niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__extract_meica_ortvec.py

@@ -0,0 +1,248 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__EXTRACT_MEICA_ORTVEC_METADATA = Metadata(
+    id="32a644ffdca9e88d2f5a1524f50f811fcef33a2e.boutiques",
+    name="@extract_meica_ortvec",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VExtractMeicaOrtvecParameters = typing.TypedDict('VExtractMeicaOrtvecParameters', {
+    "__STYX_TYPE__": typing.Literal["@extract_meica_ortvec"],
+    "prefix": str,
+    "meica_dir": typing.NotRequired[str | None],
+    "reject_ignored": typing.NotRequired[int | None],
+    "reject_midk": typing.NotRequired[int | None],
+    "work_dir": typing.NotRequired[str | None],
+    "verbosity": 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 {
+        "@extract_meica_ortvec": v__extract_meica_ortvec_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 {
+        "@extract_meica_ortvec": v__extract_meica_ortvec_outputs,
+    }.get(t)
+
+
+class VExtractMeicaOrtvecOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__extract_meica_ortvec(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Output 1D ortvec file"""
+
+
+def v__extract_meica_ortvec_params(
+    prefix: str,
+    meica_dir: str | None = None,
+    reject_ignored: int | None = None,
+    reject_midk: int | None = None,
+    work_dir: str | None = None,
+    verbosity: str | None = None,
+) -> VExtractMeicaOrtvecParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Name for output 1D ortvec file.
+        meica_dir: Directory for MEICA files.
+        reject_ignored: Do we reject ignored components (0=keep, 1=reject),\
+            default is 0.
+        reject_midk: Do we reject midk components (0=keep, 1=reject), default\
+            is 1.
+        work_dir: Sub-directory for work.
+        verbosity: Set verbosity level.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@extract_meica_ortvec",
+        "prefix": prefix,
+    }
+    if meica_dir is not None:
+        params["meica_dir"] = meica_dir
+    if reject_ignored is not None:
+        params["reject_ignored"] = reject_ignored
+    if reject_midk is not None:
+        params["reject_midk"] = reject_midk
+    if work_dir is not None:
+        params["work_dir"] = work_dir
+    if verbosity is not None:
+        params["verbosity"] = verbosity
+    return params
+
+
+def v__extract_meica_ortvec_cargs(
+    params: VExtractMeicaOrtvecParameters,
+    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("@extract_meica_ortvec")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("meica_dir") is not None:
+        cargs.extend([
+            "-meica_dir",
+            params.get("meica_dir")
+        ])
+    if params.get("reject_ignored") is not None:
+        cargs.extend([
+            "-reject_ignored",
+            str(params.get("reject_ignored"))
+        ])
+    if params.get("reject_midk") is not None:
+        cargs.extend([
+            "-reject_midk",
+            str(params.get("reject_midk"))
+        ])
+    if params.get("work_dir") is not None:
+        cargs.extend([
+            "-work_dir",
+            params.get("work_dir")
+        ])
+    if params.get("verbosity") is not None:
+        cargs.extend([
+            "-verb",
+            params.get("verbosity")
+        ])
+    return cargs
+
+
+def v__extract_meica_ortvec_outputs(
+    params: VExtractMeicaOrtvecParameters,
+    execution: Execution,
+) -> VExtractMeicaOrtvecOutputs:
+    """
+    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 = VExtractMeicaOrtvecOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("prefix") + ".1D"),
+    )
+    return ret
+
+
+def v__extract_meica_ortvec_execute(
+    params: VExtractMeicaOrtvecParameters,
+    execution: Execution,
+) -> VExtractMeicaOrtvecOutputs:
+    """
+    Project good MEICA components out of bad ones.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VExtractMeicaOrtvecOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__extract_meica_ortvec_cargs(params, execution)
+    ret = v__extract_meica_ortvec_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__extract_meica_ortvec(
+    prefix: str,
+    meica_dir: str | None = None,
+    reject_ignored: int | None = None,
+    reject_midk: int | None = None,
+    work_dir: str | None = None,
+    verbosity: str | None = None,
+    runner: Runner | None = None,
+) -> VExtractMeicaOrtvecOutputs:
+    """
+    Project good MEICA components out of bad ones.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Name for output 1D ortvec file.
