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

niwrap_mrtrix/mrtrix/mrcat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRCAT_METADATA = Metadata(
-    id="5576698dbe8f1b712d36026e63a612d70201f08f.boutiques",
+    id="18ee3a555dc21091bd71575f0cabc1362de4ece7.boutiques",
     name="mrcat",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,35 @@ MRCAT_METADATA = Metadata(
 
 
 MrcatConfigParameters = typing.TypedDict('MrcatConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+MrcatConfigParametersTagged = typing.TypedDict('MrcatConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 MrcatParameters = typing.TypedDict('MrcatParameters', {
-    "__STYXTYPE__": typing.Literal["mrcat"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/mrcat"]],
+    "axis": typing.NotRequired[int | None],
+    "datatype": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrcatConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "image1": InputPathType,
+    "image2": list[InputPathType],
+    "output": str,
+})
+MrcatParametersTagged = typing.TypedDict('MrcatParametersTagged', {
+    "@type": typing.Literal["mrtrix/mrcat"],
     "axis": typing.NotRequired[int | None],
     "datatype": typing.NotRequired[str | None],
     "info": bool,
@@ -36,45 +57,12 @@ MrcatParameters = typing.TypedDict('MrcatParameters', {
     "image2": list[InputPathType],
     "output": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mrcat": mrcat_cargs,
-        "config": mrcat_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 {
-        "mrcat": mrcat_outputs,
-    }.get(t)
 
 
 def mrcat_config_params(
     key: str,
     value: str,
-) -> MrcatConfigParameters:
+) -> MrcatConfigParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +73,7 @@ def mrcat_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -107,14 +95,14 @@ def mrcat_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 MrcatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrcat(...)`.
+    Output object returned when calling `MrcatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -136,7 +124,7 @@ def mrcat_params(
     config: list[MrcatConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MrcatParameters:
+) -> MrcatParametersTagged:
     """
     Build parameters.
     
@@ -170,7 +158,7 @@ def mrcat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrcat",
+        "@type": "mrtrix/mrcat",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -207,38 +195,38 @@ def mrcat_cargs(
     """
     cargs = []
     cargs.append("mrcat")
-    if params.get("axis") is not None:
+    if params.get("axis", None) is not None:
         cargs.extend([
             "-axis",
-            str(params.get("axis"))
+            str(params.get("axis", None))
         ])
-    if params.get("datatype") is not None:
+    if params.get("datatype", None) is not None:
         cargs.extend([
             "-datatype",
-            params.get("datatype")
+            params.get("datatype", 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 [mrcat_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("image1")))
-    cargs.extend([execution.input_file(f) for f in params.get("image2")])
-    cargs.append(params.get("output"))
+    cargs.append(execution.input_file(params.get("image1", None)))
+    cargs.extend([execution.input_file(f) for f in params.get("image2", None)])
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -257,16 +245,18 @@ def mrcat_outputs(
     """
     ret = MrcatOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def mrcat_execute(
     params: MrcatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrcatOutputs:
     """
+    mrcat
+    
     Concatenate several images into one.
     
     
@@ -281,10 +271,12 @@ def mrcat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrcatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRCAT_METADATA)
     params = execution.params(params)
     cargs = mrcat_cargs(params, execution)
     ret = mrcat_outputs(params, execution)
@@ -309,6 +301,8 @@ def mrcat(
     runner: Runner | None = None,
 ) -> MrcatOutputs:
     """
+    mrcat
+    
     Concatenate several images into one.
     
     
@@ -351,8 +345,6 @@ def mrcat(
     Returns:
         NamedTuple of outputs (described in `MrcatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRCAT_METADATA)
     params = mrcat_params(
         axis=axis,
         datatype=datatype,
@@ -368,15 +360,14 @@ def mrcat(
         image2=image2,
         output=output,
     )
-    return mrcat_execute(params, execution)
+    return mrcat_execute(params, runner)
 
