niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__simulate_motion.py

@@ -0,0 +1,350 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SIMULATE_MOTION_METADATA = Metadata(
+    id="5fc17ce508dbb62923e813f5cff61e70e1accb2d.boutiques",
+    name="@simulate_motion",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSimulateMotionParameters = typing.TypedDict('VSimulateMotionParameters', {
+    "__STYX_TYPE__": typing.Literal["@simulate_motion"],
+    "epi": InputPathType,
+    "motion_file": InputPathType,
+    "epi_timing": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "save_workdir": bool,
+    "test": bool,
+    "verb_level": typing.NotRequired[float | None],
+    "vr_base": typing.NotRequired[float | None],
+    "warp_method": typing.NotRequired[str | None],
+    "warp_1D": typing.NotRequired[InputPathType | None],
+    "warp_master": typing.NotRequired[InputPathType | None],
+    "wsinc5": bool,
+    "help": bool,
+    "hist": bool,
+    "todo": bool,
+    "ver": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@simulate_motion": v__simulate_motion_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 {
+        "@simulate_motion": v__simulate_motion_outputs,
+    }.get(t)
+
+
+class VSimulateMotionOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__simulate_motion(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    simulated_motion_output: OutputPathType | None
+    """Motion simulated EPI time series"""
+
+
+def v__simulate_motion_params(
+    epi: InputPathType,
+    motion_file: InputPathType,
+    epi_timing: InputPathType | None = None,
+    prefix: str | None = None,
+    save_workdir: bool = False,
+    test: bool = False,
+    verb_level: float | None = None,
+    vr_base: float | None = None,
+    warp_method: str | None = None,
+    warp_1_d: InputPathType | None = None,
+    warp_master: InputPathType | None = None,
+    wsinc5: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    todo: bool = False,
+    ver: bool = False,
+) -> VSimulateMotionParameters:
+    """
+    Build parameters.
+    
+    Args:
+        epi: Input EPI volume or time series (only a volreg base is needed,\
+            though more is okay).
+        motion_file: Motion parameter file (as output by 3dvolreg).
+        epi_timing: Provide EPI dataset with slice timing.
+        prefix: Prefix for data results (default = motion_sim.NUM_TRS).
+        save_workdir: Do not remove the 'work' directory.
+        test: Only test running the program, do not create a simulated motion\
+            dataset.
+        verb_level: Specify a verbose level (default = 1).
+        vr_base: 0-based index of volreg base in EPI dataset.
+        warp_method: Specify a method for forward alignment/transform.
+        warp_1_d: Specify a 12 parameter affine transformation.
+        warp_master: Specify a grid master dataset for the -warp_1D transform.
+        wsinc5: Use wsinc5 interpolation in 3dAllineate.
+        help_: Show help message.
+        hist: Show program modification history.
+        todo: Show current todo list.
+        ver: Show program version.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@simulate_motion",
+        "epi": epi,
+        "motion_file": motion_file,
+        "save_workdir": save_workdir,
+        "test": test,
+        "wsinc5": wsinc5,
+        "help": help_,
+        "hist": hist,
+        "todo": todo,
+        "ver": ver,
+    }
+    if epi_timing is not None:
+        params["epi_timing"] = epi_timing
+    if prefix is not None:
+        params["prefix"] = prefix
+    if verb_level is not None:
+        params["verb_level"] = verb_level
+    if vr_base is not None:
+        params["vr_base"] = vr_base
+    if warp_method is not None:
+        params["warp_method"] = warp_method
+    if warp_1_d is not None:
+        params["warp_1D"] = warp_1_d
+    if warp_master is not None:
+        params["warp_master"] = warp_master
+    return params
+
+
+def v__simulate_motion_cargs(
+    params: VSimulateMotionParameters,
+    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("@simulate_motion")
+    cargs.extend([
+        "-epi",
+        execution.input_file(params.get("epi"))
+    ])
+    cargs.extend([
+        "-motion_file",
+        execution.input_file(params.get("motion_file"))
+    ])
+    if params.get("epi_timing") is not None:
+        cargs.extend([
+            "-epi_timing",
+            execution.input_file(params.get("epi_timing"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("save_workdir"):
+        cargs.append("-save_workdir")
+    if params.get("test"):
+        cargs.append("-test")
+    if params.get("verb_level") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verb_level"))
+        ])
+    if params.get("vr_base") is not None:
+        cargs.extend([
+            "-vr_base",
+            str(params.get("vr_base"))
+        ])
+    if params.get("warp_method") is not None:
+        cargs.extend([
+            "-warp_method",
+            params.get("warp_method")
+        ])
+    if params.get("warp_1D") is not None:
+        cargs.extend([
+            "-warp_1D",
+            execution.input_file(params.get("warp_1D"))
+        ])
+    if params.get("warp_master") is not None:
+        cargs.extend([
+            "-warp_master",
+            execution.input_file(params.get("warp_master"))
