niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__2dwarper.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__2DWARPER_METADATA = Metadata(
+    id="00a0f14e7b2cc538eab7a1270968f6ba94c6c2e3.boutiques",
+    name="@2dwarper",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V2dwarperParameters = typing.TypedDict('V2dwarperParameters', {
+    "__STYX_TYPE__": typing.Literal["@2dwarper"],
+    "input_dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@2dwarper": v__2dwarper_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 {
+        "@2dwarper": v__2dwarper_outputs,
+    }.get(t)
+
+
+class V2dwarperOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__2dwarper(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Warped output image from the dataset"""
+
+
+def v__2dwarper_params(
+    input_dataset: InputPathType,
+) -> V2dwarperParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset (e.g., image to be warped).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@2dwarper",
+        "input_dataset": input_dataset,
+    }
+    return params
+
+
+def v__2dwarper_cargs(
+    params: V2dwarperParameters,
+    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("@2dwarper")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    return cargs
+
+
+def v__2dwarper_outputs(
+    params: V2dwarperParameters,
+    execution: Execution,
+) -> V2dwarperOutputs:
+    """
+    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 = V2dwarperOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file("warped_output"),
+    )
+    return ret
+
+
+def v__2dwarper_execute(
+    params: V2dwarperParameters,
+    execution: Execution,
+) -> V2dwarperOutputs:
+    """
+    2D image warping tool.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V2dwarperOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__2dwarper_cargs(params, execution)
+    ret = v__2dwarper_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__2dwarper(
+    input_dataset: InputPathType,
+    runner: Runner | None = None,
+) -> V2dwarperOutputs:
+    """
+    2D image warping tool.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset (e.g., image to be warped).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V2dwarperOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__2DWARPER_METADATA)
+    params = v__2dwarper_params(
+        input_dataset=input_dataset,
+    )
+    return v__2dwarper_execute(params, execution)
+
+
+__all__ = [
+    "V2dwarperOutputs",
+    "V2dwarperParameters",
+    "V__2DWARPER_METADATA",
+    "v__2dwarper",
+    "v__2dwarper_params",
+]

niwrap_afni/afni/v__2dwarper_allin.py

@@ -0,0 +1,207 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__2DWARPER_ALLIN_METADATA = Metadata(
+    id="025f4fd73449077a7f27f71bce48a9a34a8bfe9d.boutiques",
+    name="@2dwarper.Allin",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V2dwarperAllinParameters = typing.TypedDict('V2dwarperAllinParameters', {
+    "__STYX_TYPE__": typing.Literal["@2dwarper.Allin"],
+    "input_prefix": str,
+    "mask_prefix": typing.NotRequired[str | None],
+    "output_prefix": 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 {
+        "@2dwarper.Allin": v__2dwarper_allin_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 {
+        "@2dwarper.Allin": v__2dwarper_allin_outputs,
+    }.get(t)
+
+
+class V2dwarperAllinOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__2dwarper_allin(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    reg_output: OutputPathType | None
+    """Output registered dataset"""
+    param_files: OutputPathType | None
+    """Output registration parameter files"""
+
+
+def v__2dwarper_allin_params(
+    input_prefix: str,
+    mask_prefix: str | None = None,
+    output_prefix: str | None = None,
+) -> V2dwarperAllinParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_prefix: Prefix for the input 3D+time dataset.
+        mask_prefix: Prefix of an existing mask dataset.
+        output_prefix: Prefix for output datasets.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@2dwarper.Allin",
+        "input_prefix": input_prefix,
+    }
+    if mask_prefix is not None:
+        params["mask_prefix"] = mask_prefix
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    return params
+
+
+def v__2dwarper_allin_cargs(
+    params: V2dwarperAllinParameters,
+    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("@2dwarper.Allin")
+    cargs.append(params.get("input_prefix"))
+    if params.get("mask_prefix") is not None:
+        cargs.extend([
+            "-mask",
+            params.get("mask_prefix")
+        ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    return cargs
+
+
+def v__2dwarper_allin_outputs(
+    params: V2dwarperAllinParameters,
+    execution: Execution,
+) -> V2dwarperAllinOutputs:
+    """
+    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 = V2dwarperAllinOutputs(
+        root=execution.output_file("."),
+        reg_output=execution.output_file(params.get("output_prefix") + "_reg+orig.HEAD") if (params.get("output_prefix") is not None) else None,
+        param_files=execution.output_file(params.get("output_prefix") + "_param_*.1D") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v__2dwarper_allin_execute(
+    params: V2dwarperAllinParameters,
+    execution: Execution,
+) -> V2dwarperAllinOutputs:
+    """
+    Perform 2D registration on each slice of a 3D+time dataset, and combine the
+    results.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V2dwarperAllinOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__2dwarper_allin_cargs(params, execution)
+    ret = v__2dwarper_allin_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__2dwarper_allin(
+    input_prefix: str,
+    mask_prefix: str | None = None,
+    output_prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V2dwarperAllinOutputs:
+    """
+    Perform 2D registration on each slice of a 3D+time dataset, and combine the
+    results.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_prefix: Prefix for the input 3D+time dataset.
+        mask_prefix: Prefix of an existing mask dataset.
+        output_prefix: Prefix for output datasets.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V2dwarperAllinOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__2DWARPER_ALLIN_METADATA)
+    params = v__2dwarper_allin_params(
+        input_prefix=input_prefix,
+        mask_prefix=mask_prefix,
+        output_prefix=output_prefix,
+    )
+    return v__2dwarper_allin_execute(params, execution)
+
+
+__all__ = [
+    "V2dwarperAllinOutputs",
+    "V2dwarperAllinParameters",
+    "V__2DWARPER_ALLIN_METADATA",
+    "v__2dwarper_allin",
+    "v__2dwarper_allin_params",
+]

