niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_clust_count.py

@@ -0,0 +1,229 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_CLUST_COUNT_METADATA = Metadata(
+    id="98fcc8c7fba23c3985c9517555b10b2b9741fa23.boutiques",
+    name="3dClustCount",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dClustCountParameters = typing.TypedDict('V3dClustCountParameters', {
+    "__STYX_TYPE__": typing.Literal["3dClustCount"],
+    "datasets": list[InputPathType],
+    "prefix": typing.NotRequired[str | None],
+    "final": bool,
+    "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 {
+        "3dClustCount": v_3d_clust_count_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 {
+        "3dClustCount": v_3d_clust_count_outputs,
+    }.get(t)
+
+
+class V3dClustCountOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_clust_count(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    clustcount_niml: OutputPathType | None
+    """Summed results file in NIML format."""
+    clustcount_1_d: OutputPathType | None
+    """Summed results file in 1D format (when '-final' is used)."""
+    final_clustcount_niml: OutputPathType | None
+    """Summed results file in NIML format (when '-final' is used)."""
+
+
+def v_3d_clust_count_params(
+    datasets: list[InputPathType],
+    prefix: str | None = None,
+    final: bool = False,
+    quiet: bool = False,
+) -> V3dClustCountParameters:
+    """
+    Build parameters.
+    
+    Args:
+        datasets: Input datasets to be processed.
+        prefix: Prefix of the filename into which results will be summed.\
+            Actual filename will be 'sss.clustcount.niml'. If this file already\
+            exists, results from the current run will be summed into the existing\
+            results and the file then re-written.
+        final: Output results in a format similar to 3dClustSim -- as 1D and\
+            NIML formatted files with probabilities of various cluster sizes. This\
+            option can be used without any input datasets to create final output\
+            files from saved '.clustcount.niml' output file from earlier runs.
+        quiet: Suppresses progress reports and other informational messages.\
+            Should be placed first in the command line to quiet most messages.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dClustCount",
+        "datasets": datasets,
+        "final": final,
+        "quiet": quiet,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_clust_count_cargs(
+    params: V3dClustCountParameters,
+    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("3dClustCount")
+    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("final"):
+        cargs.append("-final")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3d_clust_count_outputs(
+    params: V3dClustCountParameters,
+    execution: Execution,
+) -> V3dClustCountOutputs:
+    """
+    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 = V3dClustCountOutputs(
+        root=execution.output_file("."),
+        clustcount_niml=execution.output_file(params.get("prefix") + ".clustcount.niml") if (params.get("prefix") is not None) else None,
+        clustcount_1_d=execution.output_file(params.get("prefix") + ".1D") if (params.get("prefix") is not None) else None,
+        final_clustcount_niml=execution.output_file(params.get("prefix") + ".niml") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_clust_count_execute(
+    params: V3dClustCountParameters,
+    execution: Execution,
+) -> V3dClustCountOutputs:
+    """
+    This program takes as input 1 or more datasets, thresholds them at various
+    levels, and counts up the number of clusters of various sizes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dClustCountOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_clust_count_cargs(params, execution)
+    ret = v_3d_clust_count_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_clust_count(
+    datasets: list[InputPathType],
+    prefix: str | None = None,
+    final: bool = False,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> V3dClustCountOutputs:
+    """
+    This program takes as input 1 or more datasets, thresholds them at various
+    levels, and counts up the number of clusters of various sizes.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        datasets: Input datasets to be processed.
+        prefix: Prefix of the filename into which results will be summed.\
+            Actual filename will be 'sss.clustcount.niml'. If this file already\
+            exists, results from the current run will be summed into the existing\
+            results and the file then re-written.
+        final: Output results in a format similar to 3dClustSim -- as 1D and\
+            NIML formatted files with probabilities of various cluster sizes. This\
+            option can be used without any input datasets to create final output\
+            files from saved '.clustcount.niml' output file from earlier runs.
+        quiet: Suppresses progress reports and other informational messages.\
+            Should be placed first in the command line to quiet most messages.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dClustCountOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CLUST_COUNT_METADATA)
+    params = v_3d_clust_count_params(
+        datasets=datasets,
+        prefix=prefix,
+        final=final,
+        quiet=quiet,
+    )
+    return v_3d_clust_count_execute(params, execution)
+
+
+__all__ = [
+    "V3dClustCountOutputs",
+    "V3dClustCountParameters",
+    "V_3D_CLUST_COUNT_METADATA",
+    "v_3d_clust_count",
+    "v_3d_clust_count_params",
+]

