niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/rotcom.py

@@ -0,0 +1,190 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ROTCOM_METADATA = Metadata(
+    id="65366e1283781ddcf84d07b0c61d20c1cdbf07ba.boutiques",
+    name="rotcom",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+RotcomParameters = typing.TypedDict('RotcomParameters', {
+    "__STYX_TYPE__": typing.Literal["rotcom"],
+    "rotate_ashift": str,
+    "dataset": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "rotcom": rotcom_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 {
+        "rotcom": rotcom_outputs,
+    }.get(t)
+
+
+class RotcomOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `rotcom(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    stdout: OutputPathType
+    """The 4x3 transformation matrix+vector output"""
+
+
+def rotcom_params(
+    rotate_ashift: str,
+    dataset: InputPathType | None = None,
+) -> RotcomParameters:
+    """
+    Build parameters.
+    
+    Args:
+        rotate_ashift: Combination of rotate and ashift options in a single\
+            quoted string (e.g., '-rotate 10I 0R 0A -ashift 5S 0 0').
+        dataset: Input dataset for determining coordinate order.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "rotcom",
+        "rotate_ashift": rotate_ashift,
+    }
+    if dataset is not None:
+        params["dataset"] = dataset
+    return params
+
+
+def rotcom_cargs(
+    params: RotcomParameters,
+    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("rotcom")
+    cargs.append(params.get("rotate_ashift"))
+    if params.get("dataset") is not None:
+        cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def rotcom_outputs(
+    params: RotcomParameters,
+    execution: Execution,
+) -> RotcomOutputs:
+    """
+    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 = RotcomOutputs(
+        root=execution.output_file("."),
+        stdout=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def rotcom_execute(
+    params: RotcomParameters,
+    execution: Execution,
+) -> RotcomOutputs:
+    """
+    Prints to stdout the 4x3 transformation matrix+vector that would be applied by
+    3drotate to the given dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `RotcomOutputs`).
+    """
+    params = execution.params(params)
+    cargs = rotcom_cargs(params, execution)
+    ret = rotcom_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def rotcom(
+    rotate_ashift: str,
+    dataset: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> RotcomOutputs:
+    """
+    Prints to stdout the 4x3 transformation matrix+vector that would be applied by
+    3drotate to the given dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        rotate_ashift: Combination of rotate and ashift options in a single\
+            quoted string (e.g., '-rotate 10I 0R 0A -ashift 5S 0 0').
+        dataset: Input dataset for determining coordinate order.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `RotcomOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ROTCOM_METADATA)
+    params = rotcom_params(
+        rotate_ashift=rotate_ashift,
+        dataset=dataset,
+    )
+    return rotcom_execute(params, execution)
+
+
+__all__ = [
+    "ROTCOM_METADATA",
+    "RotcomOutputs",
+    "RotcomParameters",
+    "rotcom",
+    "rotcom_params",
+]

