niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_nwarp_funcs.py

@@ -0,0 +1,232 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_NWARP_FUNCS_METADATA = Metadata(
+    id="048fa4b745e8fa4f529a924ccc5e550b16a79b2f.boutiques",
+    name="3dNwarpFuncs",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dNwarpFuncsParameters = typing.TypedDict('V3dNwarpFuncsParameters', {
+    "__STYX_TYPE__": typing.Literal["3dNwarpFuncs"],
+    "input_warp": InputPathType,
+    "output_prefix": str,
+    "bulk_flag": bool,
+    "shear_flag": bool,
+    "vorticity_flag": bool,
+    "all_flag": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dNwarpFuncs": v_3d_nwarp_funcs_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 {
+        "3dNwarpFuncs": v_3d_nwarp_funcs_outputs,
+    }.get(t)
+
+
+class V3dNwarpFuncsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_nwarp_funcs(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """The output dataset with the computed functions."""
+
+
+def v_3d_nwarp_funcs_params(
+    input_warp: InputPathType,
+    output_prefix: str,
+    bulk_flag: bool = False,
+    shear_flag: bool = False,
+    vorticity_flag: bool = False,
+    all_flag: bool = False,
+) -> V3dNwarpFuncsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_warp: 'www' is the name of the 3D warp dataset (mandatory\
+            option).
+        output_prefix: 'ppp' is the name of the new output dataset.
+        bulk_flag: Compute the (fractional) bulk volume change (Jacobian\
+            determinant minus 1).
+        shear_flag: Compute the shear energy.
+        vorticity_flag: Compute the vorticity energy.
+        all_flag: Compute all 3 functions: bulk, shear, and vorticity.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dNwarpFuncs",
+        "input_warp": input_warp,
+        "output_prefix": output_prefix,
+        "bulk_flag": bulk_flag,
+        "shear_flag": shear_flag,
+        "vorticity_flag": vorticity_flag,
+        "all_flag": all_flag,
+    }
+    return params
+
+
+def v_3d_nwarp_funcs_cargs(
+    params: V3dNwarpFuncsParameters,
+    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("3dNwarpFuncs")
+    cargs.extend([
+        "-nwarp",
+        execution.input_file(params.get("input_warp"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("output_prefix")
+    ])
+    if params.get("bulk_flag"):
+        cargs.append("-bulk")
+    if params.get("shear_flag"):
+        cargs.append("-shear")
+    if params.get("vorticity_flag"):
+        cargs.append("-vorticity")
+    if params.get("all_flag"):
+        cargs.append("-all")
+    return cargs
+
+
+def v_3d_nwarp_funcs_outputs(
+    params: V3dNwarpFuncsParameters,
+    execution: Execution,
+) -> V3dNwarpFuncsOutputs:
+    """
+    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 = V3dNwarpFuncsOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_prefix") + "_output.nii.gz"),
+    )
+    return ret
+
+
+def v_3d_nwarp_funcs_execute(
+    params: V3dNwarpFuncsParameters,
+    execution: Execution,
+) -> V3dNwarpFuncsOutputs:
+    """
+    Compute functions of 3D warp displacements, such as bulk volume change, shear
+    energy, and vorticity energy.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dNwarpFuncsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_nwarp_funcs_cargs(params, execution)
+    ret = v_3d_nwarp_funcs_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_nwarp_funcs(
+    input_warp: InputPathType,
+    output_prefix: str,
+    bulk_flag: bool = False,
+    shear_flag: bool = False,
+    vorticity_flag: bool = False,
+    all_flag: bool = False,
+    runner: Runner | None = None,
+) -> V3dNwarpFuncsOutputs:
+    """
+    Compute functions of 3D warp displacements, such as bulk volume change, shear
+    energy, and vorticity energy.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_warp: 'www' is the name of the 3D warp dataset (mandatory\
+            option).
+        output_prefix: 'ppp' is the name of the new output dataset.
+        bulk_flag: Compute the (fractional) bulk volume change (Jacobian\
+            determinant minus 1).
+        shear_flag: Compute the shear energy.
+        vorticity_flag: Compute the vorticity energy.
+        all_flag: Compute all 3 functions: bulk, shear, and vorticity.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dNwarpFuncsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NWARP_FUNCS_METADATA)
+    params = v_3d_nwarp_funcs_params(
+        input_warp=input_warp,
+        output_prefix=output_prefix,
+        bulk_flag=bulk_flag,
+        shear_flag=shear_flag,
+        vorticity_flag=vorticity_flag,
+        all_flag=all_flag,
+    )
+    return v_3d_nwarp_funcs_execute(params, execution)
+
+
+__all__ = [
+    "V3dNwarpFuncsOutputs",
+    "V3dNwarpFuncsParameters",
+    "V_3D_NWARP_FUNCS_METADATA",
+    "v_3d_nwarp_funcs",
+    "v_3d_nwarp_funcs_params",
+]