+        ])
+    if params.get("wsinc5"):
+        cargs.append("-wsinc5")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hist"):
+        cargs.append("-hist")
+    if params.get("todo"):
+        cargs.append("-todo")
+    if params.get("ver"):
+        cargs.append("-ver")
+    return cargs
+
+
+def v__simulate_motion_outputs(
+    params: VSimulateMotionParameters,
+    execution: Execution,
+) -> VSimulateMotionOutputs:
+    """
+    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 = VSimulateMotionOutputs(
+        root=execution.output_file("."),
+        simulated_motion_output=execution.output_file(params.get("prefix") + "_simulated_motion.nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__simulate_motion_execute(
+    params: VSimulateMotionParameters,
+    execution: Execution,
+) -> VSimulateMotionOutputs:
+    """
+    Create simulated motion time series in an EPI dataset based on the provided
+    motion parameters and an input volume.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSimulateMotionOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__simulate_motion_cargs(params, execution)
+    ret = v__simulate_motion_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__simulate_motion(
+    epi: InputPathType,
+    motion_file: InputPathType,
+    epi_timing: InputPathType | None = None,
+    prefix: str | None = None,
+    save_workdir: bool = False,
+    test: bool = False,
+    verb_level: float | None = None,
+    vr_base: float | None = None,
+    warp_method: str | None = None,
+    warp_1_d: InputPathType | None = None,
+    warp_master: InputPathType | None = None,
+    wsinc5: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    todo: bool = False,
+    ver: bool = False,
+    runner: Runner | None = None,
+) -> VSimulateMotionOutputs:
+    """
+    Create simulated motion time series in an EPI dataset based on the provided
+    motion parameters and an input volume.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        epi: Input EPI volume or time series (only a volreg base is needed,\
+            though more is okay).
+        motion_file: Motion parameter file (as output by 3dvolreg).
+        epi_timing: Provide EPI dataset with slice timing.
+        prefix: Prefix for data results (default = motion_sim.NUM_TRS).
+        save_workdir: Do not remove the 'work' directory.
+        test: Only test running the program, do not create a simulated motion\
+            dataset.
+        verb_level: Specify a verbose level (default = 1).
+        vr_base: 0-based index of volreg base in EPI dataset.
+        warp_method: Specify a method for forward alignment/transform.
+        warp_1_d: Specify a 12 parameter affine transformation.
+        warp_master: Specify a grid master dataset for the -warp_1D transform.
+        wsinc5: Use wsinc5 interpolation in 3dAllineate.
+        help_: Show help message.
+        hist: Show program modification history.
+        todo: Show current todo list.
+        ver: Show program version.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSimulateMotionOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SIMULATE_MOTION_METADATA)
+    params = v__simulate_motion_params(
+        epi=epi,
+        motion_file=motion_file,
+        epi_timing=epi_timing,
+        prefix=prefix,
+        save_workdir=save_workdir,
+        test=test,
+        verb_level=verb_level,
+        vr_base=vr_base,
+        warp_method=warp_method,
+        warp_1_d=warp_1_d,
+        warp_master=warp_master,
+        wsinc5=wsinc5,
+        help_=help_,
+        hist=hist,
+        todo=todo,
+        ver=ver,
+    )
+    return v__simulate_motion_execute(params, execution)
+
+
+__all__ = [
+    "VSimulateMotionOutputs",
+    "VSimulateMotionParameters",
+    "V__SIMULATE_MOTION_METADATA",
+    "v__simulate_motion",
+    "v__simulate_motion_params",
+]

niwrap_afni/afni/v__skull_strip_touch_up.py

@@ -0,0 +1,224 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__SKULL_STRIP_TOUCH_UP_METADATA = Metadata(
+    id="b6fb601a41c80b9729bd9c95da0d4f3540060f61.boutiques",
+    name="@SkullStrip_TouchUp",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VSkullStripTouchUpParameters = typing.TypedDict('VSkullStripTouchUpParameters', {
+    "__STYX_TYPE__": typing.Literal["@SkullStrip_TouchUp"],
+    "prefix": str,
+    "brain_dataset": InputPathType,
+    "head_dataset": InputPathType,
+    "mask_out": bool,
+    "orig_dim": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@SkullStrip_TouchUp": v__skull_strip_touch_up_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 {
+        "@SkullStrip_TouchUp": v__skull_strip_touch_up_outputs,
+    }.get(t)
+
+
+class VSkullStripTouchUpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__skull_strip_touch_up(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_folder: OutputPathType
+    """Output folder containing the touch-up results"""
+    output_mask: OutputPathType
+    """Output binary mask (if -mask_out flag is used)"""
+
+
+def v__skull_strip_touch_up_params(
+    prefix: str,
+    brain_dataset: InputPathType,
+    head_dataset: InputPathType,
+    mask_out: bool = False,
+    orig_dim: bool = False,
+) -> VSkullStripTouchUpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Output file and folder name.
