niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_mann_whitney.py

@@ -0,0 +1,234 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MANN_WHITNEY_METADATA = Metadata(
+    id="796cea2f9bbd9b908f3b7f4c7deae22683bec6f0.boutiques",
+    name="3dMannWhitney",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMannWhitneyParameters = typing.TypedDict('V3dMannWhitneyParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMannWhitney"],
+    "dset1_x": list[str],
+    "dset2_y": list[str],
+    "output_prefix": str,
+    "workmem": typing.NotRequired[int | None],
+    "voxel_num": typing.NotRequired[int | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dMannWhitney": v_3d_mann_whitney_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 {
+        "3dMannWhitney": v_3d_mann_whitney_outputs,
+    }.get(t)
+
+
+class V3dMannWhitneyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_mann_whitney(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType
+    """Output files for the estimated population delta and Wilcoxon-Mann-Whitney
+    statistics."""
+
+
+def v_3d_mann_whitney_params(
+    dset1_x: list[str],
+    dset2_y: list[str],
+    output_prefix: str,
+    workmem: int | None = None,
+    voxel_num: int | None = None,
+) -> V3dMannWhitneyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset1_x: Data set for X observations. Must specify 1 and only 1\
+            sub-brick.
+        dset2_y: Data set for Y observations. Must specify 1 and only 1\
+            sub-brick.
+        output_prefix: Estimated population delta and Wilcoxon-Mann-Whitney\
+            statistics written to file.
+        workmem: Number of megabytes of RAM to use for statistical workspace.
+        voxel_num: Screen output for voxel # num.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMannWhitney",
+        "dset1_x": dset1_x,
+        "dset2_y": dset2_y,
+        "output_prefix": output_prefix,
+    }
+    if workmem is not None:
+        params["workmem"] = workmem
+    if voxel_num is not None:
+        params["voxel_num"] = voxel_num
+    return params
+
+
+def v_3d_mann_whitney_cargs(
+    params: V3dMannWhitneyParameters,
+    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("3dMannWhitney")
+    cargs.extend([
+        "-dset 1",
+        *params.get("dset1_x")
+    ])
+    cargs.extend([
+        "-dset 2",
+        *params.get("dset2_y")
+    ])
+    cargs.extend([
+        "-out",
+        params.get("output_prefix")
+    ])
+    if params.get("workmem") is not None:
+        cargs.extend([
+            "-workmem",
+            str(params.get("workmem"))
+        ])
+    if params.get("voxel_num") is not None:
+        cargs.extend([
+            "-voxel",
+            str(params.get("voxel_num"))
+        ])
+    return cargs
+
+
+def v_3d_mann_whitney_outputs(
+    params: V3dMannWhitneyParameters,
+    execution: Execution,
+) -> V3dMannWhitneyOutputs:
+    """
+    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 = V3dMannWhitneyOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file(params.get("output_prefix") + "*"),
+    )
+    return ret
+
+
+def v_3d_mann_whitney_execute(
+    params: V3dMannWhitneyParameters,
+    execution: Execution,
+) -> V3dMannWhitneyOutputs:
+    """
+    Performs nonparametric Mann-Whitney two-sample test.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMannWhitneyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_mann_whitney_cargs(params, execution)
+    ret = v_3d_mann_whitney_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_mann_whitney(
+    dset1_x: list[str],
+    dset2_y: list[str],
+    output_prefix: str,
+    workmem: int | None = None,
+    voxel_num: int | None = None,
+    runner: Runner | None = None,
+) -> V3dMannWhitneyOutputs:
+    """
+    Performs nonparametric Mann-Whitney two-sample test.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset1_x: Data set for X observations. Must specify 1 and only 1\
+            sub-brick.
+        dset2_y: Data set for Y observations. Must specify 1 and only 1\
+            sub-brick.
+        output_prefix: Estimated population delta and Wilcoxon-Mann-Whitney\
+            statistics written to file.
+        workmem: Number of megabytes of RAM to use for statistical workspace.
+        voxel_num: Screen output for voxel # num.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMannWhitneyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MANN_WHITNEY_METADATA)
+    params = v_3d_mann_whitney_params(
+        dset1_x=dset1_x,
+        dset2_y=dset2_y,
+        output_prefix=output_prefix,
+        workmem=workmem,
+        voxel_num=voxel_num,
+    )
+    return v_3d_mann_whitney_execute(params, execution)
+
+
+__all__ = [
+    "V3dMannWhitneyOutputs",
+    "V3dMannWhitneyParameters",
+    "V_3D_MANN_WHITNEY_METADATA",
+    "v_3d_mann_whitney",
+    "v_3d_mann_whitney_params",
+]

