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

niwrap_freesurfer/freesurfer/mri_gcab_train.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_GCAB_TRAIN_METADATA = Metadata(
-    id="25854951f0e7de8635b58728b8a09edd107a327e.boutiques",
+    id="6ab5802648310f2f9fc90a566ab8717601903a85.boutiques",
     name="mri_gcab_train",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,53 +14,26 @@ MRI_GCAB_TRAIN_METADATA = Metadata(
 
 
 MriGcabTrainParameters = typing.TypedDict('MriGcabTrainParameters', {
-    "__STYXTYPE__": typing.Literal["mri_gcab_train"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_gcab_train"]],
+    "removed_info": typing.NotRequired[str | None],
+})
+MriGcabTrainParametersTagged = typing.TypedDict('MriGcabTrainParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_gcab_train"],
     "removed_info": 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 {
-        "mri_gcab_train": mri_gcab_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 MriGcabTrainOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_gcab_train(...)`.
+    Output object returned when calling `MriGcabTrainParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
 
 
 def mri_gcab_train_params(
-    removed_info: str | None = "mri_gcab_train has been removed from this version of freesurfer.",
-) -> MriGcabTrainParameters:
+    removed_info: str | None = None,
+) -> MriGcabTrainParametersTagged:
     """
     Build parameters.
     
@@ -72,7 +45,7 @@ def mri_gcab_train_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_gcab_train",
+        "@type": "freesurfer/mri_gcab_train",
     }
     if removed_info is not None:
         params["removed_info"] = removed_info
@@ -94,8 +67,8 @@ def mri_gcab_train_cargs(
     """
     cargs = []
     cargs.append("mri_gcab_train")
-    if params.get("removed_info") is not None:
-        cargs.append(params.get("removed_info"))
+    if params.get("removed_info", None) is not None:
+        cargs.append(params.get("removed_info", None))
     return cargs
 
 
@@ -120,9 +93,11 @@ def mri_gcab_train_outputs(
 
 def mri_gcab_train_execute(
     params: MriGcabTrainParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriGcabTrainOutputs:
     """
+    mri_gcab_train
+    
     Previously used command in FreeSurfer for training with Gaussian Classifier
     Atlas-based (GCAB) modeling; has been removed in the current version.
     
@@ -132,10 +107,12 @@ def mri_gcab_train_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriGcabTrainOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_GCAB_TRAIN_METADATA)
     params = execution.params(params)
     cargs = mri_gcab_train_cargs(params, execution)
     ret = mri_gcab_train_outputs(params, execution)
@@ -144,10 +121,12 @@ def mri_gcab_train_execute(
 
 
 def mri_gcab_train(
-    removed_info: str | None = "mri_gcab_train has been removed from this version of freesurfer.",
+    removed_info: str | None = None,
     runner: Runner | None = None,
 ) -> MriGcabTrainOutputs:
     """
+    mri_gcab_train
+    
     Previously used command in FreeSurfer for training with Gaussian Classifier
     Atlas-based (GCAB) modeling; has been removed in the current version.
     
@@ -163,18 +142,16 @@ def mri_gcab_train(
     Returns:
         NamedTuple of outputs (described in `MriGcabTrainOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_GCAB_TRAIN_METADATA)
     params = mri_gcab_train_params(
         removed_info=removed_info,
     )
-    return mri_gcab_train_execute(params, execution)
+    return mri_gcab_train_execute(params, runner)
 
 
 __all__ = [
     "MRI_GCAB_TRAIN_METADATA",
     "MriGcabTrainOutputs",
-    "MriGcabTrainParameters",
     "mri_gcab_train",
+    "mri_gcab_train_execute",
     "mri_gcab_train_params",
 ]

niwrap_freesurfer/freesurfer/mri_gcut.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_GCUT_METADATA = Metadata(
-    id="a14107292a30b2b35f5cae7aa2137f0efa242639.boutiques",
+    id="76b8b53c2ef0fb35e8dba1777373bd271dee5857.boutiques",
     name="mri_gcut",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRI_GCUT_METADATA = Metadata(
 
