niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__get_afni_version.py

@@ -0,0 +1,177 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__GET_AFNI_VERSION_METADATA = Metadata(
+    id="00b4038dc7dd30e795e94e467e6a777717d8d741.boutiques",
+    name="@get.afni.version",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VGetAfniVersionParameters = typing.TypedDict('VGetAfniVersionParameters', {
+    "__STYX_TYPE__": typing.Literal["@get.afni.version"],
+    "version": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@get.afni.version": v__get_afni_version_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.afni.version": v__get_afni_version_outputs,
+    }.get(t)
+
+
+class VGetAfniVersionOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__get_afni_version(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    src_dir: OutputPathType
+    """Directory containing the downloaded AFNI source code for the specified
+    version."""
+
+
+def v__get_afni_version_params(
+    version: str,
+) -> VGetAfniVersionParameters:
+    """
+    Build parameters.
+    
+    Args:
+        version: AFNI version number to get (e.g., 16.0.01).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@get.afni.version",
+        "version": version,
+    }
+    return params
+
+
+def v__get_afni_version_cargs(
+    params: VGetAfniVersionParameters,
+    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("@get.afni.version")
+    cargs.append(params.get("version"))
+    return cargs
+
+
+def v__get_afni_version_outputs(
+    params: VGetAfniVersionParameters,
+    execution: Execution,
+) -> VGetAfniVersionOutputs:
+    """
+    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 = VGetAfniVersionOutputs(
+        root=execution.output_file("."),
+        src_dir=execution.output_file("AFNI_" + params.get("version") + "/AFNI/src"),
+    )
+    return ret
+
+
+def v__get_afni_version_execute(
+    params: VGetAfniVersionParameters,
+    execution: Execution,
+) -> VGetAfniVersionOutputs:
+    """
+    Downloads the source code for a specified AFNI version.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VGetAfniVersionOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__get_afni_version_cargs(params, execution)
+    ret = v__get_afni_version_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__get_afni_version(
+    version: str,
+    runner: Runner | None = None,
+) -> VGetAfniVersionOutputs:
+    """
+    Downloads the source code for a specified AFNI version.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        version: AFNI version number to get (e.g., 16.0.01).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VGetAfniVersionOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__GET_AFNI_VERSION_METADATA)
+    params = v__get_afni_version_params(
+        version=version,
+    )
+    return v__get_afni_version_execute(params, execution)
+
+
+__all__ = [
+    "VGetAfniVersionOutputs",
+    "VGetAfniVersionParameters",
+    "V__GET_AFNI_VERSION_METADATA",
+    "v__get_afni_version",
+    "v__get_afni_version_params",
+]

niwrap_afni/afni/v__get_afni_view.py

@@ -0,0 +1,178 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__GET_AFNI_VIEW_METADATA = Metadata(
+    id="7a3936ebb978e01b7a83696901a1ad7e6bad42f0.boutiques",
+    name="@GetAfniView",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VGetAfniViewParameters = typing.TypedDict('VGetAfniViewParameters', {
+    "__STYX_TYPE__": typing.Literal["@GetAfniView"],
+    "dataset_name": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@GetAfniView": v__get_afni_view_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 {
+        "@GetAfniView": v__get_afni_view_outputs,
+    }.get(t)
+
+
+class VGetAfniViewOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__get_afni_view(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    afni_view: OutputPathType
+    """The AFNI view extension retrieved from the dataset name"""
+
+
+def v__get_afni_view_params(
+    dataset_name: str,
+) -> VGetAfniViewParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset_name: Name of the dataset (including path) from which to\
+            retrieve the AFNI view (+orig, +acpc, etc.).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@GetAfniView",
