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

niwrap_freesurfer/freesurfer/mri_rf_long_train.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_RF_LONG_TRAIN_METADATA = Metadata(
-    id="67ecdb74def4288562f728d10f87ede921f8ca6e.boutiques",
+    id="0f5ceedc87ea542c5819c697dd481277867096bc.boutiques",
     name="mri_rf_long_train",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ MRI_RF_LONG_TRAIN_METADATA = Metadata(
 
 
 MriRfLongTrainParameters = typing.TypedDict('MriRfLongTrainParameters', {
-    "__STYXTYPE__": typing.Literal["mri_rf_long_train"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_rf_long_train"]],
+    "seg_dir": str,
+    "xform": str,
+    "mask": typing.NotRequired[str | None],
+    "node_spacing": typing.NotRequired[float | None],
+    "prior_spacing": typing.NotRequired[float | None],
+    "input_data": typing.NotRequired[list[str] | None],
+    "check": bool,
+    "subjects": list[str],
+    "output_rfa": str,
+})
+MriRfLongTrainParametersTagged = typing.TypedDict('MriRfLongTrainParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_rf_long_train"],
     "seg_dir": str,
     "xform": str,
     "mask": typing.NotRequired[str | None],
@@ -25,43 +37,11 @@ MriRfLongTrainParameters = typing.TypedDict('MriRfLongTrainParameters', {
     "subjects": list[str],
     "output_rfa": 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_rf_long_train": mri_rf_long_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 {
-        "mri_rf_long_train": mri_rf_long_train_outputs,
-    }.get(t)
 
 
 class MriRfLongTrainOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_rf_long_train(...)`.
+    Output object returned when calling `MriRfLongTrainParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def mri_rf_long_train_params(
     prior_spacing: float | None = None,
     input_data: list[str] | None = None,
     check: bool = False,
-) -> MriRfLongTrainParameters:
+) -> MriRfLongTrainParametersTagged:
     """
     Build parameters.
     
@@ -99,7 +79,7 @@ def mri_rf_long_train_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_rf_long_train",
+        "@type": "freesurfer/mri_rf_long_train",
         "seg_dir": seg_dir,
         "xform": xform,
         "check": check,
@@ -134,36 +114,36 @@ def mri_rf_long_train_cargs(
     cargs.append("mri_rf_long_train")
     cargs.extend([
         "-seg",
-        params.get("seg_dir")
+        params.get("seg_dir", None)
     ])
     cargs.extend([
         "-xform",
-        params.get("xform")
+        params.get("xform", None)
     ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            params.get("mask")
+            params.get("mask", None)
         ])
-    if params.get("node_spacing") is not None:
+    if params.get("node_spacing", None) is not None:
         cargs.extend([
             "-node_spacing",
-            str(params.get("node_spacing"))
+            str(params.get("node_spacing", None))
         ])
-    if params.get("prior_spacing") is not None:
+    if params.get("prior_spacing", None) is not None:
         cargs.extend([
             "-prior_spacing",
-            str(params.get("prior_spacing"))
+            str(params.get("prior_spacing", None))
         ])
-    if params.get("input_data") is not None:
+    if params.get("input_data", None) is not None:
         cargs.extend([
             "-input",
-            *params.get("input_data")
+            *params.get("input_data", None)
         ])
-    if params.get("check"):
+    if params.get("check", False):
         cargs.append("-check")
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_rfa"))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_rfa", None))
     return cargs
 
 
@@ -182,16 +162,18 @@ def mri_rf_long_train_outputs(
     """
     ret = MriRfLongTrainOutputs(
         root=execution.output_file("."),
-        output_rfa_file=execution.output_file(params.get("output_rfa") + ".rfa"),
+        output_rfa_file=execution.output_file(params.get("output_rfa", None) + ".rfa"),
     )
     return ret
 
 
 def mri_rf_long_train_execute(
     params: MriRfLongTrainParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriRfLongTrainOutputs:
     """
+    mri_rf_long_train
+    
     Trains GCA data with multiple subjects for FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -200,10 +182,12 @@ def mri_rf_long_train_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriRfLongTrainOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_RF_LONG_TRAIN_METADATA)
     params = execution.params(params)
     cargs = mri_rf_long_train_cargs(params, execution)
     ret = mri_rf_long_train_outputs(params, execution)
@@ -224,6 +208,8 @@ def mri_rf_long_train(
     runner: Runner | None = None,
 ) -> MriRfLongTrainOutputs:
     """
+    mri_rf_long_train
+    
     Trains GCA data with multiple subjects for FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -246,8 +232,6 @@ def mri_rf_long_train(
     Returns:
         NamedTuple of outputs (described in `MriRfLongTrainOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_RF_LONG_TRAIN_METADATA)
     params = mri_rf_long_train_params(
         seg_dir=seg_dir,
         xform=xform,
@@ -259,13 +243,13 @@ def mri_rf_long_train(
         subjects=subjects,
         output_rfa=output_rfa,
     )
-    return mri_rf_long_train_execute(params, execution)
+    return mri_rf_long_train_execute(params, runner)
 
