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

niwrap_freesurfer/freesurfer/mris_reverse.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_REVERSE_METADATA = Metadata(
-    id="a62b3581c919ee2de9ea29c9c8f31b6b9b96227a.boutiques",
+    id="704c316990d42ff1826268cb554bb6e1cd120722.boutiques",
     name="mris_reverse",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRIS_REVERSE_METADATA = Metadata(
 
 
 MrisReverseParameters = typing.TypedDict('MrisReverseParameters', {
-    "__STYXTYPE__": typing.Literal["mris_reverse"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_reverse"]],
+    "input_surface": InputPathType,
+    "output_surface": str,
+})
+MrisReverseParametersTagged = typing.TypedDict('MrisReverseParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_reverse"],
     "input_surface": InputPathType,
     "output_surface": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_reverse": mris_reverse_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 {
-        "mris_reverse": mris_reverse_outputs,
-    }.get(t)
 
 
 class MrisReverseOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_reverse(...)`.
+    Output object returned when calling `MrisReverseParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MrisReverseOutputs(typing.NamedTuple):
 def mris_reverse_params(
     input_surface: InputPathType,
     output_surface: str,
-) -> MrisReverseParameters:
+) -> MrisReverseParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mris_reverse_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_reverse",
+        "@type": "freesurfer/mris_reverse",
         "input_surface": input_surface,
         "output_surface": output_surface,
     }
@@ -98,8 +71,8 @@ def mris_reverse_cargs(
     """
     cargs = []
     cargs.append("mris_reverse")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(params.get("output_surface"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(params.get("output_surface", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def mris_reverse_outputs(
     """
     ret = MrisReverseOutputs(
         root=execution.output_file("."),
-        reversed_surface=execution.output_file(params.get("output_surface") + ".surf"),
+        reversed_surface=execution.output_file(params.get("output_surface", None) + ".surf"),
     )
     return ret
 
 
 def mris_reverse_execute(
     params: MrisReverseParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisReverseOutputs:
     """
+    mris_reverse
+    
     This tool reverses a cortical surface.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def mris_reverse_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisReverseOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_REVERSE_METADATA)
     params = execution.params(params)
     cargs = mris_reverse_cargs(params, execution)
     ret = mris_reverse_outputs(params, execution)
@@ -153,6 +130,8 @@ def mris_reverse(
     runner: Runner | None = None,
 ) -> MrisReverseOutputs:
     """
+    mris_reverse
+    
     This tool reverses a cortical surface.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def mris_reverse(
     Returns:
         NamedTuple of outputs (described in `MrisReverseOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_REVERSE_METADATA)
     params = mris_reverse_params(
         input_surface=input_surface,
         output_surface=output_surface,
     )
-    return mris_reverse_execute(params, execution)
+    return mris_reverse_execute(params, runner)
 
 
 __all__ = [
     "MRIS_REVERSE_METADATA",
     "MrisReverseOutputs",
-    "MrisReverseParameters",
     "mris_reverse",
+    "mris_reverse_execute",
     "mris_reverse_params",
 ]

niwrap_freesurfer/freesurfer/mris_rf_label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_RF_LABEL_METADATA = Metadata(
-    id="7f1e3e28634018fe4c2b21e53465fa3c07f2cb04.boutiques",
+    id="5d227a8bccb03f1bb79adab691cff32cc55e0f38.boutiques",
     name="mris_rf_label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,26 @@ MRIS_RF_LABEL_METADATA = Metadata(
 
 
 MrisRfLabelParameters = typing.TypedDict('MrisRfLabelParameters', {
-    "__STYXTYPE__": typing.Literal["mris_rf_label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_rf_label"]],
+    "subject": str,
+    "rf_classifier": str,
+    "output_name": str,
+    "hemi": typing.NotRequired[str | None],
+    "surf": typing.NotRequired[str | None],
+})
+MrisRfLabelParametersTagged = typing.TypedDict('MrisRfLabelParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_rf_label"],
     "subject": str,
     "rf_classifier": str,
     "output_name": str,
     "hemi": typing.NotRequired[str | None],
     "surf": 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 {
-        "mris_rf_label": mris_rf_label_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 MrisRfLabelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_rf_label(...)`.
+    Output object returned when calling `MrisRfLabelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,7 +45,7 @@ def mris_rf_label_params(
     output_name: str,
     hemi: str | None = None,
     surf: str | None = None,
-) -> MrisRfLabelParameters:
+) -> MrisRfLabelParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +59,7 @@ def mris_rf_label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_rf_label",
+        "@type": "freesurfer/mris_rf_label",
         "subject": subject,
         "rf_classifier": rf_classifier,
         "output_name": output_name,
@@ -109,18 +86,18 @@ def mris_rf_label_cargs(
     """
     cargs = []
     cargs.append("mris_rf_label")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("rf_classifier"))
-    cargs.append(params.get("output_name"))
-    if params.get("hemi") is not None:
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("rf_classifier", None))
+    cargs.append(params.get("output_name", None))
+    if params.get("hemi", None) is not None:
         cargs.extend([
             "--hemi",
-            params.get("hemi")
+            params.get("hemi", None)
         ])
-    if params.get("surf") is not None:
+    if params.get("surf", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf")
+            params.get("surf", None)
         ])
     return cargs
 
@@ -146,9 +123,11 @@ def mris_rf_label_outputs(
 
 def mris_rf_label_execute(
     params: MrisRfLabelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisRfLabelOutputs:
     """
+    mris_rf_label
+    
     A tool for labeling regions of a surface using random forest classification.
     