+        "dataset_name": dataset_name,
+    }
+    return params
+
+
+def v__get_afni_view_cargs(
+    params: VGetAfniViewParameters,
+    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("@GetAfniView")
+    cargs.append(params.get("dataset_name"))
+    return cargs
+
+
+def v__get_afni_view_outputs(
+    params: VGetAfniViewParameters,
+    execution: Execution,
+) -> VGetAfniViewOutputs:
+    """
+    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 = VGetAfniViewOutputs(
+        root=execution.output_file("."),
+        afni_view=execution.output_file("view_extension.txt"),
+    )
+    return ret
+
+
+def v__get_afni_view_execute(
+    params: VGetAfniViewParameters,
+    execution: Execution,
+) -> VGetAfniViewOutputs:
+    """
+    A tool to retrieve the AFNI view of a given dataset name.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VGetAfniViewOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__get_afni_view_cargs(params, execution)
+    ret = v__get_afni_view_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__get_afni_view(
+    dataset_name: str,
+    runner: Runner | None = None,
+) -> VGetAfniViewOutputs:
+    """
+    A tool to retrieve the AFNI view of a given dataset name.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset_name: Name of the dataset (including path) from which to\
+            retrieve the AFNI view (+orig, +acpc, etc.).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VGetAfniViewOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__GET_AFNI_VIEW_METADATA)
+    params = v__get_afni_view_params(
+        dataset_name=dataset_name,
+    )
+    return v__get_afni_view_execute(params, execution)
+
+
+__all__ = [
+    "VGetAfniViewOutputs",
+    "VGetAfniViewParameters",
+    "V__GET_AFNI_VIEW_METADATA",
+    "v__get_afni_view",
+    "v__get_afni_view_params",
+]

niwrap_afni/afni/v__grad_flip_test.py

@@ -0,0 +1,359 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__GRAD_FLIP_TEST_METADATA = Metadata(
+    id="83d02b240a4d1a85f3fc3038b96542312f180177.boutiques",
+    name="@GradFlipTest",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VGradFlipTestParameters = typing.TypedDict('VGradFlipTestParameters', {
+    "__STYX_TYPE__": typing.Literal["@GradFlipTest"],
+    "dwi": InputPathType,
+    "grad_col_matT": typing.NotRequired[InputPathType | None],
+    "grad_col_matT_1": typing.NotRequired[InputPathType | None],
+    "grad_col_matT_2": typing.NotRequired[InputPathType | None],
+    "grad_col_matT_3": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "bvals": typing.NotRequired[InputPathType | None],
+    "thresh_fa": typing.NotRequired[float | None],
+    "thresh_len": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "check_abs_min": typing.NotRequired[float | None],
+    "scale_out_1000": bool,
+    "wdir": typing.NotRequired[str | None],
+    "do_clean": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@GradFlipTest": v__grad_flip_test_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 {
+        "@GradFlipTest": v__grad_flip_test_outputs,
+    }.get(t)
+
+
+class VGradFlipTestOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__grad_flip_test(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Text file that stores recommended flip option"""
+    temp_directory: OutputPathType
+    """Temporary working directory to store intermediate files"""
+
+
+def v__grad_flip_test_params(
+    dwi: InputPathType,
+    grad_col_mat_t: InputPathType | None = None,
+    grad_col_mat_t_1: InputPathType | None = None,
+    grad_col_mat_t_2: InputPathType | None = None,
+    grad_col_mat_t_3: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    bvals: InputPathType | None = None,
+    thresh_fa: float | None = None,
+    thresh_len: float | None = None,
+    prefix: str | None = None,
+    check_abs_min: float | None = None,
+    scale_out_1000: bool = False,
+    wdir: str | None = None,
+    do_clean: bool = False,
+) -> VGradFlipTestParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dwi: Set of DWIs (N total volumes).
+        grad_col_mat_t: Set of column-wise g- or b-matrix elements\
+            ("TORTOISE"-style format, "row-first").
+        grad_col_mat_t_1: Set of column-wise g- or b-matrix elements\
+            ("TORTOISE"-style format, "row-first").
