niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_rank.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_RANK_METADATA = Metadata(
+    id="05c7817af68d191ce35831e8d5e9772041297b36.boutiques",
+    name="3dRank",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dRankParameters = typing.TypedDict('V3dRankParameters', {
+    "__STYX_TYPE__": typing.Literal["3dRank"],
+    "input_datasets": list[InputPathType],
+    "output_prefix": typing.NotRequired[str | None],
+    "version_info": bool,
+    "help_info": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dRank": v_3d_rank_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 {
+        "3dRank": v_3d_rank_outputs,
+    }.get(t)
+
+
+class V3dRankOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_rank(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset_head: OutputPathType | None
+    """Main output dataset in AFNI format (.HEAD file)"""
+    output_dataset_brik: OutputPathType | None
+    """Main output dataset in AFNI format (.BRIK file)"""
+    rank_map_file: OutputPathType | None
+    """Rank map 1D file showing the mapping from the rank to the integral values
+    in the input dataset"""
+
+
+def v_3d_rank_params(
+    input_datasets: list[InputPathType],
+    output_prefix: str | None = None,
+    version_info: bool = False,
+    help_info: bool = False,
+) -> V3dRankParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_datasets: Input datasets. Acceptable data types are: byte, short,\
+            and floats.
+        output_prefix: Output prefix. If you have multiple datasets on input,\
+            the prefix is preceded by r00., r01., etc. If no prefix is given, the\
+            default is rank.DATASET1, rank.DATASET2, etc.
+        version_info: Print author and version info.
+        help_info: Print this help screen.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dRank",
+        "input_datasets": input_datasets,
+        "version_info": version_info,
+        "help_info": help_info,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    return params
+
+
+def v_3d_rank_cargs(
+    params: V3dRankParameters,
+    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("3dRank")
+    cargs.extend([execution.input_file(f) for f in params.get("input_datasets")])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("version_info"):
+        cargs.append("-ver")
+    if params.get("help_info"):
+        cargs.append("-help")
+    return cargs
+
+
+def v_3d_rank_outputs(
+    params: V3dRankParameters,
+    execution: Execution,
+) -> V3dRankOutputs:
+    """
+    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 = V3dRankOutputs(
+        root=execution.output_file("."),
+        output_dataset_head=execution.output_file(params.get("output_prefix") + "*.HEAD") if (params.get("output_prefix") is not None) else None,
+        output_dataset_brik=execution.output_file(params.get("output_prefix") + "*.BRIK") if (params.get("output_prefix") is not None) else None,
+        rank_map_file=execution.output_file(params.get("output_prefix") + "*.1D") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_rank_execute(
+    params: V3dRankParameters,
+    execution: Execution,
+) -> V3dRankOutputs:
+    """
+    Replaces voxel values by their rank in the set of values collected over all
+    voxels in all input datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dRankOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_rank_cargs(params, execution)
+    ret = v_3d_rank_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_rank(
+    input_datasets: list[InputPathType],
+    output_prefix: str | None = None,
+    version_info: bool = False,
+    help_info: bool = False,
+    runner: Runner | None = None,
+) -> V3dRankOutputs:
+    """
+    Replaces voxel values by their rank in the set of values collected over all
+    voxels in all input datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_datasets: Input datasets. Acceptable data types are: byte, short,\
+            and floats.
+        output_prefix: Output prefix. If you have multiple datasets on input,\
+            the prefix is preceded by r00., r01., etc. If no prefix is given, the\
+            default is rank.DATASET1, rank.DATASET2, etc.
+        version_info: Print author and version info.
