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

niwrap_mrtrix/mrtrix/v_5ttcheck.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_5TTCHECK_METADATA = Metadata(
-    id="173240c50f533553ebf03ac04f99f00671f6b2e7.boutiques",
+    id="c70075c5b07c488757393893376d9b30506df78c.boutiques",
     name="5ttcheck",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,32 @@ V_5TTCHECK_METADATA = Metadata(
 
 
 V5ttcheckConfigParameters = typing.TypedDict('V5ttcheckConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+V5ttcheckConfigParametersTagged = typing.TypedDict('V5ttcheckConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 V5ttcheckParameters = typing.TypedDict('V5ttcheckParameters', {
-    "__STYXTYPE__": typing.Literal["5ttcheck"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/5ttcheck"]],
+    "voxels": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[V5ttcheckConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": list[InputPathType],
+})
+V5ttcheckParametersTagged = typing.TypedDict('V5ttcheckParametersTagged', {
+    "@type": typing.Literal["mrtrix/5ttcheck"],
     "voxels": typing.NotRequired[str | None],
     "info": bool,
     "quiet": bool,
@@ -33,44 +51,12 @@ V5ttcheckParameters = typing.TypedDict('V5ttcheckParameters', {
     "version": bool,
     "input": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "5ttcheck": v_5ttcheck_cargs,
-        "config": v_5ttcheck_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 v_5ttcheck_config_params(
     key: str,
     value: str,
-) -> V5ttcheckConfigParameters:
+) -> V5ttcheckConfigParametersTagged:
     """
     Build parameters.
     
@@ -81,7 +67,7 @@ def v_5ttcheck_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -103,14 +89,14 @@ def v_5ttcheck_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 V5ttcheckOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_5ttcheck(...)`.
+    Output object returned when calling `V5ttcheckParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -127,7 +113,7 @@ def v_5ttcheck_params(
     config: list[V5ttcheckConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> V5ttcheckParameters:
+) -> V5ttcheckParametersTagged:
     """
     Build parameters.
     
@@ -151,7 +137,7 @@ def v_5ttcheck_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "5ttcheck",
+        "@type": "mrtrix/5ttcheck",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -184,31 +170,31 @@ def v_5ttcheck_cargs(
     """
     cargs = []
     cargs.append("5ttcheck")
-    if params.get("voxels") is not None:
+    if params.get("voxels", None) is not None:
         cargs.extend([
             "-voxels",
-            params.get("voxels")
+            params.get("voxels", 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_5ttcheck_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.extend([execution.input_file(f) for f in params.get("input")])
+    cargs.extend([execution.input_file(f) for f in params.get("input", None)])
     return cargs
 
 
@@ -233,9 +219,11 @@ def v_5ttcheck_outputs(
 
 def v_5ttcheck_execute(
     params: V5ttcheckParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V5ttcheckOutputs:
     """
+    5ttcheck
+    
     Thoroughly check that one or more images conform to the expected ACT
     five-tissue-type (5TT) format.
     
@@ -251,10 +239,12 @@ def v_5ttcheck_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V5ttcheckOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_5TTCHECK_METADATA)
     params = execution.params(params)
     cargs = v_5ttcheck_cargs(params, execution)
     ret = v_5ttcheck_outputs(params, execution)
@@ -276,6 +266,8 @@ def v_5ttcheck(
     runner: Runner | None = None,
 ) -> V5ttcheckOutputs:
     """
+    5ttcheck
+    
     Thoroughly check that one or more images conform to the expected ACT
     five-tissue-type (5TT) format.
     
@@ -309,8 +301,6 @@ def v_5ttcheck(
     Returns:
         NamedTuple of outputs (described in `V5ttcheckOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_5TTCHECK_METADATA)
     params = v_5ttcheck_params(
         voxels=voxels,
         info=info,
@@ -323,15 +313,14 @@ def v_5ttcheck(
         version=version,
         input_=input_,
     )
-    return v_5ttcheck_execute(params, execution)
+    return v_5ttcheck_execute(params, runner)
 
 
 __all__ = [
-    "V5ttcheckConfigParameters",
     "V5ttcheckOutputs",
-    "V5ttcheckParameters",
     "V_5TTCHECK_METADATA",
     "v_5ttcheck",
     "v_5ttcheck_config_params",
+    "v_5ttcheck_execute",
     "v_5ttcheck_params",
 ]

niwrap_mrtrix/mrtrix/v_5ttedit.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_5TTEDIT_METADATA = Metadata(
-    id="2f89d4273f8dafe192690c3eb53a171d1d583a82.boutiques",
+    id="600cbbcfcf2cf74592c61897ae8adbd5df0e6fdd.boutiques",
     name="5ttedit",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,38 @@ V_5TTEDIT_METADATA = Metadata(
 
