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

niwrap_mrtrix/mrtrix/peaks2fixel.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PEAKS2FIXEL_METADATA = Metadata(
-    id="29d2deba28f1ab844d280ad2e340fd82fd9f1c8f.boutiques",
+    id="78a8247aa596b63f8645ea73cd9578aefa56efef.boutiques",
     name="peaks2fixel",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ PEAKS2FIXEL_METADATA = Metadata(
 
 
 Peaks2fixelConfigParameters = typing.TypedDict('Peaks2fixelConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Peaks2fixelConfigParametersTagged = typing.TypedDict('Peaks2fixelConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Peaks2fixelParameters = typing.TypedDict('Peaks2fixelParameters', {
-    "__STYXTYPE__": typing.Literal["peaks2fixel"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/peaks2fixel"]],
+    "dataname": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Peaks2fixelConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "directions": InputPathType,
+    "fixels": str,
+})
+Peaks2fixelParametersTagged = typing.TypedDict('Peaks2fixelParametersTagged', {
+    "@type": typing.Literal["mrtrix/peaks2fixel"],
     "dataname": typing.NotRequired[str | None],
     "info": bool,
     "quiet": bool,
@@ -34,45 +53,12 @@ Peaks2fixelParameters = typing.TypedDict('Peaks2fixelParameters', {
     "directions": InputPathType,
     "fixels": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "peaks2fixel": peaks2fixel_cargs,
-        "config": peaks2fixel_config_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 {
-        "peaks2fixel": peaks2fixel_outputs,
-    }.get(t)
 
 
 def peaks2fixel_config_params(
     key: str,
     value: str,
-) -> Peaks2fixelConfigParameters:
+) -> Peaks2fixelConfigParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +69,7 @@ def peaks2fixel_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -105,14 +91,14 @@ def peaks2fixel_config_cargs(
     """
     cargs = []
     cargs.append("-config")
-    cargs.append(params.get("key"))
-    cargs.append(params.get("value"))
+    cargs.append(params.get("key", None))
+    cargs.append(params.get("value", None))
     return cargs
 
 
 class Peaks2fixelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `peaks2fixel(...)`.
+    Output object returned when calling `Peaks2fixelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -132,7 +118,7 @@ def peaks2fixel_params(
     config: list[Peaks2fixelConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Peaks2fixelParameters:
+) -> Peaks2fixelParametersTagged:
     """
     Build parameters.
     
@@ -158,7 +144,7 @@ def peaks2fixel_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "peaks2fixel",
+        "@type": "mrtrix/peaks2fixel",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -192,32 +178,32 @@ def peaks2fixel_cargs(
     """
     cargs = []
     cargs.append("peaks2fixel")
-    if params.get("dataname") is not None:
+    if params.get("dataname", None) is not None:
         cargs.extend([
             "-dataname",
-            params.get("dataname")
+            params.get("dataname", None)
         ])
-    if params.get("info"):
+    if params.get("info", False):
         cargs.append("-info")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("nthreads") is not None:
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "-nthreads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("config") is not None:
-        cargs.extend([a for c in [dyn_cargs(s["__STYXTYPE__"])(s, execution) for s in params.get("config")] for a in c])
-    if params.get("help"):
+    if params.get("config", None) is not None:
+        cargs.extend([a for c in [peaks2fixel_config_cargs(s, execution) for s in params.get("config", None)] for a in c])
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    cargs.append(execution.input_file(params.get("directions")))
-    cargs.append(params.get("fixels"))
+    cargs.append(execution.input_file(params.get("directions", None)))
+    cargs.append(params.get("fixels", None))
     return cargs
 
 
@@ -236,16 +222,18 @@ def peaks2fixel_outputs(
     """
     ret = Peaks2fixelOutputs(
         root=execution.output_file("."),
-        fixels=execution.output_file(params.get("fixels")),
+        fixels=execution.output_file(params.get("fixels", None)),
     )
     return ret
 
 
 def peaks2fixel_execute(
     params: Peaks2fixelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Peaks2fixelOutputs:
     """
+    peaks2fixel
+    
     Convert peak directions image to a fixel directory.
     
     
@@ -260,10 +248,12 @@ def peaks2fixel_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Peaks2fixelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PEAKS2FIXEL_METADATA)
     params = execution.params(params)
     cargs = peaks2fixel_cargs(params, execution)
     ret = peaks2fixel_outputs(params, execution)
@@ -286,6 +276,8 @@ def peaks2fixel(
     runner: Runner | None = None,
 ) -> Peaks2fixelOutputs:
     """
+    peaks2fixel
+    
     Convert peak directions image to a fixel directory.
     
