niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_slice_ndice.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_SLICE_NDICE_METADATA = Metadata(
+    id="2632d37affeb0b9dca727cb8206f5ac9def40039.boutiques",
+    name="3dSliceNDice",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSliceNdiceParameters = typing.TypedDict('V3dSliceNdiceParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSliceNDice"],
+    "infile_a": InputPathType,
+    "infile_b": InputPathType,
+    "output_prefix": str,
+    "out_domain": typing.NotRequired[typing.Literal["all", "AorB", "AandB", "Amask", "Bmask"] | None],
+    "no_cmd_echo": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dSliceNDice": v_3d_slice_ndice_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 {
+        "3dSliceNDice": v_3d_slice_ndice_outputs,
+    }.get(t)
+
+
+class V3dSliceNdiceOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_slice_ndice(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_rl: OutputPathType
+    """Output file containing Dice coefficients along the right-left axis."""
+    output_ap: OutputPathType
+    """Output file containing Dice coefficients along the anterior-posterior
+    axis."""
+    output_is: OutputPathType
+    """Output file containing Dice coefficients along the inferior-superior
+    axis."""
+
+
+def v_3d_slice_ndice_params(
+    infile_a: InputPathType,
+    infile_b: InputPathType,
+    output_prefix: str,
+    out_domain: typing.Literal["all", "AorB", "AandB", "Amask", "Bmask"] | None = None,
+    no_cmd_echo: bool = False,
+) -> V3dSliceNdiceParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile_a: Input dataset A (e.g. mask_1.nii.gz).
+        infile_b: Input dataset B (e.g. mask_2.nii.gz).
+        output_prefix: Prefix for output files (e.g. result_prefix).
+        out_domain: Specify which slices to include in the Dice coefficient\
+            report. Options are: all (default), AorB, AandB, Amask, Bmask.
+        no_cmd_echo: Turn OFF recording the command line call in the output\
+            *.1D files. Default is to do the recording.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSliceNDice",
+        "infile_a": infile_a,
+        "infile_b": infile_b,
+        "output_prefix": output_prefix,
+        "no_cmd_echo": no_cmd_echo,
+    }
+    if out_domain is not None:
+        params["out_domain"] = out_domain
+    return params
+
+
+def v_3d_slice_ndice_cargs(
+    params: V3dSliceNdiceParameters,
+    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("3dSliceNDice")
+    cargs.extend([
+        "-insetA",
+        execution.input_file(params.get("infile_a"))
+    ])
+    cargs.extend([
+        "-insetB",
+        execution.input_file(params.get("infile_b"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    if params.get("out_domain") is not None:
+        cargs.extend([
+            "-out_domain",
+            params.get("out_domain")
+        ])
+    if params.get("no_cmd_echo"):
+        cargs.append("-no_cmd_echo")
+    return cargs
+
+
+def v_3d_slice_ndice_outputs(
+    params: V3dSliceNdiceParameters,
+    execution: Execution,
+) -> V3dSliceNdiceOutputs:
+    """
+    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 = V3dSliceNdiceOutputs(
+        root=execution.output_file("."),
+        output_rl=execution.output_file(params.get("output_prefix") + "_0_RL.1D"),
+        output_ap=execution.output_file(params.get("output_prefix") + "_1_AP.1D"),
+        output_is=execution.output_file(params.get("output_prefix") + "_2_IS.1D"),
+    )
+    return ret
+
+
+def v_3d_slice_ndice_execute(
+    params: V3dSliceNdiceParameters,
+    execution: Execution,
+) -> V3dSliceNdiceOutputs:
+    """
+    Calculates the Dice coefficient between two volumes on a slice-by-slice basis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSliceNdiceOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_slice_ndice_cargs(params, execution)
+    ret = v_3d_slice_ndice_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_slice_ndice(
+    infile_a: InputPathType,
+    infile_b: InputPathType,
+    output_prefix: str,
+    out_domain: typing.Literal["all", "AorB", "AandB", "Amask", "Bmask"] | None = None,
+    no_cmd_echo: bool = False,
+    runner: Runner | None = None,
+) -> V3dSliceNdiceOutputs:
+    """
+    Calculates the Dice coefficient between two volumes on a slice-by-slice basis.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile_a: Input dataset A (e.g. mask_1.nii.gz).
