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

niwrap_freesurfer/freesurfer/mri_easyreg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_EASYREG_METADATA = Metadata(
-    id="4d4e5291ec17f7c565f30ac4c578e21520850c62.boutiques",
+    id="6ec1a94b1d91e7b7c163bd6dbc8035bf8075894c.boutiques",
     name="mri_easyreg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ MRI_EASYREG_METADATA = Metadata(
 
 
 MriEasyregParameters = typing.TypedDict('MriEasyregParameters', {
-    "__STYXTYPE__": typing.Literal["mri_easyreg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_easyreg"]],
+    "reference_image": InputPathType,
+    "reference_segmentation": typing.NotRequired[InputPathType | None],
+    "floating_image": InputPathType,
+    "floating_segmentation": typing.NotRequired[InputPathType | None],
+    "registered_reference": typing.NotRequired[InputPathType | None],
+    "registered_floating": typing.NotRequired[InputPathType | None],
+    "forward_field": typing.NotRequired[InputPathType | None],
+    "inverse_field": typing.NotRequired[InputPathType | None],
+    "affine_only": bool,
+    "threads": typing.NotRequired[float | None],
+})
+MriEasyregParametersTagged = typing.TypedDict('MriEasyregParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_easyreg"],
     "reference_image": InputPathType,
     "reference_segmentation": typing.NotRequired[InputPathType | None],
     "floating_image": InputPathType,
@@ -26,43 +39,11 @@ MriEasyregParameters = typing.TypedDict('MriEasyregParameters', {
     "affine_only": bool,
     "threads": 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_easyreg": mri_easyreg_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_easyreg": mri_easyreg_outputs,
-    }.get(t)
 
 
 class MriEasyregOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_easyreg(...)`.
+    Output object returned when calling `MriEasyregParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +68,7 @@ def mri_easyreg_params(
     inverse_field: InputPathType | None = None,
     affine_only: bool = False,
     threads: float | None = None,
-) -> MriEasyregParameters:
+) -> MriEasyregParametersTagged:
     """
     Build parameters.
     
@@ -110,7 +91,7 @@ def mri_easyreg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_easyreg",
+        "@type": "freesurfer/mri_easyreg",
         "reference_image": reference_image,
         "floating_image": floating_image,
         "affine_only": affine_only,
@@ -149,48 +130,48 @@ def mri_easyreg_cargs(
     cargs.append("mri_easyreg")
     cargs.extend([
         "--ref",
-        execution.input_file(params.get("reference_image"))
+        execution.input_file(params.get("reference_image", None))
     ])
-    if params.get("reference_segmentation") is not None:
+    if params.get("reference_segmentation", None) is not None:
         cargs.extend([
             "--ref_seg",
-            execution.input_file(params.get("reference_segmentation"))
+            execution.input_file(params.get("reference_segmentation", None))
         ])
     cargs.extend([
         "--flo",
-        execution.input_file(params.get("floating_image"))
+        execution.input_file(params.get("floating_image", None))
     ])
-    if params.get("floating_segmentation") is not None:
+    if params.get("floating_segmentation", None) is not None:
         cargs.extend([
             "--flo_seg",
-            execution.input_file(params.get("floating_segmentation"))
+            execution.input_file(params.get("floating_segmentation", None))
         ])
-    if params.get("registered_reference") is not None:
+    if params.get("registered_reference", None) is not None:
         cargs.extend([
             "--ref_reg",
-            execution.input_file(params.get("registered_reference"))
+            execution.input_file(params.get("registered_reference", None))
         ])
-    if params.get("registered_floating") is not None:
+    if params.get("registered_floating", None) is not None:
         cargs.extend([
             "--flo_reg",
-            execution.input_file(params.get("registered_floating"))
+            execution.input_file(params.get("registered_floating", None))
         ])
-    if params.get("forward_field") is not None:
+    if params.get("forward_field", None) is not None:
         cargs.extend([
             "--fwd_field",
-            execution.input_file(params.get("forward_field"))
+            execution.input_file(params.get("forward_field", None))
         ])
-    if params.get("inverse_field") is not None:
+    if params.get("inverse_field", None) is not None:
         cargs.extend([
             "--bak_field",
-            execution.input_file(params.get("inverse_field"))
+            execution.input_file(params.get("inverse_field", None))
         ])
-    if params.get("affine_only"):
+    if params.get("affine_only", False):
         cargs.append("--affine_only")
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
     return cargs
 
@@ -220,9 +201,11 @@ def mri_easyreg_outputs(
 
 def mri_easyreg_execute(
     params: MriEasyregParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriEasyregOutputs:
     """
+    mri_easyreg
+    
     EasyReg: deep learning registration simple and easy.
     