+        help_info: Print this help screen.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dRankOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RANK_METADATA)
+    params = v_3d_rank_params(
+        input_datasets=input_datasets,
+        output_prefix=output_prefix,
+        version_info=version_info,
+        help_info=help_info,
+    )
+    return v_3d_rank_execute(params, execution)
+
+
+__all__ = [
+    "V3dRankOutputs",
+    "V3dRankParameters",
+    "V_3D_RANK_METADATA",
+    "v_3d_rank",
+    "v_3d_rank_params",
+]

niwrap_afni/afni/v_3d_rankizer.py

@@ -0,0 +1,241 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_RANKIZER_METADATA = Metadata(
+    id="e854a99a853a99ed471d7da08fb007bec90426d2.boutiques",
+    name="3dRankizer",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dRankizerParameters = typing.TypedDict('V3dRankizerParameters', {
+    "__STYX_TYPE__": typing.Literal["3dRankizer"],
+    "dataset": InputPathType,
+    "base_rank": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "percentize": bool,
+    "percentize_mask": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dRankizer": v_3d_rankizer_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 {
+        "3dRankizer": v_3d_rankizer_outputs,
+    }.get(t)
+
+
+class V3dRankizerOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_rankizer(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType
+    """Output float-format dataset containing ranked voxel values"""
+
+
+def v_3d_rankizer_params(
+    dataset: InputPathType,
+    prefix: str,
+    base_rank: float | None = None,
+    mask: InputPathType | None = None,
+    percentize: bool = False,
+    percentize_mask: bool = False,
+) -> V3dRankizerParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input MRI dataset.
+        prefix: Write results into float-format output dataset.
+        base_rank: Set the 'base' rank instead of 1.
+        mask: Use the specified dataset as a mask. Only voxels with nonzero\
+            values in this mask will be used from the input dataset. Voxels outside\
+            the mask will get rank 0.
+        percentize: Divide rank by the number of voxels in the dataset and\
+            multiply by 100.0.
+        percentize_mask: Divide rank by the number of voxels in the mask and\
+            multiply by 100.0.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dRankizer",
+        "dataset": dataset,
+        "prefix": prefix,
+        "percentize": percentize,
+        "percentize_mask": percentize_mask,
+    }
+    if base_rank is not None:
+        params["base_rank"] = base_rank
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3d_rankizer_cargs(
+    params: V3dRankizerParameters,
+    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("3dRankizer")
+    cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("base_rank") is not None:
+        cargs.extend([
+            "-brank",
+            str(params.get("base_rank"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("percentize"):
+        cargs.append("-percentize")
+    if params.get("percentize_mask"):
+        cargs.append("-percentize_mask")
+    return cargs
+
+
+def v_3d_rankizer_outputs(
+    params: V3dRankizerParameters,
+    execution: Execution,
+) -> V3dRankizerOutputs:
+    """
+    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 = V3dRankizerOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + "+tlrc.HEAD"),
+    )
+    return ret
+
+
+def v_3d_rankizer_execute(
+    params: V3dRankizerParameters,
+    execution: Execution,
+) -> V3dRankizerOutputs:
+    """
+    Tool to rank each voxel as sorted into increasing value. Ties get the average
+    rank.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dRankizerOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_rankizer_cargs(params, execution)
+    ret = v_3d_rankizer_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_rankizer(
+    dataset: InputPathType,
+    prefix: str,
+    base_rank: float | None = None,
+    mask: InputPathType | None = None,
+    percentize: bool = False,
+    percentize_mask: bool = False,
+    runner: Runner | None = None,
+) -> V3dRankizerOutputs:
+    """
+    Tool to rank each voxel as sorted into increasing value. Ties get the average
+    rank.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input MRI dataset.
+        prefix: Write results into float-format output dataset.
+        base_rank: Set the 'base' rank instead of 1.
+        mask: Use the specified dataset as a mask. Only voxels with nonzero\
+            values in this mask will be used from the input dataset. Voxels outside\
+            the mask will get rank 0.
+        percentize: Divide rank by the number of voxels in the dataset and\
+            multiply by 100.0.
+        percentize_mask: Divide rank by the number of voxels in the mask and\
+            multiply by 100.0.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dRankizerOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RANKIZER_METADATA)
+    params = v_3d_rankizer_params(
+        dataset=dataset,
+        base_rank=base_rank,
+        mask=mask,
+        prefix=prefix,
+        percentize=percentize,
+        percentize_mask=percentize_mask,
+    )
+    return v_3d_rankizer_execute(params, execution)
+
+
+__all__ = [
+    "V3dRankizerOutputs",
+    "V3dRankizerParameters",
+    "V_3D_RANKIZER_METADATA",
+    "v_3d_rankizer",
+    "v_3d_rankizer_params",
+]