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

niwrap_mrtrix/mrtrix/connectome2tck.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CONNECTOME2TCK_METADATA = Metadata(
-    id="32504798f4152f6e8b935fbdd10c1918fca1272d.boutiques",
+    id="ae2ef98104119bc0342c1596e2bea3d807ec75ef.boutiques",
     name="connectome2tck",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,41 @@ CONNECTOME2TCK_METADATA = Metadata(
 
 
 Connectome2tckConfigParameters = typing.TypedDict('Connectome2tckConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+Connectome2tckConfigParametersTagged = typing.TypedDict('Connectome2tckConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 Connectome2tckParameters = typing.TypedDict('Connectome2tckParameters', {
-    "__STYXTYPE__": typing.Literal["connectome2tck"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/connectome2tck"]],
+    "nodes": typing.NotRequired[list[int] | None],
+    "exclusive": bool,
+    "files": typing.NotRequired[str | None],
+    "exemplars": typing.NotRequired[InputPathType | None],
+    "keep_unassigned": bool,
+    "keep_self": bool,
+    "tck_weights_in": typing.NotRequired[InputPathType | None],
+    "prefix_tck_weights_out": typing.NotRequired[str | None],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[Connectome2tckConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "tracks_in": InputPathType,
+    "assignments_in": InputPathType,
+    "prefix_out": str,
+})
+Connectome2tckParametersTagged = typing.TypedDict('Connectome2tckParametersTagged', {
+    "@type": typing.Literal["mrtrix/connectome2tck"],
     "nodes": typing.NotRequired[list[int] | None],
     "exclusive": bool,
     "files": typing.NotRequired[str | None],
@@ -42,44 +69,12 @@ Connectome2tckParameters = typing.TypedDict('Connectome2tckParameters', {
     "assignments_in": InputPathType,
     "prefix_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 {
-        "connectome2tck": connectome2tck_cargs,
-        "config": connectome2tck_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 connectome2tck_config_params(
     key: str,
     value: str,
-) -> Connectome2tckConfigParameters:
+) -> Connectome2tckConfigParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +85,7 @@ def connectome2tck_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -112,14 +107,14 @@ def connectome2tck_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 Connectome2tckOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `connectome2tck(...)`.
+    Output object returned when calling `Connectome2tckParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -145,7 +140,7 @@ def connectome2tck_params(
     config: list[Connectome2tckConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Connectome2tckParameters:
+) -> Connectome2tckParametersTagged:
     """
     Build parameters.
     
@@ -191,7 +186,7 @@ def connectome2tck_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "connectome2tck",
+        "@type": "mrtrix/connectome2tck",
         "exclusive": exclusive,
         "keep_unassigned": keep_unassigned,
         "keep_self": keep_self,
@@ -237,59 +232,59 @@ def connectome2tck_cargs(
     """
     cargs = []
     cargs.append("connectome2tck")
-    if params.get("nodes") is not None:
+    if params.get("nodes", None) is not None:
         cargs.extend([
             "-nodes",
-            ",".join(map(str, params.get("nodes")))
+            ",".join(map(str, params.get("nodes", None)))
         ])
-    if params.get("exclusive"):
+    if params.get("exclusive", False):
         cargs.append("-exclusive")
-    if params.get("files") is not None:
+    if params.get("files", None) is not None:
         cargs.extend([
             "-files",
-            params.get("files")
+            params.get("files", None)
         ])
-    if params.get("exemplars") is not None:
+    if params.get("exemplars", None) is not None:
         cargs.extend([
             "-exemplars",
-            execution.input_file(params.get("exemplars"))
+            execution.input_file(params.get("exemplars", None))
         ])
-    if params.get("keep_unassigned"):
+    if params.get("keep_unassigned", False):
         cargs.append("-keep_unassigned")
-    if params.get("keep_self"):
+    if params.get("keep_self", False):
         cargs.append("-keep_self")
-    if params.get("tck_weights_in") is not None:
+    if params.get("tck_weights_in", None) is not None:
         cargs.extend([
             "-tck_weights_in",
-            execution.input_file(params.get("tck_weights_in"))
+            execution.input_file(params.get("tck_weights_in", None))
         ])
-    if params.get("prefix_tck_weights_out") is not None:
+    if params.get("prefix_tck_weights_out", None) is not None:
         cargs.extend([
             "-prefix_tck_weights_out",
-            params.get("prefix_tck_weights_out")
+            params.get("prefix_tck_weights_out", 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 [connectome2tck_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("tracks_in")))
-    cargs.append(execution.input_file(params.get("assignments_in")))
-    cargs.append(params.get("prefix_out"))
+    cargs.append(execution.input_file(params.get("tracks_in", None)))
+    cargs.append(execution.input_file(params.get("assignments_in", None)))
+    cargs.append(params.get("prefix_out", None))
     return cargs
 