 
 V5tteditConfigParameters = typing.TypedDict('V5tteditConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+V5tteditConfigParametersTagged = typing.TypedDict('V5tteditConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 V5tteditParameters = typing.TypedDict('V5tteditParameters', {
-    "__STYXTYPE__": typing.Literal["5ttedit"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/5ttedit"]],
+    "cgm": typing.NotRequired[InputPathType | None],
+    "sgm": typing.NotRequired[InputPathType | None],
+    "wm": typing.NotRequired[InputPathType | None],
+    "csf": typing.NotRequired[InputPathType | None],
+    "path": typing.NotRequired[InputPathType | None],
+    "none": typing.NotRequired[InputPathType | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[V5tteditConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": InputPathType,
+    "output": str,
+})
+V5tteditParametersTagged = typing.TypedDict('V5tteditParametersTagged', {
+    "@type": typing.Literal["mrtrix/5ttedit"],
     "cgm": typing.NotRequired[InputPathType | None],
     "sgm": typing.NotRequired[InputPathType | None],
     "wm": typing.NotRequired[InputPathType | None],
@@ -39,45 +63,12 @@ V5tteditParameters = typing.TypedDict('V5tteditParameters', {
     "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 {
-        "5ttedit": v_5ttedit_cargs,
-        "config": v_5ttedit_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 {
-        "5ttedit": v_5ttedit_outputs,
-    }.get(t)
 
 
 def v_5ttedit_config_params(
     key: str,
     value: str,
-) -> V5tteditConfigParameters:
+) -> V5tteditConfigParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +79,7 @@ def v_5ttedit_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -110,14 +101,14 @@ def v_5ttedit_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 V5tteditOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_5ttedit(...)`.
+    Output object returned when calling `V5tteditParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -142,7 +133,7 @@ def v_5ttedit_params(
     config: list[V5tteditConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> V5tteditParameters:
+) -> V5tteditParametersTagged:
     """
     Build parameters.
     
@@ -175,7 +166,7 @@ def v_5ttedit_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "5ttedit",
+        "@type": "mrtrix/5ttedit",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -219,57 +210,57 @@ def v_5ttedit_cargs(
     """
     cargs = []
     cargs.append("5ttedit")
-    if params.get("cgm") is not None:
+    if params.get("cgm", None) is not None:
         cargs.extend([
             "-cgm",
-            execution.input_file(params.get("cgm"))
+            execution.input_file(params.get("cgm", None))
         ])
-    if params.get("sgm") is not None:
+    if params.get("sgm", None) is not None:
         cargs.extend([
             "-sgm",
-            execution.input_file(params.get("sgm"))
+            execution.input_file(params.get("sgm", None))
         ])
-    if params.get("wm") is not None:
+    if params.get("wm", None) is not None:
         cargs.extend([
             "-wm",
-            execution.input_file(params.get("wm"))
+            execution.input_file(params.get("wm", None))
         ])
-    if params.get("csf") is not None:
+    if params.get("csf", None) is not None:
         cargs.extend([
             "-csf",
-            execution.input_file(params.get("csf"))
+            execution.input_file(params.get("csf", None))
         ])
-    if params.get("path") is not None:
+    if params.get("path", None) is not None:
         cargs.extend([
             "-path",
-            execution.input_file(params.get("path"))
+            execution.input_file(params.get("path", None))
         ])
-    if params.get("none") is not None:
+    if params.get("none", None) is not None:
         cargs.extend([
             "-none",
-            execution.input_file(params.get("none"))
+            execution.input_file(params.get("none", 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_5ttedit_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
 
 
@@ -288,18 +279,20 @@ def v_5ttedit_outputs(
     """
     ret = V5tteditOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def v_5ttedit_execute(
     params: V5tteditParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V5tteditOutputs:
     """
-    Manually set the partial volume fractions in an ACT five-tissue-type (5TT) image
-    using mask images.
+    5ttedit
+    
+    Manually set the partial volume fractions in an ACT five-tissue-type (5TT)
+    image using mask images.
     
     
     
@@ -313,10 +306,12 @@ def v_5ttedit_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V5tteditOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_5TTEDIT_METADATA)
     params = execution.params(params)
     cargs = v_5ttedit_cargs(params, execution)
     ret = v_5ttedit_outputs(params, execution)
@@ -344,8 +339,10 @@ def v_5ttedit(
     runner: Runner | None = None,
 ) -> V5tteditOutputs:
     """
-    Manually set the partial volume fractions in an ACT five-tissue-type (5TT) image
-    using mask images.
+    5ttedit
+    
+    Manually set the partial volume fractions in an ACT five-tissue-type (5TT)
+    image using mask images.
     
     
     
@@ -386,8 +383,6 @@ def v_5ttedit(
     Returns:
         NamedTuple of outputs (described in `V5tteditOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_5TTEDIT_METADATA)
     params = v_5ttedit_params(
         cgm=cgm,
         sgm=sgm,
@@ -406,15 +401,14 @@ def v_5ttedit(
         input_=input_,
         output=output,
     )
-    return v_5ttedit_execute(params, execution)
+    return v_5ttedit_execute(params, runner)
 
 
 __all__ = [
-    "V5tteditConfigParameters",
     "V5tteditOutputs",
-    "V5tteditParameters",
     "V_5TTEDIT_METADATA",
     "v_5ttedit",
     "v_5ttedit_config_params",
+    "v_5ttedit_execute",
     "v_5ttedit_params",
 ]