niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__t1scale.py

@@ -0,0 +1,328 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__T1SCALE_METADATA = Metadata(
+    id="da9880f00af155a9d926ce79b579ac25dd00b38c.boutiques",
+    name="@T1scale",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VT1scaleParameters = typing.TypedDict('VT1scaleParameters', {
+    "__STYX_TYPE__": typing.Literal["@T1scale"],
+    "t1_volume": InputPathType,
+    "pd_volume": typing.NotRequired[InputPathType | None],
+    "output_directory": typing.NotRequired[str | None],
+    "align": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "head_mask": bool,
+    "unmasked_uni": bool,
+    "masked_uni": bool,
+    "echo": bool,
+    "help": bool,
+    "h_web": bool,
+    "h_view": bool,
+    "all_opts": bool,
+    "h_find_word": 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 {
+        "@T1scale": v__t1scale_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 {
+        "@T1scale": v__t1scale_outputs,
+    }.get(t)
+
+
+class VT1scaleOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__t1scale(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    uniformized_t1_output: OutputPathType
+    """Uniformized T1 volume output file"""
+    masked_uniformized_t1_output: OutputPathType
+    """Masked Uniformized T1 volume output file"""
+    aligned_pd_output: OutputPathType
+    """Aligned PD volume output file in alignment with T1+orig"""
+
+
+def v__t1scale_params(
+    t1_volume: InputPathType,
+    pd_volume: InputPathType | None = None,
+    output_directory: str | None = None,
+    align: bool = False,
+    mask: InputPathType | None = None,
+    head_mask: bool = False,
+    unmasked_uni: bool = False,
+    masked_uni: bool = False,
+    echo: bool = False,
+    help_: bool = False,
+    h_web: bool = False,
+    h_view: bool = False,
+    all_opts: bool = False,
+    h_find_word: str | None = None,
+) -> VT1scaleParameters:
+    """
+    Build parameters.
+    
+    Args:
+        t1_volume: The T1 volume.
+        pd_volume: The PD volume (aligned to T1).
+        output_directory: Directory where output gets dumped. Default is\
+            T1scale/.
+        align: Align PD volume to T1. Without this option, PDvol is assumed in\
+            alignment with T1vol.
+        mask: Create mask for the output. If not specified, the script will\
+            generate one with 3dAutomask on fattened PDvol.
+        head_mask: Create mask using 3dSkullStrip's -head option.
+        unmasked_uni: Do not apply masking to uniformized volume (default).
+        masked_uni: Apply masking to uniformized volume.
+        echo: Set echo.
+        help_: Display this help message and exit.
+        h_web: Open webpage with help for this program.
+        h_view: Open -help output in a GUI editor.
+        all_opts: List all of the options for this script.
+        h_find_word: Search for lines containing WORD in -help output. Search\
+            is approximate.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@T1scale",
+        "t1_volume": t1_volume,
+        "align": align,
+        "head_mask": head_mask,
+        "unmasked_uni": unmasked_uni,
+        "masked_uni": masked_uni,
+        "echo": echo,
+        "help": help_,
+        "h_web": h_web,
+        "h_view": h_view,
+        "all_opts": all_opts,
+    }
+    if pd_volume is not None:
+        params["pd_volume"] = pd_volume
+    if output_directory is not None:
+        params["output_directory"] = output_directory
+    if mask is not None:
+        params["mask"] = mask
+    if h_find_word is not None:
+        params["h_find_word"] = h_find_word
+    return params
+
+
+def v__t1scale_cargs(
+    params: VT1scaleParameters,
+    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("@T1scale")
+    cargs.extend([
+        "-T1",
+        execution.input_file(params.get("t1_volume"))
+    ])
+    if params.get("pd_volume") is not None:
+        cargs.extend([
+            "-PD",
+            execution.input_file(params.get("pd_volume"))
+        ])
+    if params.get("output_directory") is not None:
+        cargs.extend([
+            "-odir",