 
@@ -314,11 +309,13 @@ def connectome2tck_outputs(
 
 def connectome2tck_execute(
     params: Connectome2tckParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Connectome2tckOutputs:
     """
-    Extract streamlines from a tractogram based on their assignment to parcellated
-    nodes.
+    connectome2tck
+    
+    Extract streamlines from a tractogram based on their assignment to
+    parcellated nodes.
     
     The compulsory input file "assignments_in" should contain a text file where
     there is one row for each streamline, and each row contains a list of
@@ -338,10 +335,12 @@ def connectome2tck_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Connectome2tckOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONNECTOME2TCK_METADATA)
     params = execution.params(params)
     cargs = connectome2tck_cargs(params, execution)
     ret = connectome2tck_outputs(params, execution)
@@ -372,8 +371,10 @@ def connectome2tck(
     runner: Runner | None = None,
 ) -> Connectome2tckOutputs:
     """
-    Extract streamlines from a tractogram based on their assignment to parcellated
-    nodes.
+    connectome2tck
+    
+    Extract streamlines from a tractogram based on their assignment to
+    parcellated nodes.
     
     The compulsory input file "assignments_in" should contain a text file where
     there is one row for each streamline, and each row contains a list of
@@ -433,8 +434,6 @@ def connectome2tck(
     Returns:
         NamedTuple of outputs (described in `Connectome2tckOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CONNECTOME2TCK_METADATA)
     params = connectome2tck_params(
         nodes=nodes,
         exclusive=exclusive,
@@ -456,15 +455,14 @@ def connectome2tck(
         assignments_in=assignments_in,
         prefix_out=prefix_out,
     )
-    return connectome2tck_execute(params, execution)
+    return connectome2tck_execute(params, runner)
 
 
 __all__ = [
     "CONNECTOME2TCK_METADATA",
-    "Connectome2tckConfigParameters",
     "Connectome2tckOutputs",
-    "Connectome2tckParameters",
     "connectome2tck",
     "connectome2tck_config_params",
+    "connectome2tck_execute",
     "connectome2tck_params",
 ]

niwrap_mrtrix/mrtrix/connectomeedit.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CONNECTOMEEDIT_METADATA = Metadata(
-    id="a299cc4eb27663a67fd9b0e7c142c297b8c23d7f.boutiques",
+    id="7462d968f7a03c022c8bae779dc4c0ddb21e6a0f.boutiques",
     name="connectomeedit",
     package="mrtrix",
     container_image_tag="mrtrix3/mrtrix3:3.0.4",
@@ -14,14 +14,33 @@ CONNECTOMEEDIT_METADATA = Metadata(
 
 
 ConnectomeeditConfigParameters = typing.TypedDict('ConnectomeeditConfigParameters', {
-    "__STYXTYPE__": typing.Literal["config"],
+    "@type": typing.NotRequired[typing.Literal["config"]],
+    "key": str,
+    "value": str,
+})
+ConnectomeeditConfigParametersTagged = typing.TypedDict('ConnectomeeditConfigParametersTagged', {
+    "@type": typing.Literal["config"],
     "key": str,
     "value": str,
 })
 