 
 __all__ = [
     "MRI_RF_LONG_TRAIN_METADATA",
     "MriRfLongTrainOutputs",
-    "MriRfLongTrainParameters",
     "mri_rf_long_train",
+    "mri_rf_long_train_execute",
     "mri_rf_long_train_params",
 ]

niwrap_freesurfer/freesurfer/mri_rf_train.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_RF_TRAIN_METADATA = Metadata(
-    id="684653523e7ce03bf975fd3bb486ed0759a86f30.boutiques",
+    id="870f25d10067d5fd18479ccaf606dc51ef296eaf.boutiques",
     name="mri_rf_train",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ MRI_RF_TRAIN_METADATA = Metadata(
 
 
 MriRfTrainParameters = typing.TypedDict('MriRfTrainParameters', {
-    "__STYXTYPE__": typing.Literal["mri_rf_train"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_rf_train"]],
+    "seg_volume": str,
+    "atlas_transform": str,
+    "mask_volume": typing.NotRequired[str | None],
+    "node_spacing": typing.NotRequired[float | None],
+    "prior_spacing": typing.NotRequired[float | None],
+    "input_training_data": typing.NotRequired[list[str] | None],
+    "sanity_check": bool,
+    "subjects": list[str],
+    "output_rfa": str,
+})
+MriRfTrainParametersTagged = typing.TypedDict('MriRfTrainParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_rf_train"],
     "seg_volume": str,
     "atlas_transform": str,
     "mask_volume": typing.NotRequired[str | None],
@@ -25,42 +37,11 @@ MriRfTrainParameters = typing.TypedDict('MriRfTrainParameters', {
     "subjects": list[str],
     "output_rfa": 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_rf_train": mri_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 MriRfTrainOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_rf_train(...)`.
+    Output object returned when calling `MriRfTrainParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -76,7 +57,7 @@ def mri_rf_train_params(
     prior_spacing: float | None = None,
     input_training_data: list[str] | None = None,
     sanity_check: bool = False,
-) -> MriRfTrainParameters:
+) -> MriRfTrainParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +78,7 @@ def mri_rf_train_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_rf_train",
+        "@type": "freesurfer/mri_rf_train",
         "seg_volume": seg_volume,
         "atlas_transform": atlas_transform,
         "sanity_check": sanity_check,
@@ -132,36 +113,36 @@ def mri_rf_train_cargs(
     cargs.append("mri_rf_train")
     cargs.extend([
         "-seg",
-        params.get("seg_volume")
+        params.get("seg_volume", None)
     ])
     cargs.extend([
         "-xform",
-        params.get("atlas_transform")
+        params.get("atlas_transform", None)
     ])
-    if params.get("mask_volume") is not None:
+    if params.get("mask_volume", None) is not None:
         cargs.extend([
             "-mask",
-            params.get("mask_volume")
+            params.get("mask_volume", None)
         ])
-    if params.get("node_spacing") is not None:
+    if params.get("node_spacing", None) is not None:
         cargs.extend([
             "-node_spacing",
-            str(params.get("node_spacing"))
+            str(params.get("node_spacing", None))
         ])
-    if params.get("prior_spacing") is not None:
+    if params.get("prior_spacing", None) is not None:
         cargs.extend([
             "-prior_spacing",
-            str(params.get("prior_spacing"))
+            str(params.get("prior_spacing", None))
         ])
-    if params.get("input_training_data") is not None:
+    if params.get("input_training_data", None) is not None:
         cargs.extend([
             "-input",
-            *params.get("input_training_data")
+            *params.get("input_training_data", None)
         ])
-    if params.get("sanity_check"):
+    if params.get("sanity_check", False):
         cargs.append("-check")
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_rfa"))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_rfa", None))
     return cargs
 
 
@@ -186,9 +167,11 @@ def mri_rf_train_outputs(
 
 def mri_rf_train_execute(
     params: MriRfTrainParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriRfTrainOutputs:
     """
+    mri_rf_train
+    
     Trains GCA data with multiple subjects using MRI data.
     
     Author: FreeSurfer Developers
@@ -197,10 +180,12 @@ def mri_rf_train_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriRfTrainOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_RF_TRAIN_METADATA)
     params = execution.params(params)
     cargs = mri_rf_train_cargs(params, execution)
     ret = mri_rf_train_outputs(params, execution)
@@ -221,6 +206,8 @@ def mri_rf_train(
     runner: Runner | None = None,
 ) -> MriRfTrainOutputs:
     """
+    mri_rf_train
+    
     Trains GCA data with multiple subjects using MRI data.
     
