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

niwrap_mrtrix/mrtrix/v_5tt2gmwmi.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_5TT2GMWMI_METADATA = Metadata(
-    id="a49652340948d08ac441b652a0e867f85d70f9ef.boutiques",
+    id="9364810c76c939f13c428191716ed63148337a9a.boutiques",
     name="5tt2gmwmi",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ V_5TT2GMWMI_METADATA = Metadata(
 
 
 V5tt2gmwmiConfigParameters = typing.TypedDict('V5tt2gmwmiConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+V5tt2gmwmiConfigParametersTagged = typing.TypedDict('V5tt2gmwmiConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 V5tt2gmwmiParameters = typing.TypedDict('V5tt2gmwmiParameters', {
-    "__STYXTYPE__": typing.Literal["5tt2gmwmi"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/5tt2gmwmi"]],
+    "mask_in": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[V5tt2gmwmiConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "5tt_in": InputPathType,
+    "mask_out": str,
+})
+V5tt2gmwmiParametersTagged = typing.TypedDict('V5tt2gmwmiParametersTagged', {
+    "@type": typing.Literal["mrtrix/5tt2gmwmi"],
     "mask_in": typing.NotRequired[InputPathType | None],
     "info": bool,
     "quiet": bool,
@@ -34,45 +53,12 @@ V5tt2gmwmiParameters = typing.TypedDict('V5tt2gmwmiParameters', {
     "5tt_in": InputPathType,
     "mask_out": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "5tt2gmwmi": v_5tt2gmwmi_cargs,
-        "config": v_5tt2gmwmi_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 {
-        "5tt2gmwmi": v_5tt2gmwmi_outputs,
-    }.get(t)
 
 
 def v_5tt2gmwmi_config_params(
     key: str,
     value: str,
-) -> V5tt2gmwmiConfigParameters:
+) -> V5tt2gmwmiConfigParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +69,7 @@ def v_5tt2gmwmi_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -105,14 +91,14 @@ def v_5tt2gmwmi_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 V5tt2gmwmiOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_5tt2gmwmi(...)`.
+    Output object returned when calling `V5tt2gmwmiParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -132,7 +118,7 @@ def v_5tt2gmwmi_params(
     config: list[V5tt2gmwmiConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> V5tt2gmwmiParameters:
+) -> V5tt2gmwmiParametersTagged:
     """
     Build parameters.
     
@@ -159,7 +145,7 @@ def v_5tt2gmwmi_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "5tt2gmwmi",
+        "@type": "mrtrix/5tt2gmwmi",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -193,32 +179,32 @@ def v_5tt2gmwmi_cargs(
     """
     cargs = []
     cargs.append("5tt2gmwmi")
-    if params.get("mask_in") is not None:
+    if params.get("mask_in", None) is not None:
         cargs.extend([
             "-mask_in",
-            execution.input_file(params.get("mask_in"))
+            execution.input_file(params.get("mask_in", 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 [v_5tt2gmwmi_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("5tt_in")))
-    cargs.append(params.get("mask_out"))
+    cargs.append(execution.input_file(params.get("5tt_in", None)))
+    cargs.append(params.get("mask_out", None))
     return cargs
 
 
@@ -237,16 +223,18 @@ def v_5tt2gmwmi_outputs(
     """
     ret = V5tt2gmwmiOutputs(
         root=execution.output_file("."),
-        mask_out=execution.output_file(params.get("mask_out")),
+        mask_out=execution.output_file(params.get("mask_out", None)),
     )
     return ret
 
 
 def v_5tt2gmwmi_execute(
     params: V5tt2gmwmiParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V5tt2gmwmiOutputs:
     """
+    5tt2gmwmi
+    
     Generate a mask image appropriate for seeding streamlines on the grey
     matter-white matter interface.
     
@@ -265,10 +253,12 @@ def v_5tt2gmwmi_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V5tt2gmwmiOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_5TT2GMWMI_METADATA)
     params = execution.params(params)
     cargs = v_5tt2gmwmi_cargs(params, execution)
     ret = v_5tt2gmwmi_outputs(params, execution)
@@ -291,6 +281,8 @@ def v_5tt2gmwmi(
     runner: Runner | None = None,
 ) -> V5tt2gmwmiOutputs:
     """
+    5tt2gmwmi
+    
     Generate a mask image appropriate for seeding streamlines on the grey
     matter-white matter interface.
     
@@ -330,8 +322,6 @@ def v_5tt2gmwmi(
     Returns:
         NamedTuple of outputs (described in `V5tt2gmwmiOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_5TT2GMWMI_METADATA)
     params = v_5tt2gmwmi_params(
         mask_in=mask_in,
         info=info,
@@ -345,15 +335,14 @@ def v_5tt2gmwmi(
         v_5tt_in=v_5tt_in,
         mask_out=mask_out,
     )
-    return v_5tt2gmwmi_execute(params, execution)
+    return v_5tt2gmwmi_execute(params, runner)
 
 
 __all__ = [
-    "V5tt2gmwmiConfigParameters",
     "V5tt2gmwmiOutputs",
-    "V5tt2gmwmiParameters",
     "V_5TT2GMWMI_METADATA",
     "v_5tt2gmwmi",
     "v_5tt2gmwmi_config_params",
+    "v_5tt2gmwmi_execute",
     "v_5tt2gmwmi_params",
 ]

niwrap_mrtrix/mrtrix/v_5tt2vis.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_5TT2VIS_METADATA = Metadata(
-    id="03a1929197756fe6117ff3c120f0bf3a5d278522.boutiques",
+    id="79cdcbb89fc6e8b73401cd1c0d4a4e933656160a.boutiques",
     name="5tt2vis",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,38 @@ V_5TT2VIS_METADATA = Metadata(
 