niwrap_afni/afni/v_3d_clust_sim.py

@@ -0,0 +1,196 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_CLUST_SIM_METADATA = Metadata(
+    id="493de4c7d1501714af71d386a011e1fe097ca5fb.boutiques",
+    name="3dClustSim",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dClustSimParameters = typing.TypedDict('V3dClustSimParameters', {
+    "__STYX_TYPE__": typing.Literal["3dClustSim"],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dClustSim": v_3d_clust_sim_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 {
+        "3dClustSim": v_3d_clust_sim_outputs,
+    }.get(t)
+
+
+class V3dClustSimOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_clust_sim(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_nn1_1sided: OutputPathType
+    """Output file for NN1 with 1-sided thresholding"""
+    output_nn1_2sided: OutputPathType
+    """Output file for NN1 with 2-sided thresholding"""
+    output_nn1_bisided: OutputPathType
+    """Output file for NN1 with bi-sided thresholding"""
+    output_nn2_1sided: OutputPathType
+    """Output file for NN2 with 1-sided thresholding"""
+    output_nn2_2sided: OutputPathType
+    """Output file for NN2 with 2-sided thresholding"""
+    output_nn2_bisided: OutputPathType
+    """Output file for NN2 with bi-sided thresholding"""
+    output_nn3_1sided: OutputPathType
+    """Output file for NN3 with 1-sided thresholding"""
+    output_nn3_2sided: OutputPathType
+    """Output file for NN3 with 2-sided thresholding"""
+    output_nn3_bisided: OutputPathType
+    """Output file for NN3 with bi-sided thresholding"""
+    mask_compressed: OutputPathType
+    """Compressed ASCII encoding of the mask volume"""
+
+
+def v_3d_clust_sim_params(
+) -> V3dClustSimParameters:
+    """
+    Build parameters.
+    
+    Args:
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dClustSim",
+    }
+    return params
+
+
+def v_3d_clust_sim_cargs(
+    params: V3dClustSimParameters,
+    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("3dClustSim")
+    cargs.append("[OPTIONS]")
+    return cargs
+
+
+def v_3d_clust_sim_outputs(
+    params: V3dClustSimParameters,
+    execution: Execution,
+) -> V3dClustSimOutputs:
+    """
+    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 = V3dClustSimOutputs(
+        root=execution.output_file("."),
+        output_nn1_1sided=execution.output_file("[PREFIX].NN1_1sided.1D"),
+        output_nn1_2sided=execution.output_file("[PREFIX].NN1_2sided.1D"),
+        output_nn1_bisided=execution.output_file("[PREFIX].NN1_bisided.1D"),
+        output_nn2_1sided=execution.output_file("[PREFIX].NN2_1sided.1D"),
+        output_nn2_2sided=execution.output_file("[PREFIX].NN2_2sided.1D"),
+        output_nn2_bisided=execution.output_file("[PREFIX].NN2_bisided.1D"),
+        output_nn3_1sided=execution.output_file("[PREFIX].NN3_1sided.1D"),
+        output_nn3_2sided=execution.output_file("[PREFIX].NN3_2sided.1D"),
+        output_nn3_bisided=execution.output_file("[PREFIX].NN3_bisided.1D"),
+        mask_compressed=execution.output_file("[PREFIX].mask"),
+    )
+    return ret
+
+
+def v_3d_clust_sim_execute(
+    params: V3dClustSimParameters,
+    execution: Execution,
+) -> V3dClustSimOutputs:
+    """
+    Program to estimate the probability of false positive (noise-only) clusters.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dClustSimOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_clust_sim_cargs(params, execution)
+    ret = v_3d_clust_sim_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_clust_sim(
+    runner: Runner | None = None,
+) -> V3dClustSimOutputs:
+    """
+    Program to estimate the probability of false positive (noise-only) clusters.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dClustSimOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CLUST_SIM_METADATA)
+    params = v_3d_clust_sim_params(
+    )
+    return v_3d_clust_sim_execute(params, execution)
+
+
+__all__ = [
+    "V3dClustSimOutputs",
+    "V3dClustSimParameters",
+    "V_3D_CLUST_SIM_METADATA",
+    "v_3d_clust_sim",
+    "v_3d_clust_sim_params",
+]