niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__to_mni_awarp.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__TO_MNI_AWARP_METADATA = Metadata(
+    id="93b77f09cd479bf6a950c0693a066eccc0f62501.boutiques",
+    name="@toMNI_Awarp",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VToMniAwarpParameters = typing.TypedDict('VToMniAwarpParameters', {
+    "__STYX_TYPE__": typing.Literal["@toMNI_Awarp"],
+    "directory": str,
+    "datasets": 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 {
+        "@toMNI_Awarp": v__to_mni_awarp_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 {
+        "@toMNI_Awarp": v__to_mni_awarp_outputs,
+    }.get(t)
+
+
+class VToMniAwarpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__to_mni_awarp(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_datasets: OutputPathType
+    """The transformed datasets in 1x1x1 mm MNI space."""
+
+
+def v__to_mni_awarp_params(
+    directory: str,
+    datasets: list[InputPathType],
+) -> VToMniAwarpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        directory: Name of the directory to be created where results will be\
+            stored.
+        datasets: List of datasets to be transformed.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@toMNI_Awarp",
+        "directory": directory,
+        "datasets": datasets,
+    }
+    return params
+
+
+def v__to_mni_awarp_cargs(
+    params: VToMniAwarpParameters,
+    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("@toMNI_Awarp")
+    cargs.append(params.get("directory"))
+    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
+    return cargs
+
+
+def v__to_mni_awarp_outputs(
+    params: VToMniAwarpParameters,
+    execution: Execution,
+) -> VToMniAwarpOutputs:
+    """
+    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 = VToMniAwarpOutputs(
+        root=execution.output_file("."),
+        output_datasets=execution.output_file(params.get("directory") + "/*"),
+    )
+    return ret
+
+
+def v__to_mni_awarp_execute(
+    params: VToMniAwarpParameters,
+    execution: Execution,
+) -> VToMniAwarpOutputs:
+    """
+    Transforms skull-stripped datasets to 1x1x1 mm MNI space using an affine
+    transformation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VToMniAwarpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__to_mni_awarp_cargs(params, execution)
+    ret = v__to_mni_awarp_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__to_mni_awarp(
+    directory: str,
+    datasets: list[InputPathType],
+    runner: Runner | None = None,
+) -> VToMniAwarpOutputs:
+    """
+    Transforms skull-stripped datasets to 1x1x1 mm MNI space using an affine
+    transformation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        directory: Name of the directory to be created where results will be\
+            stored.
+        datasets: List of datasets to be transformed.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VToMniAwarpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__TO_MNI_AWARP_METADATA)
+    params = v__to_mni_awarp_params(
+        directory=directory,
+        datasets=datasets,
+    )
+    return v__to_mni_awarp_execute(params, execution)
+
+
+__all__ = [
+    "VToMniAwarpOutputs",
+    "VToMniAwarpParameters",
+    "V__TO_MNI_AWARP_METADATA",
+    "v__to_mni_awarp",
+    "v__to_mni_awarp_params",
+]

niwrap_afni/afni/v__to_mni_qwarpar.py

@@ -0,0 +1,170 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__TO_MNI_QWARPAR_METADATA = Metadata(
+    id="04e45eb40a57d1fc1e8c94957315562ee18d3086.boutiques",
+    name="@toMNI_Qwarpar",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VToMniQwarparParameters = typing.TypedDict('VToMniQwarparParameters', {
+    "__STYX_TYPE__": typing.Literal["@toMNI_Qwarpar"],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@toMNI_Qwarpar": v__to_mni_qwarpar_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 {
+        "@toMNI_Qwarpar": v__to_mni_qwarpar_outputs,
+    }.get(t)
+
+
+class VToMniQwarparOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__to_mni_qwarpar(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output dataset created after processing."""
+
+
+def v__to_mni_qwarpar_params(
+) -> VToMniQwarparParameters:
+    """
+    Build parameters.
+    
+    Args:
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@toMNI_Qwarpar",
+    }
+    return params
+
+
+def v__to_mni_qwarpar_cargs(
+    params: VToMniQwarparParameters,
+    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("@toMNI_Qwarpar")
+    return cargs
+
+
+def v__to_mni_qwarpar_outputs(
+    params: VToMniQwarparParameters,
+    execution: Execution,
+) -> VToMniQwarparOutputs:
+    """
+    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 = VToMniQwarparOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file("*_uni+tlrc.HEAD"),
+    )
+    return ret
+
+
+def v__to_mni_qwarpar_execute(
+    params: VToMniQwarparParameters,
+    execution: Execution,
+) -> VToMniQwarparOutputs:
+    """
+    Transforms datasets to MNI space, then collectively re-transforms them to
+    produce a refined average.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VToMniQwarparOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__to_mni_qwarpar_cargs(params, execution)
+    ret = v__to_mni_qwarpar_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__to_mni_qwarpar(
+    runner: Runner | None = None,
+) -> VToMniQwarparOutputs:
+    """
+    Transforms datasets to MNI space, then collectively re-transforms them to
+    produce a refined average.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VToMniQwarparOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__TO_MNI_QWARPAR_METADATA)
+    params = v__to_mni_qwarpar_params(
+    )
+    return v__to_mni_qwarpar_execute(params, execution)
+
+
+__all__ = [
+    "VToMniQwarparOutputs",
+    "VToMniQwarparParameters",
+    "V__TO_MNI_QWARPAR_METADATA",
+    "v__to_mni_qwarpar",
+    "v__to_mni_qwarpar_params",
+]

niwrap_afni/afni/v__to_rai.py

@@ -0,0 +1,170 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__TO_RAI_METADATA = Metadata(
+    id="ae5bb83cce00bf51d61da1e1b21d495548f69a92.boutiques",
+    name="@ToRAI",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VToRaiParameters = typing.TypedDict('VToRaiParameters', {
+    "__STYX_TYPE__": typing.Literal["@ToRAI"],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@ToRAI": v__to_rai_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 VToRaiOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__to_rai(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__to_rai_params(
+) -> VToRaiParameters:
+    """
+    Build parameters.
+    
+    Args:
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@ToRAI",
+    }
+    return params
+
+
+def v__to_rai_cargs(
+    params: VToRaiParameters,
+    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("@ToRAI")
+    cargs.append("<-xyz")
+    cargs.append("X")
+    cargs.append("Y")
+    cargs.append("Z>")
+    cargs.append("<-or")
+    cargs.append("ORIENT>")
+    return cargs
+
+
+def v__to_rai_outputs(
+    params: VToRaiParameters,
+    execution: Execution,
+) -> VToRaiOutputs:
+    """
+    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 = VToRaiOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__to_rai_execute(
+    params: VToRaiParameters,
+    execution: Execution,
+) -> VToRaiOutputs:
+    """
+    Tool to change the ORIENT coordinates to RAI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VToRaiOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__to_rai_cargs(params, execution)
+    ret = v__to_rai_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__to_rai(
+    runner: Runner | None = None,
+) -> VToRaiOutputs:
+    """
+    Tool to change the ORIENT coordinates to RAI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VToRaiOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__TO_RAI_METADATA)
+    params = v__to_rai_params(
+    )
+    return v__to_rai_execute(params, execution)
+
+
+__all__ = [
+    "VToRaiOutputs",
+    "VToRaiParameters",
+    "V__TO_RAI_METADATA",
+    "v__to_rai",
+    "v__to_rai_params",
+]