niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/adjunct_make_script_and_rst_py.py

@@ -0,0 +1,237 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ADJUNCT_MAKE_SCRIPT_AND_RST_PY_METADATA = Metadata(
+    id="b713438ba08e71d534cca42445c2bcd23acbc3af.boutiques",
+    name="adjunct_make_script_and_rst.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AdjunctMakeScriptAndRstPyParameters = typing.TypedDict('AdjunctMakeScriptAndRstPyParameters', {
+    "__STYX_TYPE__": typing.Literal["adjunct_make_script_and_rst.py"],
+    "input_script": InputPathType,
+    "prefix_rst": str,
+    "prefix_script": str,
+    "reflink": str,
+    "execute_script": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "adjunct_make_script_and_rst.py": adjunct_make_script_and_rst_py_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 {
+        "adjunct_make_script_and_rst.py": adjunct_make_script_and_rst_py_outputs,
+    }.get(t)
+
+
+class AdjunctMakeScriptAndRstPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `adjunct_make_script_and_rst_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    rst_file: OutputPathType
+    """Generated RST documentation file."""
+    script_file: OutputPathType
+    """Generated script file."""
+    output_directory: OutputPathType
+    """Output directory in Sphinx tree."""
+
+
+def adjunct_make_script_and_rst_py_params(
+    input_script: InputPathType,
+    prefix_rst: str,
+    prefix_script: str,
+    reflink: str,
+    execute_script: bool = False,
+) -> AdjunctMakeScriptAndRstPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_script: Input script file with special markup.
+        prefix_rst: Output filename including any path of the RST/Sphinx file.\
+            Must include file extension '.rst'.
+        prefix_script: Output filename of the script file. Should include file\
+            extension such as '.tcsh'.
+        reflink: A string tag that will serve as the subdirectory name holding\
+            images for the given demo, and the RST internal reference label.
+        execute_script: Flag to create the RST and script files, and also\
+            execute the script.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "adjunct_make_script_and_rst.py",
+        "input_script": input_script,
+        "prefix_rst": prefix_rst,
+        "prefix_script": prefix_script,
+        "reflink": reflink,
+        "execute_script": execute_script,
+    }
+    return params
+
+
+def adjunct_make_script_and_rst_py_cargs(
+    params: AdjunctMakeScriptAndRstPyParameters,
+    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("adjunct_make_script_and_rst.py")
+    cargs.extend([
+        "-input",
+        "-" + execution.input_file(params.get("input_script"))
+    ])
+    cargs.extend([
+        "--prefix_rst",
+        params.get("prefix_rst")
+    ])
+    cargs.extend([
+        "--prefix_script",
+        params.get("prefix_script")
+    ])
+    cargs.extend([
+        "--reflink",
+        params.get("reflink")
+    ])
+    if params.get("execute_script"):
+        cargs.append("--execute_script")
+    return cargs
+
+
+def adjunct_make_script_and_rst_py_outputs(
+    params: AdjunctMakeScriptAndRstPyParameters,
+    execution: Execution,
+) -> AdjunctMakeScriptAndRstPyOutputs:
+    """
+    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 = AdjunctMakeScriptAndRstPyOutputs(
+        root=execution.output_file("."),
+        rst_file=execution.output_file(params.get("prefix_rst")),
+        script_file=execution.output_file(params.get("prefix_script")),
+        output_directory=execution.output_file(params.get("prefix_rst") + "/media/" + params.get("reflink")),
+    )
+    return ret
+
+
+def adjunct_make_script_and_rst_py_execute(
+    params: AdjunctMakeScriptAndRstPyParameters,
+    execution: Execution,
+) -> AdjunctMakeScriptAndRstPyOutputs:
+    """
+    Program to take a script with some special markup and turn it into both an RST
+    page and a script for the online Sphinx documentation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctMakeScriptAndRstPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = adjunct_make_script_and_rst_py_cargs(params, execution)
+    ret = adjunct_make_script_and_rst_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def adjunct_make_script_and_rst_py(
+    input_script: InputPathType,
+    prefix_rst: str,
+    prefix_script: str,
+    reflink: str,
+    execute_script: bool = False,
+    runner: Runner | None = None,
+) -> AdjunctMakeScriptAndRstPyOutputs:
+    """
+    Program to take a script with some special markup and turn it into both an RST
+    page and a script for the online Sphinx documentation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_script: Input script file with special markup.
+        prefix_rst: Output filename including any path of the RST/Sphinx file.\
+            Must include file extension '.rst'.
+        prefix_script: Output filename of the script file. Should include file\
+            extension such as '.tcsh'.
+        reflink: A string tag that will serve as the subdirectory name holding\
+            images for the given demo, and the RST internal reference label.
+        execute_script: Flag to create the RST and script files, and also\
+            execute the script.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctMakeScriptAndRstPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADJUNCT_MAKE_SCRIPT_AND_RST_PY_METADATA)
+    params = adjunct_make_script_and_rst_py_params(
+        input_script=input_script,
+        prefix_rst=prefix_rst,
+        prefix_script=prefix_script,
+        reflink=reflink,
+        execute_script=execute_script,
+    )
+    return adjunct_make_script_and_rst_py_execute(params, execution)
+
+
+__all__ = [
+    "ADJUNCT_MAKE_SCRIPT_AND_RST_PY_METADATA",
+    "AdjunctMakeScriptAndRstPyOutputs",
+    "AdjunctMakeScriptAndRstPyParameters",
+    "adjunct_make_script_and_rst_py",
+    "adjunct_make_script_and_rst_py_params",
+]

