niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dmask_tool.py

@@ -0,0 +1,334 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DMASK_TOOL_METADATA = Metadata(
+    id="0ae017f62cc9cbb1c01f238cc2b3f9dd2ba732e3.boutiques",
+    name="3dmask_tool",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dmaskToolParameters = typing.TypedDict('V3dmaskToolParameters', {
+    "__STYX_TYPE__": typing.Literal["3dmask_tool"],
+    "count": bool,
+    "datum": typing.NotRequired[typing.Literal["byte", "short", "float"] | None],
+    "dilate_inputs": typing.NotRequired[str | None],
+    "dilate_results": typing.NotRequired[str | None],
+    "fill_dirs": typing.NotRequired[str | None],
+    "fill_holes": bool,
+    "frac": typing.NotRequired[float | None],
+    "in_file": InputPathType,
+    "inter": bool,
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "union": bool,
+    "verbose": 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 {
+        "3dmask_tool": v_3dmask_tool_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 {
+        "3dmask_tool": v_3dmask_tool_outputs,
+    }.get(t)
+
+
+class V3dmaskToolOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dmask_tool(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType
+    """Output image file name."""
+    out_file_: OutputPathType
+    """Mask file."""
+
+
+def v_3dmask_tool_params(
+    in_file: InputPathType,
+    count: bool = False,
+    datum: typing.Literal["byte", "short", "float"] | None = None,
+    dilate_inputs: str | None = None,
+    dilate_results: str | None = None,
+    fill_dirs: str | None = None,
+    fill_holes: bool = False,
+    frac: float | None = None,
+    inter: bool = False,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    union: bool = False,
+    verbose: int | None = None,
+) -> V3dmaskToolParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3dmask_tool.
+        count: Instead of created a binary 0/1 mask dataset, create one with\
+            counts of voxel overlap, i.e., each voxel will contain the number of\
+            masks that it is set in.
+        datum: 'byte' or 'short' or 'float'. Specify data type for output.
+        dilate_inputs: Use this option to dilate and/or erode datasets as they\
+            are read. ex. '5 -5' to dilate and erode 5 times.
+        dilate_results: Dilate and/or erode combined mask at the given levels.
+        fill_dirs: Fill holes only in the given directions. this option is for\
+            use with -fill holes. should be a single string that specifies 1-3 of\
+            the axes using {x,y,z} labels (i.e. dataset axis order), or using the\
+            labels in {r,l,a,p,i,s}.
+        fill_holes: This option can be used to fill holes in the resulting\
+            mask, i.e. after all other processing has been done.
+        frac: When combining masks (across datasets and sub-bricks), use this\
+            option to restrict the result to a certain fraction of the set of\
+            volumes.
+        inter: Intersection, this means -frac 1.0.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        union: Union, this means -frac 0.
+        verbose: Specify verbosity level, for 0 to 3.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dmask_tool",
+        "count": count,
+        "fill_holes": fill_holes,
+        "in_file": in_file,
+        "inter": inter,
+        "union": union,
+    }
+    if datum is not None:
+        params["datum"] = datum
+    if dilate_inputs is not None:
+        params["dilate_inputs"] = dilate_inputs
+    if dilate_results is not None:
+        params["dilate_results"] = dilate_results
+    if fill_dirs is not None:
+        params["fill_dirs"] = fill_dirs
+    if frac is not None:
+        params["frac"] = frac
+    if num_threads is not None:
+        params["num_threads"] = num_threads
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    if verbose is not None:
+        params["verbose"] = verbose
+    return params
+
+
+def v_3dmask_tool_cargs(
+    params: V3dmaskToolParameters,
+    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("3dmask_tool")
+    if params.get("count"):
+        cargs.append("-count")
+    if params.get("datum") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum")
+        ])
+    if params.get("dilate_inputs") is not None:
+        cargs.extend([
+            "-dilate_inputs",
+            params.get("dilate_inputs")
+        ])
+    if params.get("dilate_results") is not None:
+        cargs.extend([
+            "-dilate_results",
+            params.get("dilate_results")
+        ])
+    if params.get("fill_dirs") is not None:
+        cargs.extend([
+            "-fill_dirs",
+            params.get("fill_dirs")
+        ])
+    if params.get("fill_holes"):
+        cargs.append("-fill_holes")
+    if params.get("frac") is not None:
+        cargs.extend([
+            "-frac",
+            str(params.get("frac"))
+        ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("in_file"))
+    ])
+    if params.get("inter"):
+        cargs.append("-inter")
+    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"))
+    if params.get("union"):
+        cargs.append("-union")
+    if params.get("verbose") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbose"))
+        ])
+    return cargs
+
+
+def v_3dmask_tool_outputs(
+    params: V3dmaskToolParameters,
+    execution: Execution,
+) -> V3dmaskToolOutputs:
+    """
+    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 = V3dmaskToolOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(pathlib.Path(params.get("in_file")).name + "_mask"),
+        out_file_=execution.output_file("out_file"),
+    )
+    return ret
+
+
+def v_3dmask_tool_execute(
+    params: V3dmaskToolParameters,
+    execution: Execution,
+) -> V3dmaskToolOutputs:
+    """
+    3dmask_tool - for combining/dilating/eroding/filling masks.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dmaskToolOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dmask_tool_cargs(params, execution)
+    ret = v_3dmask_tool_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dmask_tool(
+    in_file: InputPathType,
+    count: bool = False,
+    datum: typing.Literal["byte", "short", "float"] | None = None,
+    dilate_inputs: str | None = None,
+    dilate_results: str | None = None,
+    fill_dirs: str | None = None,
+    fill_holes: bool = False,
+    frac: float | None = None,
+    inter: bool = False,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    union: bool = False,
+    verbose: int | None = None,
+    runner: Runner | None = None,
+) -> V3dmaskToolOutputs:
+    """
+    3dmask_tool - for combining/dilating/eroding/filling masks.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3dmask_tool.
+        count: Instead of created a binary 0/1 mask dataset, create one with\
+            counts of voxel overlap, i.e., each voxel will contain the number of\
+            masks that it is set in.
+        datum: 'byte' or 'short' or 'float'. Specify data type for output.
+        dilate_inputs: Use this option to dilate and/or erode datasets as they\
+            are read. ex. '5 -5' to dilate and erode 5 times.
+        dilate_results: Dilate and/or erode combined mask at the given levels.
+        fill_dirs: Fill holes only in the given directions. this option is for\
+            use with -fill holes. should be a single string that specifies 1-3 of\
+            the axes using {x,y,z} labels (i.e. dataset axis order), or using the\
+            labels in {r,l,a,p,i,s}.
+        fill_holes: This option can be used to fill holes in the resulting\
+            mask, i.e. after all other processing has been done.
+        frac: When combining masks (across datasets and sub-bricks), use this\
+            option to restrict the result to a certain fraction of the set of\
+            volumes.
+        inter: Intersection, this means -frac 1.0.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        union: Union, this means -frac 0.
+        verbose: Specify verbosity level, for 0 to 3.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dmaskToolOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMASK_TOOL_METADATA)
+    params = v_3dmask_tool_params(
+        count=count,
+        datum=datum,
+        dilate_inputs=dilate_inputs,
+        dilate_results=dilate_results,
+        fill_dirs=fill_dirs,
+        fill_holes=fill_holes,
+        frac=frac,
+        in_file=in_file,
+        inter=inter,
+        num_threads=num_threads,
+        outputtype=outputtype,
+        union=union,
+        verbose=verbose,
+    )
+    return v_3dmask_tool_execute(params, execution)
+
+
+__all__ = [
+    "V3dmaskToolOutputs",
+    "V3dmaskToolParameters",
+    "V_3DMASK_TOOL_METADATA",
+    "v_3dmask_tool",
+    "v_3dmask_tool_params",
+]