     Author: FreeSurfer Developers
@@ -231,10 +214,12 @@ def mri_easyreg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriEasyregOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EASYREG_METADATA)
     params = execution.params(params)
     cargs = mri_easyreg_cargs(params, execution)
     ret = mri_easyreg_outputs(params, execution)
@@ -256,6 +241,8 @@ def mri_easyreg(
     runner: Runner | None = None,
 ) -> MriEasyregOutputs:
     """
+    mri_easyreg
+    
     EasyReg: deep learning registration simple and easy.
     
     Author: FreeSurfer Developers
@@ -281,8 +268,6 @@ def mri_easyreg(
     Returns:
         NamedTuple of outputs (described in `MriEasyregOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_EASYREG_METADATA)
     params = mri_easyreg_params(
         reference_image=reference_image,
         reference_segmentation=reference_segmentation,
@@ -295,13 +280,13 @@ def mri_easyreg(
         affine_only=affine_only,
         threads=threads,
     )
-    return mri_easyreg_execute(params, execution)
+    return mri_easyreg_execute(params, runner)
 
 
 __all__ = [
     "MRI_EASYREG_METADATA",
     "MriEasyregOutputs",
-    "MriEasyregParameters",
     "mri_easyreg",
+    "mri_easyreg_execute",
     "mri_easyreg_params",
 ]

niwrap_freesurfer/freesurfer/mri_easywarp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_EASYWARP_METADATA = Metadata(
-    id="6f60813ddf4e27961ba032e4927aafbdbf0d9186.boutiques",
+    id="c8820066f7e2a7b0f0629dfb2fbeb1cce057ae2e.boutiques",
     name="mri_easywarp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRI_EASYWARP_METADATA = Metadata(
 
 
 MriEasywarpParameters = typing.TypedDict('MriEasywarpParameters', {
-    "__STYXTYPE__": typing.Literal["mri_easywarp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_easywarp"]],
+    "input_image": InputPathType,
+    "output_image": str,
+    "deformation_field": typing.NotRequired[InputPathType | None],
+    "nearest_neighbor": bool,
+    "num_threads": typing.NotRequired[float | None],
+})
+MriEasywarpParametersTagged = typing.TypedDict('MriEasywarpParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_easywarp"],
     "input_image": InputPathType,
     "output_image": str,
     "deformation_field": typing.NotRequired[InputPathType | None],
     "nearest_neighbor": bool,
     "num_threads": 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_easywarp": mri_easywarp_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_easywarp": mri_easywarp_outputs,
-    }.get(t)
 
 
 class MriEasywarpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_easywarp(...)`.
+    Output object returned when calling `MriEasywarpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mri_easywarp_params(
     deformation_field: InputPathType | None = None,
     nearest_neighbor: bool = False,
     num_threads: float | None = None,
-) -> MriEasywarpParameters:
+) -> MriEasywarpParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +63,7 @@ def mri_easywarp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_easywarp",
+        "@type": "freesurfer/mri_easywarp",
         "input_image": input_image,
         "output_image": output_image,
         "nearest_neighbor": nearest_neighbor,
@@ -116,23 +92,23 @@ def mri_easywarp_cargs(
     cargs.append("mri_easywarp")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_image"))
+        execution.input_file(params.get("input_image", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output_image")
+        params.get("output_image", None)
     ])
-    if params.get("deformation_field") is not None:
+    if params.get("deformation_field", None) is not None:
         cargs.extend([
             "--field",
-            execution.input_file(params.get("deformation_field"))
+            execution.input_file(params.get("deformation_field", None))
         ])
-    if params.get("nearest_neighbor"):
+    if params.get("nearest_neighbor", False):
         cargs.append("--nearest")
-    if params.get("num_threads") is not None:
+    if params.get("num_threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("num_threads"))
+            str(params.get("num_threads", None))
         ])
     return cargs
 
@@ -152,16 +128,18 @@ def mri_easywarp_outputs(
     """
     ret = MriEasywarpOutputs(
         root=execution.output_file("."),
-        output_deformed_image=execution.output_file(params.get("output_image") + ".nii.gz"),
+        output_deformed_image=execution.output_file(params.get("output_image", None) + ".nii.gz"),
     )
     return ret
 
 
 def mri_easywarp_execute(
     params: MriEasywarpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriEasywarpOutputs:
     """
+    mri_easywarp
+    
     EasyReg: deep learning registration simple and easy.
     
     Author: FreeSurfer Developers
@@ -170,10 +148,12 @@ def mri_easywarp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriEasywarpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EASYWARP_METADATA)
     params = execution.params(params)
     cargs = mri_easywarp_cargs(params, execution)
     ret = mri_easywarp_outputs(params, execution)
@@ -190,6 +170,8 @@ def mri_easywarp(
     runner: Runner | None = None,
 ) -> MriEasywarpOutputs:
     """
+    mri_easywarp
+    
     EasyReg: deep learning registration simple and easy.
     