+        infile_b: Input dataset B (e.g. mask_2.nii.gz).
+        output_prefix: Prefix for output files (e.g. result_prefix).
+        out_domain: Specify which slices to include in the Dice coefficient\
+            report. Options are: all (default), AorB, AandB, Amask, Bmask.
+        no_cmd_echo: Turn OFF recording the command line call in the output\
+            *.1D files. Default is to do the recording.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSliceNdiceOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SLICE_NDICE_METADATA)
+    params = v_3d_slice_ndice_params(
+        infile_a=infile_a,
+        infile_b=infile_b,
+        output_prefix=output_prefix,
+        out_domain=out_domain,
+        no_cmd_echo=no_cmd_echo,
+    )
+    return v_3d_slice_ndice_execute(params, execution)
+
+
+__all__ = [
+    "V3dSliceNdiceOutputs",
+    "V3dSliceNdiceParameters",
+    "V_3D_SLICE_NDICE_METADATA",
+    "v_3d_slice_ndice",
+    "v_3d_slice_ndice_params",
+]

niwrap_afni/afni/v_3d_space_time_corr.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_SPACE_TIME_CORR_METADATA = Metadata(
+    id="8dd159ea37a52b08625a393a1f0450d03271fcfd.boutiques",
+    name="3dSpaceTimeCorr",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dSpaceTimeCorrParameters = typing.TypedDict('V3dSpaceTimeCorrParameters', {
+    "__STYX_TYPE__": typing.Literal["3dSpaceTimeCorr"],
+    "insetA": InputPathType,
+    "insetB": InputPathType,
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "out_Zcorr": bool,
+    "freeze_insetA_ijk": typing.NotRequired[list[float] | None],
+    "freeze_insetA_xyz": typing.NotRequired[list[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 {
+        "3dSpaceTimeCorr": v_3d_space_time_corr_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 {
+        "3dSpaceTimeCorr": v_3d_space_time_corr_outputs,
+    }.get(t)
+
+
+class V3dSpaceTimeCorrOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_space_time_corr(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """Output data set with space-time correlation coefficients."""
+
+
+def v_3d_space_time_corr_params(
+    inset_a: InputPathType,
+    inset_b: InputPathType,
+    prefix: str,
+    mask: InputPathType | None = None,
+    out_zcorr: bool = False,
+    freeze_inset_a_ijk: list[float] | None = None,
+    freeze_inset_a_xyz: list[float] | None = None,
+) -> V3dSpaceTimeCorrParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inset_a: First 4D data set.
+        inset_b: Second 4D data set. Must have the same spatial dimensions and\
+            number of time points as insetA.
+        prefix: Output filename/base.
+        mask: Optional mask for calculations. Recommended for speed and\
+            interpretability.
+        out_zcorr: Switch to output Fisher Z transform of spatial map\
+            correlation instead of Pearson r values.
+        freeze_inset_a_ijk: Freeze the seed voxel location in the insetA data\
+            set using ijk indices while the seed location in insetB moves\
+            throughout the volume or mask. Provide three ijk values.
