niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_spat_norm.py

@@ -0,0 +1,265 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_SPAT_NORM_METADATA = Metadata(
+    id="3dfa068ac2f6a03026257ba621a4c3d853de135b.boutiques",
+    name="3dSpatNorm",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSpatNormParameters = typing.TypedDict('V3dSpatNormParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSpatNorm"],
+    "dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "orig_space": bool,
+    "verbose": bool,
+    "monkey": bool,
+    "marmot": bool,
+    "rat": bool,
+    "human": bool,
+    "bottom_cuts": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dSpatNorm": v_3d_spat_norm_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 {
+        "3dSpatNorm": v_3d_spat_norm_outputs,
+    }.get(t)
+
+
+class V3dSpatNormOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_spat_norm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_head: OutputPathType | None
+    """Output dataset (HEAD file)"""
+    out_brik: OutputPathType | None
+    """Output dataset (BRIK file)"""
+
+
+def v_3d_spat_norm_params(
+    dataset: InputPathType,
+    prefix: str | None = None,
+    orig_space: bool = False,
+    verbose: bool = False,
+    monkey: bool = False,
+    marmot: bool = False,
+    rat: bool = False,
+    human: bool = False,
+    bottom_cuts: str | None = None,
+) -> V3dSpatNormParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset.
+        prefix: Write output dataset using 'ppp' for the prefix.
+        orig_space: Write output dataset using the same grid as dataset.
+        verbose: Write out progress reports.
+        monkey: Monkey business.
+        marmot: Marmoset head.
+        rat: Rat head.
+        human: Bone head (default).
+        bottom_cuts: Make approximate cuts at the bottom to shave non-brain\
+            areas. CUTFLAGS is a string of characters indicating which sides to\
+            cut: 'A' for anterior, 'P' for posterior, 'R' for right, 'L' for left.\
+            Example: -bottom_cuts APLR.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSpatNorm",
+        "dataset": dataset,
+        "orig_space": orig_space,
+        "verbose": verbose,
+        "monkey": monkey,
+        "marmot": marmot,
+        "rat": rat,
+        "human": human,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if bottom_cuts is not None:
+        params["bottom_cuts"] = bottom_cuts
+    return params
+
+
+def v_3d_spat_norm_cargs(
+    params: V3dSpatNormParameters,
+    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("3dSpatNorm")
+    cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("orig_space"):
+        cargs.append("-orig_space")
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("monkey"):
+        cargs.append("-monkey")
+    if params.get("marmot"):
+        cargs.append("-marmost")
+    if params.get("rat"):
+        cargs.append("-rat")
+    if params.get("human"):
+        cargs.append("-human")
+    if params.get("bottom_cuts") is not None:
+        cargs.extend([
+            "-bottom_cuts",
+            params.get("bottom_cuts")
+        ])
+    return cargs
+
+
+def v_3d_spat_norm_outputs(
+    params: V3dSpatNormParameters,
+    execution: Execution,
+) -> V3dSpatNormOutputs:
+    """
+    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 = V3dSpatNormOutputs(
+        root=execution.output_file("."),
+        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        out_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_spat_norm_execute(
+    params: V3dSpatNormParameters,
+    execution: Execution,
+) -> V3dSpatNormOutputs:
+    """
+    An obsolete tool for spatial normalization.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSpatNormOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_spat_norm_cargs(params, execution)
+    ret = v_3d_spat_norm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_spat_norm(
+    dataset: InputPathType,
+    prefix: str | None = None,
+    orig_space: bool = False,
+    verbose: bool = False,
+    monkey: bool = False,
+    marmot: bool = False,
+    rat: bool = False,
+    human: bool = False,
+    bottom_cuts: str | None = None,
+    runner: Runner | None = None,
+) -> V3dSpatNormOutputs:
+    """
+    An obsolete tool for spatial normalization.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset.
+        prefix: Write output dataset using 'ppp' for the prefix.
+        orig_space: Write output dataset using the same grid as dataset.
+        verbose: Write out progress reports.
+        monkey: Monkey business.
+        marmot: Marmoset head.
+        rat: Rat head.
+        human: Bone head (default).
+        bottom_cuts: Make approximate cuts at the bottom to shave non-brain\
+            areas. CUTFLAGS is a string of characters indicating which sides to\
+            cut: 'A' for anterior, 'P' for posterior, 'R' for right, 'L' for left.\
+            Example: -bottom_cuts APLR.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSpatNormOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SPAT_NORM_METADATA)
+    params = v_3d_spat_norm_params(
+        dataset=dataset,
+        prefix=prefix,
+        orig_space=orig_space,
+        verbose=verbose,
+        monkey=monkey,
+        marmot=marmot,
+        rat=rat,
+        human=human,
+        bottom_cuts=bottom_cuts,
+    )
+    return v_3d_spat_norm_execute(params, execution)
+
+
+__all__ = [
+    "V3dSpatNormOutputs",
+    "V3dSpatNormParameters",
+    "V_3D_SPAT_NORM_METADATA",
+    "v_3d_spat_norm",
+    "v_3d_spat_norm_params",
+]