niwrap_afni/afni/v_3d_mask_to_ascii.py

@@ -0,0 +1,189 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MASK_TO_ASCII_METADATA = Metadata(
+    id="00c7066c6c38f027299750536983f490b1c220de.boutiques",
+    name="3dMaskToASCII",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMaskToAsciiParameters = typing.TypedDict('V3dMaskToAsciiParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMaskToASCII"],
+    "tobin_flag": bool,
+    "dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dMaskToASCII": v_3d_mask_to_ascii_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 {
+        "3dMaskToASCII": v_3d_mask_to_ascii_outputs,
+    }.get(t)
+
+
+class V3dMaskToAsciiOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_mask_to_ascii(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outputfile: OutputPathType
+    """Output file where ASCII string mask or binary mask will be written."""
+
+
+def v_3d_mask_to_ascii_params(
+    dataset: InputPathType,
+    tobin_flag: bool = False,
+) -> V3dMaskToAsciiParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset (e.g. mask.nii.gz).
+        tobin_flag: Read ASCII mask, expand it to byte-valued dataset, and\
+            write to stdout.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMaskToASCII",
+        "tobin_flag": tobin_flag,
+        "dataset": dataset,
+    }
+    return params
+
+
+def v_3d_mask_to_ascii_cargs(
+    params: V3dMaskToAsciiParameters,
+    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("3dMaskToASCII")
+    if params.get("tobin_flag"):
+        cargs.append("-tobin")
+    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(">")
+    cargs.append("[OUTPUTFILE]")
+    return cargs
+
+
+def v_3d_mask_to_ascii_outputs(
+    params: V3dMaskToAsciiParameters,
+    execution: Execution,
+) -> V3dMaskToAsciiOutputs:
+    """
+    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 = V3dMaskToAsciiOutputs(
+        root=execution.output_file("."),
+        outputfile=execution.output_file("[OUTPUTFILE]"),
+    )
+    return ret
+
+
+def v_3d_mask_to_ascii_execute(
+    params: V3dMaskToAsciiParameters,
+    execution: Execution,
+) -> V3dMaskToAsciiOutputs:
+    """
+    Converts a byte-valued 0/1 dataset into an ASCII string, or vice versa.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMaskToAsciiOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_mask_to_ascii_cargs(params, execution)
+    ret = v_3d_mask_to_ascii_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_mask_to_ascii(
+    dataset: InputPathType,
+    tobin_flag: bool = False,
+    runner: Runner | None = None,
+) -> V3dMaskToAsciiOutputs:
+    """
+    Converts a byte-valued 0/1 dataset into an ASCII string, or vice versa.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset (e.g. mask.nii.gz).
+        tobin_flag: Read ASCII mask, expand it to byte-valued dataset, and\
+            write to stdout.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMaskToAsciiOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MASK_TO_ASCII_METADATA)
+    params = v_3d_mask_to_ascii_params(
+        tobin_flag=tobin_flag,
+        dataset=dataset,
+    )
+    return v_3d_mask_to_ascii_execute(params, execution)
+
+
+__all__ = [
+    "V3dMaskToAsciiOutputs",
+    "V3dMaskToAsciiParameters",
+    "V_3D_MASK_TO_ASCII_METADATA",
+    "v_3d_mask_to_ascii",
+    "v_3d_mask_to_ascii_params",
+]

