            analysis_results.txt).
+        segmentation: Flag to apply genome segmentation.
+        filter_: Flag to apply data filtering.
+        threshold: Threshold level for data filtering; default=0.5.
+        smoothing: Apply smoothing with specified kernel size.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSignatures",
+        "infile": infile,
+        "outfile": outfile,
+        "segmentation": segmentation,
+        "filter": filter_,
+    }
+    if threshold is not None:
+        params["threshold"] = threshold
+    if smoothing is not None:
+        params["smoothing"] = smoothing
+    return params
+
+
+def v_3d_signatures_cargs(
+    params: V3dSignaturesParameters,
+    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("3dSignatures")
+    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(params.get("outfile"))
+    if params.get("segmentation"):
+        cargs.append("--segmentation")
+    if params.get("filter"):
+        cargs.append("--filter")
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "--threshold",
+            str(params.get("threshold"))
+        ])
+    if params.get("smoothing") is not None:
+        cargs.extend([
+            "--smoothing",
+            str(params.get("smoothing"))
+        ])
+    return cargs
+
+
+def v_3d_signatures_outputs(
+    params: V3dSignaturesParameters,
+    execution: Execution,
+) -> V3dSignaturesOutputs:
+    """
+    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 = V3dSignaturesOutputs(
+        root=execution.output_file("."),
+        results_file=execution.output_file(params.get("outfile") + ".txt"),
+    )
+    return ret
+
+
+def v_3d_signatures_execute(
+    params: V3dSignaturesParameters,
+    execution: Execution,
+) -> V3dSignaturesOutputs:
+    """
+    3dSignatures analysis tool for 3D genome organization.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSignaturesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_signatures_cargs(params, execution)
+    ret = v_3d_signatures_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_signatures(
+    infile: InputPathType,
+    outfile: str,
+    segmentation: bool = False,
+    filter_: bool = False,
+    threshold: float | None = None,
+    smoothing: float | None = None,
+    runner: Runner | None = None,
+) -> V3dSignaturesOutputs:
+    """
+    3dSignatures analysis tool for 3D genome organization.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input file containing 3D genome data (e.g. genome_data.txt).
+        outfile: Output file to store analysis results (e.g.\
+            analysis_results.txt).
+        segmentation: Flag to apply genome segmentation.
+        filter_: Flag to apply data filtering.
+        threshold: Threshold level for data filtering; default=0.5.
+        smoothing: Apply smoothing with specified kernel size.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSignaturesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SIGNATURES_METADATA)
+    params = v_3d_signatures_params(
+        infile=infile,
+        outfile=outfile,
+        segmentation=segmentation,
+        filter_=filter_,
+        threshold=threshold,
+        smoothing=smoothing,
+    )
+    return v_3d_signatures_execute(params, execution)
+
+
+__all__ = [
+    "V3dSignaturesOutputs",
+    "V3dSignaturesParameters",
+    "V_3D_SIGNATURES_METADATA",
+    "v_3d_signatures",
+    "v_3d_signatures_params",
+]

niwrap_afni/afni/v_3d_skull_strip.py

@@ -0,0 +1,204 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_SKULL_STRIP_METADATA = Metadata(
+    id="df6efe15ce597ef9d7e30605580718458f380555.boutiques",
+    name="3dSkullStrip",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSkullStripParameters = typing.TypedDict('V3dSkullStripParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSkullStrip"],
+    "in_file": InputPathType,
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dSkullStrip": v_3d_skull_strip_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 {
+        "3dSkullStrip": v_3d_skull_strip_outputs,
+    }.get(t)
+
+
+class V3dSkullStripOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_skull_strip(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType
+    """Output image file name."""
+    out_file_: OutputPathType
+    """Output file."""
+
+
+def v_3d_skull_strip_params(
+    in_file: InputPathType,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+) -> V3dSkullStripParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3dskullstrip.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSkullStrip",
+        "in_file": in_file,
+    }
+    if num_threads is not None:
+        params["num_threads"] = num_threads
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    return params
+
+
+def v_3d_skull_strip_cargs(
+    params: V3dSkullStripParameters,
+    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("3dSkullStrip")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("in_file"))
+    ])
+    if params.get("num_threads") is not None:
+        cargs.append(str(params.get("num_threads")))
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    return cargs
+
+
+def v_3d_skull_strip_outputs(
+    params: V3dSkullStripParameters,
+    execution: Execution,
+) -> V3dSkullStripOutputs:
+    """
+    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 = V3dSkullStripOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(pathlib.Path(params.get("in_file")).name + "_skullstrip"),
+        out_file_=execution.output_file("out_file"),
+    )
+    return ret
+
+
+def v_3d_skull_strip_execute(
+    params: V3dSkullStripParameters,
+    execution: Execution,
+) -> V3dSkullStripOutputs:
+    """
+    A program to extract the brain from surrounding tissue from MRI T1-weighted
+    images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSkullStripOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_skull_strip_cargs(params, execution)
+    ret = v_3d_skull_strip_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_skull_strip(
+    in_file: InputPathType,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    runner: Runner | None = None,
+) -> V3dSkullStripOutputs:
+    """
+    A program to extract the brain from surrounding tissue from MRI T1-weighted
+    images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3dskullstrip.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSkullStripOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SKULL_STRIP_METADATA)
+    params = v_3d_skull_strip_params(
+        in_file=in_file,
+        num_threads=num_threads,
+        outputtype=outputtype,
+    )
+    return v_3d_skull_strip_execute(params, execution)
+
+
+__all__ = [
+    "V3dSkullStripOutputs",
+    "V3dSkullStripParameters",
+    "V_3D_SKULL_STRIP_METADATA",
+    "v_3d_skull_strip",
+    "v_3d_skull_strip_params",
+]