niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dkmeans.py

@@ -0,0 +1,449 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DKMEANS_METADATA = Metadata(
+    id="4536293f2db1b50ebead4293161f46a508afd8a7.boutiques",
+    name="3dkmeans",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dkmeansParameters = typing.TypedDict('V3dkmeansParameters', {
+    "__STYX_TYPE__": typing.Literal["3dkmeans"],
+    "version": bool,
+    "input": list[InputPathType],
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_range": typing.NotRequired[list[float] | None],
+    "cmask": typing.NotRequired[str | None],
+    "jobname": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "distance_measure": typing.NotRequired[float | None],
+    "num_clusters": typing.NotRequired[float | None],
+    "remap_method": typing.NotRequired[str | None],
+    "labeltable": typing.NotRequired[InputPathType | None],
+    "clabels": typing.NotRequired[list[str] | None],
+    "clust_init": typing.NotRequired[InputPathType | None],
+    "num_repeats": typing.NotRequired[float | None],
+    "rsigs": typing.NotRequired[InputPathType | None],
+    "verbose": bool,
+    "write_dists": bool,
+    "voxdbg": typing.NotRequired[list[float] | None],
+    "seed": 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 {
+        "3dkmeans": v_3dkmeans_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 {
+        "3dkmeans": v_3dkmeans_outputs,
+    }.get(t)
+
+
+class V3dkmeansOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dkmeans(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    cluster_membership: OutputPathType | None
+    """Output volume for the cluster membership."""
+    cluster_distance: OutputPathType | None
+    """Output volume for the cluster distance measures."""
+    distances_text_file: OutputPathType
+    """Output text file containing distances between clusters."""
+    centroids_text_file: OutputPathType
+    """Output text file containing cluster centroids."""
+    within_cluster_sum_text_file: OutputPathType
+    """Output text file containing within cluster sum of distances."""
+    max_distance_text_file: OutputPathType
+    """Output text file containing maximum distance within each cluster."""
+    voxel_distance_to_centroid: OutputPathType
+    """Output text file containing distance from voxel to its centroid."""
+
+
+def v_3dkmeans_params(
+    input_: list[InputPathType],
+    version: bool = False,
+    mask: InputPathType | None = None,
+    mask_range: list[float] | None = None,
+    cmask: str | None = None,
+    jobname: str | None = None,
+    prefix: str | None = None,
+    distance_measure: float | None = None,
+    num_clusters: float | None = None,
+    remap_method: str | None = None,
+    labeltable: InputPathType | None = None,
+    clabels: list[str] | None = None,
+    clust_init: InputPathType | None = None,
+    num_repeats: float | None = None,
+    rsigs: InputPathType | None = None,
+    verbose: bool = False,
+    write_dists: bool = False,
+    voxdbg: list[float] | None = None,
+    seed: float | None = None,
+) -> V3dkmeansParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Input data to be clustered. You can specify multiple filenames\
+            in sequence and they will be concatenated internally.
+        version:.
+        mask: Dataset to be used as a mask; only voxels with nonzero values in\
+            'mset' will be used.
+        mask_range: Restrict the voxels from 'mset' to only those mask values\
+            between 'a' and 'b' (inclusive).
+        cmask: Execute the options enclosed in single quotes as a 3dcalc-like\
+            program to produce a mask from the resulting 3D brick.
+        jobname: Specify a different name for the output files. Default is\
+            derived from the input file name.
+        prefix: Specify a prefix for the output volumes. Default is the same as\
+            jobname.
+        distance_measure: Specifies distance measure for clustering. Supported\
+            values: 0 (No clustering), 1 (Uncentered correlation distance), 2\
+            (Pearson distance), 3 (Uncentered correlation distance, absolute\
+            value), 4 (Pearson distance, absolute value), 5 (Spearman's rank\
+            distance), 6 (Kendall's distance), 7 (Euclidean distance), 8\
+            (City-block distance).