 
 MriGcutParameters = typing.TypedDict('MriGcutParameters', {
-    "__STYXTYPE__": typing.Literal["mri_gcut"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_gcut"]],
+    "wmmask_110": bool,
+    "mult_file": typing.NotRequired[InputPathType | None],
+    "threshold_value": typing.NotRequired[float | None],
+    "infile": InputPathType,
+    "outfile": str,
+})
+MriGcutParametersTagged = typing.TypedDict('MriGcutParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_gcut"],
     "wmmask_110": bool,
     "mult_file": typing.NotRequired[InputPathType | None],
     "threshold_value": typing.NotRequired[float | None],
     "infile": InputPathType,
     "outfile": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_gcut": mri_gcut_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 {
-        "mri_gcut": mri_gcut_outputs,
-    }.get(t)
 
 
 class MriGcutOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_gcut(...)`.
+    Output object returned when calling `MriGcutParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mri_gcut_params(
     wmmask_110: bool = False,
     mult_file: InputPathType | None = None,
     threshold_value: float | None = None,
-) -> MriGcutParameters:
+) -> MriGcutParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +65,7 @@ def mri_gcut_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_gcut",
+        "@type": "freesurfer/mri_gcut",
         "wmmask_110": wmmask_110,
         "infile": infile,
         "outfile": outfile,
@@ -116,20 +92,20 @@ def mri_gcut_cargs(
     """
     cargs = []
     cargs.append("mri_gcut")
-    if params.get("wmmask_110"):
+    if params.get("wmmask_110", False):
         cargs.append("-110")
-    if params.get("mult_file") is not None:
+    if params.get("mult_file", None) is not None:
         cargs.extend([
             "-mult",
-            execution.input_file(params.get("mult_file"))
+            execution.input_file(params.get("mult_file", None))
         ])
-    if params.get("threshold_value") is not None:
+    if params.get("threshold_value", None) is not None:
         cargs.extend([
             "-T",
-            str(params.get("threshold_value"))
+            str(params.get("threshold_value", None))
         ])
-    cargs.append(execution.input_file(params.get("infile")))
-    cargs.append(params.get("outfile"))
+    cargs.append(execution.input_file(params.get("infile", None)))
+    cargs.append(params.get("outfile", None))
     return cargs
 
 
@@ -148,16 +124,18 @@ def mri_gcut_outputs(
     """
     ret = MriGcutOutputs(
         root=execution.output_file("."),
-        output_mask_file=execution.output_file(params.get("outfile")),
+        output_mask_file=execution.output_file(params.get("outfile", None)),
     )
     return ret
 
 
 def mri_gcut_execute(
     params: MriGcutParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriGcutOutputs:
     """
+    mri_gcut
+    
     Skull stripping algorithm based on graph cuts.
     
     Author: FreeSurfer Developers
@@ -166,10 +144,12 @@ def mri_gcut_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriGcutOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_GCUT_METADATA)
     params = execution.params(params)
     cargs = mri_gcut_cargs(params, execution)
     ret = mri_gcut_outputs(params, execution)
@@ -186,6 +166,8 @@ def mri_gcut(
     runner: Runner | None = None,
 ) -> MriGcutOutputs:
     """
+    mri_gcut
+    
     Skull stripping algorithm based on graph cuts.
     
