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

niwrap_mrtrix/mrtrix/fixelconnectivity.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIXELCONNECTIVITY_METADATA = Metadata(
-    id="a28812763f98c83cba5bf32daac94ae191c3ce0f.boutiques",
+    id="00a3b63e9ba975a20fec13986503b3adc2b7f0f5.boutiques",
     name="fixelconnectivity",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,36 @@ FIXELCONNECTIVITY_METADATA = Metadata(
 
 
 FixelconnectivityConfigParameters = typing.TypedDict('FixelconnectivityConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+FixelconnectivityConfigParametersTagged = typing.TypedDict('FixelconnectivityConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 FixelconnectivityParameters = typing.TypedDict('FixelconnectivityParameters', {
-    "__STYXTYPE__": typing.Literal["fixelconnectivity"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/fixelconnectivity"]],
+    "threshold": typing.NotRequired[float | None],
+    "angle": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelconnectivityConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "fixel_directory": InputPathType,
+    "tracks": InputPathType,
+    "matrix": str,
+})
+FixelconnectivityParametersTagged = typing.TypedDict('FixelconnectivityParametersTagged', {
+    "@type": typing.Literal["mrtrix/fixelconnectivity"],
     "threshold": typing.NotRequired[float | None],
     "angle": typing.NotRequired[float | None],
     "mask": typing.NotRequired[InputPathType | None],
@@ -37,45 +59,12 @@ FixelconnectivityParameters = typing.TypedDict('FixelconnectivityParameters', {
     "tracks": InputPathType,
     "matrix": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fixelconnectivity": fixelconnectivity_cargs,
-        "config": fixelconnectivity_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 {
-        "fixelconnectivity": fixelconnectivity_outputs,
-    }.get(t)
 
 
 def fixelconnectivity_config_params(
     key: str,
     value: str,
-) -> FixelconnectivityConfigParameters:
+) -> FixelconnectivityConfigParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +75,7 @@ def fixelconnectivity_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -108,14 +97,14 @@ def fixelconnectivity_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 FixelconnectivityOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fixelconnectivity(...)`.
+    Output object returned when calling `FixelconnectivityParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -138,7 +127,7 @@ def fixelconnectivity_params(
     config: list[FixelconnectivityConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> FixelconnectivityParameters:
+) -> FixelconnectivityParametersTagged:
     """
     Build parameters.
     
@@ -169,7 +158,7 @@ def fixelconnectivity_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fixelconnectivity",
+        "@type": "mrtrix/fixelconnectivity",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -208,43 +197,43 @@ def fixelconnectivity_cargs(
     """
     cargs = []
     cargs.append("fixelconnectivity")
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-threshold",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("angle") is not None:
+    if params.get("angle", None) is not None:
         cargs.extend([
             "-angle",
-            str(params.get("angle"))
+            str(params.get("angle", None))
         ])
-    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("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 [fixelconnectivity_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("fixel_directory")))
-    cargs.append(execution.input_file(params.get("tracks")))
-    cargs.append(params.get("matrix"))
+    cargs.append(execution.input_file(params.get("fixel_directory", None)))
+    cargs.append(execution.input_file(params.get("tracks", None)))
+    cargs.append(params.get("matrix", None))
     return cargs
 
 
@@ -263,16 +252,18 @@ def fixelconnectivity_outputs(
     """
     ret = FixelconnectivityOutputs(
         root=execution.output_file("."),
-        matrix=execution.output_file(params.get("matrix")),
+        matrix=execution.output_file(params.get("matrix", None)),
     )
     return ret
 
 
 def fixelconnectivity_execute(
     params: FixelconnectivityParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FixelconnectivityOutputs:
     """
+    fixelconnectivity
+    
     Generate a fixel-fixel connectivity matrix.
     
     This command will generate a directory containing three images, which
@@ -289,10 +280,12 @@ def fixelconnectivity_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FixelconnectivityOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELCONNECTIVITY_METADATA)
     params = execution.params(params)
     cargs = fixelconnectivity_cargs(params, execution)
     ret = fixelconnectivity_outputs(params, execution)
@@ -318,6 +311,8 @@ def fixelconnectivity(
     runner: Runner | None = None,
 ) -> FixelconnectivityOutputs:
     """
+    fixelconnectivity
+    
     Generate a fixel-fixel connectivity matrix.
     
     This command will generate a directory containing three images, which
@@ -359,8 +354,6 @@ def fixelconnectivity(
     Returns:
         NamedTuple of outputs (described in `FixelconnectivityOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIXELCONNECTIVITY_METADATA)
     params = fixelconnectivity_params(
         threshold=threshold,
         angle=angle,
@@ -377,15 +370,14 @@ def fixelconnectivity(
         tracks=tracks,
         matrix=matrix,
     )
-    return fixelconnectivity_execute(params, execution)
+    return fixelconnectivity_execute(params, runner)
 
 
 __all__ = [
     "FIXELCONNECTIVITY_METADATA",
-    "FixelconnectivityConfigParameters",
     "FixelconnectivityOutputs",
-    "FixelconnectivityParameters",
     "fixelconnectivity",
     "fixelconnectivity_config_params",
+    "fixelconnectivity_execute",
     "fixelconnectivity_params",
 ]