 
 ConnectomeeditParameters = typing.TypedDict('ConnectomeeditParameters', {
-    "__STYXTYPE__": typing.Literal["connectomeedit"],
+    "@type": typing.NotRequired[typing.Literal["mrtrix/connectomeedit"]],
+    "info": bool,
+    "quiet": bool,
+    "debug": bool,
+    "force": bool,
+    "nthreads": typing.NotRequired[int | None],
+    "config": typing.NotRequired[list[ConnectomeeditConfigParameters] | None],
+    "help": bool,
+    "version": bool,
+    "input": str,
+    "operation": str,
+    "output": str,
+})
+ConnectomeeditParametersTagged = typing.TypedDict('ConnectomeeditParametersTagged', {
+    "@type": typing.Literal["mrtrix/connectomeedit"],
     "info": bool,
     "quiet": bool,
     "debug": bool,
@@ -34,44 +53,12 @@ ConnectomeeditParameters = typing.TypedDict('ConnectomeeditParameters', {
     "operation": str,
     "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 {
-        "connectomeedit": connectomeedit_cargs,
-        "config": connectomeedit_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 connectomeedit_config_params(
     key: str,
     value: str,
-) -> ConnectomeeditConfigParameters:
+) -> ConnectomeeditConfigParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +69,7 @@ def connectomeedit_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "config",
+        "@type": "config",
         "key": key,
         "value": value,
     }
@@ -104,14 +91,14 @@ def connectomeedit_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 ConnectomeeditOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `connectomeedit(...)`.
+    Output object returned when calling `ConnectomeeditParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -129,7 +116,7 @@ def connectomeedit_params(
     config: list[ConnectomeeditConfigParameters] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> ConnectomeeditParameters:
+) -> ConnectomeeditParametersTagged:
     """
     Build parameters.
     
@@ -154,7 +141,7 @@ def connectomeedit_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "connectomeedit",
+        "@type": "mrtrix/connectomeedit",
         "info": info,
         "quiet": quiet,
         "debug": debug,
@@ -187,28 +174,28 @@ def connectomeedit_cargs(
     """
     cargs = []
     cargs.append("connectomeedit")
-    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 [connectomeedit_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(params.get("input"))
-    cargs.append(params.get("operation"))
-    cargs.append(params.get("output"))
+    cargs.append(params.get("input", None))
+    cargs.append(params.get("operation", None))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -233,9 +220,11 @@ def connectomeedit_outputs(
 
 def connectomeedit_execute(
     params: ConnectomeeditParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ConnectomeeditOutputs:
     """
+    connectomeedit
+    
     Perform basic operations on a connectome.
     
     
@@ -250,10 +239,12 @@ def connectomeedit_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ConnectomeeditOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONNECTOMEEDIT_METADATA)
     params = execution.params(params)
     cargs = connectomeedit_cargs(params, execution)
     ret = connectomeedit_outputs(params, execution)
@@ -276,6 +267,8 @@ def connectomeedit(
     runner: Runner | None = None,
 ) -> ConnectomeeditOutputs:
     """
+    connectomeedit
+    
     Perform basic operations on a connectome.
     
     
@@ -309,8 +302,6 @@ def connectomeedit(
     Returns:
         NamedTuple of outputs (described in `ConnectomeeditOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CONNECTOMEEDIT_METADATA)
     params = connectomeedit_params(
         info=info,
         quiet=quiet,
@@ -324,15 +315,14 @@ def connectomeedit(
         operation=operation,
         output=output,
     )
-    return connectomeedit_execute(params, execution)
+    return connectomeedit_execute(params, runner)
 
 
 __all__ = [
     "CONNECTOMEEDIT_METADATA",
-    "ConnectomeeditConfigParameters",
     "ConnectomeeditOutputs",
-    "ConnectomeeditParameters",
     "connectomeedit",
     "connectomeedit_config_params",
+    "connectomeedit_execute",
     "connectomeedit_params",
 ]