+        num_clusters: Specify number of clusters.
+        remap_method: Reassign clusters numbers based on METHOD: NONE\
+            (default), COUNT, iCOUNT, MAG, iMAG.
+        labeltable: Attach labeltable to clustering output.
+        clabels: Provide a label for each cluster. Labels cannot start with\
+            '-'.
+        clust_init: Specify a dataset to initialize clustering. If provided,\
+            sets -r 0.
+        num_repeats: Number of times the k-means clustering algorithm is run.
+        rsigs: Calculate distances from each voxel's signature to the\
+            signatures in this multi-column file. No clustering done.
+        verbose: Enable verbose mode.
+        write_dists: Output text files containing various distance measures.
+        voxdbg: Output debugging info for specified voxel (I J K).
+        seed: Seed for the random number generator. Default is 1234567.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dkmeans",
+        "version": version,
+        "input": input_,
+        "verbose": verbose,
+        "write_dists": write_dists,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if mask_range is not None:
+        params["mask_range"] = mask_range
+    if cmask is not None:
+        params["cmask"] = cmask
+    if jobname is not None:
+        params["jobname"] = jobname
+    if prefix is not None:
+        params["prefix"] = prefix
+    if distance_measure is not None:
+        params["distance_measure"] = distance_measure
+    if num_clusters is not None:
+        params["num_clusters"] = num_clusters
+    if remap_method is not None:
+        params["remap_method"] = remap_method
+    if labeltable is not None:
+        params["labeltable"] = labeltable
+    if clabels is not None:
+        params["clabels"] = clabels
+    if clust_init is not None:
+        params["clust_init"] = clust_init
+    if num_repeats is not None:
+        params["num_repeats"] = num_repeats
+    if rsigs is not None:
+        params["rsigs"] = rsigs
+    if voxdbg is not None:
+        params["voxdbg"] = voxdbg
+    if seed is not None:
+        params["seed"] = seed
+    return params
+
+
+def v_3dkmeans_cargs(
+    params: V3dkmeansParameters,
+    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("3dkmeans")
+    if params.get("version"):
+        cargs.append("--version")
+    cargs.extend([
+        "-f",
+        *[execution.input_file(f) for f in params.get("input")]
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("mask_range") is not None:
+        cargs.extend([
+            "-mrange",
+            *map(str, params.get("mask_range"))
+        ])
+    if params.get("cmask") is not None:
+        cargs.extend([
+            "-cmask",
+            params.get("cmask")
+        ])
+    if params.get("jobname") is not None:
+        cargs.extend([
+            "-u",
+            params.get("jobname")
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("distance_measure") is not None:
+        cargs.extend([
+            "-g",
+            str(params.get("distance_measure"))
+        ])
+    if params.get("num_clusters") is not None:
+        cargs.extend([
+            "-k",
+            str(params.get("num_clusters"))
+        ])
+    if params.get("remap_method") is not None:
+        cargs.extend([
+            "-remap",
+            params.get("remap_method")
+        ])
+    if params.get("labeltable") is not None:
+        cargs.extend([
+            "-labeltable",
+            execution.input_file(params.get("labeltable"))
+        ])
+    if params.get("clabels") is not None:
+        cargs.extend([
+            "-clabels",
+            *params.get("clabels")
+        ])
+    if params.get("clust_init") is not None:
+        cargs.extend([
+            "-clust_init",
+            execution.input_file(params.get("clust_init"))
+        ])
+    if params.get("num_repeats") is not None:
+        cargs.extend([
+            "-r",
+            str(params.get("num_repeats"))
+        ])
+    if params.get("rsigs") is not None:
+        cargs.extend([
+            "-rsigs",
+            execution.input_file(params.get("rsigs"))
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("write_dists"):
+        cargs.append("-write_dists")