+        freeze_inset_a_xyz: Freeze the seed voxel location in the insetA data\
+            set using xyz coordinates while the seed location in insetB moves\
+            throughout the volume or mask. Provide three xyz values.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dSpaceTimeCorr",
+        "insetA": inset_a,
+        "insetB": inset_b,
+        "prefix": prefix,
+        "out_Zcorr": out_zcorr,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if freeze_inset_a_ijk is not None:
+        params["freeze_insetA_ijk"] = freeze_inset_a_ijk
+    if freeze_inset_a_xyz is not None:
+        params["freeze_insetA_xyz"] = freeze_inset_a_xyz
+    return params
+
+
+def v_3d_space_time_corr_cargs(
+    params: V3dSpaceTimeCorrParameters,
+    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("3dSpaceTimeCorr")
+    cargs.extend([
+        "-insetA",
+        execution.input_file(params.get("insetA"))
+    ])
+    cargs.extend([
+        "-insetB",
+        execution.input_file(params.get("insetB"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("out_Zcorr"):
+        cargs.append("-out_Zcorr")
+    if params.get("freeze_insetA_ijk") is not None:
+        cargs.extend([
+            "-freeze_insetA_ijk",
+            *map(str, params.get("freeze_insetA_ijk"))
+        ])
+    if params.get("freeze_insetA_xyz") is not None:
+        cargs.extend([
+            "-freeze_insetA_xyz",
+            *map(str, params.get("freeze_insetA_xyz"))
+        ])
+    return cargs
+
+
+def v_3d_space_time_corr_outputs(
+    params: V3dSpaceTimeCorrParameters,
+    execution: Execution,
+) -> V3dSpaceTimeCorrOutputs:
+    """
+    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 = V3dSpaceTimeCorrOutputs(
+        root=execution.output_file("."),
+        output=execution.output_file(params.get("prefix") + ".nii.gz"),
+    )
+    return ret
+
+
+def v_3d_space_time_corr_execute(
+    params: V3dSpaceTimeCorrParameters,
+    execution: Execution,
+) -> V3dSpaceTimeCorrOutputs:
+    """
+    Calculates correlation coefficients between two 4D datasets using space+time
+    patterns.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dSpaceTimeCorrOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_space_time_corr_cargs(params, execution)
+    ret = v_3d_space_time_corr_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_space_time_corr(
+    inset_a: InputPathType,
+    inset_b: InputPathType,
+    prefix: str,
+    mask: InputPathType | None = None,
+    out_zcorr: bool = False,
+    freeze_inset_a_ijk: list[float] | None = None,
+    freeze_inset_a_xyz: list[float] | None = None,
+    runner: Runner | None = None,
+) -> V3dSpaceTimeCorrOutputs:
+    """
+    Calculates correlation coefficients between two 4D datasets using space+time
+    patterns.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        inset_a: First 4D data set.
+        inset_b: Second 4D data set. Must have the same spatial dimensions and\
+            number of time points as insetA.
+        prefix: Output filename/base.
+        mask: Optional mask for calculations. Recommended for speed and\
+            interpretability.
+        out_zcorr: Switch to output Fisher Z transform of spatial map\
+            correlation instead of Pearson r values.
+        freeze_inset_a_ijk: Freeze the seed voxel location in the insetA data\
+            set using ijk indices while the seed location in insetB moves\
+            throughout the volume or mask. Provide three ijk values.
+        freeze_inset_a_xyz: Freeze the seed voxel location in the insetA data\
+            set using xyz coordinates while the seed location in insetB moves\
+            throughout the volume or mask. Provide three xyz values.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dSpaceTimeCorrOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SPACE_TIME_CORR_METADATA)
+    params = v_3d_space_time_corr_params(
+        inset_a=inset_a,
+        inset_b=inset_b,
+        prefix=prefix,
+        mask=mask,
+        out_zcorr=out_zcorr,
+        freeze_inset_a_ijk=freeze_inset_a_ijk,
+        freeze_inset_a_xyz=freeze_inset_a_xyz,
+    )
+    return v_3d_space_time_corr_execute(params, execution)
+
+
+__all__ = [
+    "V3dSpaceTimeCorrOutputs",
+    "V3dSpaceTimeCorrParameters",
+    "V_3D_SPACE_TIME_CORR_METADATA",
+    "v_3d_space_time_corr",
+    "v_3d_space_time_corr_params",
+]