     Author: FreeSurfer Developers
@@ -157,10 +136,12 @@ def mris_rf_label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisRfLabelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_RF_LABEL_METADATA)
     params = execution.params(params)
     cargs = mris_rf_label_cargs(params, execution)
     ret = mris_rf_label_outputs(params, execution)
@@ -177,6 +158,8 @@ def mris_rf_label(
     runner: Runner | None = None,
 ) -> MrisRfLabelOutputs:
     """
+    mris_rf_label
+    
     A tool for labeling regions of a surface using random forest classification.
     
     Author: FreeSurfer Developers
@@ -193,8 +176,6 @@ def mris_rf_label(
     Returns:
         NamedTuple of outputs (described in `MrisRfLabelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_RF_LABEL_METADATA)
     params = mris_rf_label_params(
         subject=subject,
         rf_classifier=rf_classifier,
@@ -202,13 +183,13 @@ def mris_rf_label(
         hemi=hemi,
         surf=surf,
     )
-    return mris_rf_label_execute(params, execution)
+    return mris_rf_label_execute(params, runner)
 
 
 __all__ = [
     "MRIS_RF_LABEL_METADATA",
     "MrisRfLabelOutputs",
-    "MrisRfLabelParameters",
     "mris_rf_label",
+    "mris_rf_label_execute",
     "mris_rf_label_params",
 ]

niwrap_freesurfer/freesurfer/mris_rf_train.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_RF_TRAIN_METADATA = Metadata(
-    id="ed47732236da2816714345ea0516a2a3309483a8.boutiques",
+    id="bf5f4317681a309ec278b22f75586f1d97e41b50.boutiques",
     name="mris_rf_train",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ MRIS_RF_TRAIN_METADATA = Metadata(
 
 
 MrisRfTrainParameters = typing.TypedDict('MrisRfTrainParameters', {
-    "__STYXTYPE__": typing.Literal["mris_rf_train"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_rf_train"]],
+    "subjects": list[str],
+    "output_name": str,
+    "hemi": typing.NotRequired[str | None],
+    "surf": typing.NotRequired[str | None],
+})
+MrisRfTrainParametersTagged = typing.TypedDict('MrisRfTrainParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_rf_train"],
     "subjects": list[str],
     "output_name": str,
     "hemi": typing.NotRequired[str | None],
     "surf": 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 {
-        "mris_rf_train": mris_rf_train_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 MrisRfTrainOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_rf_train(...)`.
+    Output object returned when calling `MrisRfTrainParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def mris_rf_train_params(
     output_name: str,
     hemi: str | None = None,
     surf: str | None = None,
-) -> MrisRfTrainParameters:
+) -> MrisRfTrainParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +56,7 @@ def mris_rf_train_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_rf_train",
+        "@type": "freesurfer/mris_rf_train",
         "subjects": subjects,
         "output_name": output_name,
     }
@@ -106,17 +82,17 @@ def mris_rf_train_cargs(
     """
     cargs = []
     cargs.append("mris_rf_train")
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_name"))
-    if params.get("hemi") is not None:
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_name", None))
+    if params.get("hemi", None) is not None:
         cargs.extend([
             "--hemi",
-            params.get("hemi")
+            params.get("hemi", None)
         ])
-    if params.get("surf") is not None:
+    if params.get("surf", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf")
+            params.get("surf", None)
         ])
     return cargs
 
@@ -142,9 +118,11 @@ def mris_rf_train_outputs(
 
 def mris_rf_train_execute(
     params: MrisRfTrainParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisRfTrainOutputs:
     """
+    mris_rf_train
+    
     Tool for training a random forest classifier using MRIS surface data.
     
     Author: FreeSurfer Developers
@@ -153,10 +131,12 @@ def mris_rf_train_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisRfTrainOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_RF_TRAIN_METADATA)
     params = execution.params(params)
     cargs = mris_rf_train_cargs(params, execution)
     ret = mris_rf_train_outputs(params, execution)
@@ -172,6 +152,8 @@ def mris_rf_train(
     runner: Runner | None = None,
 ) -> MrisRfTrainOutputs:
     """
+    mris_rf_train
+    
     Tool for training a random forest classifier using MRIS surface data.
     