niwrap_afni/afni/v__4_daverage.py

@@ -0,0 +1,173 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__4_DAVERAGE_METADATA = Metadata(
+    id="539f6118b726725db3041382540750353fc522e5.boutiques",
+    name="@4Daverage",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V4DaverageParameters = typing.TypedDict('V4DaverageParameters', {
+    "__STYX_TYPE__": typing.Literal["@4Daverage"],
+    "output_prefix": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@4Daverage": v__4_daverage_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 V4DaverageOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__4_daverage(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__4_daverage_params(
+    output_prefix: str,
+) -> V4DaverageParameters:
+    """
+    Build parameters.
+    
+    Args:
+        output_prefix: Prefix for the output 3D+t brick.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@4Daverage",
+        "output_prefix": output_prefix,
+    }
+    return params
+
+
+def v__4_daverage_cargs(
+    params: V4DaverageParameters,
+    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("@4Daverage")
+    cargs.append(params.get("output_prefix"))
+    cargs.append("[INPUT_FILES...]")
+    return cargs
+
+
+def v__4_daverage_outputs(
+    params: V4DaverageParameters,
+    execution: Execution,
+) -> V4DaverageOutputs:
+    """
+    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 = V4DaverageOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__4_daverage_execute(
+    params: V4DaverageParameters,
+    execution: Execution,
+) -> V4DaverageOutputs:
+    """
+    Script for computing average 3D+time bricks using 3Dcalc.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V4DaverageOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__4_daverage_cargs(params, execution)
+    ret = v__4_daverage_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__4_daverage(
+    output_prefix: str,
+    runner: Runner | None = None,
+) -> V4DaverageOutputs:
+    """
+    Script for computing average 3D+time bricks using 3Dcalc.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        output_prefix: Prefix for the output 3D+t brick.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V4DaverageOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__4_DAVERAGE_METADATA)
+    params = v__4_daverage_params(
+        output_prefix=output_prefix,
+    )
+    return v__4_daverage_execute(params, execution)
+
+
+__all__ = [
+    "V4DaverageOutputs",
+    "V4DaverageParameters",
+    "V__4_DAVERAGE_METADATA",
+    "v__4_daverage",
+    "v__4_daverage_params",
+]