niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_zcat.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_3D_ZCAT_METADATA = Metadata(
+    id="a00d1d033ba00163e081549b0d7b74b2c667d65a.boutiques",
+    name="3dZcat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dZcatParameters = typing.TypedDict('V3dZcatParameters', {
+    "__STYX_TYPE__": typing.Literal["3dZcat"],
+    "prefix": typing.NotRequired[str | None],
+    "datum": typing.NotRequired[typing.Literal["byte", "short", "float"] | None],
+    "fscale": bool,
+    "nscale": bool,
+    "verb": bool,
+    "frugal": bool,
+    "input_files": 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 {
+        "3dZcat": v_3d_zcat_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 {
+        "3dZcat": v_3d_zcat_outputs,
+    }.get(t)
+
+
+class V3dZcatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_zcat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_head: OutputPathType | None
+    """AFNI HEAD file of the output dataset"""
+    out_brik: OutputPathType | None
+    """AFNI BRIK file of the output dataset"""
+
+
+def v_3d_zcat_params(
+    input_files: list[InputPathType],
+    prefix: str | None = None,
+    datum: typing.Literal["byte", "short", "float"] | None = None,
+    fscale: bool = False,
+    nscale: bool = False,
+    verb: bool = False,
+    frugal: bool = False,
+) -> V3dZcatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input datasets.
+        prefix: Use 'pname' for the output dataset prefix name.\
+            [default='zcat'].
+        datum: Coerce the output data to be stored as the given type, which may\
+            be byte, short, or float.
+        fscale: Force scaling of the output to the maximum integer range. This\
+            only has effect if the output datum is byte or short (either forced or\
+            defaulted). This option is sometimes necessary to eliminate unpleasant\
+            truncation artifacts.
+        nscale: Don't do any scaling on output to byte or short datasets. This\
+            may be especially useful when operating on mask datasets whose output\
+            values are only 0's and 1's.
+        verb: Print out some verbosity as the program proceeds.
+        frugal: Be 'frugal' in the use of memory, at the cost of I/O time. Only\
+            needed if the program runs out of memory. Note frugality cannot be\
+            combined with NIFTI output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dZcat",
+        "fscale": fscale,
+        "nscale": nscale,
+        "verb": verb,
+        "frugal": frugal,
+        "input_files": input_files,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if datum is not None:
+        params["datum"] = datum
+    return params
+
+
+def v_3d_zcat_cargs(
+    params: V3dZcatParameters,
+    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("3dZcat")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("datum") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum")
+        ])
+    if params.get("fscale"):
+        cargs.append("-fscale")
+    if params.get("nscale"):
+        cargs.append("-nscale")
+    if params.get("verb"):
+        cargs.append("-verb")
+    if params.get("frugal"):
+        cargs.append("-frugal")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    return cargs
+
+
+def v_3d_zcat_outputs(
+    params: V3dZcatParameters,
+    execution: Execution,
+) -> V3dZcatOutputs:
+    """
+    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 = V3dZcatOutputs(
+        root=execution.output_file("."),
+        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        out_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_zcat_execute(
+    params: V3dZcatParameters,
+    execution: Execution,
+) -> V3dZcatOutputs:
+    """
+    Concatenates datasets in the slice (z) direction.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dZcatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_zcat_cargs(params, execution)
+    ret = v_3d_zcat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_zcat(
+    input_files: list[InputPathType],
+    prefix: str | None = None,
+    datum: typing.Literal["byte", "short", "float"] | None = None,
+    fscale: bool = False,
+    nscale: bool = False,
+    verb: bool = False,
+    frugal: bool = False,
+    runner: Runner | None = None,
+) -> V3dZcatOutputs:
+    """
+    Concatenates datasets in the slice (z) direction.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input datasets.
+        prefix: Use 'pname' for the output dataset prefix name.\
+            [default='zcat'].
+        datum: Coerce the output data to be stored as the given type, which may\
+            be byte, short, or float.
+        fscale: Force scaling of the output to the maximum integer range. This\
+            only has effect if the output datum is byte or short (either forced or\
+            defaulted). This option is sometimes necessary to eliminate unpleasant\
+            truncation artifacts.