niwrap_afni/afni/adjunct_select_str_py.py

@@ -0,0 +1,188 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ADJUNCT_SELECT_STR_PY_METADATA = Metadata(
+    id="51bd0c93e4c33858ebe75938263e1d88647851a7.boutiques",
+    name="adjunct_select_str.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AdjunctSelectStrPyParameters = typing.TypedDict('AdjunctSelectStrPyParameters', {
+    "__STYX_TYPE__": typing.Literal["adjunct_select_str.py"],
+    "input_file": InputPathType,
+    "num_bricks": float,
+    "output_file": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "adjunct_select_str.py": adjunct_select_str_py_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 AdjunctSelectStrPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `adjunct_select_str_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def adjunct_select_str_py_params(
+    input_file: InputPathType,
+    num_bricks: float,
+    output_file: str,
+) -> AdjunctSelectStrPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: File containing a list of integers.
+        num_bricks: The number N of bricks in the dataset (so max index is N-1).
+        output_file: Output file name.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "adjunct_select_str.py",
+        "input_file": input_file,
+        "num_bricks": num_bricks,
+        "output_file": output_file,
+    }
+    return params
+
+
+def adjunct_select_str_py_cargs(
+    params: AdjunctSelectStrPyParameters,
+    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("adjunct_select_str.py")
+    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(str(params.get("num_bricks")))
+    cargs.append(params.get("output_file"))
+    return cargs
+
+
+def adjunct_select_str_py_outputs(
+    params: AdjunctSelectStrPyParameters,
+    execution: Execution,
+) -> AdjunctSelectStrPyOutputs:
+    """
+    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 = AdjunctSelectStrPyOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def adjunct_select_str_py_execute(
+    params: AdjunctSelectStrPyParameters,
+    execution: Execution,
+) -> AdjunctSelectStrPyOutputs:
+    """
+    A simple helper function for the fat_proc* scripts.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctSelectStrPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = adjunct_select_str_py_cargs(params, execution)
+    ret = adjunct_select_str_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def adjunct_select_str_py(
+    input_file: InputPathType,
+    num_bricks: float,
+    output_file: str,
+    runner: Runner | None = None,
+) -> AdjunctSelectStrPyOutputs:
+    """
+    A simple helper function for the fat_proc* scripts.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: File containing a list of integers.
+        num_bricks: The number N of bricks in the dataset (so max index is N-1).
+        output_file: Output file name.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctSelectStrPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADJUNCT_SELECT_STR_PY_METADATA)
+    params = adjunct_select_str_py_params(
+        input_file=input_file,
+        num_bricks=num_bricks,
+        output_file=output_file,
+    )
+    return adjunct_select_str_py_execute(params, execution)
+
+
+__all__ = [
+    "ADJUNCT_SELECT_STR_PY_METADATA",
+    "AdjunctSelectStrPyOutputs",
+    "AdjunctSelectStrPyParameters",
+    "adjunct_select_str_py",
+    "adjunct_select_str_py_params",
+]

niwrap_afni/afni/adjunct_simplify_cost.py

@@ -0,0 +1,172 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ADJUNCT_SIMPLIFY_COST_METADATA = Metadata(
+    id="0291c293f6b2eaf6626f15fdc0c7c7079ef500e7.boutiques",
+    name="adjunct_simplify_cost",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AdjunctSimplifyCostParameters = typing.TypedDict('AdjunctSimplifyCostParameters', {
+    "__STYX_TYPE__": typing.Literal["adjunct_simplify_cost"],
+    "cost_function": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "adjunct_simplify_cost": adjunct_simplify_cost_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 AdjunctSimplifyCostOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `adjunct_simplify_cost(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def adjunct_simplify_cost_params(
+    cost_function: str,
+) -> AdjunctSimplifyCostParameters:
+    """
+    Build parameters.
+    
+    Args:
+        cost_function: The cost function name to be simplified.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "adjunct_simplify_cost",
+        "cost_function": cost_function,
+    }
+    return params
+
+
+def adjunct_simplify_cost_cargs(
+    params: AdjunctSimplifyCostParameters,
+    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("adjunct_simplify_cost.py")
+    cargs.append(params.get("cost_function"))
+    return cargs
+
+
+def adjunct_simplify_cost_outputs(
+    params: AdjunctSimplifyCostParameters,
+    execution: Execution,
+) -> AdjunctSimplifyCostOutputs:
+    """
+    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 = AdjunctSimplifyCostOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def adjunct_simplify_cost_execute(
+    params: AdjunctSimplifyCostParameters,
+    execution: Execution,
+) -> AdjunctSimplifyCostOutputs:
+    """
+    Simplifies a cost function name by removing the '+' and anything following it.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctSimplifyCostOutputs`).
+    """
+    params = execution.params(params)
+    cargs = adjunct_simplify_cost_cargs(params, execution)
+    ret = adjunct_simplify_cost_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def adjunct_simplify_cost(
+    cost_function: str,
+    runner: Runner | None = None,
+) -> AdjunctSimplifyCostOutputs:
+    """
+    Simplifies a cost function name by removing the '+' and anything following it.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        cost_function: The cost function name to be simplified.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AdjunctSimplifyCostOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADJUNCT_SIMPLIFY_COST_METADATA)
+    params = adjunct_simplify_cost_params(
+        cost_function=cost_function,
+    )
+    return adjunct_simplify_cost_execute(params, execution)
+
+
+__all__ = [
+    "ADJUNCT_SIMPLIFY_COST_METADATA",
+    "AdjunctSimplifyCostOutputs",
+    "AdjunctSimplifyCostParameters",
+    "adjunct_simplify_cost",
+    "adjunct_simplify_cost_params",
+]