     Author: FreeSurfer Developers
@@ -208,8 +190,6 @@ def mri_easywarp(
     Returns:
         NamedTuple of outputs (described in `MriEasywarpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_EASYWARP_METADATA)
     params = mri_easywarp_params(
         input_image=input_image,
         output_image=output_image,
@@ -217,13 +197,13 @@ def mri_easywarp(
         nearest_neighbor=nearest_neighbor,
         num_threads=num_threads,
     )
-    return mri_easywarp_execute(params, execution)
+    return mri_easywarp_execute(params, runner)
 
 
 __all__ = [
     "MRI_EASYWARP_METADATA",
     "MriEasywarpOutputs",
-    "MriEasywarpParameters",
     "mri_easywarp",
+    "mri_easywarp_execute",
     "mri_easywarp_params",
 ]

niwrap_freesurfer/freesurfer/mri_edit_segmentation.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_EDIT_SEGMENTATION_METADATA = Metadata(
-    id="4268d37b37ec0629a95cd2fcd649fc7fa4c4561c.boutiques",
+    id="ec740c47f3a29897bf1472d70ad26803f8a74c15.boutiques",
     name="mri_edit_segmentation",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_EDIT_SEGMENTATION_METADATA = Metadata(
 
 
 MriEditSegmentationParameters = typing.TypedDict('MriEditSegmentationParameters', {
-    "__STYXTYPE__": typing.Literal["mri_edit_segmentation"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_edit_segmentation"]],
+    "input_segmentation": InputPathType,
+    "t1_volume": InputPathType,
+    "output_segmentation": str,
+})
+MriEditSegmentationParametersTagged = typing.TypedDict('MriEditSegmentationParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_edit_segmentation"],
     "input_segmentation": InputPathType,
     "t1_volume": InputPathType,
     "output_segmentation": 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_edit_segmentation": mri_edit_segmentation_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_edit_segmentation": mri_edit_segmentation_outputs,
-    }.get(t)
 
 
 class MriEditSegmentationOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_edit_segmentation(...)`.
+    Output object returned when calling `MriEditSegmentationParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_edit_segmentation_params(
     input_segmentation: InputPathType,
     t1_volume: InputPathType,
     output_segmentation: str,
-) -> MriEditSegmentationParameters:
+) -> MriEditSegmentationParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mri_edit_segmentation_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_edit_segmentation",
+        "@type": "freesurfer/mri_edit_segmentation",
         "input_segmentation": input_segmentation,
         "t1_volume": t1_volume,
         "output_segmentation": output_segmentation,
@@ -102,9 +76,9 @@ def mri_edit_segmentation_cargs(
     """
     cargs = []
     cargs.append("mri_edit_segmentation")
-    cargs.append(execution.input_file(params.get("input_segmentation")))
-    cargs.append(execution.input_file(params.get("t1_volume")))
-    cargs.append(params.get("output_segmentation"))
+    cargs.append(execution.input_file(params.get("input_segmentation", None)))
+    cargs.append(execution.input_file(params.get("t1_volume", None)))
+    cargs.append(params.get("output_segmentation", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def mri_edit_segmentation_outputs(
     """
     ret = MriEditSegmentationOutputs(
         root=execution.output_file("."),
-        output_segmentation_file=execution.output_file(params.get("output_segmentation")),
+        output_segmentation_file=execution.output_file(params.get("output_segmentation", None)),
     )
     return ret
 
 
 def mri_edit_segmentation_execute(
     params: MriEditSegmentationParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriEditSegmentationOutputs:
     """
+    mri_edit_segmentation
+    
     A tool used for editing segmentations.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def mri_edit_segmentation_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriEditSegmentationOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EDIT_SEGMENTATION_METADATA)
     params = execution.params(params)
     cargs = mri_edit_segmentation_cargs(params, execution)
     ret = mri_edit_segmentation_outputs(params, execution)
@@ -159,6 +137,8 @@ def mri_edit_segmentation(
     runner: Runner | None = None,
 ) -> MriEditSegmentationOutputs:
     """
+    mri_edit_segmentation
+    
     A tool used for editing segmentations.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def mri_edit_segmentation(
     Returns:
         NamedTuple of outputs (described in `MriEditSegmentationOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_EDIT_SEGMENTATION_METADATA)
     params = mri_edit_segmentation_params(
         input_segmentation=input_segmentation,
         t1_volume=t1_volume,
         output_segmentation=output_segmentation,
     )
-    return mri_edit_segmentation_execute(params, execution)
+    return mri_edit_segmentation_execute(params, runner)
 
 
 __all__ = [
     "MRI_EDIT_SEGMENTATION_METADATA",
     "MriEditSegmentationOutputs",
-    "MriEditSegmentationParameters",
     "mri_edit_segmentation",
+    "mri_edit_segmentation_execute",
     "mri_edit_segmentation_params",
 ]