niwrap-freesurfer 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/inflate_subject_new_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INFLATE_SUBJECT_NEW_RH_METADATA = Metadata(
-    id="3037b7690756cae99cf0b6e186eebe74d51160c7.boutiques",
+    id="d1e34d6eb3e7d1be418620a47b88a358aecca528.boutiques",
     name="inflate_subject_new-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ INFLATE_SUBJECT_NEW_RH_METADATA = Metadata(
 
 
 InflateSubjectNewRhParameters = typing.TypedDict('InflateSubjectNewRhParameters', {
-    "__STYXTYPE__": typing.Literal["inflate_subject_new-rh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/inflate_subject_new-rh"]],
+    "args": typing.NotRequired[str | None],
+})
+InflateSubjectNewRhParametersTagged = typing.TypedDict('InflateSubjectNewRhParametersTagged', {
+    "@type": typing.Literal["freesurfer/inflate_subject_new-rh"],
     "args": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "inflate_subject_new-rh": inflate_subject_new_rh_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)
 
 
 class InflateSubjectNewRhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `inflate_subject_new_rh(...)`.
+    Output object returned when calling `InflateSubjectNewRhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class InflateSubjectNewRhOutputs(typing.NamedTuple):
 
 def inflate_subject_new_rh_params(
     args: str | None = None,
-) -> InflateSubjectNewRhParameters:
+) -> InflateSubjectNewRhParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def inflate_subject_new_rh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "inflate_subject_new-rh",
+        "@type": "freesurfer/inflate_subject_new-rh",
     }
     if args is not None:
         params["args"] = args
@@ -92,10 +65,10 @@ def inflate_subject_new_rh_cargs(
     """
     cargs = []
     cargs.append("inflate_subject_new-rh")
-    if params.get("args") is not None:
+    if params.get("args", None) is not None:
         cargs.extend([
             "-rh",
-            params.get("args")
+            params.get("args", None)
         ])
     return cargs
 
@@ -121,12 +94,14 @@ def inflate_subject_new_rh_outputs(
 
 def inflate_subject_new_rh_execute(
     params: InflateSubjectNewRhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> InflateSubjectNewRhOutputs:
     """
-    This is a placeholder descriptor for the 'inflate_subject_new-rh' command. The
-    tool appears to be part of FreeSurfer but the specific inputs, outputs or
-    options couldn't be extracted from the help text.
+    inflate_subject_new-rh
+    
+    This is a placeholder descriptor for the 'inflate_subject_new-rh' command.
+    The tool appears to be part of FreeSurfer but the specific inputs, outputs
+    or options couldn't be extracted from the help text.
     
     Author: FreeSurfer Developers
     
@@ -134,10 +109,12 @@ def inflate_subject_new_rh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `InflateSubjectNewRhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INFLATE_SUBJECT_NEW_RH_METADATA)
     params = execution.params(params)
     cargs = inflate_subject_new_rh_cargs(params, execution)
     ret = inflate_subject_new_rh_outputs(params, execution)
@@ -150,9 +127,11 @@ def inflate_subject_new_rh(
     runner: Runner | None = None,
 ) -> InflateSubjectNewRhOutputs:
     """
-    This is a placeholder descriptor for the 'inflate_subject_new-rh' command. The
-    tool appears to be part of FreeSurfer but the specific inputs, outputs or
-    options couldn't be extracted from the help text.
+    inflate_subject_new-rh
+    
+    This is a placeholder descriptor for the 'inflate_subject_new-rh' command.
+    The tool appears to be part of FreeSurfer but the specific inputs, outputs
+    or options couldn't be extracted from the help text.
     
     Author: FreeSurfer Developers
     
@@ -164,18 +143,16 @@ def inflate_subject_new_rh(
     Returns:
         NamedTuple of outputs (described in `InflateSubjectNewRhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(INFLATE_SUBJECT_NEW_RH_METADATA)
     params = inflate_subject_new_rh_params(
         args=args,
     )
-    return inflate_subject_new_rh_execute(params, execution)
+    return inflate_subject_new_rh_execute(params, runner)
 
 
 __all__ = [
     "INFLATE_SUBJECT_NEW_RH_METADATA",
     "InflateSubjectNewRhOutputs",
-    "InflateSubjectNewRhParameters",
     "inflate_subject_new_rh",
+    "inflate_subject_new_rh_execute",
     "inflate_subject_new_rh_params",
 ]

niwrap_freesurfer/freesurfer/inflate_subject_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INFLATE_SUBJECT_RH_METADATA = Metadata(
-    id="28e53c36f45c8022dda8ede70eb4400f88349ad3.boutiques",
+    id="588165724a07807cbcd41c87e107c7dcf3252184.boutiques",
     name="inflate_subject-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ INFLATE_SUBJECT_RH_METADATA = Metadata(
 
