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

niwrap_freesurfer/freesurfer/mri_tessellate.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_TESSELLATE_METADATA = Metadata(
-    id="f45ebf91c0ba77da8568b9b11d9468a5d80fa341.boutiques",
+    id="317340698b3037c109130e654835bfde8ad2763f.boutiques",
     name="mri_tessellate",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRI_TESSELLATE_METADATA = Metadata(
 
 
 MriTessellateParameters = typing.TypedDict('MriTessellateParameters', {
-    "__STYXTYPE__": typing.Literal["mri_tessellate"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_tessellate"]],
+    "input_volume": InputPathType,
+    "label_value": int,
+    "output_surf": str,
+    "different_labels": bool,
+    "max_vertices": typing.NotRequired[int | None],
+    "real_ras": bool,
+})
+MriTessellateParametersTagged = typing.TypedDict('MriTessellateParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_tessellate"],
     "input_volume": InputPathType,
     "label_value": int,
     "output_surf": str,
@@ -22,43 +31,11 @@ MriTessellateParameters = typing.TypedDict('MriTessellateParameters', {
     "max_vertices": typing.NotRequired[int | None],
     "real_ras": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_tessellate": mri_tessellate_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_tessellate": mri_tessellate_outputs,
-    }.get(t)
 
 
 class MriTessellateOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_tessellate(...)`.
+    Output object returned when calling `MriTessellateParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mri_tessellate_params(
     different_labels: bool = False,
     max_vertices: int | None = None,
     real_ras: bool = False,
-) -> MriTessellateParameters:
+) -> MriTessellateParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +68,7 @@ def mri_tessellate_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_tessellate",
+        "@type": "freesurfer/mri_tessellate",
         "input_volume": input_volume,
         "label_value": label_value,
         "output_surf": output_surf,
@@ -118,17 +95,17 @@ def mri_tessellate_cargs(
     """
     cargs = []
     cargs.append("mri_tessellate")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(str(params.get("label_value")))
-    cargs.append(params.get("output_surf"))
-    if params.get("different_labels"):
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(str(params.get("label_value", None)))
+    cargs.append(params.get("output_surf", None))
+    if params.get("different_labels", False):
         cargs.append("-a")
-    if params.get("max_vertices") is not None:
+    if params.get("max_vertices", None) is not None:
         cargs.extend([
             "-maxv",
-            str(params.get("max_vertices"))
+            str(params.get("max_vertices", None))
         ])
-    if params.get("real_ras"):
+    if params.get("real_ras", False):
         cargs.append("-n")
     return cargs
 
@@ -148,16 +125,18 @@ def mri_tessellate_outputs(
     """
     ret = MriTessellateOutputs(
         root=execution.output_file("."),
-        output_surface_file=execution.output_file(params.get("output_surf")),
+        output_surface_file=execution.output_file(params.get("output_surf", None)),
     )
     return ret
 
 
 def mri_tessellate_execute(
     params: MriTessellateParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriTessellateOutputs:
     """
+    mri_tessellate
+    
     This program creates a surface by tessellating a given input volume.
     
     Author: FreeSurfer Developers
@@ -166,10 +145,12 @@ def mri_tessellate_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriTessellateOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_TESSELLATE_METADATA)
     params = execution.params(params)
     cargs = mri_tessellate_cargs(params, execution)
     ret = mri_tessellate_outputs(params, execution)
@@ -187,6 +168,8 @@ def mri_tessellate(
     runner: Runner | None = None,
 ) -> MriTessellateOutputs:
     """
+    mri_tessellate
+    
     This program creates a surface by tessellating a given input volume.
     
     Author: FreeSurfer Developers
@@ -207,8 +190,6 @@ def mri_tessellate(
     Returns:
         NamedTuple of outputs (described in `MriTessellateOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_TESSELLATE_METADATA)
     params = mri_tessellate_params(
         input_volume=input_volume,
         label_value=label_value,
@@ -217,13 +198,13 @@ def mri_tessellate(
         max_vertices=max_vertices,
         real_ras=real_ras,
     )
-    return mri_tessellate_execute(params, execution)
+    return mri_tessellate_execute(params, runner)
 
 
 __all__ = [
     "MRI_TESSELLATE_METADATA",
     "MriTessellateOutputs",
-    "MriTessellateParameters",
     "mri_tessellate",
+    "mri_tessellate_execute",
     "mri_tessellate_params",
 ]

niwrap_freesurfer/freesurfer/mri_threshold.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_THRESHOLD_METADATA = Metadata(
-    id="18118adc25493a185a902418d2d12f7e965b7d74.boutiques",
+    id="62baf41ab3970c5b8c42316e743a468c342edf72.boutiques",
     name="mri_threshold",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRI_THRESHOLD_METADATA = Metadata(
 