+        meica_dir: Directory for MEICA files.
+        reject_ignored: Do we reject ignored components (0=keep, 1=reject),\
+            default is 0.
+        reject_midk: Do we reject midk components (0=keep, 1=reject), default\
+            is 1.
+        work_dir: Sub-directory for work.
+        verbosity: Set verbosity level.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VExtractMeicaOrtvecOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__EXTRACT_MEICA_ORTVEC_METADATA)
+    params = v__extract_meica_ortvec_params(
+        prefix=prefix,
+        meica_dir=meica_dir,
+        reject_ignored=reject_ignored,
+        reject_midk=reject_midk,
+        work_dir=work_dir,
+        verbosity=verbosity,
+    )
+    return v__extract_meica_ortvec_execute(params, execution)
+
+
+__all__ = [
+    "VExtractMeicaOrtvecOutputs",
+    "VExtractMeicaOrtvecParameters",
+    "V__EXTRACT_MEICA_ORTVEC_METADATA",
+    "v__extract_meica_ortvec",
+    "v__extract_meica_ortvec_params",
+]

niwrap_afni/afni/v__fast_roi.py

@@ -0,0 +1,290 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__FAST_ROI_METADATA = Metadata(
+    id="3e8aa0aa33715b8e34aca3647b6dda45cf739777.boutiques",
+    name="@fast_roi",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VFastRoiParameters = typing.TypedDict('VFastRoiParameters', {
+    "__STYX_TYPE__": typing.Literal["@fast_roi"],
+    "region": list[str],
+    "drawn_roi": typing.NotRequired[InputPathType | None],
+    "anat": InputPathType,
+    "anat_ns": typing.NotRequired[InputPathType | None],
+    "base": InputPathType,
+    "roi_grid": InputPathType,
+    "prefix": str,
+    "time": bool,
+    "twopass": bool,
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@fast_roi": v__fast_roi_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 {
+        "@fast_roi": v__fast_roi_outputs,
+    }.get(t)
+
+
+class VFastRoiOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__fast_roi(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    roi_output: OutputPathType
+    """ROI output volume with the specified prefix."""
+
+
+def v__fast_roi_params(
+    region: list[str],
+    anat: InputPathType,
+    base: InputPathType,
+    roi_grid: InputPathType,
+    prefix: str,
+    drawn_roi: InputPathType | None = None,
+    anat_ns: InputPathType | None = None,
+    time_: bool = False,
+    twopass: bool = False,
+    help_: bool = False,
+) -> VFastRoiParameters:
+    """
+    Build parameters.
+    
+    Args:
+        region: Symbolic atlas-based region name. Use repeated instances to\
+            specify a mask of numerous regions. Each region is assigned a power of\
+            2 integer in the output mask.
+        anat: ANAT is the volume to be put in standard space. If ANAT is\
+            already in TLRC space, there is no need for -base option.
+        base: Name of the reference TLRC volume.
+        roi_grid: The volume that defines the final ROI's grid.
+        prefix: Prefix used to tag the names the ROIs output.
+        drawn_roi: A user drawn ROI in standard (tlrc) space. This ROI gets\
+            added with the REGION ROI.
+        anat_ns: Same as -anat, but indicates that the skull has been removed\
+            already.
+        time_: Output elapsed time reports.
+        twopass: Make TLRC transformation more robust. Use it if TLRC transform\
+            step fails.