+        brain_dataset: Skull stripped data set to touch up.
+        head_dataset: Whole head anatomical data set.
+        mask_out: Output a binary mask in addition to actual data.
+        orig_dim: Edit in the original image dimensions.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@SkullStrip_TouchUp",
+        "prefix": prefix,
+        "brain_dataset": brain_dataset,
+        "head_dataset": head_dataset,
+        "mask_out": mask_out,
+        "orig_dim": orig_dim,
+    }
+    return params
+
+
+def v__skull_strip_touch_up_cargs(
+    params: VSkullStripTouchUpParameters,
+    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("@SkullStrip_TouchUp")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-brain",
+        execution.input_file(params.get("brain_dataset"))
+    ])
+    cargs.extend([
+        "-head",
+        execution.input_file(params.get("head_dataset"))
+    ])
+    if params.get("mask_out"):
+        cargs.append("-mask_out")
+    if params.get("orig_dim"):
+        cargs.append("-orig_dim")
+    return cargs
+
+
+def v__skull_strip_touch_up_outputs(
+    params: VSkullStripTouchUpParameters,
+    execution: Execution,
+) -> VSkullStripTouchUpOutputs:
+    """
+    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 = VSkullStripTouchUpOutputs(
+        root=execution.output_file("."),
+        output_folder=execution.output_file(params.get("prefix") + "_SS_touch_up"),
+        output_mask=execution.output_file(params.get("prefix") + "_mask.nii.gz"),
+    )
+    return ret
+
+
+def v__skull_strip_touch_up_execute(
+    params: VSkullStripTouchUpParameters,
+    execution: Execution,
+) -> VSkullStripTouchUpOutputs:
+    """
+    Helper program to touch up failed skull stripping by resampling data, allowing
+    manual edits, and outputting corrected data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VSkullStripTouchUpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__skull_strip_touch_up_cargs(params, execution)
+    ret = v__skull_strip_touch_up_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__skull_strip_touch_up(
+    prefix: str,
+    brain_dataset: InputPathType,
+    head_dataset: InputPathType,
+    mask_out: bool = False,
+    orig_dim: bool = False,
+    runner: Runner | None = None,
+) -> VSkullStripTouchUpOutputs:
+    """
+    Helper program to touch up failed skull stripping by resampling data, allowing
+    manual edits, and outputting corrected data.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Output file and folder name.
+        brain_dataset: Skull stripped data set to touch up.
+        head_dataset: Whole head anatomical data set.
+        mask_out: Output a binary mask in addition to actual data.
+        orig_dim: Edit in the original image dimensions.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VSkullStripTouchUpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SKULL_STRIP_TOUCH_UP_METADATA)
+    params = v__skull_strip_touch_up_params(
+        prefix=prefix,
+        brain_dataset=brain_dataset,
+        head_dataset=head_dataset,
+        mask_out=mask_out,
+        orig_dim=orig_dim,
+    )
+    return v__skull_strip_touch_up_execute(params, execution)
+
+
+__all__ = [
+    "VSkullStripTouchUpOutputs",
+    "VSkullStripTouchUpParameters",
+    "V__SKULL_STRIP_TOUCH_UP_METADATA",
+    "v__skull_strip_touch_up",
+    "v__skull_strip_touch_up_params",
+]