niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dbucket.py

@@ -0,0 +1,266 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DBUCKET_METADATA = Metadata(
+    id="a07bb3d6d6114eb899f05be41e593f262e6cd274.boutiques",
+    name="3dbucket",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dbucketParameters = typing.TypedDict('V3dbucketParameters', {
+    "__STYX_TYPE__": typing.Literal["3dbucket"],
+    "prefix": typing.NotRequired[str | None],
+    "session": typing.NotRequired[str | None],
+    "glueto": typing.NotRequired[str | None],
+    "aglueto": typing.NotRequired[str | None],
+    "dry": bool,
+    "verbose": bool,
+    "fbuc": bool,
+    "abuc": bool,
+    "input_files": list[str],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dbucket": v_3dbucket_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 V3dbucketOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dbucket(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3dbucket_params(
+    input_files: list[str],
+    prefix: str | None = None,
+    session: str | None = None,
+    glueto: str | None = None,
+    aglueto: str | None = None,
+    dry: bool = False,
+    verbose: bool = False,
+    fbuc: bool = False,
+    abuc: bool = False,
+) -> V3dbucketParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input datasets with optional sub-brick selection.
+        prefix: Use 'pname' for the output dataset prefix name.
+        session: Use 'dir' for the output dataset session directory.\
+            [default='./'=current working directory].
+        glueto: Append bricks to the end of the 'fname' dataset.
+        aglueto: If fname dataset does not exist, create it (like -prefix).\
+            Otherwise append to fname (like -glueto).
+        dry: Execute a 'dry run'; only print out what would be done.
+        verbose: Print out some verbose output as the program proceeds.
+        fbuc: Create a functional bucket.
+        abuc: Create an anatomical bucket. If neither of these options is\
+            given, the output type is determined from the first input type.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dbucket",
+        "dry": dry,
+        "verbose": verbose,
+        "fbuc": fbuc,
+        "abuc": abuc,
+        "input_files": input_files,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if session is not None:
+        params["session"] = session
+    if glueto is not None:
+        params["glueto"] = glueto
+    if aglueto is not None:
+        params["aglueto"] = aglueto
+    return params
+
+
+def v_3dbucket_cargs(
+    params: V3dbucketParameters,
+    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("3dbucket")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("session") is not None:
+        cargs.extend([
+            "-session",
+            params.get("session")
+        ])
+    if params.get("glueto") is not None:
+        cargs.extend([
+            "-glueto",
+            params.get("glueto")
+        ])
+    if params.get("aglueto") is not None:
+        cargs.extend([
+            "-aglueto",
+            params.get("aglueto")
+        ])
+    if params.get("dry"):
+        cargs.append("-dry")
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("fbuc"):
+        cargs.append("-fbuc")
+    if params.get("abuc"):
+        cargs.append("-abuc")
+    cargs.extend(params.get("input_files"))
+    return cargs
+
+
+def v_3dbucket_outputs(
+    params: V3dbucketParameters,
+    execution: Execution,
+) -> V3dbucketOutputs:
+    """
+    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 = V3dbucketOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3dbucket_execute(
+    params: V3dbucketParameters,
+    execution: Execution,
+) -> V3dbucketOutputs:
+    """
+    Concatenate sub-bricks from input datasets into one big bucket dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dbucketOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dbucket_cargs(params, execution)
+    ret = v_3dbucket_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dbucket(
+    input_files: list[str],
+    prefix: str | None = None,
+    session: str | None = None,
+    glueto: str | None = None,
+    aglueto: str | None = None,
+    dry: bool = False,
+    verbose: bool = False,
+    fbuc: bool = False,
+    abuc: bool = False,
+    runner: Runner | None = None,
+) -> V3dbucketOutputs:
+    """
+    Concatenate sub-bricks from input datasets into one big bucket dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input datasets with optional sub-brick selection.
+        prefix: Use 'pname' for the output dataset prefix name.
+        session: Use 'dir' for the output dataset session directory.\
+            [default='./'=current working directory].
+        glueto: Append bricks to the end of the 'fname' dataset.
+        aglueto: If fname dataset does not exist, create it (like -prefix).\
+            Otherwise append to fname (like -glueto).
+        dry: Execute a 'dry run'; only print out what would be done.
+        verbose: Print out some verbose output as the program proceeds.
+        fbuc: Create a functional bucket.
+        abuc: Create an anatomical bucket. If neither of these options is\
+            given, the output type is determined from the first input type.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dbucketOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DBUCKET_METADATA)
+    params = v_3dbucket_params(
+        prefix=prefix,
+        session=session,
+        glueto=glueto,
+        aglueto=aglueto,
+        dry=dry,
+        verbose=verbose,
+        fbuc=fbuc,
+        abuc=abuc,
+        input_files=input_files,
+    )
+    return v_3dbucket_execute(params, execution)
+
+
+__all__ = [
+    "V3dbucketOutputs",
+    "V3dbucketParameters",
+    "V_3DBUCKET_METADATA",
+    "v_3dbucket",
+    "v_3dbucket_params",
+]