 
 InflateSubjectRhParameters = typing.TypedDict('InflateSubjectRhParameters', {
-    "__STYXTYPE__": typing.Literal["inflate_subject-rh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/inflate_subject-rh"]],
+    "arguments": typing.NotRequired[str | None],
+})
+InflateSubjectRhParametersTagged = typing.TypedDict('InflateSubjectRhParametersTagged', {
+    "@type": typing.Literal["freesurfer/inflate_subject-rh"],
     "arguments": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "inflate_subject-rh": inflate_subject_rh_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)
 
 
 class InflateSubjectRhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `inflate_subject_rh(...)`.
+    Output object returned when calling `InflateSubjectRhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class InflateSubjectRhOutputs(typing.NamedTuple):
 
 def inflate_subject_rh_params(
     arguments: str | None = None,
-) -> InflateSubjectRhParameters:
+) -> InflateSubjectRhParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def inflate_subject_rh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "inflate_subject-rh",
+        "@type": "freesurfer/inflate_subject-rh",
     }
     if arguments is not None:
         params["arguments"] = arguments
@@ -93,10 +66,10 @@ def inflate_subject_rh_cargs(
     """
     cargs = []
     cargs.append("inflate_subject-rh")
-    if params.get("arguments") is not None:
+    if params.get("arguments", None) is not None:
         cargs.extend([
             "-rh",
-            params.get("arguments")
+            params.get("arguments", None)
         ])
     return cargs
 
@@ -122,9 +95,11 @@ def inflate_subject_rh_outputs(
 
 def inflate_subject_rh_execute(
     params: InflateSubjectRhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> InflateSubjectRhOutputs:
     """
+    inflate_subject-rh
+    
     Freesurfer command to perform an operation on the right hemisphere of a
     subject's brain image data.
     
@@ -134,10 +109,12 @@ def inflate_subject_rh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `InflateSubjectRhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INFLATE_SUBJECT_RH_METADATA)
     params = execution.params(params)
     cargs = inflate_subject_rh_cargs(params, execution)
     ret = inflate_subject_rh_outputs(params, execution)
@@ -150,6 +127,8 @@ def inflate_subject_rh(
     runner: Runner | None = None,
 ) -> InflateSubjectRhOutputs:
     """
+    inflate_subject-rh
+    
     Freesurfer command to perform an operation on the right hemisphere of a
     subject's brain image data.
     
@@ -164,18 +143,16 @@ def inflate_subject_rh(
     Returns:
         NamedTuple of outputs (described in `InflateSubjectRhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(INFLATE_SUBJECT_RH_METADATA)
     params = inflate_subject_rh_params(
         arguments=arguments,
     )
-    return inflate_subject_rh_execute(params, execution)
+    return inflate_subject_rh_execute(params, runner)
 
 
 __all__ = [
     "INFLATE_SUBJECT_RH_METADATA",
     "InflateSubjectRhOutputs",
-    "InflateSubjectRhParameters",
     "inflate_subject_rh",
+    "inflate_subject_rh_execute",
     "inflate_subject_rh_params",
 ]

niwrap_freesurfer/freesurfer/inflate_subject_sc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 INFLATE_SUBJECT_SC_METADATA = Metadata(
-    id="374b86b399ea8397082f6fd310e5b358a734f923.boutiques",
+    id="3ef1078ec04b8330bcd6cfd0c6ff057cd09f46bd.boutiques",
     name="inflate_subject_sc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ INFLATE_SUBJECT_SC_METADATA = Metadata(
 
 
 InflateSubjectScParameters = typing.TypedDict('InflateSubjectScParameters', {
-    "__STYXTYPE__": typing.Literal["inflate_subject_sc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/inflate_subject_sc"]],
+    "subject_dir": str,
+    "verbose": bool,
+    "debug": bool,
+})
+InflateSubjectScParametersTagged = typing.TypedDict('InflateSubjectScParametersTagged', {
+    "@type": typing.Literal["freesurfer/inflate_subject_sc"],
     "subject_dir": str,
     "verbose": bool,
     "debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "inflate_subject_sc": inflate_subject_sc_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 {
-        "inflate_subject_sc": inflate_subject_sc_outputs,
-    }.get(t)
 
 
 class InflateSubjectScOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `inflate_subject_sc(...)`.
+    Output object returned when calling `InflateSubjectScParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def inflate_subject_sc_params(
     subject_dir: str,
     verbose: bool = False,
     debug: bool = False,
-) -> InflateSubjectScParameters:
+) -> InflateSubjectScParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def inflate_subject_sc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "inflate_subject_sc",
+        "@type": "freesurfer/inflate_subject_sc",
         "subject_dir": subject_dir,
         "verbose": verbose,
         "debug": debug,
@@ -102,10 +76,10 @@ def inflate_subject_sc_cargs(
     """
     cargs = []
     cargs.append("inflate_subject_sc")
-    cargs.append(params.get("subject_dir"))
-    if params.get("verbose"):
+    cargs.append(params.get("subject_dir", None))
+    if params.get("verbose", False):
         cargs.append("--verbose")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
     return cargs
 
@@ -125,16 +99,18 @@ def inflate_subject_sc_outputs(
     """
     ret = InflateSubjectScOutputs(
         root=execution.output_file("."),
-        inflated_output=execution.output_file(params.get("subject_dir") + "/inflated_output"),
+        inflated_output=execution.output_file(params.get("subject_dir", None) + "/inflated_output"),
     )
     return ret
 
 
 def inflate_subject_sc_execute(
     params: InflateSubjectScParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> InflateSubjectScOutputs:
     """
+    inflate_subject_sc
+    
     Inferred description: Tool for inflating subject surfaces, specific details
     unavailable.
     