niwrap_afni/afni/v_3d_match.py

@@ -0,0 +1,300 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MATCH_METADATA = Metadata(
+    id="5e79a849f1f76bbe598dfba4e01f90d83d62deb0.boutiques",
+    name="3dMatch",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMatchParameters = typing.TypedDict('V3dMatchParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMatch"],
+    "inset": InputPathType,
+    "refset": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "in_min": typing.NotRequired[float | None],
+    "in_max": typing.NotRequired[float | None],
+    "ref_min": typing.NotRequired[float | None],
+    "ref_max": typing.NotRequired[float | None],
+    "prefix": str,
+    "only_dice_thr": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dMatch": v_3d_match_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 {
+        "3dMatch": v_3d_match_outputs,
+    }.get(t)
+
+
+class V3dMatchOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_match(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    ref_brik: OutputPathType
+    """AFNI BRIK file with the same number of subbricks as the refset file, with
+    highest weighted correlation."""
+    ref_coeff_vals: OutputPathType
+    """Text file recording original indices and coefficients."""
+    in_brik: OutputPathType
+    """AFNI BRIK file with the same number of subbricks as the inset file, with
+    highest weighted correlation."""
+    in_coeff_vals: OutputPathType
+    """Text file recording original indices and coefficients."""
+
+
+def v_3d_match_params(
+    inset: InputPathType,
+    refset: InputPathType,
+    prefix: str,
+    mask: InputPathType | None = None,
+    in_min: float | None = None,
+    in_max: float | None = None,
+    ref_min: float | None = None,
+    ref_max: float | None = None,
+    only_dice_thr: bool = False,
+) -> V3dMatchParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inset: File with M subbricks of data to match against another file.
+        refset: File with N subbricks, serving as a reference for INPUT_FILE.
+        prefix: Prefix for output name for BRIK/HEAD files and *_coeff.vals\
+            text files.
+        mask: A mask of regions to include in the correlation of datasets.
+        in_min: Threshold below which values in INPUT_FILE will be zeroed\
+            during analysis.
+        in_max: Threshold above which values in INPUT_FILE will be zeroed\
+            during analysis.
+        ref_min: Threshold below which values in REF_FILE will be zeroed during\
+            analysis.
+        ref_max: Threshold above which values in REF_FILE will be zeroed during\
+            analysis.
+        only_dice_thr: Apply thresholding only during Dice evaluation, not\
+            during spatial correlation.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMatch",
+        "inset": inset,
+        "refset": refset,
+        "prefix": prefix,
+        "only_dice_thr": only_dice_thr,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if in_min is not None:
+        params["in_min"] = in_min
+    if in_max is not None:
+        params["in_max"] = in_max
+    if ref_min is not None:
+        params["ref_min"] = ref_min
+    if ref_max is not None:
+        params["ref_max"] = ref_max
+    return params
+
+
+def v_3d_match_cargs(
+    params: V3dMatchParameters,
+    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("3dMatch")
+    cargs.extend([
+        "-inset",
+        execution.input_file(params.get("inset"))
+    ])
+    cargs.extend([
+        "-refset",
+        execution.input_file(params.get("refset"))
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("in_min") is not None:
+        cargs.extend([
+            "-in_min",
+            str(params.get("in_min"))
+        ])
+    if params.get("in_max") is not None:
+        cargs.extend([
+            "-in_max",
+            str(params.get("in_max"))
+        ])
+    if params.get("ref_min") is not None:
+        cargs.extend([
+            "-ref_min",
+            str(params.get("ref_min"))
+        ])
+    if params.get("ref_max") is not None:
+        cargs.extend([
+            "-ref_max",
+            str(params.get("ref_max"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("only_dice_thr"):
+        cargs.append("-only_dice_thr")
+    return cargs
+
+
+def v_3d_match_outputs(
+    params: V3dMatchParameters,
+    execution: Execution,
+) -> V3dMatchOutputs:
+    """
+    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 = V3dMatchOutputs(
+        root=execution.output_file("."),
+        ref_brik=execution.output_file(params.get("prefix") + "_REF+orig.BRIK"),
+        ref_coeff_vals=execution.output_file(params.get("prefix") + "_REF_coeff.vals"),
+        in_brik=execution.output_file(params.get("prefix") + "_IN+orig.BRIK"),
+        in_coeff_vals=execution.output_file(params.get("prefix") + "_IN_coeff.vals"),
+    )
+    return ret
+
+
+def v_3d_match_execute(
+    params: V3dMatchParameters,
+    execution: Execution,
+) -> V3dMatchOutputs:
+    """
+    Find similar subbricks and rearrange order to ease comparison. Part of FATCAT in
+    AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMatchOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_match_cargs(params, execution)
+    ret = v_3d_match_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_match(
+    inset: InputPathType,
+    refset: InputPathType,
+    prefix: str,
+    mask: InputPathType | None = None,
+    in_min: float | None = None,
+    in_max: float | None = None,
+    ref_min: float | None = None,
+    ref_max: float | None = None,
+    only_dice_thr: bool = False,
+    runner: Runner | None = None,
+) -> V3dMatchOutputs:
+    """
+    Find similar subbricks and rearrange order to ease comparison. Part of FATCAT in
+    AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        inset: File with M subbricks of data to match against another file.
+        refset: File with N subbricks, serving as a reference for INPUT_FILE.
+        prefix: Prefix for output name for BRIK/HEAD files and *_coeff.vals\
+            text files.
+        mask: A mask of regions to include in the correlation of datasets.
+        in_min: Threshold below which values in INPUT_FILE will be zeroed\
+            during analysis.
+        in_max: Threshold above which values in INPUT_FILE will be zeroed\
+            during analysis.
+        ref_min: Threshold below which values in REF_FILE will be zeroed during\
+            analysis.
+        ref_max: Threshold above which values in REF_FILE will be zeroed during\
+            analysis.
+        only_dice_thr: Apply thresholding only during Dice evaluation, not\
+            during spatial correlation.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMatchOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MATCH_METADATA)
+    params = v_3d_match_params(
+        inset=inset,
+        refset=refset,
+        mask=mask,
+        in_min=in_min,
+        in_max=in_max,
+        ref_min=ref_min,
+        ref_max=ref_max,
+        prefix=prefix,
+        only_dice_thr=only_dice_thr,
+    )
+    return v_3d_match_execute(params, execution)
+
+
+__all__ = [
+    "V3dMatchOutputs",
+    "V3dMatchParameters",
+    "V_3D_MATCH_METADATA",
+    "v_3d_match",
+    "v_3d_match_params",
+]