+        grad_col_mat_t_2: Set of column-wise g- or b-matrix elements\
+            ("TORTOISE"-style format, "row-first").
+        grad_col_mat_t_3: Set of column-wise g- or b-matrix elements\
+            ("TORTOISE"-style format, "row-first").
+        mask: Optional mask (probably whole brain); otherwise, automasking is\
+            performed.
+        bvals: Can input bvals, if necessary (but shouldn't be necessary?).
+        thresh_fa: Set minimum FA value for tracking (default X=0.2).
+        thresh_len: Set minimum tract length to keep a tract when propagating\
+            (default L=30mm).
+        prefix: Output name of text file that stores recommended flip option.
+        check_abs_min: Handle tiny negative values in gradient vectors.
+        scale_out_1000: Scale output to 1000, as in 3dDWItoDT (probably not\
+            necessary).
+        wdir: Rename working directory output; useful if running multiple\
+            iterations.
+        do_clean: Remove temporary directory.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@GradFlipTest",
+        "dwi": dwi,
+        "scale_out_1000": scale_out_1000,
+        "do_clean": do_clean,
+    }
+    if grad_col_mat_t is not None:
+        params["grad_col_matT"] = grad_col_mat_t
+    if grad_col_mat_t_1 is not None:
+        params["grad_col_matT_1"] = grad_col_mat_t_1
+    if grad_col_mat_t_2 is not None:
+        params["grad_col_matT_2"] = grad_col_mat_t_2
+    if grad_col_mat_t_3 is not None:
+        params["grad_col_matT_3"] = grad_col_mat_t_3
+    if mask is not None:
+        params["mask"] = mask
+    if bvals is not None:
+        params["bvals"] = bvals
+    if thresh_fa is not None:
+        params["thresh_fa"] = thresh_fa
+    if thresh_len is not None:
+        params["thresh_len"] = thresh_len
+    if prefix is not None:
+        params["prefix"] = prefix
+    if check_abs_min is not None:
+        params["check_abs_min"] = check_abs_min
+    if wdir is not None:
+        params["wdir"] = wdir
+    return params
+
+
+def v__grad_flip_test_cargs(
+    params: VGradFlipTestParameters,
+    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("@GradFlipTest")
+    cargs.extend([
+        "-in_dwi",
+        execution.input_file(params.get("dwi"))
+    ])
+    if params.get("grad_col_matT") is not None:
+        cargs.extend([
+            "-in_col_matT",
+            execution.input_file(params.get("grad_col_matT"))
+        ])
+    if params.get("grad_col_matT_1") is not None:
+        cargs.extend([
+            "-in_col_matT",
+            execution.input_file(params.get("grad_col_matT_1"))
+        ])
+    if params.get("grad_col_matT_2") is not None:
+        cargs.extend([
+            "-in_col_matT",
+            execution.input_file(params.get("grad_col_matT_2"))
+        ])
+    if params.get("grad_col_matT_3") is not None:
+        cargs.extend([
+            "-in_col_matT",
+            execution.input_file(params.get("grad_col_matT_3"))
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("bvals") is not None:
+        cargs.extend([
+            "-in_bvals",
+            execution.input_file(params.get("bvals"))
+        ])
+    if params.get("thresh_fa") is not None:
+        cargs.extend([
+            "-alg_Thresh_FA",
+            str(params.get("thresh_fa"))
+        ])
+    if params.get("thresh_len") is not None:
+        cargs.extend([
+            "-alg_Thresh_Len",
+            str(params.get("thresh_len"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("check_abs_min") is not None:
+        cargs.extend([
+            "-check_abs_min",
+            str(params.get("check_abs_min"))
+        ])
+    if params.get("scale_out_1000"):
+        cargs.append("-scale_out_1000")
+    if params.get("wdir") is not None:
+        cargs.extend([
+            "-wdir",
+            params.get("wdir")
+        ])
