niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/imstat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IMSTAT_METADATA = Metadata(
-    id="89246952930bbc473cd12fb8e5446fc4fdc11065.boutiques",
+    id="4da535ce4141bcf89f5877ae61702c19f674a35c.boutiques",
     name="imstat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ IMSTAT_METADATA = Metadata(
 
 
 ImstatParameters = typing.TypedDict('ImstatParameters', {
-    "__STYXTYPE__": typing.Literal["imstat"],
+    "@type": typing.NotRequired[typing.Literal["afni/imstat"]],
+    "no_label": bool,
+    "quiet": bool,
+    "pixstat_prefix": typing.NotRequired[str | None],
+    "image_files": list[InputPathType],
+})
+ImstatParametersTagged = typing.TypedDict('ImstatParametersTagged', {
+    "@type": typing.Literal["afni/imstat"],
     "no_label": bool,
     "quiet": bool,
     "pixstat_prefix": typing.NotRequired[str | None],
     "image_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 {
-        "imstat": imstat_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 {
-        "imstat": imstat_outputs,
-    }.get(t)
 
 
 class ImstatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `imstat(...)`.
+    Output object returned when calling `ImstatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +47,7 @@ def imstat_params(
     no_label: bool = False,
     quiet: bool = False,
     pixstat_prefix: str | None = None,
-) -> ImstatParameters:
+) -> ImstatParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +63,7 @@ def imstat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "imstat",
+        "@type": "afni/imstat",
         "no_label": no_label,
         "quiet": quiet,
         "image_files": image_files,
@@ -113,16 +88,16 @@ def imstat_cargs(
     """
     cargs = []
     cargs.append("imstat")
-    if params.get("no_label"):
+    if params.get("no_label", False):
         cargs.append("-nolabel")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("pixstat_prefix") is not None:
+    if params.get("pixstat_prefix", None) is not None:
         cargs.extend([
             "-pixstat",
-            params.get("pixstat_prefix")
+            params.get("pixstat_prefix", None)
         ])
-    cargs.extend([execution.input_file(f) for f in params.get("image_files")])
+    cargs.extend([execution.input_file(f) for f in params.get("image_files", None)])
     return cargs
 
 
@@ -141,17 +116,19 @@ def imstat_outputs(
     """
     ret = ImstatOutputs(
         root=execution.output_file("."),
-        mean_output=execution.output_file(params.get("pixstat_prefix") + ".mean") if (params.get("pixstat_prefix") is not None) else None,
-        sdev_output=execution.output_file(params.get("pixstat_prefix") + ".sdev") if (params.get("pixstat_prefix") is not None) else None,
+        mean_output=execution.output_file(params.get("pixstat_prefix", None) + ".mean") if (params.get("pixstat_prefix") is not None) else None,
+        sdev_output=execution.output_file(params.get("pixstat_prefix", None) + ".sdev") if (params.get("pixstat_prefix") is not None) else None,
     )
     return ret
 
 
 def imstat_execute(
     params: ImstatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ImstatOutputs:
     """
+    imstat
+    
     Calculation of statistics of one or more images.
     
     Author: AFNI Developers
@@ -160,10 +137,12 @@ def imstat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ImstatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMSTAT_METADATA)
     params = execution.params(params)
     cargs = imstat_cargs(params, execution)
     ret = imstat_outputs(params, execution)
@@ -179,6 +158,8 @@ def imstat(
     runner: Runner | None = None,
 ) -> ImstatOutputs:
     """
+    imstat
+    
     Calculation of statistics of one or more images.
     
     Author: AFNI Developers
@@ -197,21 +178,19 @@ def imstat(
     Returns:
         NamedTuple of outputs (described in `ImstatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IMSTAT_METADATA)
     params = imstat_params(
         no_label=no_label,
         quiet=quiet,
         pixstat_prefix=pixstat_prefix,
         image_files=image_files,
     )
-    return imstat_execute(params, execution)
+    return imstat_execute(params, runner)
 
 
 __all__ = [
     "IMSTAT_METADATA",
     "ImstatOutputs",
-    "ImstatParameters",
     "imstat",
+    "imstat_execute",
     "imstat_params",
 ]

niwrap_afni/afni/imupsam.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IMUPSAM_METADATA = Metadata(
-    id="d769dae1e4c21af6509b731daf0c2ab2e1688ccf.boutiques",
+    id="c9b1972bc2d4e437f46d0e160e05368c4300769c.boutiques",
     name="imupsam",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ IMUPSAM_METADATA = Metadata(
 