niwrap_afni/afni/v_3dmaskave.py

@@ -0,0 +1,223 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DMASKAVE_METADATA = Metadata(
+    id="f43e3dde7ed7ffaf36c08fedc037f88f0b2a842f.boutiques",
+    name="3dmaskave",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dmaskaveParameters = typing.TypedDict('V3dmaskaveParameters', {
+    "__STYX_TYPE__": typing.Literal["3dmaskave"],
+    "in_file": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "quiet": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dmaskave": v_3dmaskave_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 {
+        "3dmaskave": v_3dmaskave_outputs,
+    }.get(t)
+
+
+class V3dmaskaveOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dmaskave(...)`.
+    """
+    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_3dmaskave_params(
+    in_file: InputPathType,
+    mask: InputPathType | None = None,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    quiet: bool = False,
+) -> V3dmaskaveParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3dmaskave.
+        mask: Matrix to align input file.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        quiet: Matrix to align input file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dmaskave",
+        "in_file": in_file,
+        "quiet": quiet,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if num_threads is not None:
+        params["num_threads"] = num_threads
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    return params
+
+
+def v_3dmaskave_cargs(
+    params: V3dmaskaveParameters,
+    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("3dmaskave")
+    cargs.append(execution.input_file(params.get("in_file")))
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    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"))
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3dmaskave_outputs(
+    params: V3dmaskaveParameters,
+    execution: Execution,
+) -> V3dmaskaveOutputs:
+    """
+    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 = V3dmaskaveOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(pathlib.Path(params.get("in_file")).name + "_maskave.1D"),
+        out_file_=execution.output_file("out_file"),
+    )
+    return ret
+
+
+def v_3dmaskave_execute(
+    params: V3dmaskaveParameters,
+    execution: Execution,
+) -> V3dmaskaveOutputs:
+    """
+    Computes average of all voxels in the input dataset which satisfy the criterion
+    in the options list.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dmaskaveOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dmaskave_cargs(params, execution)
+    ret = v_3dmaskave_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dmaskave(
+    in_file: InputPathType,
+    mask: InputPathType | None = None,
+    num_threads: int | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> V3dmaskaveOutputs:
+    """
+    Computes average of all voxels in the input dataset which satisfy the criterion
+    in the options list.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3dmaskave.
+        mask: Matrix to align input file.
+        num_threads: Set number of threads.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        quiet: Matrix to align input file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dmaskaveOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMASKAVE_METADATA)
+    params = v_3dmaskave_params(
+        in_file=in_file,
+        mask=mask,
+        num_threads=num_threads,
+        outputtype=outputtype,
+        quiet=quiet,
+    )
+    return v_3dmaskave_execute(params, execution)
+
+
+__all__ = [
+    "V3dmaskaveOutputs",
+    "V3dmaskaveParameters",
+    "V_3DMASKAVE_METADATA",
+    "v_3dmaskave",
+    "v_3dmaskave_params",
+]