niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dclust.py

@@ -0,0 +1,380 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DCLUST_METADATA = Metadata(
+    id="3ce8cefee5cef3ba7b1a972b0fcad6cd5a2fd94f.boutiques",
+    name="3dclust",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dclustParameters = typing.TypedDict('V3dclustParameters', {
+    "__STYX_TYPE__": typing.Literal["3dclust"],
+    "rmm": typing.NotRequired[float | None],
+    "vmul": typing.NotRequired[float | None],
+    "datasets": list[InputPathType],
+    "nn1": bool,
+    "nn2": bool,
+    "nn3": bool,
+    "noabs": bool,
+    "summarize": bool,
+    "nosum": bool,
+    "verb": bool,
+    "oned_format": bool,
+    "no_oned_format": bool,
+    "quiet": bool,
+    "mni": bool,
+    "isovalue": bool,
+    "isomerge": bool,
+    "inmask": bool,
+    "prefix": typing.NotRequired[str | None],
+    "savemask": typing.NotRequired[str | None],
+    "binary": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dclust": v_3dclust_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 {
+        "3dclust": v_3dclust_outputs,
+    }.get(t)
+
+
+class V3dclustOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dclust(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    prefixed_output: OutputPathType | None
+    """New dataset with clusters set to zero based on prefix."""
+    ordered_mask_output: OutputPathType | None
+    """Ordered mask dataset based on savemask prefix."""
+
+
+def v_3dclust_params(
+    datasets: list[InputPathType],
+    rmm: float | None = None,
+    vmul: float | None = None,
+    nn1: bool = False,
+    nn2: bool = False,
+    nn3: bool = False,
+    noabs: bool = False,
+    summarize: bool = False,
+    nosum: bool = False,
+    verb: bool = False,
+    oned_format: bool = False,
+    no_oned_format: bool = False,
+    quiet: bool = False,
+    mni: bool = False,
+    isovalue: bool = False,
+    isomerge: bool = False,
+    inmask: bool = False,
+    prefix: str | None = None,
+    savemask: str | None = None,
+    binary: bool = False,
+) -> V3dclustParameters:
+    """
+    Build parameters.
+    
+    Args:
+        datasets: Input dataset(s). More than one allowed, but only the first\
+            sub-brick of the dataset.
+        rmm: Cluster connection radius in millimeters.
+        vmul: Minimum cluster volume in micro-liters or minimum number of\
+            voxels if negative.
+        nn1: 1st nearest-neighbor clustering (faces touching).
+        nn2: 2nd nearest-neighbor clustering (edges touching).
+        nn3: 3rd nearest-neighbor clustering (corners touching).
+        noabs: Use the signed voxel intensities for calculations.
+        summarize: Write out only the total nonzero voxel count and volume for\
+            each dataset.
+        nosum: Suppress printout of the totals.
+        verb: Print out a progress report to stderr as computations proceed.
+        oned_format: Write output in 1D format (default).
+        no_oned_format: Do not write output in 1D format.
+        quiet: Suppress all non-essential output.
+        mni: Transform output xyz-coordinates from TLRC to MNI space if the\
+            input dataset has the +tlrc view.
+        isovalue: Clusters will be formed only from contiguous voxels that also\
+            have the same value.
+        isomerge: Clusters will be formed from each distinct value in the\
+            dataset; spatial contiguity will not be used.
+        inmask: Use an internal mask from the dataset to eliminate voxels\
+            before clustering.
+        prefix: Write a new dataset that is a copy of the input, but with all\
+            voxels not in a cluster set to zero; provide a prefix for the new\
+            dataset.
+        savemask: Write a new dataset that is an ordered mask where the largest\
+            cluster is labeled '1', the next largest '2', and so forth.