+        help_: Output help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@fast_roi",
+        "region": region,
+        "anat": anat,
+        "base": base,
+        "roi_grid": roi_grid,
+        "prefix": prefix,
+        "time": time_,
+        "twopass": twopass,
+        "help": help_,
+    }
+    if drawn_roi is not None:
+        params["drawn_roi"] = drawn_roi
+    if anat_ns is not None:
+        params["anat_ns"] = anat_ns
+    return params
+
+
+def v__fast_roi_cargs(
+    params: VFastRoiParameters,
+    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("@fast_roi")
+    cargs.extend([
+        "-region",
+        *params.get("region")
+    ])
+    if params.get("drawn_roi") is not None:
+        cargs.extend([
+            "-drawn_roi",
+            execution.input_file(params.get("drawn_roi"))
+        ])
+    cargs.extend([
+        "-anat",
+        execution.input_file(params.get("anat"))
+    ])
+    if params.get("anat_ns") is not None:
+        cargs.extend([
+            "-anat_ns",
+            execution.input_file(params.get("anat_ns"))
+        ])
+    cargs.extend([
+        "-base",
+        execution.input_file(params.get("base"))
+    ])
+    cargs.extend([
+        "-roi_grid",
+        execution.input_file(params.get("roi_grid"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("time"):
+        cargs.append("--time")
+    if params.get("twopass"):
+        cargs.append("--twopass")
+    if params.get("help"):
+        cargs.append("--help")
+    return cargs
+
+
+def v__fast_roi_outputs(
+    params: VFastRoiParameters,
+    execution: Execution,
+) -> VFastRoiOutputs:
+    """
+    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 = VFastRoiOutputs(
+        root=execution.output_file("."),
+        roi_output=execution.output_file("ROI." + params.get("prefix") + "+orig"),
+    )
+    return ret
+
+
+def v__fast_roi_execute(
+    params: VFastRoiParameters,
+    execution: Execution,
+) -> VFastRoiOutputs:
+    """
+    Creates Atlas-based ROI masked in ANAT's original space. The script executes
+    rapidly for realtime fMRI applications.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VFastRoiOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__fast_roi_cargs(params, execution)
+    ret = v__fast_roi_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__fast_roi(
+    region: list[str],
+    anat: InputPathType,
+    base: InputPathType,
+    roi_grid: InputPathType,
+    prefix: str,
+    drawn_roi: InputPathType | None = None,
+    anat_ns: InputPathType | None = None,
+    time_: bool = False,
+    twopass: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> VFastRoiOutputs:
+    """
+    Creates Atlas-based ROI masked in ANAT's original space. The script executes
+    rapidly for realtime fMRI applications.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        region: Symbolic atlas-based region name. Use repeated instances to\
+            specify a mask of numerous regions. Each region is assigned a power of\
+            2 integer in the output mask.
+        anat: ANAT is the volume to be put in standard space. If ANAT is\
+            already in TLRC space, there is no need for -base option.
+        base: Name of the reference TLRC volume.
+        roi_grid: The volume that defines the final ROI's grid.
+        prefix: Prefix used to tag the names the ROIs output.
+        drawn_roi: A user drawn ROI in standard (tlrc) space. This ROI gets\
+            added with the REGION ROI.
+        anat_ns: Same as -anat, but indicates that the skull has been removed\
+            already.
+        time_: Output elapsed time reports.
+        twopass: Make TLRC transformation more robust. Use it if TLRC transform\
+            step fails.
+        help_: Output help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VFastRoiOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FAST_ROI_METADATA)
+    params = v__fast_roi_params(
+        region=region,
+        drawn_roi=drawn_roi,
+        anat=anat,
+        anat_ns=anat_ns,
+        base=base,
+        roi_grid=roi_grid,
+        prefix=prefix,
+        time_=time_,
+        twopass=twopass,
+        help_=help_,
+    )
+    return v__fast_roi_execute(params, execution)
+
+
+__all__ = [
+    "VFastRoiOutputs",
+    "VFastRoiParameters",
+    "V__FAST_ROI_METADATA",
+    "v__fast_roi",
+    "v__fast_roi_params",
+]