niwrap_afni/afni/v_3dcalc.py

@@ -0,0 +1,278 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DCALC_METADATA = Metadata(
+    id="3a17cb5cc1d3b991065054ac23d926bf8d3018c8.boutiques",
+    name="3dcalc",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dcalcParameters = typing.TypedDict('V3dcalcParameters', {
+    "__STYX_TYPE__": typing.Literal["3dcalc"],
+    "in_file_a": InputPathType,
+    "in_file_b": typing.NotRequired[InputPathType | None],
+    "in_file_c": typing.NotRequired[InputPathType | None],
+    "other": typing.NotRequired[InputPathType | None],
+    "overwrite": bool,
+    "single_idx": typing.NotRequired[int | None],
+    "start_idx": typing.NotRequired[int | None],
+    "stop_idx": typing.NotRequired[int | None],
+    "expr": str,
+    "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 {
+        "3dcalc": v_3dcalc_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 {
+        "3dcalc": v_3dcalc_outputs,
+    }.get(t)
+
+
+class V3dcalcOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dcalc(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Output image file name."""
+
+
+def v_3dcalc_params(
+    in_file_a: InputPathType,
+    expr: str,
+    in_file_b: InputPathType | None = None,
+    in_file_c: InputPathType | None = None,
+    other: InputPathType | None = None,
+    overwrite: bool = False,
+    single_idx: int | None = None,
+    start_idx: int | None = None,
+    stop_idx: int | None = None,
+    prefix: str | None = None,
+) -> V3dcalcParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file_a: Input file to 3dcalc.
+        expr: Expr.
+        in_file_b: Operand file to 3dcalc.
+        in_file_c: Operand file to 3dcalc.
+        other: Other options.
+        overwrite: Overwrite output.
+        single_idx: Volume index for in_file_a.
+        start_idx: Start index for in_file_a.
+        stop_idx: Stop index for in_file_a.
+        prefix: Output image file name.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dcalc",
+        "in_file_a": in_file_a,
+        "overwrite": overwrite,
+        "expr": expr,
+    }
+    if in_file_b is not None:
+        params["in_file_b"] = in_file_b
+    if in_file_c is not None:
+        params["in_file_c"] = in_file_c
+    if other is not None:
+        params["other"] = other
+    if single_idx is not None:
+        params["single_idx"] = single_idx
+    if start_idx is not None:
+        params["start_idx"] = start_idx
+    if stop_idx is not None:
+        params["stop_idx"] = stop_idx
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3dcalc_cargs(
+    params: V3dcalcParameters,
+    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("3dcalc")
+    cargs.extend([
+        "-a",
+        execution.input_file(params.get("in_file_a"))
+    ])
+    if params.get("in_file_b") is not None:
+        cargs.extend([
+            "-b",
+            execution.input_file(params.get("in_file_b"))
+        ])
+    if params.get("in_file_c") is not None:
+        cargs.extend([
+            "-c",
+            execution.input_file(params.get("in_file_c"))
+        ])
+    if params.get("other") is not None:
+        cargs.append(execution.input_file(params.get("other")))
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    if params.get("single_idx") is not None:
+        cargs.append(str(params.get("single_idx")))
+    if params.get("start_idx") is not None:
+        cargs.append(str(params.get("start_idx")))
+    if params.get("stop_idx") is not None:
+        cargs.append(str(params.get("stop_idx")))
+    cargs.extend([
+        "-expr",
+        params.get("expr")
+    ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    return cargs
+
+
+def v_3dcalc_outputs(
+    params: V3dcalcParameters,
+    execution: Execution,
+) -> V3dcalcOutputs:
+    """
+    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 = V3dcalcOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3dcalc_execute(
+    params: V3dcalcParameters,
+    execution: Execution,
+) -> V3dcalcOutputs:
+    """
+    AFNI's calculator program.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dcalcOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dcalc_cargs(params, execution)
+    ret = v_3dcalc_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dcalc(
+    in_file_a: InputPathType,
+    expr: str,
+    in_file_b: InputPathType | None = None,
+    in_file_c: InputPathType | None = None,
+    other: InputPathType | None = None,
+    overwrite: bool = False,
+    single_idx: int | None = None,
+    start_idx: int | None = None,
+    stop_idx: int | None = None,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dcalcOutputs:
+    """
+    AFNI's calculator program.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file_a: Input file to 3dcalc.
+        expr: Expr.
+        in_file_b: Operand file to 3dcalc.
+        in_file_c: Operand file to 3dcalc.
+        other: Other options.
+        overwrite: Overwrite output.
+        single_idx: Volume index for in_file_a.
+        start_idx: Start index for in_file_a.
+        stop_idx: Stop index for in_file_a.
+        prefix: Output image file name.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dcalcOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DCALC_METADATA)
+    params = v_3dcalc_params(
+        in_file_a=in_file_a,
+        in_file_b=in_file_b,
+        in_file_c=in_file_c,
+        other=other,
+        overwrite=overwrite,
+        single_idx=single_idx,
+        start_idx=start_idx,
+        stop_idx=stop_idx,
+        expr=expr,
+        prefix=prefix,
+    )
+    return v_3dcalc_execute(params, execution)
+
+
+__all__ = [
+    "V3dcalcOutputs",
+    "V3dcalcParameters",
+    "V_3DCALC_METADATA",
+    "v_3dcalc",
+    "v_3dcalc_params",
+]