+    if params.get("voxdbg") is not None:
+        cargs.extend([
+            "-voxdbg",
+            *map(str, params.get("voxdbg"))
+        ])
+    if params.get("seed") is not None:
+        cargs.extend([
+            "-seed",
+            str(params.get("seed"))
+        ])
+    return cargs
+
+
+def v_3dkmeans_outputs(
+    params: V3dkmeansParameters,
+    execution: Execution,
+) -> V3dkmeansOutputs:
+    """
+    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 = V3dkmeansOutputs(
+        root=execution.output_file("."),
+        cluster_membership=execution.output_file(params.get("jobname") + "_membership.nii.gz") if (params.get("jobname") is not None) else None,
+        cluster_distance=execution.output_file(params.get("jobname") + "_distance.nii.gz") if (params.get("jobname") is not None) else None,
+        distances_text_file=execution.output_file("FILE.dis.1D"),
+        centroids_text_file=execution.output_file("FILE.cen.1D"),
+        within_cluster_sum_text_file=execution.output_file("FILE.info1.1D"),
+        max_distance_text_file=execution.output_file("FILE.info2.1D"),
+        voxel_distance_to_centroid=execution.output_file("FILE.vcd.1D"),
+    )
+    return ret
+
+
+def v_3dkmeans_execute(
+    params: V3dkmeansParameters,
+    execution: Execution,
+) -> V3dkmeansOutputs:
+    """
+    3d+t Clustering segmentation based on The C clustering library.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dkmeansOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dkmeans_cargs(params, execution)
+    ret = v_3dkmeans_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dkmeans(
+    input_: list[InputPathType],
+    version: bool = False,
+    mask: InputPathType | None = None,
+    mask_range: list[float] | None = None,
+    cmask: str | None = None,
+    jobname: str | None = None,
+    prefix: str | None = None,
+    distance_measure: float | None = None,
+    num_clusters: float | None = None,
+    remap_method: str | None = None,
+    labeltable: InputPathType | None = None,
+    clabels: list[str] | None = None,
+    clust_init: InputPathType | None = None,
+    num_repeats: float | None = None,
+    rsigs: InputPathType | None = None,
+    verbose: bool = False,
+    write_dists: bool = False,
+    voxdbg: list[float] | None = None,
+    seed: float | None = None,
+    runner: Runner | None = None,
+) -> V3dkmeansOutputs:
+    """
+    3d+t Clustering segmentation based on The C clustering library.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Input data to be clustered. You can specify multiple filenames\
+            in sequence and they will be concatenated internally.
+        version:.
+        mask: Dataset to be used as a mask; only voxels with nonzero values in\
+            'mset' will be used.
+        mask_range: Restrict the voxels from 'mset' to only those mask values\
+            between 'a' and 'b' (inclusive).
+        cmask: Execute the options enclosed in single quotes as a 3dcalc-like\
+            program to produce a mask from the resulting 3D brick.
+        jobname: Specify a different name for the output files. Default is\
+            derived from the input file name.
+        prefix: Specify a prefix for the output volumes. Default is the same as\
+            jobname.
+        distance_measure: Specifies distance measure for clustering. Supported\
+            values: 0 (No clustering), 1 (Uncentered correlation distance), 2\
+            (Pearson distance), 3 (Uncentered correlation distance, absolute\
+            value), 4 (Pearson distance, absolute value), 5 (Spearman's rank\
+            distance), 6 (Kendall's distance), 7 (Euclidean distance), 8\
+            (City-block distance).
+        num_clusters: Specify number of clusters.
+        remap_method: Reassign clusters numbers based on METHOD: NONE\
+            (default), COUNT, iCOUNT, MAG, iMAG.
+        labeltable: Attach labeltable to clustering output.
+        clabels: Provide a label for each cluster. Labels cannot start with\
+            '-'.
+        clust_init: Specify a dataset to initialize clustering. If provided,\
+            sets -r 0.
+        num_repeats: Number of times the k-means clustering algorithm is run.