+    if params.get("do_clean"):
+        cargs.append("-do_clean")
+    return cargs
+
+
+def v__grad_flip_test_outputs(
+    params: VGradFlipTestParameters,
+    execution: Execution,
+) -> VGradFlipTestOutputs:
+    """
+    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 = VGradFlipTestOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".txt") if (params.get("prefix") is not None) else None,
+        temp_directory=execution.output_file("_tmp_TESTFLIP"),
+    )
+    return ret
+
+
+def v__grad_flip_test_execute(
+    params: VGradFlipTestParameters,
+    execution: Execution,
+) -> VGradFlipTestOutputs:
+    """
+    Script to test the correct flip for a data set when using 1dDW_Grad_o_Mat++.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VGradFlipTestOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__grad_flip_test_cargs(params, execution)
+    ret = v__grad_flip_test_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__grad_flip_test(
+    dwi: InputPathType,
+    grad_col_mat_t: InputPathType | None = None,
+    grad_col_mat_t_1: InputPathType | None = None,
+    grad_col_mat_t_2: InputPathType | None = None,
+    grad_col_mat_t_3: InputPathType | None = None,
+    mask: InputPathType | None = None,
+    bvals: InputPathType | None = None,
+    thresh_fa: float | None = None,
+    thresh_len: float | None = None,
+    prefix: str | None = None,
+    check_abs_min: float | None = None,
+    scale_out_1000: bool = False,
+    wdir: str | None = None,
+    do_clean: bool = False,
+    runner: Runner | None = None,
+) -> VGradFlipTestOutputs:
+    """
+    Script to test the correct flip for a data set when using 1dDW_Grad_o_Mat++.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dwi: Set of DWIs (N total volumes).
+        grad_col_mat_t: Set of column-wise g- or b-matrix elements\
+            ("TORTOISE"-style format, "row-first").
+        grad_col_mat_t_1: Set of column-wise g- or b-matrix elements\
+            ("TORTOISE"-style format, "row-first").
+        grad_col_mat_t_2: Set of column-wise g- or b-matrix elements\
+            ("TORTOISE"-style format, "row-first").
+        grad_col_mat_t_3: Set of column-wise g- or b-matrix elements\
+            ("TORTOISE"-style format, "row-first").
+        mask: Optional mask (probably whole brain); otherwise, automasking is\
+            performed.
+        bvals: Can input bvals, if necessary (but shouldn't be necessary?).
+        thresh_fa: Set minimum FA value for tracking (default X=0.2).
+        thresh_len: Set minimum tract length to keep a tract when propagating\
+            (default L=30mm).
+        prefix: Output name of text file that stores recommended flip option.
+        check_abs_min: Handle tiny negative values in gradient vectors.
+        scale_out_1000: Scale output to 1000, as in 3dDWItoDT (probably not\
+            necessary).
+        wdir: Rename working directory output; useful if running multiple\
+            iterations.
+        do_clean: Remove temporary directory.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VGradFlipTestOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__GRAD_FLIP_TEST_METADATA)
+    params = v__grad_flip_test_params(
+        dwi=dwi,
+        grad_col_mat_t=grad_col_mat_t,
+        grad_col_mat_t_1=grad_col_mat_t_1,
+        grad_col_mat_t_2=grad_col_mat_t_2,
+        grad_col_mat_t_3=grad_col_mat_t_3,
+        mask=mask,
+        bvals=bvals,
+        thresh_fa=thresh_fa,
+        thresh_len=thresh_len,
+        prefix=prefix,
+        check_abs_min=check_abs_min,
+        scale_out_1000=scale_out_1000,
+        wdir=wdir,
+        do_clean=do_clean,
+    )
+    return v__grad_flip_test_execute(params, execution)
+
+
+__all__ = [
+    "VGradFlipTestOutputs",
+    "VGradFlipTestParameters",
+    "V__GRAD_FLIP_TEST_METADATA",
+    "v__grad_flip_test",
+    "v__grad_flip_test_params",
+]