niwrap_afni/afni/v_3d_nwarp_xyz.py

@@ -0,0 +1,193 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_NWARP_XYZ_METADATA = Metadata(
+    id="5a16d2bee46238f64451cbe6e0fea267dd5ecf53.boutiques",
+    name="3dNwarpXYZ",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dNwarpXyzParameters = typing.TypedDict('V3dNwarpXyzParameters', {
+    "__STYX_TYPE__": typing.Literal["3dNwarpXYZ"],
+    "warp_spec": str,
+    "xyzfile": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dNwarpXYZ": v_3d_nwarp_xyz_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 {
+        "3dNwarpXYZ": v_3d_nwarp_xyz_outputs,
+    }.get(t)
+
+
+class V3dNwarpXyzOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_nwarp_xyz(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Warped XYZ coordinates output file"""
+
+
+def v_3d_nwarp_xyz_params(
+    warp_spec: str,
+    xyzfile: InputPathType,
+) -> V3dNwarpXyzParameters:
+    """
+    Build parameters.
+    
+    Args:
+        warp_spec: Warp specification as in 3dNwarpApply.
+        xyzfile: XYZ coordinate file containing 3 columns.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dNwarpXYZ",
+        "warp_spec": warp_spec,
+        "xyzfile": xyzfile,
+    }
+    return params
+
+
+def v_3d_nwarp_xyz_cargs(
+    params: V3dNwarpXyzParameters,
+    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("3dNwarpXYZ")
+    cargs.append("[OPTIONS]")
+    cargs.append("-nwarp")
+    cargs.extend([
+        "-nwarp",
+        params.get("warp_spec")
+    ])
+    cargs.append(execution.input_file(params.get("xyzfile")))
+    cargs.append(">")
+    cargs.append("[OUTPUT_FILE]")
+    return cargs
+
+
+def v_3d_nwarp_xyz_outputs(
+    params: V3dNwarpXyzParameters,
+    execution: Execution,
+) -> V3dNwarpXyzOutputs:
+    """
+    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 = V3dNwarpXyzOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file("[OUTPUT_FILE]"),
+    )
+    return ret
+
+
+def v_3d_nwarp_xyz_execute(
+    params: V3dNwarpXyzParameters,
+    execution: Execution,
+) -> V3dNwarpXyzOutputs:
+    """
+    Transforms the DICOM xyz coordinates in the input XYZfile.1D based on specified
+    warp.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dNwarpXyzOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_nwarp_xyz_cargs(params, execution)
+    ret = v_3d_nwarp_xyz_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_nwarp_xyz(
+    warp_spec: str,
+    xyzfile: InputPathType,
+    runner: Runner | None = None,
+) -> V3dNwarpXyzOutputs:
+    """
+    Transforms the DICOM xyz coordinates in the input XYZfile.1D based on specified
+    warp.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        warp_spec: Warp specification as in 3dNwarpApply.
+        xyzfile: XYZ coordinate file containing 3 columns.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dNwarpXyzOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NWARP_XYZ_METADATA)
+    params = v_3d_nwarp_xyz_params(
+        warp_spec=warp_spec,
+        xyzfile=xyzfile,
+    )
+    return v_3d_nwarp_xyz_execute(params, execution)
+
+
+__all__ = [
+    "V3dNwarpXyzOutputs",
+    "V3dNwarpXyzParameters",
+    "V_3D_NWARP_XYZ_METADATA",
+    "v_3d_nwarp_xyz",
+    "v_3d_nwarp_xyz_params",
+]

niwrap_afni/afni/v_3d_overlap.py

@@ -0,0 +1,188 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_OVERLAP_METADATA = Metadata(
+    id="a1bc040d8dc7e5b89536a75a10ba6ad55a1ecc95.boutiques",
+    name="3dOverlap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dOverlapParameters = typing.TypedDict('V3dOverlapParameters', {
+    "__STYX_TYPE__": typing.Literal["3dOverlap"],
+    "dataset1": InputPathType,
+    "dataset2": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dOverlap": v_3d_overlap_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 {
+        "3dOverlap": v_3d_overlap_outputs,
+    }.get(t)
+
+
+class V3dOverlapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_overlap(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_brik: OutputPathType
+    """BRIK file with count of overlaps at each voxel (if -save is used)"""
+    output_head: OutputPathType
+    """HEAD file with count of overlaps at each voxel (if -save is used)"""
+
+
+def v_3d_overlap_params(
+    dataset1: InputPathType,
+    dataset2: list[InputPathType],
+) -> V3dOverlapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset1: First input dataset (e.g. dset1+orig).
+        dataset2: Second input dataset (e.g. dset2+orig).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dOverlap",
+        "dataset1": dataset1,
+        "dataset2": dataset2,
+    }
+    return params
+
+
+def v_3d_overlap_cargs(
+    params: V3dOverlapParameters,
+    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("3dOverlap")
+    cargs.append("[OPTIONS]")
+    cargs.append(execution.input_file(params.get("dataset1")))
+    cargs.extend([execution.input_file(f) for f in params.get("dataset2")])
+    return cargs
+
+
+def v_3d_overlap_outputs(
+    params: V3dOverlapParameters,
+    execution: Execution,
+) -> V3dOverlapOutputs:
+    """
+    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 = V3dOverlapOutputs(
+        root=execution.output_file("."),
+        output_brik=execution.output_file("[SAVE_PREFIX]+orig.BRIK"),
+        output_head=execution.output_file("[SAVE_PREFIX]+orig.HEAD"),
+    )
+    return ret
+
+
+def v_3d_overlap_execute(
+    params: V3dOverlapParameters,
+    execution: Execution,
+) -> V3dOverlapOutputs:
+    """
+    Counts the number of voxels that are nonzero 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 `V3dOverlapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_overlap_cargs(params, execution)
+    ret = v_3d_overlap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_overlap(
+    dataset1: InputPathType,
+    dataset2: list[InputPathType],
+    runner: Runner | None = None,
+) -> V3dOverlapOutputs:
+    """
+    Counts the number of voxels that are nonzero in all input datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset1: First input dataset (e.g. dset1+orig).
+        dataset2: Second input dataset (e.g. dset2+orig).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dOverlapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_OVERLAP_METADATA)
+    params = v_3d_overlap_params(
+        dataset1=dataset1,
+        dataset2=dataset2,
+    )
+    return v_3d_overlap_execute(params, execution)
+
+
+__all__ = [
+    "V3dOverlapOutputs",
+    "V3dOverlapParameters",
+    "V_3D_OVERLAP_METADATA",
+    "v_3d_overlap",
+    "v_3d_overlap_params",
+]