 
 __all__ = [
     "MRCAT_METADATA",
-    "MrcatConfigParameters",
     "MrcatOutputs",
-    "MrcatParameters",
     "mrcat",
     "mrcat_config_params",
+    "mrcat_execute",
     "mrcat_params",
 ]

niwrap_mrtrix/mrtrix/mrcentroid.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRCENTROID_METADATA = Metadata(
-    id="f917eb70b8105e988cc147a312518157cd650728.boutiques",
+    id="3db7f938efa26f30a08814f6c0e6329316866d53.boutiques",
     name="mrcentroid",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ MRCENTROID_METADATA = Metadata(
 
 
 MrcentroidConfigParameters = typing.TypedDict('MrcentroidConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+MrcentroidConfigParametersTagged = typing.TypedDict('MrcentroidConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 MrcentroidParameters = typing.TypedDict('MrcentroidParameters', {
-    "__STYXTYPE__": typing.Literal["mrcentroid"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/mrcentroid"]],
+    "mask": typing.NotRequired[InputPathType | None],
+    "voxelspace": bool,
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[MrcentroidConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+})
+MrcentroidParametersTagged = typing.TypedDict('MrcentroidParametersTagged', {
+    "@type": typing.Literal["mrtrix/mrcentroid"],
     "mask": typing.NotRequired[InputPathType | None],
     "voxelspace": bool,
     "info": bool,
@@ -34,44 +53,12 @@ MrcentroidParameters = typing.TypedDict('MrcentroidParameters', {
     "version": bool,
     "input": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mrcentroid": mrcentroid_cargs,
-        "config": mrcentroid_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 {
-    }.get(t)
 
 
 def mrcentroid_config_params(
     key: str,
     value: str,
-) -> MrcentroidConfigParameters:
+) -> MrcentroidConfigParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +69,7 @@ def mrcentroid_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -104,14 +91,14 @@ def mrcentroid_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 MrcentroidOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrcentroid(...)`.
+    Output object returned when calling `MrcentroidParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -129,7 +116,7 @@ def mrcentroid_params(
     config: list[MrcentroidConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MrcentroidParameters:
+) -> MrcentroidParametersTagged:
     """
     Build parameters.
     
@@ -154,7 +141,7 @@ def mrcentroid_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrcentroid",
+        "@type": "mrtrix/mrcentroid",
         "voxelspace": voxelspace,
         "info": info,
         "quiet": quiet,
@@ -188,33 +175,33 @@ def mrcentroid_cargs(
     """
     cargs = []
     cargs.append("mrcentroid")
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("voxelspace"):
+    if params.get("voxelspace", False):
         cargs.append("-voxelspace")
-    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 [mrcentroid_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("input")))
+    cargs.append(execution.input_file(params.get("input", None)))
     return cargs
 
 
@@ -239,9 +226,11 @@ def mrcentroid_outputs(
 
 def mrcentroid_execute(
     params: MrcentroidParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrcentroidOutputs:
     """
+    mrcentroid
+    
     Determine the centre of mass / centre of gravity of an image.
     
     
@@ -256,10 +245,12 @@ def mrcentroid_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrcentroidOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRCENTROID_METADATA)
     params = execution.params(params)
     cargs = mrcentroid_cargs(params, execution)
     ret = mrcentroid_outputs(params, execution)
@@ -282,6 +273,8 @@ def mrcentroid(
     runner: Runner | None = None,
 ) -> MrcentroidOutputs:
     """
+    mrcentroid
+    
     Determine the centre of mass / centre of gravity of an image.
     
     
@@ -315,8 +308,6 @@ def mrcentroid(
     Returns:
         NamedTuple of outputs (described in `MrcentroidOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRCENTROID_METADATA)
     params = mrcentroid_params(
         mask=mask,
         voxelspace=voxelspace,
@@ -330,15 +321,14 @@ def mrcentroid(
         version=version,
         input_=input_,
     )
-    return mrcentroid_execute(params, execution)
+    return mrcentroid_execute(params, runner)
 
 
 __all__ = [
     "MRCENTROID_METADATA",
-    "MrcentroidConfigParameters",
     "MrcentroidOutputs",
-    "MrcentroidParameters",
     "mrcentroid",
     "mrcentroid_config_params",
+    "mrcentroid_execute",
     "mrcentroid_params",
 ]