     Author: FreeSurfer Developers
@@ -244,8 +231,6 @@ def mri_rf_train(
     Returns:
         NamedTuple of outputs (described in `MriRfTrainOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_RF_TRAIN_METADATA)
     params = mri_rf_train_params(
         seg_volume=seg_volume,
         atlas_transform=atlas_transform,
@@ -257,13 +242,13 @@ def mri_rf_train(
         subjects=subjects,
         output_rfa=output_rfa,
     )
-    return mri_rf_train_execute(params, execution)
+    return mri_rf_train_execute(params, runner)
 
 
 __all__ = [
     "MRI_RF_TRAIN_METADATA",
     "MriRfTrainOutputs",
-    "MriRfTrainParameters",
     "mri_rf_train",
+    "mri_rf_train_execute",
     "mri_rf_train_params",
 ]

niwrap_freesurfer/freesurfer/mri_ribbon.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_RIBBON_METADATA = Metadata(
-    id="2304da93e8c915d7208416df97d57e92ea3d0bd3.boutiques",
+    id="a40554737433b3d1d89c707652c1ac81b900e449.boutiques",
     name="mri_ribbon",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRI_RIBBON_METADATA = Metadata(
 
 
 MriRibbonParameters = typing.TypedDict('MriRibbonParameters', {
-    "__STYXTYPE__": typing.Literal["mri_ribbon"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_ribbon"]],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "inner_surface": InputPathType,
+    "outer_surface": InputPathType,
+    "input_volume": str,
+    "output_volume": str,
+})
+MriRibbonParametersTagged = typing.TypedDict('MriRibbonParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_ribbon"],
     "label_file": typing.NotRequired[InputPathType | None],
     "inner_surface": InputPathType,
     "outer_surface": InputPathType,
     "input_volume": str,
     "output_volume": 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_ribbon": mri_ribbon_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_ribbon": mri_ribbon_outputs,
-    }.get(t)
 
 
 class MriRibbonOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_ribbon(...)`.
+    Output object returned when calling `MriRibbonParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mri_ribbon_params(
     input_volume: str,
     output_volume: str,
     label_file: InputPathType | None = None,
-) -> MriRibbonParameters:
+) -> MriRibbonParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def mri_ribbon_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_ribbon",
+        "@type": "freesurfer/mri_ribbon",
         "inner_surface": inner_surface,
         "outer_surface": outer_surface,
         "input_volume": input_volume,
@@ -111,15 +87,15 @@ def mri_ribbon_cargs(
     """
     cargs = []
     cargs.append("mri_ribbon")
-    if params.get("label_file") is not None:
+    if params.get("label_file", None) is not None:
         cargs.extend([
             "-l",
-            execution.input_file(params.get("label_file"))
+            execution.input_file(params.get("label_file", None))
         ])
-    cargs.append(execution.input_file(params.get("inner_surface")))
-    cargs.append(execution.input_file(params.get("outer_surface")))
-    cargs.append(params.get("input_volume"))
-    cargs.append(params.get("output_volume"))
+    cargs.append(execution.input_file(params.get("inner_surface", None)))
+    cargs.append(execution.input_file(params.get("outer_surface", None)))
+    cargs.append(params.get("input_volume", None))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -138,16 +114,18 @@ def mri_ribbon_outputs(
     """
     ret = MriRibbonOutputs(
         root=execution.output_file("."),
-        ribbon_output=execution.output_file(params.get("output_volume") + "_ribbon.nii.gz"),
+        ribbon_output=execution.output_file(params.get("output_volume", None) + "_ribbon.nii.gz"),
     )
     return ret
 
 
 def mri_ribbon_execute(
     params: MriRibbonParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriRibbonOutputs:
     """
+    mri_ribbon
+    
     MRI Ribbon tool to create ribbon volumes from surface files.
     
     Author: FreeSurfer Developers
@@ -156,10 +134,12 @@ def mri_ribbon_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriRibbonOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_RIBBON_METADATA)
     params = execution.params(params)
     cargs = mri_ribbon_cargs(params, execution)
     ret = mri_ribbon_outputs(params, execution)
@@ -176,6 +156,8 @@ def mri_ribbon(
     runner: Runner | None = None,
 ) -> MriRibbonOutputs:
     """
+    mri_ribbon
+    
     MRI Ribbon tool to create ribbon volumes from surface files.
     
     Author: FreeSurfer Developers
@@ -192,8 +174,6 @@ def mri_ribbon(
     Returns:
         NamedTuple of outputs (described in `MriRibbonOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_RIBBON_METADATA)
     params = mri_ribbon_params(
         label_file=label_file,
         inner_surface=inner_surface,
@@ -201,13 +181,13 @@ def mri_ribbon(
         input_volume=input_volume,
         output_volume=output_volume,
     )
-    return mri_ribbon_execute(params, execution)
+    return mri_ribbon_execute(params, runner)
 
 
 __all__ = [
     "MRI_RIBBON_METADATA",
     "MriRibbonOutputs",
-    "MriRibbonParameters",
     "mri_ribbon",
+    "mri_ribbon_execute",
     "mri_ribbon_params",
 ]