@@ -144,10 +120,12 @@ def inflate_subject_sc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `InflateSubjectScOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(INFLATE_SUBJECT_SC_METADATA)
     params = execution.params(params)
     cargs = inflate_subject_sc_cargs(params, execution)
     ret = inflate_subject_sc_outputs(params, execution)
@@ -162,6 +140,8 @@ def inflate_subject_sc(
     runner: Runner | None = None,
 ) -> InflateSubjectScOutputs:
     """
+    inflate_subject_sc
+    
     Inferred description: Tool for inflating subject surfaces, specific details
     unavailable.
     
@@ -177,20 +157,18 @@ def inflate_subject_sc(
     Returns:
         NamedTuple of outputs (described in `InflateSubjectScOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(INFLATE_SUBJECT_SC_METADATA)
     params = inflate_subject_sc_params(
         subject_dir=subject_dir,
         verbose=verbose,
         debug=debug,
     )
-    return inflate_subject_sc_execute(params, execution)
+    return inflate_subject_sc_execute(params, runner)
 
 
 __all__ = [
     "INFLATE_SUBJECT_SC_METADATA",
     "InflateSubjectScOutputs",
-    "InflateSubjectScParameters",
     "inflate_subject_sc",
+    "inflate_subject_sc_execute",
     "inflate_subject_sc_params",
 ]

niwrap_freesurfer/freesurfer/irepifitvol.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 IREPIFITVOL_METADATA = Metadata(
-    id="663ec789ed974f373b832bb8e7b325af94880c4a.boutiques",
+    id="6bb0f5048cbb49c24ae87b3a07b4ba8f29ce9886.boutiques",
     name="irepifitvol",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ IREPIFITVOL_METADATA = Metadata(
 
 
 IrepifitvolParameters = typing.TypedDict('IrepifitvolParameters', {
-    "__STYXTYPE__": typing.Literal["irepifitvol"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/irepifitvol"]],
+    "input_file": InputPathType,
+    "output_file": str,
+})
+IrepifitvolParametersTagged = typing.TypedDict('IrepifitvolParametersTagged', {
+    "@type": typing.Literal["freesurfer/irepifitvol"],
     "input_file": InputPathType,
     "output_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "irepifitvol": irepifitvol_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 {
-        "irepifitvol": irepifitvol_outputs,
-    }.get(t)
 
 
 class IrepifitvolOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `irepifitvol(...)`.
+    Output object returned when calling `IrepifitvolParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class IrepifitvolOutputs(typing.NamedTuple):
 def irepifitvol_params(
     input_file: InputPathType,
     output_file: str = "fitted_output",
-) -> IrepifitvolParameters:
+) -> IrepifitvolParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def irepifitvol_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "irepifitvol",
+        "@type": "freesurfer/irepifitvol",
         "input_file": input_file,
         "output_file": output_file,
     }
@@ -98,8 +71,8 @@ def irepifitvol_cargs(
     """
     cargs = []
     cargs.append("irepifitvol")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", "fitted_output"))
     return cargs
 
 
@@ -118,16 +91,18 @@ def irepifitvol_outputs(
     """
     ret = IrepifitvolOutputs(
         root=execution.output_file("."),
-        fitted_output=execution.output_file(params.get("output_file") + ".ext"),
+        fitted_output=execution.output_file(params.get("output_file", "fitted_output") + ".ext"),
     )
     return ret
 
 
 def irepifitvol_execute(
     params: IrepifitvolParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> IrepifitvolOutputs:
     """
+    irepifitvol
+    
     A tool for 3D volume fitting.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def irepifitvol_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `IrepifitvolOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(IREPIFITVOL_METADATA)
     params = execution.params(params)
     cargs = irepifitvol_cargs(params, execution)
     ret = irepifitvol_outputs(params, execution)
@@ -153,6 +130,8 @@ def irepifitvol(
     runner: Runner | None = None,
 ) -> IrepifitvolOutputs:
     """
+    irepifitvol
+    
     A tool for 3D volume fitting.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def irepifitvol(
     Returns:
         NamedTuple of outputs (described in `IrepifitvolOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(IREPIFITVOL_METADATA)
     params = irepifitvol_params(
         input_file=input_file,
         output_file=output_file,
     )
-    return irepifitvol_execute(params, execution)
+    return irepifitvol_execute(params, runner)
 
 
 __all__ = [
     "IREPIFITVOL_METADATA",
     "IrepifitvolOutputs",
-    "IrepifitvolParameters",
     "irepifitvol",
+    "irepifitvol_execute",
     "irepifitvol_params",
 ]