niwrap-afni 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/scale_to_map.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SCALE_TO_MAP_METADATA = Metadata(
-    id="9a992db39f38d17e9c86690f3d2805363790bd24.boutiques",
+    id="06ba06811b98fb7d08d9ac952d96068b1af51f39.boutiques",
     name="ScaleToMap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,14 +14,51 @@ SCALE_TO_MAP_METADATA = Metadata(
 
 
 ScaleToMapTraceParameters = typing.TypedDict('ScaleToMapTraceParameters', {
-    "__STYXTYPE__": typing.Literal["trace"],
+    "@type": typing.NotRequired[typing.Literal["trace"]],
+    "trace": bool,
+    "TRACE": bool,
+})
+ScaleToMapTraceParametersTagged = typing.TypedDict('ScaleToMapTraceParametersTagged', {
+    "@type": typing.Literal["trace"],
     "trace": bool,
     "TRACE": bool,
 })
 
 
 ScaleToMapParameters = typing.TypedDict('ScaleToMapParameters', {
-    "__STYXTYPE__": typing.Literal["ScaleToMap"],
+    "@type": typing.NotRequired[typing.Literal["afni/ScaleToMap"]],
+    "input_file": InputPathType,
+    "icol": float,
+    "vcol": float,
+    "cmap": typing.NotRequired[str | None],
+    "cmapfile": typing.NotRequired[InputPathType | None],
+    "cmapdb": typing.NotRequired[InputPathType | None],
+    "frf": bool,
+    "clp": typing.NotRequired[list[float] | None],
+    "perc_clp": typing.NotRequired[list[float] | None],
+    "apr": typing.NotRequired[float | None],
+    "anr": typing.NotRequired[float | None],
+    "interp": bool,
+    "nointerp": bool,
+    "direct": bool,
+    "msk_zero": bool,
+    "msk": typing.NotRequired[list[float] | None],
+    "msk_col": typing.NotRequired[list[float] | None],
+    "nomsk_col": bool,
+    "br": typing.NotRequired[float | None],
+    "help": bool,
+    "verbose": bool,
+    "showmap": bool,
+    "showdb": bool,
+    "novolreg": bool,
+    "noxform": bool,
+    "setenv": typing.NotRequired[str | None],
+    "trace": typing.NotRequired[ScaleToMapTraceParameters | None],
+    "nomall": bool,
+    "yesmall": bool,
+})
+ScaleToMapParametersTagged = typing.TypedDict('ScaleToMapParametersTagged', {
+    "@type": typing.Literal["afni/ScaleToMap"],
     "input_file": InputPathType,
     "icol": float,
     "vcol": float,
@@ -52,44 +89,12 @@ ScaleToMapParameters = typing.TypedDict('ScaleToMapParameters', {
     "nomall": bool,
     "yesmall": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "ScaleToMap": scale_to_map_cargs,
-        "trace": scale_to_map_trace_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)
 
 
 def scale_to_map_trace_params(
     trace_: bool = False,
     trace_2: bool = False,
-) -> ScaleToMapTraceParameters:
+) -> ScaleToMapTraceParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +106,7 @@ def scale_to_map_trace_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "trace",
+        "@type": "trace",
         "trace": trace_,
         "TRACE": trace_2,
     }
@@ -122,16 +127,16 @@ def scale_to_map_trace_cargs(
         Command-line arguments.
     """
     cargs = []
-    if params.get("trace"):
+    if params.get("trace", False):
         cargs.append("-trace")
-    if params.get("TRACE"):
+    if params.get("TRACE", False):
         cargs.append("-TRACE")
     return cargs
 
 
 class ScaleToMapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `scale_to_map(...)`.
+    Output object returned when calling `ScaleToMapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -167,7 +172,7 @@ def scale_to_map_params(
     trace_: ScaleToMapTraceParameters | None = None,
     nomall: bool = False,
     yesmall: bool = False,
-) -> ScaleToMapParameters:
+) -> ScaleToMapParametersTagged:
     """
     Build parameters.
     