+            params.get("output_directory")
+        ])
+    if params.get("align"):
+        cargs.append("-align")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("head_mask"):
+        cargs.append("-head_mask")
+    if params.get("unmasked_uni"):
+        cargs.append("-unmasked_uni")
+    if params.get("masked_uni"):
+        cargs.append("-masked_uni")
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("h_web"):
+        cargs.append("-h_web")
+    if params.get("h_view"):
+        cargs.append("-hview")
+    if params.get("all_opts"):
+        cargs.append("-all_opts")
+    if params.get("h_find_word") is not None:
+        cargs.extend([
+            "-h_find",
+            params.get("h_find_word")
+        ])
+    return cargs
+
+
+def v__t1scale_outputs(
+    params: VT1scaleParameters,
+    execution: Execution,
+) -> VT1scaleOutputs:
+    """
+    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 = VT1scaleOutputs(
+        root=execution.output_file("."),
+        uniformized_t1_output=execution.output_file("T1.uni+orig"),
+        masked_uniformized_t1_output=execution.output_file("T1_uni_masked+orig"),
+        aligned_pd_output=execution.output_file("PD+orig"),
+    )
+    return ret
+
+
+def v__t1scale_execute(
+    params: VT1scaleParameters,
+    execution: Execution,
+) -> VT1scaleOutputs:
+    """
+    Fix bias field shading in T1 by scaling it with PD image. You can also get a
+    decent result even without the PD volume.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VT1scaleOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__t1scale_cargs(params, execution)
+    ret = v__t1scale_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__t1scale(
+    t1_volume: InputPathType,
+    pd_volume: InputPathType | None = None,
+    output_directory: str | None = None,
+    align: bool = False,
+    mask: InputPathType | None = None,
+    head_mask: bool = False,
+    unmasked_uni: bool = False,
+    masked_uni: bool = False,
+    echo: bool = False,
+    help_: bool = False,
+    h_web: bool = False,
+    h_view: bool = False,
+    all_opts: bool = False,
+    h_find_word: str | None = None,
+    runner: Runner | None = None,
+) -> VT1scaleOutputs:
+    """
+    Fix bias field shading in T1 by scaling it with PD image. You can also get a
+    decent result even without the PD volume.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        t1_volume: The T1 volume.
+        pd_volume: The PD volume (aligned to T1).
+        output_directory: Directory where output gets dumped. Default is\
+            T1scale/.
+        align: Align PD volume to T1. Without this option, PDvol is assumed in\
+            alignment with T1vol.
+        mask: Create mask for the output. If not specified, the script will\
+            generate one with 3dAutomask on fattened PDvol.
+        head_mask: Create mask using 3dSkullStrip's -head option.
+        unmasked_uni: Do not apply masking to uniformized volume (default).
+        masked_uni: Apply masking to uniformized volume.
+        echo: Set echo.
+        help_: Display this help message and exit.
+        h_web: Open webpage with help for this program.
+        h_view: Open -help output in a GUI editor.
+        all_opts: List all of the options for this script.
+        h_find_word: Search for lines containing WORD in -help output. Search\
+            is approximate.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VT1scaleOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__T1SCALE_METADATA)
+    params = v__t1scale_params(
+        t1_volume=t1_volume,
+        pd_volume=pd_volume,
+        output_directory=output_directory,
+        align=align,
+        mask=mask,
+        head_mask=head_mask,
+        unmasked_uni=unmasked_uni,
+        masked_uni=masked_uni,
+        echo=echo,
+        help_=help_,
+        h_web=h_web,
+        h_view=h_view,
+        all_opts=all_opts,
+        h_find_word=h_find_word,
+    )
+    return v__t1scale_execute(params, execution)
+
+
+__all__ = [
+    "VT1scaleOutputs",
+    "VT1scaleParameters",
+    "V__T1SCALE_METADATA",
+    "v__t1scale",
+    "v__t1scale_params",
+]