 
 ImupsamParameters = typing.TypedDict('ImupsamParameters', {
-    "__STYXTYPE__": typing.Literal["imupsam"],
+    "@type": typing.NotRequired[typing.Literal["afni/imupsam"]],
+    "ascii_flag": bool,
+    "factor": int,
+    "input_image": InputPathType,
+    "output_image": str,
+})
+ImupsamParametersTagged = typing.TypedDict('ImupsamParametersTagged', {
+    "@type": typing.Literal["afni/imupsam"],
     "ascii_flag": bool,
     "factor": int,
     "input_image": InputPathType,
     "output_image": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "imupsam": imupsam_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 {
-        "imupsam": imupsam_outputs,
-    }.get(t)
 
 
 class ImupsamOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `imupsam(...)`.
+    Output object returned when calling `ImupsamParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def imupsam_params(
     input_image: InputPathType,
     output_image: str,
     ascii_flag: bool = False,
-) -> ImupsamParameters:
+) -> ImupsamParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +59,7 @@ def imupsam_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "imupsam",
+        "@type": "afni/imupsam",
         "ascii_flag": ascii_flag,
         "factor": factor,
         "input_image": input_image,
@@ -108,11 +83,11 @@ def imupsam_cargs(
     """
     cargs = []
     cargs.append("imupsam")
-    if params.get("ascii_flag"):
+    if params.get("ascii_flag", False):
         cargs.append("-A")
-    cargs.append(str(params.get("factor")))
-    cargs.append(execution.input_file(params.get("input_image")))
-    cargs.append(params.get("output_image"))
+    cargs.append(str(params.get("factor", None)))
+    cargs.append(execution.input_file(params.get("input_image", None)))
+    cargs.append(params.get("output_image", None))
     return cargs
 
 
@@ -131,16 +106,18 @@ def imupsam_outputs(
     """
     ret = ImupsamOutputs(
         root=execution.output_file("."),
-        output_image_file=execution.output_file(params.get("output_image")),
+        output_image_file=execution.output_file(params.get("output_image", None)),
     )
     return ret
 
 
 def imupsam_execute(
     params: ImupsamParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ImupsamOutputs:
     """
+    imupsam
+    
     Upsamples a 2D image by a specified factor.
     
     Author: AFNI Developers
@@ -149,10 +126,12 @@ def imupsam_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ImupsamOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IMUPSAM_METADATA)
     params = execution.params(params)
     cargs = imupsam_cargs(params, execution)
     ret = imupsam_outputs(params, execution)
@@ -168,6 +147,8 @@ def imupsam(
     runner: Runner | None = None,
 ) -> ImupsamOutputs:
     """
+    imupsam
+    
     Upsamples a 2D image by a specified factor.
     
     Author: AFNI Developers
@@ -185,21 +166,19 @@ def imupsam(
     Returns:
         NamedTuple of outputs (described in `ImupsamOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IMUPSAM_METADATA)
     params = imupsam_params(
         ascii_flag=ascii_flag,
         factor=factor,
         input_image=input_image,
         output_image=output_image,
     )
-    return imupsam_execute(params, execution)
+    return imupsam_execute(params, runner)
 
 
 __all__ = [
     "IMUPSAM_METADATA",
     "ImupsamOutputs",
-    "ImupsamParameters",
     "imupsam",
+    "imupsam_execute",
     "imupsam_params",
 ]

niwrap_afni/afni/init_user_dotfiles_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INIT_USER_DOTFILES_PY_METADATA = Metadata(
-    id="7836d6bef57cb420a1e85769b6dd3d108f252382.boutiques",
+    id="c50e66cb3d9bf43cacbd6da9a67ba68c68f7904d.boutiques",
     name="init_user_dotfiles.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,27 @@ INIT_USER_DOTFILES_PY_METADATA = Metadata(
 
 
 InitUserDotfilesPyParameters = typing.TypedDict('InitUserDotfilesPyParameters', {
-    "__STYXTYPE__": typing.Literal["init_user_dotfiles.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/init_user_dotfiles.py"]],
+    "help": bool,
+    "help_dotfiles_all": bool,
+    "help_dotfiles_mod": bool,
+    "help_shells": bool,
+    "hist": bool,
+    "show_valid_opts": bool,
+    "ver": bool,
+    "dot_files_list": typing.NotRequired[list[str] | None],
+    "dir_bin": typing.NotRequired[str | None],
+    "dir_dot": typing.NotRequired[str | None],
+    "do_updates": typing.NotRequired[list[str] | None],
+    "dry_run": bool,
+    "force": bool,
+    "make_backup": typing.NotRequired[str | None],
+    "shell_list": typing.NotRequired[list[str] | None],
+    "test": bool,
+    "verbosity_level": typing.NotRequired[int | None],
+})
+InitUserDotfilesPyParametersTagged = typing.TypedDict('InitUserDotfilesPyParametersTagged', {
+    "@type": typing.Literal["afni/init_user_dotfiles.py"],
     "help": bool,
     "help_dotfiles_all": bool,
     "help_dotfiles_mod": bool,
@@ -33,42 +53,11 @@ InitUserDotfilesPyParameters = typing.TypedDict('InitUserDotfilesPyParameters',
     "test": bool,
     "verbosity_level": typing.NotRequired[int | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "init_user_dotfiles.py": init_user_dotfiles_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 InitUserDotfilesPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `init_user_dotfiles_py(...)`.
+    Output object returned when calling `InitUserDotfilesPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -92,7 +81,7 @@ def init_user_dotfiles_py_params(
     shell_list: list[str] | None = None,
     test: bool = False,
     verbosity_level: int | None = None,
-) -> InitUserDotfilesPyParameters:
+) -> InitUserDotfilesPyParametersTagged:
     """
     Build parameters.
     
