niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/strblast.py

@@ -0,0 +1,239 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+STRBLAST_METADATA = Metadata(
+    id="a2cee2c629b430408b17d4c3a5b48c6d60070e17.boutiques",
+    name="strblast",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+StrblastParameters = typing.TypedDict('StrblastParameters', {
+    "__STYX_TYPE__": typing.Literal["strblast"],
+    "targetstring": str,
+    "input_files": list[InputPathType],
+    "new_char": typing.NotRequired[str | None],
+    "new_string": typing.NotRequired[str | None],
+    "unescape": bool,
+    "quiet": bool,
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "strblast": strblast_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 StrblastOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `strblast(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def strblast_params(
+    targetstring: str,
+    input_files: list[InputPathType],
+    new_char: str | None = None,
+    new_string: str | None = None,
+    unescape: bool = False,
+    quiet: bool = False,
+    help_: bool = False,
+) -> StrblastParameters:
+    """
+    Build parameters.
+    
+    Args:
+        targetstring: Target string to search for in the input files.
+        input_files: Input files to search for the target string.
+        new_char: Replace TARGETSTRING with CHAR (repeated).
+        new_string: Replace TARGETSTRING with STRING.
+        unescape: Parse TARGETSTRING for escaped characters (includes '\\t',\
+            '\\n', '\\r').
+        quiet: Do not report files with no strings found. Use -quiet -quiet to\
+            avoid any reporting.
+        help_: Show help message and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "strblast",
+        "targetstring": targetstring,
+        "input_files": input_files,
+        "unescape": unescape,
+        "quiet": quiet,
+        "help": help_,
+    }
+    if new_char is not None:
+        params["new_char"] = new_char
+    if new_string is not None:
+        params["new_string"] = new_string
+    return params
+
+
+def strblast_cargs(
+    params: StrblastParameters,
+    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("strblast")
+    cargs.append(params.get("targetstring"))
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("new_char") is not None:
+        cargs.extend([
+            "-new_char",
+            params.get("new_char")
+        ])
+    if params.get("new_string") is not None:
+        cargs.extend([
+            "-new_string",
+            params.get("new_string")
+        ])
+    if params.get("unescape"):
+        cargs.append("-unescape")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def strblast_outputs(
+    params: StrblastParameters,
+    execution: Execution,
+) -> StrblastOutputs:
+    """
+    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 = StrblastOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def strblast_execute(
+    params: StrblastParameters,
+    execution: Execution,
+) -> StrblastOutputs:
+    """
+    Finds exact copies of the target string in each of the input files, and replaces
+    all characters with some junk string.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `StrblastOutputs`).
+    """
+    params = execution.params(params)
+    cargs = strblast_cargs(params, execution)
+    ret = strblast_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def strblast(
+    targetstring: str,
+    input_files: list[InputPathType],
+    new_char: str | None = None,
+    new_string: str | None = None,
+    unescape: bool = False,
+    quiet: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> StrblastOutputs:
+    """
+    Finds exact copies of the target string in each of the input files, and replaces
+    all characters with some junk string.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        targetstring: Target string to search for in the input files.
+        input_files: Input files to search for the target string.
+        new_char: Replace TARGETSTRING with CHAR (repeated).
+        new_string: Replace TARGETSTRING with STRING.
+        unescape: Parse TARGETSTRING for escaped characters (includes '\\t',\
+            '\\n', '\\r').
+        quiet: Do not report files with no strings found. Use -quiet -quiet to\
+            avoid any reporting.
+        help_: Show help message and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `StrblastOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(STRBLAST_METADATA)
+    params = strblast_params(
+        targetstring=targetstring,
+        input_files=input_files,
+        new_char=new_char,
+        new_string=new_string,
+        unescape=unescape,
+        quiet=quiet,
+        help_=help_,
+    )
+    return strblast_execute(params, execution)
+
+
+__all__ = [
+    "STRBLAST_METADATA",
+    "StrblastOutputs",
+    "StrblastParameters",
+    "strblast",
+    "strblast_params",
+]