niwrap_afni/afni/v_3d_stat_clust.py

@@ -0,0 +1,257 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_STAT_CLUST_METADATA = Metadata(
+    id="fc722addfbc175c71d3a318d604f19ee64fdb599.boutiques",
+    name="3dStatClust",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dStatClustParameters = typing.TypedDict('V3dStatClustParameters', {
+    "__STYX_TYPE__": typing.Literal["3dStatClust"],
+    "prefix": typing.NotRequired[str | None],
+    "session_dir": typing.NotRequired[str | None],
+    "verbose": bool,
+    "dist_cor": bool,
+    "thresh": str,
+    "nclust": float,
+    "datasets": list[str],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dStatClust": v_3d_stat_clust_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 {
+        "3dStatClust": v_3d_stat_clust_outputs,
+    }.get(t)
+
+
+class V3dStatClustOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_stat_clust(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_head: OutputPathType | None
+    """Output dataset header"""
+    output_brick: OutputPathType | None
+    """Output dataset brick"""
+
+
+def v_3d_stat_clust_params(
+    thresh: str,
+    nclust: float,
+    datasets: list[str],
+    prefix: str | None = None,
+    session_dir: str | None = None,
+    verbose: bool = False,
+    dist_cor: bool = False,
+) -> V3dStatClustParameters:
+    """
+    Build parameters.
+    
+    Args:
+        thresh: Threshold statistic from file tname. Only voxels whose\
+            threshold statistic is greater than t in absolute value will be\
+            considered. If file tname contains more than 1 sub-brick, the threshold\
+            stat. sub-brick must be specified.
+        nclust: Maximum number of clusters for output (= number of sub-bricks\
+            in output dataset).
+        datasets: Parameter datasets.
+        prefix: Use 'pname' for the output dataset prefix name.
+        session_dir: Use 'dir' for the output dataset session directory.
+        verbose: Print out verbose output as the program proceeds.
+        dist_cor: Statistical distance for correlated parameters.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dStatClust",
+        "verbose": verbose,
+        "dist_cor": dist_cor,
+        "thresh": thresh,
+        "nclust": nclust,
+        "datasets": datasets,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if session_dir is not None:
+        params["session_dir"] = session_dir
+    return params
+
+
+def v_3d_stat_clust_cargs(
+    params: V3dStatClustParameters,
+    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("3dStatClust")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("session_dir") is not None:
+        cargs.extend([
+            "-session",
+            params.get("session_dir")
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("dist_cor"):
+        cargs.append("-dist_cor")
+    cargs.extend([
+        "-thresh",
+        params.get("thresh")
+    ])
+    cargs.extend([
+        "-nclust",
+        str(params.get("nclust"))
+    ])
+    cargs.extend(params.get("datasets"))
+    return cargs
+
+
+def v_3d_stat_clust_outputs(
+    params: V3dStatClustParameters,
+    execution: Execution,
+) -> V3dStatClustOutputs:
+    """
+    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 = V3dStatClustOutputs(
+        root=execution.output_file("."),
+        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        output_brick=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_stat_clust_execute(
+    params: V3dStatClustParameters,
+    execution: Execution,
+) -> V3dStatClustOutputs:
+    """
+    Perform agglomerative hierarchical clustering for user specified parameter
+    sub-bricks, for all voxels whose threshold statistic is above a user specified
+    value.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dStatClustOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_stat_clust_cargs(params, execution)
+    ret = v_3d_stat_clust_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_stat_clust(
+    thresh: str,
+    nclust: float,
+    datasets: list[str],
+    prefix: str | None = None,
+    session_dir: str | None = None,
+    verbose: bool = False,
+    dist_cor: bool = False,
+    runner: Runner | None = None,
+) -> V3dStatClustOutputs:
+    """
+    Perform agglomerative hierarchical clustering for user specified parameter
+    sub-bricks, for all voxels whose threshold statistic is above a user specified
+    value.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        thresh: Threshold statistic from file tname. Only voxels whose\
+            threshold statistic is greater than t in absolute value will be\
+            considered. If file tname contains more than 1 sub-brick, the threshold\
+            stat. sub-brick must be specified.
+        nclust: Maximum number of clusters for output (= number of sub-bricks\
+            in output dataset).
+        datasets: Parameter datasets.
+        prefix: Use 'pname' for the output dataset prefix name.
+        session_dir: Use 'dir' for the output dataset session directory.
+        verbose: Print out verbose output as the program proceeds.
+        dist_cor: Statistical distance for correlated parameters.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dStatClustOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_STAT_CLUST_METADATA)
+    params = v_3d_stat_clust_params(
+        prefix=prefix,
+        session_dir=session_dir,
+        verbose=verbose,
+        dist_cor=dist_cor,
+        thresh=thresh,
+        nclust=nclust,
+        datasets=datasets,
+    )
+    return v_3d_stat_clust_execute(params, execution)
+
+
+__all__ = [
+    "V3dStatClustOutputs",
+    "V3dStatClustParameters",
+    "V_3D_STAT_CLUST_METADATA",
+    "v_3d_stat_clust",
+    "v_3d_stat_clust_params",
+]