 
 MriThresholdParameters = typing.TypedDict('MriThresholdParameters', {
-    "__STYXTYPE__": typing.Literal["mri_threshold"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_threshold"]],
+    "input_vol": InputPathType,
+    "threshold": float,
+    "output_vol": str,
+    "binarize": typing.NotRequired[float | None],
+    "upper_threshold": bool,
+    "frame_number": typing.NotRequired[float | None],
+})
+MriThresholdParametersTagged = typing.TypedDict('MriThresholdParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_threshold"],
     "input_vol": InputPathType,
     "threshold": float,
     "output_vol": str,
@@ -22,43 +31,11 @@ MriThresholdParameters = typing.TypedDict('MriThresholdParameters', {
     "upper_threshold": bool,
     "frame_number": typing.NotRequired[float | 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_threshold": mri_threshold_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_threshold": mri_threshold_outputs,
-    }.get(t)
 
 
 class MriThresholdOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_threshold(...)`.
+    Output object returned when calling `MriThresholdParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mri_threshold_params(
     binarize: float | None = None,
     upper_threshold: bool = False,
     frame_number: float | None = None,
-) -> MriThresholdParameters:
+) -> MriThresholdParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +66,7 @@ def mri_threshold_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_threshold",
+        "@type": "freesurfer/mri_threshold",
         "input_vol": input_vol,
         "threshold": threshold,
         "output_vol": output_vol,
@@ -117,20 +94,20 @@ def mri_threshold_cargs(
     """
     cargs = []
     cargs.append("mri_threshold")
-    cargs.append(execution.input_file(params.get("input_vol")))
-    cargs.append(str(params.get("threshold")))
-    cargs.append(params.get("output_vol"))
-    if params.get("binarize") is not None:
+    cargs.append(execution.input_file(params.get("input_vol", None)))
+    cargs.append(str(params.get("threshold", None)))
+    cargs.append(params.get("output_vol", None))
+    if params.get("binarize", None) is not None:
         cargs.extend([
             "-B",
-            str(params.get("binarize"))
+            str(params.get("binarize", None))
         ])
-    if params.get("upper_threshold"):
+    if params.get("upper_threshold", False):
         cargs.append("-U")
-    if params.get("frame_number") is not None:
+    if params.get("frame_number", None) is not None:
         cargs.extend([
             "-F",
-            str(params.get("frame_number"))
+            str(params.get("frame_number", None))
         ])
     return cargs
 
@@ -150,16 +127,18 @@ def mri_threshold_outputs(
     """
     ret = MriThresholdOutputs(
         root=execution.output_file("."),
-        output_vol_file=execution.output_file(params.get("output_vol")),
+        output_vol_file=execution.output_file(params.get("output_vol", None)),
     )
     return ret
 
 
 def mri_threshold_execute(
     params: MriThresholdParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriThresholdOutputs:
     """
+    mri_threshold
+    
     This program will lower threshold an input volume.
     
     Author: FreeSurfer Developers
@@ -168,10 +147,12 @@ def mri_threshold_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriThresholdOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_THRESHOLD_METADATA)
     params = execution.params(params)
     cargs = mri_threshold_cargs(params, execution)
     ret = mri_threshold_outputs(params, execution)
@@ -189,6 +170,8 @@ def mri_threshold(
     runner: Runner | None = None,
 ) -> MriThresholdOutputs:
     """
+    mri_threshold
+    
     This program will lower threshold an input volume.
     
     Author: FreeSurfer Developers
@@ -207,8 +190,6 @@ def mri_threshold(
     Returns:
         NamedTuple of outputs (described in `MriThresholdOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_THRESHOLD_METADATA)
     params = mri_threshold_params(
         input_vol=input_vol,
         threshold=threshold,
@@ -217,13 +198,13 @@ def mri_threshold(
         upper_threshold=upper_threshold,
         frame_number=frame_number,
     )
-    return mri_threshold_execute(params, execution)
+    return mri_threshold_execute(params, runner)
 
 
 __all__ = [
     "MRI_THRESHOLD_METADATA",
     "MriThresholdOutputs",
-    "MriThresholdParameters",
     "mri_threshold",
+    "mri_threshold_execute",
     "mri_threshold_params",
 ]

niwrap_freesurfer/freesurfer/mri_topologycorrection.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_TOPOLOGYCORRECTION_METADATA = Metadata(
-    id="40a7e8816236f767c7c17e74f2b35d577fe73190.boutiques",
+    id="5f5adcd820a3d0675b0294a701f5d9eebf40f347.boutiques",
     name="mri_topologycorrection",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRI_TOPOLOGYCORRECTION_METADATA = Metadata(
 
 
 MriTopologycorrectionParameters = typing.TypedDict('MriTopologycorrectionParameters', {
-    "__STYXTYPE__": typing.Literal["mri_topologycorrection"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_topologycorrection"]],
+    "input_orig_file": InputPathType,
+    "input_segmented_file": InputPathType,
+})
+MriTopologycorrectionParametersTagged = typing.TypedDict('MriTopologycorrectionParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_topologycorrection"],
     "input_orig_file": InputPathType,
     "input_segmented_file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_topologycorrection": mri_topologycorrection_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_topologycorrection": mri_topologycorrection_outputs,
-    }.get(t)
 