niwrap_afni/afni/suma_change_spec.py

@@ -0,0 +1,225 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SUMA_CHANGE_SPEC_METADATA = Metadata(
+    id="4bf222ffae950010f81275acc0be3c92fdd2d01c.boutiques",
+    name="suma_change_spec",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SumaChangeSpecParameters = typing.TypedDict('SumaChangeSpecParameters', {
+    "__STYX_TYPE__": typing.Literal["suma_change_spec"],
+    "input": InputPathType,
+    "state": str,
+    "domainparent": typing.NotRequired[str | None],
+    "output": typing.NotRequired[str | None],
+    "remove": bool,
+    "anatomical": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "suma_change_spec": suma_change_spec_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 {
+        "suma_change_spec": suma_change_spec_outputs,
+    }.get(t)
+
+
+class SumaChangeSpecOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `suma_change_spec(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_spec: OutputPathType | None
+    """New Spec file"""
+    backup_spec: OutputPathType
+    """Backup of the original Spec file"""
+
+
+def suma_change_spec_params(
+    input_: InputPathType,
+    state: str,
+    domainparent: str | None = None,
+    output: str | None = None,
+    remove: bool = False,
+    anatomical: bool = False,
+) -> SumaChangeSpecParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: SUMA Spec file to change.
+        state: State within the Spec file to change.
+        domainparent: New Domain Parent for the state within the Spec file.
+        output: Name to which the new Spec file will be temporarily written.
+        remove: Remove the automatically created backup.
+        anatomical: Add 'Anatomical = Y' to the selected SurfaceState.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "suma_change_spec",
+        "input": input_,
+        "state": state,
+        "remove": remove,
+        "anatomical": anatomical,
+    }
+    if domainparent is not None:
+        params["domainparent"] = domainparent
+    if output is not None:
+        params["output"] = output
+    return params
+
+
+def suma_change_spec_cargs(
+    params: SumaChangeSpecParameters,
+    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("suma_change_spec")
+    cargs.append(execution.input_file(params.get("input")))
+    cargs.append(params.get("state"))
+    if params.get("domainparent") is not None:
+        cargs.append(params.get("domainparent"))
+    if params.get("output") is not None:
+        cargs.append(params.get("output"))
+    if params.get("remove"):
+        cargs.append("-remove")
+    if params.get("anatomical"):
+        cargs.append("-anatomical")
+    return cargs
+
+
+def suma_change_spec_outputs(
+    params: SumaChangeSpecParameters,
+    execution: Execution,
+) -> SumaChangeSpecOutputs:
+    """
+    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 = SumaChangeSpecOutputs(
+        root=execution.output_file("."),
+        output_spec=execution.output_file(params.get("output")) if (params.get("output") is not None) else None,
+        backup_spec=execution.output_file(pathlib.Path(params.get("input")).name + ".bkp"),
+    )
+    return ret
+
+
+def suma_change_spec_execute(
+    params: SumaChangeSpecParameters,
+    execution: Execution,
+) -> SumaChangeSpecOutputs:
+    """
+    This program changes SUMA's surface specification (Spec) files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SumaChangeSpecOutputs`).
+    """
+    params = execution.params(params)
+    cargs = suma_change_spec_cargs(params, execution)
+    ret = suma_change_spec_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def suma_change_spec(
+    input_: InputPathType,
+    state: str,
+    domainparent: str | None = None,
+    output: str | None = None,
+    remove: bool = False,
+    anatomical: bool = False,
+    runner: Runner | None = None,
+) -> SumaChangeSpecOutputs:
+    """
+    This program changes SUMA's surface specification (Spec) files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: SUMA Spec file to change.
+        state: State within the Spec file to change.
+        domainparent: New Domain Parent for the state within the Spec file.
+        output: Name to which the new Spec file will be temporarily written.
+        remove: Remove the automatically created backup.
+        anatomical: Add 'Anatomical = Y' to the selected SurfaceState.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SumaChangeSpecOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SUMA_CHANGE_SPEC_METADATA)
+    params = suma_change_spec_params(
+        input_=input_,
+        state=state,
+        domainparent=domainparent,
+        output=output,
+        remove=remove,
+        anatomical=anatomical,
+    )
+    return suma_change_spec_execute(params, execution)
+
+
+__all__ = [
+    "SUMA_CHANGE_SPEC_METADATA",
+    "SumaChangeSpecOutputs",
+    "SumaChangeSpecParameters",
+    "suma_change_spec",
+    "suma_change_spec_params",
+]

niwrap_afni/afni/suma_glxdino.py

@@ -0,0 +1,175 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SUMA_GLXDINO_METADATA = Metadata(
+    id="010ab925596263ceb26cb004e13fc1698878aefc.boutiques",
+    name="SUMA_glxdino",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SumaGlxdinoParameters = typing.TypedDict('SumaGlxdinoParameters', {
+    "__STYX_TYPE__": typing.Literal["SUMA_glxdino"],
+    "verbose": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "SUMA_glxdino": suma_glxdino_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 SumaGlxdinoOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `suma_glxdino(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def suma_glxdino_params(
+    verbose: bool = False,
+) -> SumaGlxdinoParameters:
+    """
+    Build parameters.
+    
+    Args:
+        verbose: Switch on diagnostic messages.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SUMA_glxdino",
+        "verbose": verbose,
+    }
+    return params
+
+
+def suma_glxdino_cargs(
+    params: SumaGlxdinoParameters,
+    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("SUMA_glxdino")
+    if params.get("verbose"):
+        cargs.append("-v")
+    return cargs
+
+
+def suma_glxdino_outputs(
+    params: SumaGlxdinoParameters,
+    execution: Execution,
+) -> SumaGlxdinoOutputs:
+    """
+    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 = SumaGlxdinoOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def suma_glxdino_execute(
+    params: SumaGlxdinoParameters,
+    execution: Execution,
+) -> SumaGlxdinoOutputs:
+    """
+    A simple openGL test program using GLX. If it does not run, then SUMA certainly
+    won't.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SumaGlxdinoOutputs`).
+    """
+    params = execution.params(params)
+    cargs = suma_glxdino_cargs(params, execution)
+    ret = suma_glxdino_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def suma_glxdino(
+    verbose: bool = False,
+    runner: Runner | None = None,
+) -> SumaGlxdinoOutputs:
+    """
+    A simple openGL test program using GLX. If it does not run, then SUMA certainly
+    won't.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        verbose: Switch on diagnostic messages.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SumaGlxdinoOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SUMA_GLXDINO_METADATA)
+    params = suma_glxdino_params(
+        verbose=verbose,
+    )
+    return suma_glxdino_execute(params, execution)
+
+
+__all__ = [
+    "SUMA_GLXDINO_METADATA",
+    "SumaGlxdinoOutputs",
+    "SumaGlxdinoParameters",
+    "suma_glxdino",
+    "suma_glxdino_params",
+]