@@ -209,7 +214,7 @@ def scale_to_map_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ScaleToMap",
+        "@type": "afni/ScaleToMap",
         "input_file": input_file,
         "icol": icol,
         "vcol": vcol,
@@ -270,93 +275,93 @@ def scale_to_map_cargs(
     """
     cargs = []
     cargs.append("ScaleToMap")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(str(params.get("icol")))
-    cargs.append(str(params.get("vcol")))
-    if params.get("cmap") is not None:
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(str(params.get("icol", None)))
+    cargs.append(str(params.get("vcol", None)))
+    if params.get("cmap", None) is not None:
         cargs.extend([
             "-cmap",
-            params.get("cmap")
+            params.get("cmap", None)
         ])
-    if params.get("cmapfile") is not None:
+    if params.get("cmapfile", None) is not None:
         cargs.extend([
             "-cmapfile",
-            execution.input_file(params.get("cmapfile"))
+            execution.input_file(params.get("cmapfile", None))
         ])
-    if params.get("cmapdb") is not None:
+    if params.get("cmapdb", None) is not None:
         cargs.extend([
             "-cmapdb",
-            execution.input_file(params.get("cmapdb"))
+            execution.input_file(params.get("cmapdb", None))
         ])
-    if params.get("frf"):
+    if params.get("frf", False):
         cargs.append("-frf")
-    if params.get("clp") is not None:
+    if params.get("clp", None) is not None:
         cargs.extend([
             "-clp",
-            *map(str, params.get("clp"))
+            *map(str, params.get("clp", None))
         ])
-    if params.get("perc_clp") is not None:
+    if params.get("perc_clp", None) is not None:
         cargs.extend([
             "-perc_clp",
-            *map(str, params.get("perc_clp"))
+            *map(str, params.get("perc_clp", None))
         ])
-    if params.get("apr") is not None:
+    if params.get("apr", None) is not None:
         cargs.extend([
             "-apr",
-            str(params.get("apr"))
+            str(params.get("apr", None))
         ])
-    if params.get("anr") is not None:
+    if params.get("anr", None) is not None:
         cargs.extend([
             "-anr",
-            str(params.get("anr"))
+            str(params.get("anr", None))
         ])
-    if params.get("interp"):
+    if params.get("interp", False):
         cargs.append("-interp")
-    if params.get("nointerp"):
+    if params.get("nointerp", False):
         cargs.append("-nointerp")
-    if params.get("direct"):
+    if params.get("direct", False):
         cargs.append("-direct")
-    if params.get("msk_zero"):
+    if params.get("msk_zero", False):
         cargs.append("-msk_zero")
-    if params.get("msk") is not None:
+    if params.get("msk", None) is not None:
         cargs.extend([
             "-msk",
-            *map(str, params.get("msk"))
+            *map(str, params.get("msk", None))
         ])
-    if params.get("msk_col") is not None:
+    if params.get("msk_col", None) is not None:
         cargs.extend([
             "-msk_col",
-            *map(str, params.get("msk_col"))
+            *map(str, params.get("msk_col", None))
         ])
-    if params.get("nomsk_col"):
+    if params.get("nomsk_col", False):
         cargs.append("-nomsk_col")
-    if params.get("br") is not None:
+    if params.get("br", None) is not None:
         cargs.extend([
             "-br",
-            str(params.get("br"))
+            str(params.get("br", None))
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-h")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("showmap"):
+    if params.get("showmap", False):
         cargs.append("-showmap")
-    if params.get("showdb"):
+    if params.get("showdb", False):
         cargs.append("-showdb")
-    if params.get("novolreg"):
+    if params.get("novolreg", False):
         cargs.append("-novolreg")
-    if params.get("noxform"):
+    if params.get("noxform", False):
         cargs.append("-noxform")
-    if params.get("setenv") is not None:
+    if params.get("setenv", None) is not None:
         cargs.extend([
             "-setenv",
-            params.get("setenv")
+            params.get("setenv", None)
         ])
-    if params.get("trace") is not None:
-        cargs.extend(dyn_cargs(params.get("trace")["__STYXTYPE__"])(params.get("trace"), execution))
-    if params.get("nomall"):
+    if params.get("trace", None) is not None:
+        cargs.extend(scale_to_map_trace_cargs(params.get("trace", None), execution))
+    if params.get("nomall", False):
         cargs.append("-nomall")
-    if params.get("yesmall"):
+    if params.get("yesmall", False):
         cargs.append("-yesmall")
     return cargs
 
@@ -382,9 +387,11 @@ def scale_to_map_outputs(
 
 def scale_to_map_execute(
     params: ScaleToMapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ScaleToMapOutputs:
     """
+    ScaleToMap
+    
     Tool to scale values to a color map.
     
     Author: AFNI Developers
@@ -393,10 +400,12 @@ def scale_to_map_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ScaleToMapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SCALE_TO_MAP_METADATA)
     params = execution.params(params)
     cargs = scale_to_map_cargs(params, execution)
     ret = scale_to_map_outputs(params, execution)
@@ -437,6 +446,8 @@ def scale_to_map(
     runner: Runner | None = None,
 ) -> ScaleToMapOutputs:
     """
+    ScaleToMap
+    
     Tool to scale values to a color map.
     
     Author: AFNI Developers
@@ -481,8 +492,6 @@ def scale_to_map(
     Returns:
         NamedTuple of outputs (described in `ScaleToMapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SCALE_TO_MAP_METADATA)
     params = scale_to_map_params(
         input_file=input_file,
         icol=icol,
@@ -514,15 +523,14 @@ def scale_to_map(
         nomall=nomall,
         yesmall=yesmall,
     )
-    return scale_to_map_execute(params, execution)
+    return scale_to_map_execute(params, runner)
 
 
 __all__ = [
     "SCALE_TO_MAP_METADATA",
     "ScaleToMapOutputs",
-    "ScaleToMapParameters",
-    "ScaleToMapTraceParameters",
     "scale_to_map",
+    "scale_to_map_execute",
     "scale_to_map_params",
     "scale_to_map_trace_params",
 ]

niwrap_afni/afni/serial_helper.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SERIAL_HELPER_METADATA = Metadata(
-    id="8178f88c2d781af8e9aeb5797401a6ba061486fd.boutiques",
+    id="570f1612d9ad639e31e198a69206c0ff9f24f06a.boutiques",
     name="serial_helper",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ SERIAL_HELPER_METADATA = Metadata(
 