niwrap_afni/afni/v__thickness_master.py

@@ -0,0 +1,213 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__THICKNESS_MASTER_METADATA = Metadata(
+    id="7cbe201588fb28fa02cdf63392c9f32c09dd8fea.boutiques",
+    name="@thickness_master",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VThicknessMasterParameters = typing.TypedDict('VThicknessMasterParameters', {
+    "__STYX_TYPE__": typing.Literal["@thickness_master"],
+    "maskset": InputPathType,
+    "surfset": InputPathType,
+    "outdir": 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 {
+        "@thickness_master": v__thickness_master_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 {
+        "@thickness_master": v__thickness_master_outputs,
+    }.get(t)
+
+
+class VThicknessMasterOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__thickness_master(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_bb_dir: OutputPathType | None
+    """Output directory for ball and box method"""
+    output_erode_dir: OutputPathType | None
+    """Output directory for erosion method"""
+    output_in2out_dir: OutputPathType | None
+    """Output directory for in2out method"""
+
+
+def v__thickness_master_params(
+    maskset: InputPathType,
+    surfset: InputPathType,
+    outdir: str | None = None,
+) -> VThicknessMasterParameters:
+    """
+    Build parameters.
+    
+    Args:
+        maskset: Mask dataset to find thickness.
+        surfset: Surface dataset to use for normals into the volume.
+        outdir: Output directory base name. The output will be placed in a\
+            directory with thick_base in its name (e.g., mmmm_bb, mmmm_erode,\
+            mmmm_in2out).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@thickness_master",
+        "maskset": maskset,
+        "surfset": surfset,
+    }
+    if outdir is not None:
+        params["outdir"] = outdir
+    return params
+
+
+def v__thickness_master_cargs(
+    params: VThicknessMasterParameters,
+    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("@thickness_master")
+    cargs.extend([
+        "-maskset",
+        execution.input_file(params.get("maskset"))
+    ])
+    cargs.extend([
+        "-surfset",
+        execution.input_file(params.get("surfset"))
+    ])
+    if params.get("outdir") is not None:
+        cargs.extend([
+            "-outdir",
+            params.get("outdir")
+        ])
+    return cargs
+
+
+def v__thickness_master_outputs(
+    params: VThicknessMasterParameters,
+    execution: Execution,
+) -> VThicknessMasterOutputs:
+    """
+    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 = VThicknessMasterOutputs(
+        root=execution.output_file("."),
+        output_bb_dir=execution.output_file(params.get("outdir") + "_bb/") if (params.get("outdir") is not None) else None,
+        output_erode_dir=execution.output_file(params.get("outdir") + "_erode/") if (params.get("outdir") is not None) else None,
+        output_in2out_dir=execution.output_file(params.get("outdir") + "_in2out/") if (params.get("outdir") is not None) else None,
+    )
+    return ret
+
+
+def v__thickness_master_execute(
+    params: VThicknessMasterParameters,
+    execution: Execution,
+) -> VThicknessMasterOutputs:
+    """
+    Compute cortical thickness using mask and surface datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VThicknessMasterOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__thickness_master_cargs(params, execution)
+    ret = v__thickness_master_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__thickness_master(
+    maskset: InputPathType,
+    surfset: InputPathType,
+    outdir: str | None = None,
+    runner: Runner | None = None,
+) -> VThicknessMasterOutputs:
+    """
+    Compute cortical thickness using mask and surface datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        maskset: Mask dataset to find thickness.
+        surfset: Surface dataset to use for normals into the volume.
+        outdir: Output directory base name. The output will be placed in a\
+            directory with thick_base in its name (e.g., mmmm_bb, mmmm_erode,\
+            mmmm_in2out).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VThicknessMasterOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__THICKNESS_MASTER_METADATA)
+    params = v__thickness_master_params(
+        maskset=maskset,
+        surfset=surfset,
+        outdir=outdir,
+    )
+    return v__thickness_master_execute(params, execution)
+
+
+__all__ = [
+    "VThicknessMasterOutputs",
+    "VThicknessMasterParameters",
+    "V__THICKNESS_MASTER_METADATA",
+    "v__thickness_master",
+    "v__thickness_master_params",
+]

niwrap_afni/afni/v__time_diff.py

@@ -0,0 +1,180 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__TIME_DIFF_METADATA = Metadata(
+    id="7889ba0aeecc01a9a55b923b84e149e7cec9417e.boutiques",
+    name="@TimeDiff",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VTimeDiffParameters = typing.TypedDict('VTimeDiffParameters', {
+    "__STYX_TYPE__": typing.Literal["@TimeDiff"],
+    "file1": InputPathType,
+    "file2": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@TimeDiff": v__time_diff_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 VTimeDiffOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__time_diff(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__time_diff_params(
+    file1: InputPathType,
+    file2: InputPathType,
+) -> VTimeDiffParameters:
+    """
+    Build parameters.
+    
+    Args:
+        file1: First file to compare (e.g., file1.txt).
+        file2: Second file to compare (e.g., file2.txt).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@TimeDiff",
+        "file1": file1,
+        "file2": file2,
+    }
+    return params
+
+
+def v__time_diff_cargs(
+    params: VTimeDiffParameters,
+    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("@TimeDiff")
+    cargs.append(execution.input_file(params.get("file1")))
+    cargs.append(execution.input_file(params.get("file2")))
+    return cargs
+
+
+def v__time_diff_outputs(
+    params: VTimeDiffParameters,
+    execution: Execution,
+) -> VTimeDiffOutputs:
+    """
+    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 = VTimeDiffOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__time_diff_execute(
+    params: VTimeDiffParameters,
+    execution: Execution,
+) -> VTimeDiffOutputs:
+    """
+    A tool to compare the modification times of two files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VTimeDiffOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__time_diff_cargs(params, execution)
+    ret = v__time_diff_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__time_diff(
+    file1: InputPathType,
+    file2: InputPathType,
+    runner: Runner | None = None,
+) -> VTimeDiffOutputs:
+    """
+    A tool to compare the modification times of two files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        file1: First file to compare (e.g., file1.txt).
+        file2: Second file to compare (e.g., file2.txt).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VTimeDiffOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__TIME_DIFF_METADATA)
+    params = v__time_diff_params(
+        file1=file1,
+        file2=file2,
+    )
+    return v__time_diff_execute(params, execution)
+
+
+__all__ = [
+    "VTimeDiffOutputs",
+    "VTimeDiffParameters",
+    "V__TIME_DIFF_METADATA",
+    "v__time_diff",
+    "v__time_diff_params",
+]