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

niwrap_mrtrix/mrtrix/fixelcorrespondence.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIXELCORRESPONDENCE_METADATA = Metadata(
-    id="e8b9ecaf4d43ab1afe6a42a47e88079ef6be0ada.boutiques",
+    id="0cdb6d5a0f6fc504a73335d26a91aed6bead44ba.boutiques",
     name="fixelcorrespondence",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,35 @@ FIXELCORRESPONDENCE_METADATA = Metadata(
 
 
 FixelcorrespondenceConfigParameters = typing.TypedDict('FixelcorrespondenceConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+FixelcorrespondenceConfigParametersTagged = typing.TypedDict('FixelcorrespondenceConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 FixelcorrespondenceParameters = typing.TypedDict('FixelcorrespondenceParameters', {
-    "__STYXTYPE__": typing.Literal["fixelcorrespondence"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/fixelcorrespondence"]],
+    "angle": typing.NotRequired[float | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelcorrespondenceConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "subject_data": InputPathType,
+    "template_directory": InputPathType,
+    "output_directory": str,
+    "output_data": str,
+})
+FixelcorrespondenceParametersTagged = typing.TypedDict('FixelcorrespondenceParametersTagged', {
+    "@type": typing.Literal["mrtrix/fixelcorrespondence"],
     "angle": typing.NotRequired[float | None],
     "info": bool,
     "quiet": bool,
@@ -36,44 +57,12 @@ FixelcorrespondenceParameters = typing.TypedDict('FixelcorrespondenceParameters'
     "output_directory": str,
     "output_data": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fixelcorrespondence": fixelcorrespondence_cargs,
-        "config": fixelcorrespondence_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 fixelcorrespondence_config_params(
     key: str,
     value: str,
-) -> FixelcorrespondenceConfigParameters:
+) -> FixelcorrespondenceConfigParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +73,7 @@ def fixelcorrespondence_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -106,14 +95,14 @@ def fixelcorrespondence_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 FixelcorrespondenceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fixelcorrespondence(...)`.
+    Output object returned when calling `FixelcorrespondenceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -133,7 +122,7 @@ def fixelcorrespondence_params(
     config: list[FixelcorrespondenceConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> FixelcorrespondenceParameters:
+) -> FixelcorrespondenceParametersTagged:
     """
     Build parameters.
     
@@ -163,7 +152,7 @@ def fixelcorrespondence_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fixelcorrespondence",
+        "@type": "mrtrix/fixelcorrespondence",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -199,34 +188,34 @@ def fixelcorrespondence_cargs(
     """
     cargs = []
     cargs.append("fixelcorrespondence")
-    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("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 [fixelcorrespondence_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("subject_data")))
-    cargs.append(execution.input_file(params.get("template_directory")))
-    cargs.append(params.get("output_directory"))
-    cargs.append(params.get("output_data"))
+    cargs.append(execution.input_file(params.get("subject_data", None)))
+    cargs.append(execution.input_file(params.get("template_directory", None)))
+    cargs.append(params.get("output_directory", None))
+    cargs.append(params.get("output_data", None))
     return cargs
 
 
@@ -251,11 +240,13 @@ def fixelcorrespondence_outputs(
 
 def fixelcorrespondence_execute(
     params: FixelcorrespondenceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FixelcorrespondenceOutputs:
     """
-    Obtain fixel-fixel correpondence between a subject fixel image and a template
-    fixel mask.
+    fixelcorrespondence
+    
+    Obtain fixel-fixel correpondence between a subject fixel image and a
+    template fixel mask.
     
     It is assumed that the subject image has already been spatially normalised
     and is aligned with the template. The output fixel image will have the same
@@ -271,10 +262,12 @@ def fixelcorrespondence_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FixelcorrespondenceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELCORRESPONDENCE_METADATA)
     params = execution.params(params)
     cargs = fixelcorrespondence_cargs(params, execution)
     ret = fixelcorrespondence_outputs(params, execution)
@@ -299,8 +292,10 @@ def fixelcorrespondence(
     runner: Runner | None = None,
 ) -> FixelcorrespondenceOutputs:
     """
-    Obtain fixel-fixel correpondence between a subject fixel image and a template
-    fixel mask.
+    fixelcorrespondence
+    
+    Obtain fixel-fixel correpondence between a subject fixel image and a
+    template fixel mask.
     
