niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_normality_test.py

@@ -0,0 +1,209 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_NORMALITY_TEST_METADATA = Metadata(
+    id="25ece735fc7f7a81d4c52176a3e16fdc401aa190.boutiques",
+    name="3dNormalityTest",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dNormalityTestParameters = typing.TypedDict('V3dNormalityTestParameters', {
+    "__STYX_TYPE__": typing.Literal["3dNormalityTest"],
+    "input": InputPathType,
+    "prefix": str,
+    "noexp": bool,
+    "pval": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dNormalityTest": v_3d_normality_test_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 {
+        "3dNormalityTest": v_3d_normality_test_outputs,
+    }.get(t)
+
+
+class V3dNormalityTestOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_normality_test(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType
+    """Output dataset with results"""
+
+
+def v_3d_normality_test_params(
+    input_: InputPathType,
+    prefix: str,
+    noexp: bool = False,
+    pval: bool = False,
+) -> V3dNormalityTestParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Specifies the input dataset.
+        prefix: Specifies the name for the output dataset.
+        noexp: Do not convert the A-D statistic to an exponentially distributed\
+            value.
+        pval: Output the results as a pure (estimated) p-value.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dNormalityTest",
+        "input": input_,
+        "prefix": prefix,
+        "noexp": noexp,
+        "pval": pval,
+    }
+    return params
+
+
+def v_3d_normality_test_cargs(
+    params: V3dNormalityTestParameters,
+    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("3dNormalityTest")
+    cargs.append(execution.input_file(params.get("input")))
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("noexp"):
+        cargs.append("-noexp")
+    if params.get("pval"):
+        cargs.append("-pval")
+    return cargs
+
+
+def v_3d_normality_test_outputs(
+    params: V3dNormalityTestParameters,
+    execution: Execution,
+) -> V3dNormalityTestOutputs:
+    """
+    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 = V3dNormalityTestOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + "+orig.*"),
+    )
+    return ret
+
+
+def v_3d_normality_test_execute(
+    params: V3dNormalityTestParameters,
+    execution: Execution,
+) -> V3dNormalityTestOutputs:
+    """
+    This program tests the input values at each voxel for normality using the
+    Anderson-Darling method.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dNormalityTestOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_normality_test_cargs(params, execution)
+    ret = v_3d_normality_test_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_normality_test(
+    input_: InputPathType,
+    prefix: str,
+    noexp: bool = False,
+    pval: bool = False,
+    runner: Runner | None = None,
+) -> V3dNormalityTestOutputs:
+    """
+    This program tests the input values at each voxel for normality using the
+    Anderson-Darling method.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Specifies the input dataset.
+        prefix: Specifies the name for the output dataset.
+        noexp: Do not convert the A-D statistic to an exponentially distributed\
+            value.
+        pval: Output the results as a pure (estimated) p-value.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dNormalityTestOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NORMALITY_TEST_METADATA)
+    params = v_3d_normality_test_params(
+        input_=input_,
+        prefix=prefix,
+        noexp=noexp,
+        pval=pval,
+    )
+    return v_3d_normality_test_execute(params, execution)
+
+
+__all__ = [
+    "V3dNormalityTestOutputs",
+    "V3dNormalityTestParameters",
+    "V_3D_NORMALITY_TEST_METADATA",
+    "v_3d_normality_test",
+    "v_3d_normality_test_params",
+]