     
@@ -320,8 +312,6 @@ def peaks2fixel(
     Returns:
         NamedTuple of outputs (described in `Peaks2fixelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(PEAKS2FIXEL_METADATA)
     params = peaks2fixel_params(
         dataname=dataname,
         info=info,
@@ -335,15 +325,14 @@ def peaks2fixel(
         directions=directions,
         fixels=fixels,
     )
-    return peaks2fixel_execute(params, execution)
+    return peaks2fixel_execute(params, runner)
 
 
 __all__ = [
     "PEAKS2FIXEL_METADATA",
-    "Peaks2fixelConfigParameters",
     "Peaks2fixelOutputs",
-    "Peaks2fixelParameters",
     "peaks2fixel",
     "peaks2fixel_config_params",
+    "peaks2fixel_execute",
     "peaks2fixel_params",
 ]

niwrap_mrtrix/mrtrix/responsemean.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RESPONSEMEAN_METADATA = Metadata(
-    id="81ec998971b969a494c27142aa2c763ec1e1ab0f.boutiques",
+    id="580e677d66de76d497b1d37c93d76dd82a169d45.boutiques",
     name="responsemean",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,7 +14,24 @@ RESPONSEMEAN_METADATA = Metadata(
 
 
 ResponsemeanParameters = typing.TypedDict('ResponsemeanParameters', {
-    "__STYXTYPE__": typing.Literal["responsemean"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/responsemean"]],
+    "input_response": list[InputPathType],
+    "output_response": str,
+    "legacy": bool,
+    "nocleanup": bool,
+    "scratch_dir": typing.NotRequired[InputPathType | None],
+    "continue_scratch_dir": typing.NotRequired[list[InputPathType] | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[float | None],
+    "config": typing.NotRequired[list[str] | None],
+    "help": bool,
+    "version": bool,
+})
+ResponsemeanParametersTagged = typing.TypedDict('ResponsemeanParametersTagged', {
+    "@type": typing.Literal["mrtrix/responsemean"],
     "input_response": list[InputPathType],
     "output_response": str,
     "legacy": bool,
@@ -30,43 +47,11 @@ ResponsemeanParameters = typing.TypedDict('ResponsemeanParameters', {
     "help": 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 {
-        "responsemean": responsemean_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 {
-        "responsemean": responsemean_outputs,
-    }.get(t)
 
 
 class ResponsemeanOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `responsemean(...)`.
+    Output object returned when calling `ResponsemeanParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +74,7 @@ def responsemean_params(
     config: list[str] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> ResponsemeanParameters:
+) -> ResponsemeanParametersTagged:
     """
     Build parameters.
     
@@ -116,7 +101,7 @@ def responsemean_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "responsemean",
+        "@type": "mrtrix/responsemean",
         "input_response": input_response,
         "output_response": output_response,
         "legacy": legacy,
@@ -154,43 +139,43 @@ def responsemean_cargs(
     """
     cargs = []
     cargs.append("responsemean")
-    cargs.extend([execution.input_file(f) for f in params.get("input_response")])
-    cargs.append(params.get("output_response"))
-    if params.get("legacy"):
+    cargs.extend([execution.input_file(f) for f in params.get("input_response", None)])
+    cargs.append(params.get("output_response", None))
+    if params.get("legacy", False):
         cargs.append("-legacy")
-    if params.get("nocleanup"):
+    if params.get("nocleanup", False):
         cargs.append("-nocleanup")
-    if params.get("scratch_dir") is not None:
+    if params.get("scratch_dir", None) is not None:
         cargs.extend([
             "-scratch",
-            execution.input_file(params.get("scratch_dir"))
+            execution.input_file(params.get("scratch_dir", None))
         ])
-    if params.get("continue_scratch_dir") is not None:
+    if params.get("continue_scratch_dir", None) is not None:
         cargs.extend([
             "-continue",
-            *[execution.input_file(f) for f in params.get("continue_scratch_dir")]
+            *[execution.input_file(f) for f in params.get("continue_scratch_dir", None)]
         ])
-    if params.get("info"):
+    if params.get("info", False):
         cargs.append("-info")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("-force")
-    if params.get("nthreads") is not None:
+    if params.get("nthreads", None) is not None:
         cargs.extend([
             "-nthreads",
-            str(params.get("nthreads"))
+            str(params.get("nthreads", None))
         ])
-    if params.get("config") is not None:
+    if params.get("config", None) is not None:
         cargs.extend([
             "-config",
-            *params.get("config")
+            *params.get("config", None)
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
     return cargs
 
@@ -210,16 +195,18 @@ def responsemean_outputs(
     """
     ret = ResponsemeanOutputs(
         root=execution.output_file("."),
-        output_response_file=execution.output_file(params.get("output_response")),
+        output_response_file=execution.output_file(params.get("output_response", None)),
     )
     return ret
 
 
 def responsemean_execute(
     params: ResponsemeanParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ResponsemeanOutputs:
     """
+    responsemean
+    
     Calculate the mean response function from a set of text files.
     
     Author: MRTrix3 Developers
@@ -228,10 +215,12 @@ def responsemean_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ResponsemeanOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RESPONSEMEAN_METADATA)
     params = execution.params(params)
     cargs = responsemean_cargs(params, execution)
     ret = responsemean_outputs(params, execution)
@@ -257,6 +246,8 @@ def responsemean(
     runner: Runner | None = None,
 ) -> ResponsemeanOutputs:
     """
+    responsemean
+    
     Calculate the mean response function from a set of text files.
     
     Author: MRTrix3 Developers
@@ -286,8 +277,6 @@ def responsemean(
     Returns:
         NamedTuple of outputs (described in `ResponsemeanOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RESPONSEMEAN_METADATA)
     params = responsemean_params(
         input_response=input_response,
         output_response=output_response,
@@ -304,13 +293,13 @@ def responsemean(
         help_=help_,
         version=version,
     )
-    return responsemean_execute(params, execution)
+    return responsemean_execute(params, runner)
 
 
 __all__ = [
     "RESPONSEMEAN_METADATA",
     "ResponsemeanOutputs",
-    "ResponsemeanParameters",
     "responsemean",
+    "responsemean_execute",
     "responsemean_params",
 ]