     It is assumed that the subject image has already been spatially normalised
     and is aligned with the template. The output fixel image will have the same
@@ -340,8 +335,6 @@ def fixelcorrespondence(
     Returns:
         NamedTuple of outputs (described in `FixelcorrespondenceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIXELCORRESPONDENCE_METADATA)
     params = fixelcorrespondence_params(
         angle=angle,
         info=info,
@@ -357,15 +350,14 @@ def fixelcorrespondence(
         output_directory=output_directory,
         output_data=output_data,
     )
-    return fixelcorrespondence_execute(params, execution)
+    return fixelcorrespondence_execute(params, runner)
 
 
 __all__ = [
     "FIXELCORRESPONDENCE_METADATA",
-    "FixelcorrespondenceConfigParameters",
     "FixelcorrespondenceOutputs",
-    "FixelcorrespondenceParameters",
     "fixelcorrespondence",
     "fixelcorrespondence_config_params",
+    "fixelcorrespondence_execute",
     "fixelcorrespondence_params",
 ]

niwrap_mrtrix/mrtrix/fixelcrop.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIXELCROP_METADATA = Metadata(
-    id="a9dc6e85d8f2c07ebac3e15d9b3d6120feff0aaf.boutiques",
+    id="d70da385bb1143b77638a918a070ee631393b7f4.boutiques",
     name="fixelcrop",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ FIXELCROP_METADATA = Metadata(
 
 
 FixelcropConfigParameters = typing.TypedDict('FixelcropConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+FixelcropConfigParametersTagged = typing.TypedDict('FixelcropConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 FixelcropParameters = typing.TypedDict('FixelcropParameters', {
-    "__STYXTYPE__": typing.Literal["fixelcrop"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/fixelcrop"]],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[FixelcropConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input_fixel_directory": InputPathType,
+    "input_fixel_mask": InputPathType,
+    "output_fixel_directory": str,
+})
+FixelcropParametersTagged = typing.TypedDict('FixelcropParametersTagged', {
+    "@type": typing.Literal["mrtrix/fixelcrop"],
     "info": bool,
     "quiet": bool,
     "debug": bool,
@@ -34,45 +53,12 @@ FixelcropParameters = typing.TypedDict('FixelcropParameters', {
     "input_fixel_mask": InputPathType,
     "output_fixel_directory": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fixelcrop": fixelcrop_cargs,
-        "config": fixelcrop_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 {
-        "fixelcrop": fixelcrop_outputs,
-    }.get(t)
 
 
 def fixelcrop_config_params(
     key: str,
     value: str,
-) -> FixelcropConfigParameters:
+) -> FixelcropConfigParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +69,7 @@ def fixelcrop_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -105,14 +91,14 @@ def fixelcrop_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 FixelcropOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fixelcrop(...)`.
+    Output object returned when calling `FixelcropParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -132,7 +118,7 @@ def fixelcrop_params(
     config: list[FixelcropConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> FixelcropParameters:
+) -> FixelcropParametersTagged:
     """
     Build parameters.
     
@@ -159,7 +145,7 @@ def fixelcrop_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fixelcrop",
+        "@type": "mrtrix/fixelcrop",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -192,28 +178,28 @@ def fixelcrop_cargs(
     """
     cargs = []
     cargs.append("fixelcrop")
-    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 [fixelcrop_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_fixel_directory")))
-    cargs.append(execution.input_file(params.get("input_fixel_mask")))
-    cargs.append(params.get("output_fixel_directory"))
+    cargs.append(execution.input_file(params.get("input_fixel_directory", None)))
+    cargs.append(execution.input_file(params.get("input_fixel_mask", None)))
+    cargs.append(params.get("output_fixel_directory", None))
     return cargs
 
 
@@ -232,16 +218,18 @@ def fixelcrop_outputs(
     """
     ret = FixelcropOutputs(
         root=execution.output_file("."),
-        output_fixel_directory=execution.output_file(params.get("output_fixel_directory")),
+        output_fixel_directory=execution.output_file(params.get("output_fixel_directory", None)),
     )
     return ret
 
 
 def fixelcrop_execute(
     params: FixelcropParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FixelcropOutputs:
     """
+    fixelcrop
+    
     Crop/remove fixels from sparse fixel image using a binary fixel mask.
     
     The mask must be input as a fixel data file the same dimensions as the fixel
@@ -257,10 +245,12 @@ def fixelcrop_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FixelcropOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIXELCROP_METADATA)
     params = execution.params(params)
     cargs = fixelcrop_cargs(params, execution)
     ret = fixelcrop_outputs(params, execution)
@@ -283,6 +273,8 @@ def fixelcrop(
     runner: Runner | None = None,
 ) -> FixelcropOutputs:
     """
+    fixelcrop
+    
     Crop/remove fixels from sparse fixel image using a binary fixel mask.
     
     The mask must be input as a fixel data file the same dimensions as the fixel
@@ -319,8 +311,6 @@ def fixelcrop(
     Returns:
         NamedTuple of outputs (described in `FixelcropOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIXELCROP_METADATA)
     params = fixelcrop_params(
         info=info,
         quiet=quiet,
@@ -334,15 +324,14 @@ def fixelcrop(
         input_fixel_mask=input_fixel_mask,
         output_fixel_directory=output_fixel_directory,
     )
-    return fixelcrop_execute(params, execution)
+    return fixelcrop_execute(params, runner)
 
 
 __all__ = [
     "FIXELCROP_METADATA",
-    "FixelcropConfigParameters",
     "FixelcropOutputs",
-    "FixelcropParameters",
     "fixelcrop",
     "fixelcrop_config_params",
+    "fixelcrop_execute",
     "fixelcrop_params",
 ]