     Author: FreeSurfer Developers
@@ -206,8 +188,6 @@ def mri_gcut(
     Returns:
         NamedTuple of outputs (described in `MriGcutOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_GCUT_METADATA)
     params = mri_gcut_params(
         wmmask_110=wmmask_110,
         mult_file=mult_file,
@@ -215,13 +195,13 @@ def mri_gcut(
         infile=infile,
         outfile=outfile,
     )
-    return mri_gcut_execute(params, execution)
+    return mri_gcut_execute(params, runner)
 
 
 __all__ = [
     "MRI_GCUT_METADATA",
     "MriGcutOutputs",
-    "MriGcutParameters",
     "mri_gcut",
+    "mri_gcut_execute",
     "mri_gcut_params",
 ]

niwrap_freesurfer/freesurfer/mri_gdfglm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_GDFGLM_METADATA = Metadata(
-    id="dafcf252ee11d371e4e1d7050ccaf3d1ecfa51d0.boutiques",
+    id="1f66601024a6edf8664437309e6f8ea6af7c6553.boutiques",
     name="mri_gdfglm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ MRI_GDFGLM_METADATA = Metadata(
 
 
 MriGdfglmParameters = typing.TypedDict('MriGdfglmParameters', {
-    "__STYXTYPE__": typing.Literal["mri_gdfglm"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_gdfglm"]],
+    "inputs": typing.NotRequired[str | None],
+})
+MriGdfglmParametersTagged = typing.TypedDict('MriGdfglmParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_gdfglm"],
     "inputs": 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 {
-        "mri_gdfglm": mri_gdfglm_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 {
-        "mri_gdfglm": mri_gdfglm_outputs,
-    }.get(t)
 
 
 class MriGdfglmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_gdfglm(...)`.
+    Output object returned when calling `MriGdfglmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +36,7 @@ class MriGdfglmOutputs(typing.NamedTuple):
 
 def mri_gdfglm_params(
     inputs: str | None = None,
-) -> MriGdfglmParameters:
+) -> MriGdfglmParametersTagged:
     """
     Build parameters.
     
@@ -75,7 +47,7 @@ def mri_gdfglm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_gdfglm",
+        "@type": "freesurfer/mri_gdfglm",
     }
     if inputs is not None:
         params["inputs"] = inputs
@@ -97,8 +69,8 @@ def mri_gdfglm_cargs(
     """
     cargs = []
     cargs.append("mri_gdfglm")
-    if params.get("inputs") is not None:
-        cargs.append(params.get("inputs"))
+    if params.get("inputs", None) is not None:
+        cargs.append(params.get("inputs", None))
     return cargs
 
 
@@ -124,10 +96,13 @@ def mri_gdfglm_outputs(
 
 def mri_gdfglm_execute(
     params: MriGdfglmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriGdfglmOutputs:
     """
-    The mri_gdfglm command has been removed from the current version of FreeSurfer.
+    mri_gdfglm
+    
+    The mri_gdfglm command has been removed from the current version of
+    FreeSurfer.
     
     Author: FreeSurfer Developers
     
@@ -135,10 +110,12 @@ def mri_gdfglm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriGdfglmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_GDFGLM_METADATA)
     params = execution.params(params)
     cargs = mri_gdfglm_cargs(params, execution)
     ret = mri_gdfglm_outputs(params, execution)
@@ -151,7 +128,10 @@ def mri_gdfglm(
     runner: Runner | None = None,
 ) -> MriGdfglmOutputs:
     """
-    The mri_gdfglm command has been removed from the current version of FreeSurfer.
+    mri_gdfglm
+    
+    The mri_gdfglm command has been removed from the current version of
+    FreeSurfer.
     
     Author: FreeSurfer Developers
     
@@ -164,18 +144,16 @@ def mri_gdfglm(
     Returns:
         NamedTuple of outputs (described in `MriGdfglmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_GDFGLM_METADATA)
     params = mri_gdfglm_params(
         inputs=inputs,
     )
-    return mri_gdfglm_execute(params, execution)
+    return mri_gdfglm_execute(params, runner)
 
 
 __all__ = [
     "MRI_GDFGLM_METADATA",
     "MriGdfglmOutputs",
-    "MriGdfglmParameters",
     "mri_gdfglm",
+    "mri_gdfglm_execute",
     "mri_gdfglm_params",
 ]