niwrap_afni/afni/v_3d_notes.py

@@ -0,0 +1,246 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_NOTES_METADATA = Metadata(
+    id="940bc1c01a30bd95a8de66900c6eff7191dde7e1.boutiques",
+    name="3dNotes",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dNotesParameters = typing.TypedDict('V3dNotesParameters', {
+    "__STYX_TYPE__": typing.Literal["3dNotes"],
+    "add_note": typing.NotRequired[str | None],
+    "append_history": typing.NotRequired[str | None],
+    "replace_history": typing.NotRequired[str | None],
+    "delete_note": typing.NotRequired[float | None],
+    "print_notes": bool,
+    "help": bool,
+    "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 {
+        "3dNotes": v_3d_notes_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 V3dNotesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_notes(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_notes_params(
+    dataset: InputPathType,
+    add_note: str | None = None,
+    append_history: str | None = None,
+    replace_history: str | None = None,
+    delete_note: float | None = None,
+    print_notes: bool = False,
+    help_: bool = False,
+) -> V3dNotesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: AFNI compatible dataset [required].
+        add_note: Add the string 'str' to the list of notes.
+        append_history: Append the string 'str' to the dataset's history. This\
+            can only appear once on the command line.
+        replace_history: Replace any existing history note with 'str'. This\
+            option cannot be used with '-h'.
+        delete_note: Deletes note number num.
+        print_notes: Print to stdout the expanded notes.
+        help_: Displays this help screen.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dNotes",
+        "print_notes": print_notes,
+        "help": help_,
+        "dataset": dataset,
+    }
+    if add_note is not None:
+        params["add_note"] = add_note
+    if append_history is not None:
+        params["append_history"] = append_history
+    if replace_history is not None:
+        params["replace_history"] = replace_history
+    if delete_note is not None:
+        params["delete_note"] = delete_note
+    return params
+
+
+def v_3d_notes_cargs(
+    params: V3dNotesParameters,
+    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("3dNotes")
+    if params.get("add_note") is not None:
+        cargs.extend([
+            "-a",
+            params.get("add_note")
+        ])
+    if params.get("append_history") is not None:
+        cargs.extend([
+            "-h",
+            params.get("append_history")
+        ])
+    if params.get("replace_history") is not None:
+        cargs.extend([
+            "-HH",
+            params.get("replace_history")
+        ])
+    if params.get("delete_note") is not None:
+        cargs.extend([
+            "-d",
+            str(params.get("delete_note"))
+        ])
+    if params.get("print_notes"):
+        cargs.append("-ses")
+    if params.get("help"):
+        cargs.append("-help")
+    cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def v_3d_notes_outputs(
+    params: V3dNotesParameters,
+    execution: Execution,
+) -> V3dNotesOutputs:
+    """
+    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 = V3dNotesOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_notes_execute(
+    params: V3dNotesParameters,
+    execution: Execution,
+) -> V3dNotesOutputs:
+    """
+    A program to add, delete and show notes for AFNI datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dNotesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_notes_cargs(params, execution)
+    ret = v_3d_notes_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_notes(
+    dataset: InputPathType,
+    add_note: str | None = None,
+    append_history: str | None = None,
+    replace_history: str | None = None,
+    delete_note: float | None = None,
+    print_notes: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> V3dNotesOutputs:
+    """
+    A program to add, delete and show notes for AFNI datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: AFNI compatible dataset [required].
+        add_note: Add the string 'str' to the list of notes.
+        append_history: Append the string 'str' to the dataset's history. This\
+            can only appear once on the command line.
+        replace_history: Replace any existing history note with 'str'. This\
+            option cannot be used with '-h'.
+        delete_note: Deletes note number num.
+        print_notes: Print to stdout the expanded notes.
+        help_: Displays this help screen.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dNotesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NOTES_METADATA)
+    params = v_3d_notes_params(
+        add_note=add_note,
+        append_history=append_history,
+        replace_history=replace_history,
+        delete_note=delete_note,
+        print_notes=print_notes,
+        help_=help_,
+        dataset=dataset,
+    )
+    return v_3d_notes_execute(params, execution)
+
+
+__all__ = [
+    "V3dNotesOutputs",
+    "V3dNotesParameters",
+    "V_3D_NOTES_METADATA",
+    "v_3d_notes",
+    "v_3d_notes_params",
+]