+        rsigs: Calculate distances from each voxel's signature to the\
+            signatures in this multi-column file. No clustering done.
+        verbose: Enable verbose mode.
+        write_dists: Output text files containing various distance measures.
+        voxdbg: Output debugging info for specified voxel (I J K).
+        seed: Seed for the random number generator. Default is 1234567.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dkmeansOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DKMEANS_METADATA)
+    params = v_3dkmeans_params(
+        version=version,
+        input_=input_,
+        mask=mask,
+        mask_range=mask_range,
+        cmask=cmask,
+        jobname=jobname,
+        prefix=prefix,
+        distance_measure=distance_measure,
+        num_clusters=num_clusters,
+        remap_method=remap_method,
+        labeltable=labeltable,
+        clabels=clabels,
+        clust_init=clust_init,
+        num_repeats=num_repeats,
+        rsigs=rsigs,
+        verbose=verbose,
+        write_dists=write_dists,
+        voxdbg=voxdbg,
+        seed=seed,
+    )
+    return v_3dkmeans_execute(params, execution)
+
+
+__all__ = [
+    "V3dkmeansOutputs",
+    "V3dkmeansParameters",
+    "V_3DKMEANS_METADATA",
+    "v_3dkmeans",
+    "v_3dkmeans_params",
+]

niwrap_afni/afni/v_3dmask_svd.py

@@ -0,0 +1,179 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DMASK_SVD_METADATA = Metadata(
+    id="5cc0ef9b4df81bcbe1689588ddbddf9e81594730.boutiques",
+    name="3dmaskSVD",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dmaskSvdParameters = typing.TypedDict('V3dmaskSvdParameters', {
+    "__STYX_TYPE__": typing.Literal["3dmaskSVD"],
+    "input_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 {
+        "3dmaskSVD": v_3dmask_svd_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 {
+        "3dmaskSVD": v_3dmask_svd_outputs,
+    }.get(t)
+
+
+class V3dmaskSvdOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dmask_svd(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    svd_output: OutputPathType
+    """Singular vector output redirected to this file"""
+
+
+def v_3dmask_svd_params(
+    input_dataset: InputPathType,
+) -> V3dmaskSvdParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dmaskSVD",
+        "input_dataset": input_dataset,
+    }
+    return params
+
+
+def v_3dmask_svd_cargs(
+    params: V3dmaskSvdParameters,
+    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("3dmaskSVD")
+    cargs.append("[OPTIONS]")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    return cargs
+
+
+def v_3dmask_svd_outputs(
+    params: V3dmaskSvdParameters,
+    execution: Execution,
+) -> V3dmaskSvdOutputs:
+    """
+    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 = V3dmaskSvdOutputs(
+        root=execution.output_file("."),
+        svd_output=execution.output_file("../stdout"),
+    )
+    return ret
+
+
+def v_3dmask_svd_execute(
+    params: V3dmaskSvdParameters,
+    execution: Execution,
+) -> V3dmaskSvdOutputs:
+    """
+    Computes the principal singular vector of the time series vectors extracted from
+    the input dataset over the input mask.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dmaskSvdOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dmask_svd_cargs(params, execution)
+    ret = v_3dmask_svd_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dmask_svd(
+    input_dataset: InputPathType,
+    runner: Runner | None = None,
+) -> V3dmaskSvdOutputs:
+    """
+    Computes the principal singular vector of the time series vectors extracted from
+    the input dataset over the input mask.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dmaskSvdOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMASK_SVD_METADATA)
+    params = v_3dmask_svd_params(
+        input_dataset=input_dataset,
+    )
+    return v_3dmask_svd_execute(params, execution)
+
+
+__all__ = [
+    "V3dmaskSvdOutputs",
+    "V3dmaskSvdParameters",
+    "V_3DMASK_SVD_METADATA",
+    "v_3dmask_svd",
+    "v_3dmask_svd_params",
+]