 
 V5tt2visConfigParameters = typing.TypedDict('V5tt2visConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+V5tt2visConfigParametersTagged = typing.TypedDict('V5tt2visConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 V5tt2visParameters = typing.TypedDict('V5tt2visParameters', {
-    "__STYXTYPE__": typing.Literal["5tt2vis"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/5tt2vis"]],
+    "bg": typing.NotRequired[float | None],
+    "cgm": typing.NotRequired[float | None],
+    "sgm": typing.NotRequired[float | None],
+    "wm": typing.NotRequired[float | None],
+    "csf": typing.NotRequired[float | None],
+    "path": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[V5tt2visConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+V5tt2visParametersTagged = typing.TypedDict('V5tt2visParametersTagged', {
+    "@type": typing.Literal["mrtrix/5tt2vis"],
     "bg": typing.NotRequired[float | None],
     "cgm": typing.NotRequired[float | None],
     "sgm": typing.NotRequired[float | None],
@@ -39,45 +63,12 @@ V5tt2visParameters = typing.TypedDict('V5tt2visParameters', {
     "input": 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 {
-        "5tt2vis": v_5tt2vis_cargs,
-        "config": v_5tt2vis_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 {
-        "5tt2vis": v_5tt2vis_outputs,
-    }.get(t)
 
 
 def v_5tt2vis_config_params(
     key: str,
     value: str,
-) -> V5tt2visConfigParameters:
+) -> V5tt2visConfigParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +79,7 @@ def v_5tt2vis_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -110,14 +101,14 @@ def v_5tt2vis_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 V5tt2visOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_5tt2vis(...)`.
+    Output object returned when calling `V5tt2visParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -142,7 +133,7 @@ def v_5tt2vis_params(
     config: list[V5tt2visConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> V5tt2visParameters:
+) -> V5tt2visParametersTagged:
     """
     Build parameters.
     
@@ -171,7 +162,7 @@ def v_5tt2vis_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "5tt2vis",
+        "@type": "mrtrix/5tt2vis",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -215,57 +206,57 @@ def v_5tt2vis_cargs(
     """
     cargs = []
     cargs.append("5tt2vis")
-    if params.get("bg") is not None:
+    if params.get("bg", None) is not None:
         cargs.extend([
             "-bg",
-            str(params.get("bg"))
+            str(params.get("bg", None))
         ])
-    if params.get("cgm") is not None:
+    if params.get("cgm", None) is not None:
         cargs.extend([
             "-cgm",
-            str(params.get("cgm"))
+            str(params.get("cgm", None))
         ])
-    if params.get("sgm") is not None:
+    if params.get("sgm", None) is not None:
         cargs.extend([
             "-sgm",
-            str(params.get("sgm"))
+            str(params.get("sgm", None))
         ])
-    if params.get("wm") is not None:
+    if params.get("wm", None) is not None:
         cargs.extend([
             "-wm",
-            str(params.get("wm"))
+            str(params.get("wm", None))
         ])
-    if params.get("csf") is not None:
+    if params.get("csf", None) is not None:
         cargs.extend([
             "-csf",
-            str(params.get("csf"))
+            str(params.get("csf", None))
         ])
-    if params.get("path") is not None:
+    if params.get("path", None) is not None:
         cargs.extend([
             "-path",
-            str(params.get("path"))
+            str(params.get("path", 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 [v_5tt2vis_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(params.get("output"))
+    cargs.append(execution.input_file(params.get("input", None)))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -284,16 +275,18 @@ def v_5tt2vis_outputs(
     """
     ret = V5tt2visOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def v_5tt2vis_execute(
     params: V5tt2visParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V5tt2visOutputs:
     """
+    5tt2vis
+    
     Generate an image for visualisation purposes from an ACT 5TT segmented
     anatomical image.
     
@@ -309,10 +302,12 @@ def v_5tt2vis_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V5tt2visOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_5TT2VIS_METADATA)
     params = execution.params(params)
     cargs = v_5tt2vis_cargs(params, execution)
     ret = v_5tt2vis_outputs(params, execution)
@@ -340,6 +335,8 @@ def v_5tt2vis(
     runner: Runner | None = None,
 ) -> V5tt2visOutputs:
     """
+    5tt2vis
+    
     Generate an image for visualisation purposes from an ACT 5TT segmented
     anatomical image.
     
@@ -378,8 +375,6 @@ def v_5tt2vis(
     Returns:
         NamedTuple of outputs (described in `V5tt2visOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_5TT2VIS_METADATA)
     params = v_5tt2vis_params(
         bg=bg,
         cgm=cgm,
@@ -398,15 +393,14 @@ def v_5tt2vis(
         input_=input_,
         output=output,
     )
-    return v_5tt2vis_execute(params, execution)
+    return v_5tt2vis_execute(params, runner)
 
 
 __all__ = [
-    "V5tt2visConfigParameters",
     "V5tt2visOutputs",
-    "V5tt2visParameters",
     "V_5TT2VIS_METADATA",
     "v_5tt2vis",
     "v_5tt2vis_config_params",
+    "v_5tt2vis_execute",
     "v_5tt2vis_params",
 ]