niwrap_afni/afni/v_3d_nwarp_adjust.py

@@ -0,0 +1,218 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_NWARP_ADJUST_METADATA = Metadata(
+    id="0c3ecbaf201c4034c9ca75f6bc8b7c5f5190cfaf.boutiques",
+    name="3dNwarpAdjust",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dNwarpAdjustParameters = typing.TypedDict('V3dNwarpAdjustParameters', {
+    "__STYX_TYPE__": typing.Literal["3dNwarpAdjust"],
+    "input_warps": list[InputPathType],
+    "source_datasets": typing.NotRequired[list[InputPathType] | None],
+    "output_prefix": 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 {
+        "3dNwarpAdjust": v_3d_nwarp_adjust_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 {
+        "3dNwarpAdjust": v_3d_nwarp_adjust_outputs,
+    }.get(t)
+
+
+class V3dNwarpAdjustOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_nwarp_adjust(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_brik: OutputPathType | None
+    """Output mean dataset BRIK file"""
+    output_head: OutputPathType | None
+    """Output mean dataset HEAD file"""
+
+
+def v_3d_nwarp_adjust_params(
+    input_warps: list[InputPathType],
+    source_datasets: list[InputPathType] | None = None,
+    output_prefix: str | None = None,
+) -> V3dNwarpAdjustParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_warps: List of input 3D warp datasets (at least 5).
+        source_datasets: List of input 3D datasets to be warped by the adjusted\
+            warp datasets. There must be exactly as many of these datasets as there\
+            are input warps.
+        output_prefix: Prefix for the output mean dataset (only needed if the\
+            '-source' option is also given).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dNwarpAdjust",
+        "input_warps": input_warps,
+    }
+    if source_datasets is not None:
+        params["source_datasets"] = source_datasets
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    return params
+
+
+def v_3d_nwarp_adjust_cargs(
+    params: V3dNwarpAdjustParameters,
+    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("3dNwarpAdjust")
+    cargs.extend([
+        "-nwarp",
+        *[execution.input_file(f) for f in params.get("input_warps")]
+    ])
+    if params.get("source_datasets") is not None:
+        cargs.extend([
+            "-source",
+            *[execution.input_file(f) for f in params.get("source_datasets")]
+        ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    return cargs
+
+
+def v_3d_nwarp_adjust_outputs(
+    params: V3dNwarpAdjustParameters,
+    execution: Execution,
+) -> V3dNwarpAdjustOutputs:
+    """
+    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 = V3dNwarpAdjustOutputs(
+        root=execution.output_file("."),
+        output_brik=execution.output_file(params.get("output_prefix") + "+tlrc.BRIK") if (params.get("output_prefix") is not None) else None,
+        output_head=execution.output_file(params.get("output_prefix") + "+tlrc.HEAD") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_nwarp_adjust_execute(
+    params: V3dNwarpAdjustParameters,
+    execution: Execution,
+) -> V3dNwarpAdjustOutputs:
+    """
+    Program to adjust 3D warp datasets by composing them with the inverse of their
+    average, optionally warping input datasets and generating an output mean
+    dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dNwarpAdjustOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_nwarp_adjust_cargs(params, execution)
+    ret = v_3d_nwarp_adjust_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_nwarp_adjust(
+    input_warps: list[InputPathType],
+    source_datasets: list[InputPathType] | None = None,
+    output_prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dNwarpAdjustOutputs:
+    """
+    Program to adjust 3D warp datasets by composing them with the inverse of their
+    average, optionally warping input datasets and generating an output mean
+    dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_warps: List of input 3D warp datasets (at least 5).
+        source_datasets: List of input 3D datasets to be warped by the adjusted\
+            warp datasets. There must be exactly as many of these datasets as there\
+            are input warps.
+        output_prefix: Prefix for the output mean dataset (only needed if the\
+            '-source' option is also given).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dNwarpAdjustOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NWARP_ADJUST_METADATA)
+    params = v_3d_nwarp_adjust_params(
+        input_warps=input_warps,
+        source_datasets=source_datasets,
+        output_prefix=output_prefix,
+    )
+    return v_3d_nwarp_adjust_execute(params, execution)
+
+
+__all__ = [
+    "V3dNwarpAdjustOutputs",
+    "V3dNwarpAdjustParameters",
+    "V_3D_NWARP_ADJUST_METADATA",
+    "v_3d_nwarp_adjust",
+    "v_3d_nwarp_adjust_params",
+]