+        binary: Turn the output of '-savemask' into a binary (0 or 1) mask.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dclust",
+        "datasets": datasets,
+        "nn1": nn1,
+        "nn2": nn2,
+        "nn3": nn3,
+        "noabs": noabs,
+        "summarize": summarize,
+        "nosum": nosum,
+        "verb": verb,
+        "oned_format": oned_format,
+        "no_oned_format": no_oned_format,
+        "quiet": quiet,
+        "mni": mni,
+        "isovalue": isovalue,
+        "isomerge": isomerge,
+        "inmask": inmask,
+        "binary": binary,
+    }
+    if rmm is not None:
+        params["rmm"] = rmm
+    if vmul is not None:
+        params["vmul"] = vmul
+    if prefix is not None:
+        params["prefix"] = prefix
+    if savemask is not None:
+        params["savemask"] = savemask
+    return params
+
+
+def v_3dclust_cargs(
+    params: V3dclustParameters,
+    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("3dclust")
+    if params.get("rmm") is not None:
+        cargs.append(str(params.get("rmm")))
+    if params.get("vmul") is not None:
+        cargs.append(str(params.get("vmul")))
+    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
+    if params.get("nn1"):
+        cargs.append("-NN1")
+    if params.get("nn2"):
+        cargs.append("-NN2")
+    if params.get("nn3"):
+        cargs.append("-NN3")
+    if params.get("noabs"):
+        cargs.append("-noabs")
+    if params.get("summarize"):
+        cargs.append("-summarize")
+    if params.get("nosum"):
+        cargs.append("-nosum")
+    if params.get("verb"):
+        cargs.append("-verb")
+    if params.get("oned_format"):
+        cargs.append("-1Dformat")
+    if params.get("no_oned_format"):
+        cargs.append("-no_1Dformat")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("mni"):
+        cargs.append("-mni")
+    if params.get("isovalue"):
+        cargs.append("-isovalue")
+    if params.get("isomerge"):
+        cargs.append("-isomerge")
+    if params.get("inmask"):
+        cargs.append("-inmask")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("savemask") is not None:
+        cargs.extend([
+            "-savemask",
+            params.get("savemask")
+        ])
+    if params.get("binary"):
+        cargs.append("-binary")
+    return cargs
+
+
+def v_3dclust_outputs(
+    params: V3dclustParameters,
+    execution: Execution,
+) -> V3dclustOutputs:
+    """
+    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 = V3dclustOutputs(
+        root=execution.output_file("."),
+        prefixed_output=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        ordered_mask_output=execution.output_file(params.get("savemask") + ".nii.gz") if (params.get("savemask") is not None) else None,
+    )
+    return ret
+
+
+def v_3dclust_execute(
+    params: V3dclustParameters,
+    execution: Execution,
+) -> V3dclustOutputs:
+    """
+    Performs simple-minded cluster detection in 3D datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dclustOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dclust_cargs(params, execution)
+    ret = v_3dclust_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dclust(
+    datasets: list[InputPathType],
+    rmm: float | None = None,
+    vmul: float | None = None,
+    nn1: bool = False,
+    nn2: bool = False,
+    nn3: bool = False,
+    noabs: bool = False,
+    summarize: bool = False,
+    nosum: bool = False,
+    verb: bool = False,
+    oned_format: bool = False,
+    no_oned_format: bool = False,
+    quiet: bool = False,
+    mni: bool = False,
+    isovalue: bool = False,
+    isomerge: bool = False,
+    inmask: bool = False,
+    prefix: str | None = None,
+    savemask: str | None = None,
+    binary: bool = False,
+    runner: Runner | None = None,
+) -> V3dclustOutputs:
+    """
+    Performs simple-minded cluster detection in 3D datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        datasets: Input dataset(s). More than one allowed, but only the first\
+            sub-brick of the dataset.
+        rmm: Cluster connection radius in millimeters.
+        vmul: Minimum cluster volume in micro-liters or minimum number of\
+            voxels if negative.
+        nn1: 1st nearest-neighbor clustering (faces touching).
+        nn2: 2nd nearest-neighbor clustering (edges touching).
+        nn3: 3rd nearest-neighbor clustering (corners touching).
+        noabs: Use the signed voxel intensities for calculations.
+        summarize: Write out only the total nonzero voxel count and volume for\
+            each dataset.
+        nosum: Suppress printout of the totals.
+        verb: Print out a progress report to stderr as computations proceed.
+        oned_format: Write output in 1D format (default).