 
 class MriTopologycorrectionOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_topologycorrection(...)`.
+    Output object returned when calling `MriTopologycorrectionParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MriTopologycorrectionOutputs(typing.NamedTuple):
 def mri_topologycorrection_params(
     input_orig_file: InputPathType,
     input_segmented_file: InputPathType,
-) -> MriTopologycorrectionParameters:
+) -> MriTopologycorrectionParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mri_topologycorrection_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_topologycorrection",
+        "@type": "freesurfer/mri_topologycorrection",
         "input_orig_file": input_orig_file,
         "input_segmented_file": input_segmented_file,
     }
@@ -98,8 +71,8 @@ def mri_topologycorrection_cargs(
     """
     cargs = []
     cargs.append("mri_topologycorrection")
-    cargs.append(execution.input_file(params.get("input_orig_file")))
-    cargs.append(execution.input_file(params.get("input_segmented_file")))
+    cargs.append(execution.input_file(params.get("input_orig_file", None)))
+    cargs.append(execution.input_file(params.get("input_segmented_file", None)))
     return cargs
 
 
@@ -125,9 +98,11 @@ def mri_topologycorrection_outputs(
 
 def mri_topologycorrection_execute(
     params: MriTopologycorrectionParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriTopologycorrectionOutputs:
     """
+    mri_topologycorrection
+    
     Corrects the topology of segmented MRI images.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def mri_topologycorrection_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriTopologycorrectionOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_TOPOLOGYCORRECTION_METADATA)
     params = execution.params(params)
     cargs = mri_topologycorrection_cargs(params, execution)
     ret = mri_topologycorrection_outputs(params, execution)
@@ -153,6 +130,8 @@ def mri_topologycorrection(
     runner: Runner | None = None,
 ) -> MriTopologycorrectionOutputs:
     """
+    mri_topologycorrection
+    
     Corrects the topology of segmented MRI images.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def mri_topologycorrection(
     Returns:
         NamedTuple of outputs (described in `MriTopologycorrectionOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_TOPOLOGYCORRECTION_METADATA)
     params = mri_topologycorrection_params(
         input_orig_file=input_orig_file,
         input_segmented_file=input_segmented_file,
     )
-    return mri_topologycorrection_execute(params, execution)
+    return mri_topologycorrection_execute(params, runner)
 
 
 __all__ = [
     "MRI_TOPOLOGYCORRECTION_METADATA",
     "MriTopologycorrectionOutputs",
-    "MriTopologycorrectionParameters",
     "mri_topologycorrection",
+    "mri_topologycorrection_execute",
     "mri_topologycorrection_params",
 ]

niwrap_freesurfer/freesurfer/mri_train.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_TRAIN_METADATA = Metadata(
-    id="d0941b64d4a6f238b895b5763048b0ed9578d676.boutiques",
+    id="b7429817b01262357da9a5d34e39a1deef382fad.boutiques",
     name="mri_train",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRI_TRAIN_METADATA = Metadata(
 
 
 MriTrainParameters = typing.TypedDict('MriTrainParameters', {
-    "__STYXTYPE__": typing.Literal["mri_train"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_train"]],
+    "training_file": InputPathType,
+    "output_file": str,
+})
+MriTrainParametersTagged = typing.TypedDict('MriTrainParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_train"],
     "training_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 {
-        "mri_train": mri_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_train": mri_train_outputs,
-    }.get(t)
 
 
 class MriTrainOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_train(...)`.
+    Output object returned when calling `MriTrainParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MriTrainOutputs(typing.NamedTuple):
 def mri_train_params(
     training_file: InputPathType,
     output_file: str,
-) -> MriTrainParameters:
+) -> MriTrainParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mri_train_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_train",
+        "@type": "freesurfer/mri_train",
         "training_file": training_file,
         "output_file": output_file,
     }
@@ -98,8 +71,8 @@ def mri_train_cargs(
     """
     cargs = []
     cargs.append("mri_train")
-    cargs.append(execution.input_file(params.get("training_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(execution.input_file(params.get("training_file", None)))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def mri_train_outputs(
     """
     ret = MriTrainOutputs(
         root=execution.output_file("."),
-        output_file_generated=execution.output_file(params.get("output_file")),
+        output_file_generated=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mri_train_execute(
     params: MriTrainParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriTrainOutputs:
     """
+    mri_train
+    
     Tool for training with MRI data in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def mri_train_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriTrainOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_TRAIN_METADATA)
     params = execution.params(params)
     cargs = mri_train_cargs(params, execution)
     ret = mri_train_outputs(params, execution)
@@ -153,6 +130,8 @@ def mri_train(
     runner: Runner | None = None,
 ) -> MriTrainOutputs:
     """
+    mri_train
+    
     Tool for training with MRI data in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def mri_train(
     Returns:
         NamedTuple of outputs (described in `MriTrainOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_TRAIN_METADATA)
     params = mri_train_params(
         training_file=training_file,
         output_file=output_file,
     )
-    return mri_train_execute(params, execution)
+    return mri_train_execute(params, runner)
 
 
 __all__ = [
     "MRI_TRAIN_METADATA",
     "MriTrainOutputs",
-    "MriTrainParameters",
     "mri_train",
+    "mri_train_execute",
     "mri_train_params",
 ]