@@ -121,7 +110,7 @@ def init_user_dotfiles_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "init_user_dotfiles.py",
+        "@type": "afni/init_user_dotfiles.py",
         "help": help_,
         "help_dotfiles_all": help_dotfiles_all,
         "help_dotfiles_mod": help_dotfiles_mod,
@@ -165,60 +154,60 @@ def init_user_dotfiles_py_cargs(
     """
     cargs = []
     cargs.append("init_user_dotfiles.py")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("help_dotfiles_all"):
+    if params.get("help_dotfiles_all", False):
         cargs.append("-help_dotfiles_all")
-    if params.get("help_dotfiles_mod"):
+    if params.get("help_dotfiles_mod", False):
         cargs.append("-help_dotfiles_mod")
-    if params.get("help_shells"):
+    if params.get("help_shells", False):
         cargs.append("-help_shells")
-    if params.get("hist"):
+    if params.get("hist", False):
         cargs.append("-hist")
-    if params.get("show_valid_opts"):
+    if params.get("show_valid_opts", False):
         cargs.append("-show_valid_opts")
-    if params.get("ver"):
+    if params.get("ver", False):
         cargs.append("-ver")
-    if params.get("dot_files_list") is not None:
+    if params.get("dot_files_list", None) is not None:
         cargs.extend([
             "-dflist",
-            *params.get("dot_files_list")
+            *params.get("dot_files_list", None)
         ])
-    if params.get("dir_bin") is not None:
+    if params.get("dir_bin", None) is not None:
         cargs.extend([
             "-dir_bin",
-            params.get("dir_bin")
+            params.get("dir_bin", None)
         ])
-    if params.get("dir_dot") is not None:
+    if params.get("dir_dot", None) is not None:
         cargs.extend([
             "-dir_dot",
-            params.get("dir_dot")
+            params.get("dir_dot", None)
         ])
-    if params.get("do_updates") is not None:
+    if params.get("do_updates", None) is not None:
         cargs.extend([
             "-do_updates",
-            *params.get("do_updates")
+            *params.get("do_updates", None)
         ])
-    if params.get("dry_run"):
+    if params.get("dry_run", False):
         cargs.append("-dry_run")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("make_backup") is not None:
+    if params.get("make_backup", None) is not None:
         cargs.extend([
             "-make_backup",
-            params.get("make_backup")
+            params.get("make_backup", None)
         ])
-    if params.get("shell_list") is not None:
+    if params.get("shell_list", None) is not None:
         cargs.extend([
             "-shell_list",
-            *params.get("shell_list")
+            *params.get("shell_list", None)
         ])
-    if params.get("test"):
+    if params.get("test", False):
         cargs.append("-test")
-    if params.get("verbosity_level") is not None:
+    if params.get("verbosity_level", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity_level"))
+            str(params.get("verbosity_level", None))
         ])
     return cargs
 
@@ -244,9 +233,11 @@ def init_user_dotfiles_py_outputs(
 
 def init_user_dotfiles_py_execute(
     params: InitUserDotfilesPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> InitUserDotfilesPyOutputs:
     """
+    init_user_dotfiles.py
+    
     Initialize or evaluate user dot files (.cshrc, .bashrc, ...) for system
     settings.
     
@@ -256,10 +247,12 @@ def init_user_dotfiles_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `InitUserDotfilesPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INIT_USER_DOTFILES_PY_METADATA)
     params = execution.params(params)
     cargs = init_user_dotfiles_py_cargs(params, execution)
     ret = init_user_dotfiles_py_outputs(params, execution)
@@ -288,6 +281,8 @@ def init_user_dotfiles_py(
     runner: Runner | None = None,
 ) -> InitUserDotfilesPyOutputs:
     """
+    init_user_dotfiles.py
+    
     Initialize or evaluate user dot files (.cshrc, .bashrc, ...) for system
     settings.
     
@@ -320,8 +315,6 @@ def init_user_dotfiles_py(
     Returns:
         NamedTuple of outputs (described in `InitUserDotfilesPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(INIT_USER_DOTFILES_PY_METADATA)
     params = init_user_dotfiles_py_params(
         help_=help_,
         help_dotfiles_all=help_dotfiles_all,
@@ -341,13 +334,13 @@ def init_user_dotfiles_py(
         test=test,
         verbosity_level=verbosity_level,
     )
-    return init_user_dotfiles_py_execute(params, execution)
+    return init_user_dotfiles_py_execute(params, runner)
 
 
 __all__ = [
     "INIT_USER_DOTFILES_PY_METADATA",
     "InitUserDotfilesPyOutputs",
-    "InitUserDotfilesPyParameters",
     "init_user_dotfiles_py",
+    "init_user_dotfiles_py_execute",
     "init_user_dotfiles_py_params",
 ]