+        no_oned_format: Do not write output in 1D format.
+        quiet: Suppress all non-essential output.
+        mni: Transform output xyz-coordinates from TLRC to MNI space if the\
+            input dataset has the +tlrc view.
+        isovalue: Clusters will be formed only from contiguous voxels that also\
+            have the same value.
+        isomerge: Clusters will be formed from each distinct value in the\
+            dataset; spatial contiguity will not be used.
+        inmask: Use an internal mask from the dataset to eliminate voxels\
+            before clustering.
+        prefix: Write a new dataset that is a copy of the input, but with all\
+            voxels not in a cluster set to zero; provide a prefix for the new\
+            dataset.
+        savemask: Write a new dataset that is an ordered mask where the largest\
+            cluster is labeled '1', the next largest '2', and so forth.
+        binary: Turn the output of '-savemask' into a binary (0 or 1) mask.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dclustOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DCLUST_METADATA)
+    params = v_3dclust_params(
+        rmm=rmm,
+        vmul=vmul,
+        datasets=datasets,
+        nn1=nn1,
+        nn2=nn2,
+        nn3=nn3,
+        noabs=noabs,
+        summarize=summarize,
+        nosum=nosum,
+        verb=verb,
+        oned_format=oned_format,
+        no_oned_format=no_oned_format,
+        quiet=quiet,
+        mni=mni,
+        isovalue=isovalue,
+        isomerge=isomerge,
+        inmask=inmask,
+        prefix=prefix,
+        savemask=savemask,
+        binary=binary,
+    )
+    return v_3dclust_execute(params, execution)
+
+
+__all__ = [
+    "V3dclustOutputs",
+    "V3dclustParameters",
+    "V_3DCLUST_METADATA",
+    "v_3dclust",
+    "v_3dclust_params",
+]

niwrap_afni/afni/v_3dcopy.py

@@ -0,0 +1,184 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DCOPY_METADATA = Metadata(
+    id="4b8187d004c6f4ba95518e709ad1f9b3eb4ed322.boutiques",
+    name="3dcopy",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dcopyParameters = typing.TypedDict('V3dcopyParameters', {
+    "__STYX_TYPE__": typing.Literal["3dcopy"],
+    "verbose": bool,
+    "denote": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dcopy": v_3dcopy_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 V3dcopyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dcopy(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3dcopy_params(
+    verbose: bool = False,
+    denote: bool = False,
+) -> V3dcopyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        verbose: Print progress reports.
+        denote: Remove any Notes from the file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dcopy",
+        "verbose": verbose,
+        "denote": denote,
+    }
+    return params
+
+
+def v_3dcopy_cargs(
+    params: V3dcopyParameters,
+    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("3dcopy")
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("denote"):
+        cargs.append("-denote")
+    cargs.append("{OLD_PREFIX}+{VIEW}")
+    cargs.append("{NEW_PREFIX}")
+    return cargs
+
+
+def v_3dcopy_outputs(
+    params: V3dcopyParameters,
+    execution: Execution,
+) -> V3dcopyOutputs:
+    """
+    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 = V3dcopyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3dcopy_execute(
+    params: V3dcopyParameters,
+    execution: Execution,
+) -> V3dcopyOutputs:
+    """
+    3dcopy copies datasets with or without altering prefixes and converting formats.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dcopyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dcopy_cargs(params, execution)
+    ret = v_3dcopy_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dcopy(
+    verbose: bool = False,
+    denote: bool = False,
+    runner: Runner | None = None,
+) -> V3dcopyOutputs:
+    """
+    3dcopy copies datasets with or without altering prefixes and converting formats.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        verbose: Print progress reports.
+        denote: Remove any Notes from the file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dcopyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DCOPY_METADATA)
+    params = v_3dcopy_params(
+        verbose=verbose,
+        denote=denote,
+    )
+    return v_3dcopy_execute(params, execution)
+
+
+__all__ = [
+    "V3dcopyOutputs",
+    "V3dcopyParameters",
+    "V_3DCOPY_METADATA",
+    "v_3dcopy",
+    "v_3dcopy_params",
+]