+        nscale: Don't do any scaling on output to byte or short datasets. This\
+            may be especially useful when operating on mask datasets whose output\
+            values are only 0's and 1's.
+        verb: Print out some verbosity as the program proceeds.
+        frugal: Be 'frugal' in the use of memory, at the cost of I/O time. Only\
+            needed if the program runs out of memory. Note frugality cannot be\
+            combined with NIFTI output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dZcatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ZCAT_METADATA)
+    params = v_3d_zcat_params(
+        prefix=prefix,
+        datum=datum,
+        fscale=fscale,
+        nscale=nscale,
+        verb=verb,
+        frugal=frugal,
+        input_files=input_files,
+    )
+    return v_3d_zcat_execute(params, execution)
+
+
+__all__ = [
+    "V3dZcatOutputs",
+    "V3dZcatParameters",
+    "V_3D_ZCAT_METADATA",
+    "v_3d_zcat",
+    "v_3d_zcat_params",
+]

niwrap_afni/afni/v_3d_zcutup.py

@@ -0,0 +1,209 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_ZCUTUP_METADATA = Metadata(
+    id="9f4c5ae0e2d25b35b3ce4085901c813b8cd03916.boutiques",
+    name="3dZcutup",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dZcutupParameters = typing.TypedDict('V3dZcutupParameters', {
+    "__STYX_TYPE__": typing.Literal["3dZcutup"],
+    "keep_slices": str,
+    "prefix": typing.NotRequired[str | None],
+    "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 {
+        "3dZcutup": v_3d_zcutup_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 {
+        "3dZcutup": v_3d_zcutup_outputs,
+    }.get(t)
+
+
+class V3dZcutupOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_zcutup(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_head: OutputPathType | None
+    """The output dataset HEAD file"""
+    output_brik: OutputPathType | None
+    """The output dataset BRIK file"""
+
+
+def v_3d_zcutup_params(
+    keep_slices: str,
+    dataset: InputPathType,
+    prefix: str | None = None,
+) -> V3dZcutupParameters:
+    """
+    Build parameters.
+    
+    Args:
+        keep_slices: Keep slices numbered 'b' through 't', inclusive. This is a\
+            mandatory option. Slice numbers start at 0.
+        dataset: The input dataset (e.g., epi07+orig). You can use a sub-brick\
+            selector on the input dataset.
+        prefix: Write result into dataset with the given prefix [default =\
+            'zcutup'].
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dZcutup",
+        "keep_slices": keep_slices,
+        "dataset": dataset,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_zcutup_cargs(
+    params: V3dZcutupParameters,
+    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("3dZcutup")
+    cargs.extend([
+        "-keep",
+        params.get("keep_slices")
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def v_3d_zcutup_outputs(
+    params: V3dZcutupParameters,
+    execution: Execution,
+) -> V3dZcutupOutputs:
+    """
+    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 = V3dZcutupOutputs(
+        root=execution.output_file("."),
+        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_zcutup_execute(
+    params: V3dZcutupParameters,
+    execution: Execution,
+) -> V3dZcutupOutputs:
+    """
+    Cut slices off a dataset in its z-direction and write a new dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dZcutupOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_zcutup_cargs(params, execution)
+    ret = v_3d_zcutup_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_zcutup(
+    keep_slices: str,
+    dataset: InputPathType,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dZcutupOutputs:
+    """
+    Cut slices off a dataset in its z-direction and write a new dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        keep_slices: Keep slices numbered 'b' through 't', inclusive. This is a\
+            mandatory option. Slice numbers start at 0.
+        dataset: The input dataset (e.g., epi07+orig). You can use a sub-brick\
+            selector on the input dataset.
+        prefix: Write result into dataset with the given prefix [default =\
+            'zcutup'].
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dZcutupOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ZCUTUP_METADATA)
+    params = v_3d_zcutup_params(
+        keep_slices=keep_slices,
+        prefix=prefix,
+        dataset=dataset,
+    )
+    return v_3d_zcutup_execute(params, execution)
+
+
+__all__ = [
+    "V3dZcutupOutputs",
+    "V3dZcutupParameters",
+    "V_3D_ZCUTUP_METADATA",
+    "v_3d_zcutup",
+    "v_3d_zcutup_params",
+]