 
 SerialHelperParameters = typing.TypedDict('SerialHelperParameters', {
-    "__STYXTYPE__": typing.Literal["serial_helper"],
+    "@type": typing.NotRequired[typing.Literal["afni/serial_helper"]],
+    "serial_port": str,
+    "sock_num": typing.NotRequired[float | None],
+    "mp_max": typing.NotRequired[float | None],
+    "mp_min": typing.NotRequired[float | None],
+    "num_extra": typing.NotRequired[float | None],
+    "disp_all": typing.NotRequired[float | None],
+    "debug": typing.NotRequired[float | None],
+    "show_times": bool,
+    "help": bool,
+    "hist": bool,
+    "no_serial": bool,
+    "version": bool,
+})
+SerialHelperParametersTagged = typing.TypedDict('SerialHelperParametersTagged', {
+    "@type": typing.Literal["afni/serial_helper"],
     "serial_port": str,
     "sock_num": typing.NotRequired[float | None],
     "mp_max": typing.NotRequired[float | None],
@@ -28,42 +43,11 @@ SerialHelperParameters = typing.TypedDict('SerialHelperParameters', {
     "no_serial": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "serial_helper": serial_helper_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 SerialHelperOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `serial_helper(...)`.
+    Output object returned when calling `SerialHelperParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -82,7 +66,7 @@ def serial_helper_params(
     hist: bool = False,
     no_serial: bool = False,
     version: bool = False,
-) -> SerialHelperParameters:
+) -> SerialHelperParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +87,7 @@ def serial_helper_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "serial_helper",
+        "@type": "afni/serial_helper",
         "serial_port": serial_port,
         "show_times": show_times,
         "help": help_,
@@ -143,47 +127,47 @@ def serial_helper_cargs(
     cargs.append("serial_helper")
     cargs.extend([
         "-serial_port",
-        params.get("serial_port")
+        params.get("serial_port", None)
     ])
-    if params.get("sock_num") is not None:
+    if params.get("sock_num", None) is not None:
         cargs.extend([
             "-sock_num",
-            str(params.get("sock_num"))
+            str(params.get("sock_num", None))
         ])
-    if params.get("mp_max") is not None:
+    if params.get("mp_max", None) is not None:
         cargs.extend([
             "-mp_max",
-            str(params.get("mp_max"))
+            str(params.get("mp_max", None))
         ])
-    if params.get("mp_min") is not None:
+    if params.get("mp_min", None) is not None:
         cargs.extend([
             "-mp_min",
-            str(params.get("mp_min"))
+            str(params.get("mp_min", None))
         ])
-    if params.get("num_extra") is not None:
+    if params.get("num_extra", None) is not None:
         cargs.extend([
             "-num_extra",
-            str(params.get("num_extra"))
+            str(params.get("num_extra", None))
         ])
-    if params.get("disp_all") is not None:
+    if params.get("disp_all", None) is not None:
         cargs.extend([
             "-disp_all",
-            str(params.get("disp_all"))
+            str(params.get("disp_all", None))
         ])
-    if params.get("debug") is not None:
+    if params.get("debug", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug"))
+            str(params.get("debug", None))
         ])
-    if params.get("show_times"):
+    if params.get("show_times", False):
         cargs.append("-show_times")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("hist"):
+    if params.get("hist", False):
         cargs.append("-hist")
-    if params.get("no_serial"):
+    if params.get("no_serial", False):
         cargs.append("-no_serial")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
     return cargs
 
@@ -209,9 +193,11 @@ def serial_helper_outputs(
 
 def serial_helper_execute(
     params: SerialHelperParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SerialHelperOutputs:
     """
+    serial_helper
+    
     Passes motion parameters from socket to serial port.
     
     Author: AFNI Developers
@@ -220,10 +206,12 @@ def serial_helper_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SerialHelperOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SERIAL_HELPER_METADATA)
     params = execution.params(params)
     cargs = serial_helper_cargs(params, execution)
     ret = serial_helper_outputs(params, execution)
@@ -247,6 +235,8 @@ def serial_helper(
     runner: Runner | None = None,
 ) -> SerialHelperOutputs:
     """
+    serial_helper
+    
     Passes motion parameters from socket to serial port.
     
     Author: AFNI Developers
@@ -270,8 +260,6 @@ def serial_helper(
     Returns:
         NamedTuple of outputs (described in `SerialHelperOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SERIAL_HELPER_METADATA)
     params = serial_helper_params(
         serial_port=serial_port,
         sock_num=sock_num,
@@ -286,13 +274,13 @@ def serial_helper(
         no_serial=no_serial,
         version=version,
     )
-    return serial_helper_execute(params, execution)
+    return serial_helper_execute(params, runner)
 
 
 __all__ = [
     "SERIAL_HELPER_METADATA",
     "SerialHelperOutputs",
-    "SerialHelperParameters",
     "serial_helper",
+    "serial_helper_execute",
     "serial_helper_params",
 ]