niwrap_afni/afni/rsfgen.py

@@ -0,0 +1,330 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+RSFGEN_METADATA = Metadata(
+    id="42de4c95300ddfa6a27f2ddbc5b6d9dc63cdd292.boutiques",
+    name="RSFgen",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+RsfgenParameters = typing.TypedDict('RsfgenParameters', {
+    "__STYX_TYPE__": typing.Literal["RSFgen"],
+    "length": int,
+    "num_experimental_conditions": int,
+    "block_length": typing.NotRequired[str | None],
+    "random_seed": typing.NotRequired[float | None],
+    "suppress_output_flag": bool,
+    "single_file_flag": bool,
+    "single_column_flag": bool,
+    "output_prefix": typing.NotRequired[str | None],
+    "num_reps": typing.NotRequired[str | None],
+    "permutation_seed": typing.NotRequired[float | None],
+    "markov_file": typing.NotRequired[InputPathType | None],
+    "prob_zero": typing.NotRequired[float | None],
+    "input_table": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "RSFgen": rsfgen_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 {
+        "RSFgen": rsfgen_outputs,
+    }.get(t)
+
+
+class RsfgenOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `rsfgen(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType | None
+    """Output .1D stimulus function files prefixed with the provided output
+    prefix."""
+
+
+def rsfgen_params(
+    length: int,
+    num_experimental_conditions: int,
+    block_length: str | None = None,
+    random_seed: float | None = None,
+    suppress_output_flag: bool = False,
+    single_file_flag: bool = False,
+    single_column_flag: bool = False,
+    output_prefix: str | None = None,
+    num_reps: str | None = None,
+    permutation_seed: float | None = None,
+    markov_file: InputPathType | None = None,
+    prob_zero: float | None = None,
+    input_table: InputPathType | None = None,
+) -> RsfgenParameters:
+    """
+    Build parameters.
+    
+    Args:
+        length: Length of time series.
+        num_experimental_conditions: Number of input stimuli (experimental\
+            conditions).
+        block_length: Block length for stimulus. Must specify stimulus index\
+            and length. Example: -nblock 1 5.
+        random_seed: Random number seed.
+        suppress_output_flag: Flag to suppress screen output.
+        single_file_flag: Place stimulus functions into a single .1D file.
+        single_column_flag: Write stimulus functions as a single column of\
+            decimal integers.
+        output_prefix: Prefix for output .1D stimulus functions.
+        num_reps: Number of repetitions for stimulus.
+        permutation_seed: Stim label permutation random number seed.
+        markov_file: File containing the transition probability matrix.
+        prob_zero: Probability of a zero (i.e., null) state (default: 0).
+        input_table: Filename of column or table of numbers. All other input\
+            options (except -seed and -prefix) are ignored with this option.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "RSFgen",
+        "length": length,
+        "num_experimental_conditions": num_experimental_conditions,
+        "suppress_output_flag": suppress_output_flag,
+        "single_file_flag": single_file_flag,
+        "single_column_flag": single_column_flag,
+    }
+    if block_length is not None:
+        params["block_length"] = block_length
+    if random_seed is not None:
+        params["random_seed"] = random_seed
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if num_reps is not None:
+        params["num_reps"] = num_reps
+    if permutation_seed is not None:
+        params["permutation_seed"] = permutation_seed
+    if markov_file is not None:
+        params["markov_file"] = markov_file
+    if prob_zero is not None:
+        params["prob_zero"] = prob_zero
+    if input_table is not None:
+        params["input_table"] = input_table
+    return params
+
+
+def rsfgen_cargs(
+    params: RsfgenParameters,
+    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("RSFgen")
+    cargs.extend([
+        "-nt",
+        str(params.get("length"))
+    ])
+    cargs.extend([
+        "-num_stimts",
+        str(params.get("num_experimental_conditions"))
+    ])
+    if params.get("block_length") is not None:
+        cargs.extend([
+            "-nblock",
+            params.get("block_length")
+        ])
+    if params.get("random_seed") is not None:
+        cargs.extend([
+            "-seed",
+            str(params.get("random_seed"))
+        ])
+    if params.get("suppress_output_flag"):
+        cargs.append("-quiet")
+    if params.get("single_file_flag"):
+        cargs.append("-one_file")
+    if params.get("single_column_flag"):
+        cargs.append("-one_col")
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("num_reps") is not None:
+        cargs.extend([
+            "-nreps",
+            params.get("num_reps")
+        ])
+    if params.get("permutation_seed") is not None:
+        cargs.extend([
+            "-pseed",
+            str(params.get("permutation_seed"))
+        ])
+    if params.get("markov_file") is not None:
+        cargs.extend([
+            "-markov",
+            execution.input_file(params.get("markov_file"))
+        ])
+    if params.get("prob_zero") is not None:
+        cargs.extend([
+            "-pzero",
+            str(params.get("prob_zero"))
+        ])
+    if params.get("input_table") is not None:
+        cargs.extend([
+            "-table",
+            execution.input_file(params.get("input_table"))
+        ])
+    return cargs
+
+
+def rsfgen_outputs(
+    params: RsfgenParameters,
+    execution: Execution,
+) -> RsfgenOutputs:
+    """
+    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 = RsfgenOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file(params.get("output_prefix") + "1.1D") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def rsfgen_execute(
+    params: RsfgenParameters,
+    execution: Execution,
+) -> RsfgenOutputs:
+    """
+    Program to generate random stimulus functions.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `RsfgenOutputs`).
+    """
+    params = execution.params(params)
+    cargs = rsfgen_cargs(params, execution)
+    ret = rsfgen_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def rsfgen(
+    length: int,
+    num_experimental_conditions: int,
+    block_length: str | None = None,
+    random_seed: float | None = None,
+    suppress_output_flag: bool = False,
+    single_file_flag: bool = False,
+    single_column_flag: bool = False,
+    output_prefix: str | None = None,
+    num_reps: str | None = None,
+    permutation_seed: float | None = None,
+    markov_file: InputPathType | None = None,
+    prob_zero: float | None = None,
+    input_table: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> RsfgenOutputs:
+    """
+    Program to generate random stimulus functions.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        length: Length of time series.
+        num_experimental_conditions: Number of input stimuli (experimental\
+            conditions).
+        block_length: Block length for stimulus. Must specify stimulus index\
+            and length. Example: -nblock 1 5.
+        random_seed: Random number seed.
+        suppress_output_flag: Flag to suppress screen output.
+        single_file_flag: Place stimulus functions into a single .1D file.
+        single_column_flag: Write stimulus functions as a single column of\
+            decimal integers.
+        output_prefix: Prefix for output .1D stimulus functions.
+        num_reps: Number of repetitions for stimulus.
+        permutation_seed: Stim label permutation random number seed.
+        markov_file: File containing the transition probability matrix.
+        prob_zero: Probability of a zero (i.e., null) state (default: 0).
+        input_table: Filename of column or table of numbers. All other input\
+            options (except -seed and -prefix) are ignored with this option.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `RsfgenOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RSFGEN_METADATA)
+    params = rsfgen_params(
+        length=length,
+        num_experimental_conditions=num_experimental_conditions,
+        block_length=block_length,
+        random_seed=random_seed,
+        suppress_output_flag=suppress_output_flag,
+        single_file_flag=single_file_flag,
+        single_column_flag=single_column_flag,
+        output_prefix=output_prefix,
+        num_reps=num_reps,
+        permutation_seed=permutation_seed,
+        markov_file=markov_file,
+        prob_zero=prob_zero,
+        input_table=input_table,
+    )
+    return rsfgen_execute(params, execution)
+
+
+__all__ = [
+    "RSFGEN_METADATA",
+    "RsfgenOutputs",
+    "RsfgenParameters",
+    "rsfgen",
+    "rsfgen_params",
+]