     Author: FreeSurfer Developers
@@ -188,21 +170,19 @@ def mris_rf_train(
     Returns:
         NamedTuple of outputs (described in `MrisRfTrainOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_RF_TRAIN_METADATA)
     params = mris_rf_train_params(
         subjects=subjects,
         output_name=output_name,
         hemi=hemi,
         surf=surf,
     )
-    return mris_rf_train_execute(params, execution)
+    return mris_rf_train_execute(params, runner)
 
 
 __all__ = [
     "MRIS_RF_TRAIN_METADATA",
     "MrisRfTrainOutputs",
-    "MrisRfTrainParameters",
     "mris_rf_train",
+    "mris_rf_train_execute",
     "mris_rf_train_params",
 ]

niwrap_freesurfer/freesurfer/mris_rotate.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_ROTATE_METADATA = Metadata(
-    id="d9c070a5b188c09d84fb30d4647745da84c963b5.boutiques",
+    id="43cfae1ef796fac2dcfd8e23fbce456de3e8b830.boutiques",
     name="mris_rotate",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRIS_ROTATE_METADATA = Metadata(
 
 
 MrisRotateParameters = typing.TypedDict('MrisRotateParameters', {
-    "__STYXTYPE__": typing.Literal["mris_rotate"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_rotate"]],
+    "input_surface": InputPathType,
+    "alpha_deg": float,
+    "beta_deg": float,
+    "gamma_deg": float,
+    "output_surface": str,
+    "regfile": typing.NotRequired[InputPathType | None],
+    "invalidate_geometry": bool,
+})
+MrisRotateParametersTagged = typing.TypedDict('MrisRotateParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_rotate"],
     "input_surface": InputPathType,
     "alpha_deg": float,
     "beta_deg": float,
@@ -23,43 +33,11 @@ MrisRotateParameters = typing.TypedDict('MrisRotateParameters', {
     "regfile": typing.NotRequired[InputPathType | None],
     "invalidate_geometry": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_rotate": mris_rotate_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 {
-        "mris_rotate": mris_rotate_outputs,
-    }.get(t)
 
 
 class MrisRotateOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_rotate(...)`.
+    Output object returned when calling `MrisRotateParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mris_rotate_params(
     output_surface: str,
     regfile: InputPathType | None = None,
     invalidate_geometry: bool = False,
-) -> MrisRotateParameters:
+) -> MrisRotateParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +70,7 @@ def mris_rotate_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_rotate",
+        "@type": "freesurfer/mris_rotate",
         "input_surface": input_surface,
         "alpha_deg": alpha_deg,
         "beta_deg": beta_deg,
@@ -120,17 +98,17 @@ def mris_rotate_cargs(
     """
     cargs = []
     cargs.append("mris_rotate")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(str(params.get("alpha_deg")))
-    cargs.append(str(params.get("beta_deg")))
-    cargs.append(str(params.get("gamma_deg")))
-    cargs.append(params.get("output_surface"))
-    if params.get("regfile") is not None:
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(str(params.get("alpha_deg", None)))
+    cargs.append(str(params.get("beta_deg", None)))
+    cargs.append(str(params.get("gamma_deg", None)))
+    cargs.append(params.get("output_surface", None))
+    if params.get("regfile", None) is not None:
         cargs.extend([
             "-r",
-            execution.input_file(params.get("regfile"))
+            execution.input_file(params.get("regfile", None))
         ])
-    if params.get("invalidate_geometry"):
+    if params.get("invalidate_geometry", False):
         cargs.append("-n")
     return cargs
 
@@ -150,16 +128,18 @@ def mris_rotate_outputs(
     """
     ret = MrisRotateOutputs(
         root=execution.output_file("."),
-        rotated_surface=execution.output_file(params.get("output_surface")),
+        rotated_surface=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mris_rotate_execute(
     params: MrisRotateParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisRotateOutputs:
     """
+    mris_rotate
+    
     Rotate a surface given three angles.
     
     Author: FreeSurfer Developers
@@ -168,10 +148,12 @@ def mris_rotate_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisRotateOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_ROTATE_METADATA)
     params = execution.params(params)
     cargs = mris_rotate_cargs(params, execution)
     ret = mris_rotate_outputs(params, execution)
@@ -190,6 +172,8 @@ def mris_rotate(
     runner: Runner | None = None,
 ) -> MrisRotateOutputs:
     """
+    mris_rotate
+    
     Rotate a surface given three angles.
     
     Author: FreeSurfer Developers
@@ -209,8 +193,6 @@ def mris_rotate(
     Returns:
         NamedTuple of outputs (described in `MrisRotateOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_ROTATE_METADATA)
     params = mris_rotate_params(
         input_surface=input_surface,
         alpha_deg=alpha_deg,
@@ -220,13 +202,13 @@ def mris_rotate(
         regfile=regfile,
         invalidate_geometry=invalidate_geometry,
     )
-    return mris_rotate_execute(params, execution)
+    return mris_rotate_execute(params, runner)
 
 
 __all__ = [
     "MRIS_ROTATE_METADATA",
     "MrisRotateOutputs",
-    "MrisRotateParameters",
     "mris_rotate",
+    "mris_rotate_execute",
     "mris_rotate_params",
 ]