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

niwrap_freesurfer/freesurfer/mri_transform.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_TRANSFORM_METADATA = Metadata(
-    id="22b17ef4c1a157e2633827e670c9f3297b49ab98.boutiques",
+    id="9fe411f8dfb45289644c71c21317deb81a0cb83a.boutiques",
     name="mri_transform",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRI_TRANSFORM_METADATA = Metadata(
 
 
 MriTransformParameters = typing.TypedDict('MriTransformParameters', {
-    "__STYXTYPE__": typing.Literal["mri_transform"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_transform"]],
+    "input_volume": InputPathType,
+    "lta_file": InputPathType,
+    "output_file": str,
+    "out_like": typing.NotRequired[InputPathType | None],
+    "invert": bool,
+})
+MriTransformParametersTagged = typing.TypedDict('MriTransformParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_transform"],
     "input_volume": InputPathType,
     "lta_file": InputPathType,
     "output_file": str,
     "out_like": typing.NotRequired[InputPathType | None],
     "invert": 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_transform": mri_transform_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_transform": mri_transform_outputs,
-    }.get(t)
 
 
 class MriTransformOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_transform(...)`.
+    Output object returned when calling `MriTransformParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mri_transform_params(
     output_file: str,
     out_like: InputPathType | None = None,
     invert: bool = False,
-) -> MriTransformParameters:
+) -> MriTransformParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def mri_transform_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_transform",
+        "@type": "freesurfer/mri_transform",
         "input_volume": input_volume,
         "lta_file": lta_file,
         "output_file": output_file,
@@ -111,15 +87,15 @@ def mri_transform_cargs(
     """
     cargs = []
     cargs.append("mri_transform")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(execution.input_file(params.get("lta_file")))
-    cargs.append(params.get("output_file"))
-    if params.get("out_like") is not None:
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(execution.input_file(params.get("lta_file", None)))
+    cargs.append(params.get("output_file", None))
+    if params.get("out_like", None) is not None:
         cargs.extend([
             "-out_like",
-            execution.input_file(params.get("out_like"))
+            execution.input_file(params.get("out_like", None))
         ])
-    if params.get("invert"):
+    if params.get("invert", False):
         cargs.append("-I")
     return cargs
 
@@ -139,16 +115,18 @@ def mri_transform_outputs(
     """
     ret = MriTransformOutputs(
         root=execution.output_file("."),
-        transformed_output=execution.output_file(params.get("output_file")),
+        transformed_output=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mri_transform_execute(
     params: MriTransformParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriTransformOutputs:
     """
+    mri_transform
+    
     Applies a linear transform to an MRI volume and writes out the result.
     
     Author: FreeSurfer Developers
@@ -157,10 +135,12 @@ def mri_transform_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriTransformOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_TRANSFORM_METADATA)
     params = execution.params(params)
     cargs = mri_transform_cargs(params, execution)
     ret = mri_transform_outputs(params, execution)
@@ -177,6 +157,8 @@ def mri_transform(
     runner: Runner | None = None,
 ) -> MriTransformOutputs:
     """
+    mri_transform
+    
     Applies a linear transform to an MRI volume and writes out the result.
     
     Author: FreeSurfer Developers
@@ -193,8 +175,6 @@ def mri_transform(
     Returns:
         NamedTuple of outputs (described in `MriTransformOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_TRANSFORM_METADATA)
     params = mri_transform_params(
         input_volume=input_volume,
         lta_file=lta_file,
@@ -202,13 +182,13 @@ def mri_transform(
         out_like=out_like,
         invert=invert,
     )
-    return mri_transform_execute(params, execution)
+    return mri_transform_execute(params, runner)
 
 
 __all__ = [
     "MRI_TRANSFORM_METADATA",
     "MriTransformOutputs",
-    "MriTransformParameters",
     "mri_transform",
+    "mri_transform_execute",
     "mri_transform_params",
 ]

niwrap_freesurfer/freesurfer/mri_twoclass.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_TWOCLASS_METADATA = Metadata(
-    id="a4bd1f841f3834d6bee43f67f3cc687cf2b8aec8.boutiques",
+    id="1f5933526ae351fb97dfc4ae02bbe3f2c10f5407.boutiques",
     name="mri_twoclass",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRI_TWOCLASS_METADATA = Metadata(
 
 
 MriTwoclassParameters = typing.TypedDict('MriTwoclassParameters', {
-    "__STYXTYPE__": typing.Literal["mri_twoclass"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_twoclass"]],
+    "segmentation_volume": InputPathType,
+    "output_subject": str,
+    "output_volume": str,
+    "c1_subjects": list[str],
+    "c2_subjects": list[str],
+    "f_threshold": typing.NotRequired[float | None],
+    "bonferroni_correction": bool,
+})
+MriTwoclassParametersTagged = typing.TypedDict('MriTwoclassParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_twoclass"],
     "segmentation_volume": InputPathType,
     "output_subject": str,
     "output_volume": str,
@@ -23,43 +33,11 @@ MriTwoclassParameters = typing.TypedDict('MriTwoclassParameters', {
     "f_threshold": typing.NotRequired[float | None],
     "bonferroni_correction": 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_twoclass": mri_twoclass_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_twoclass": mri_twoclass_outputs,
-    }.get(t)
 
 
 class MriTwoclassOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_twoclass(...)`.
+    Output object returned when calling `MriTwoclassParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mri_twoclass_params(
     c2_subjects: list[str],
     f_threshold: float | None = None,
     bonferroni_correction: bool = False,
-) -> MriTwoclassParameters:
+) -> MriTwoclassParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +69,7 @@ def mri_twoclass_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_twoclass",
+        "@type": "freesurfer/mri_twoclass",
         "segmentation_volume": segmentation_volume,
         "output_subject": output_subject,
         "output_volume": output_volume,
@@ -119,17 +97,17 @@ def mri_twoclass_cargs(
     """
     cargs = []
     cargs.append("mri_twoclass")
-    cargs.append(execution.input_file(params.get("segmentation_volume")))
-    cargs.append(params.get("output_subject"))
-    cargs.append(params.get("output_volume"))
-    cargs.extend(params.get("c1_subjects"))
-    cargs.extend(params.get("c2_subjects"))
-    if params.get("f_threshold") is not None:
+    cargs.append(execution.input_file(params.get("segmentation_volume", None)))
+    cargs.append(params.get("output_subject", None))
+    cargs.append(params.get("output_volume", None))
+    cargs.extend(params.get("c1_subjects", None))
+    cargs.extend(params.get("c2_subjects", None))
+    if params.get("f_threshold", None) is not None:
         cargs.extend([
             "-t",
-            str(params.get("f_threshold"))
+            str(params.get("f_threshold", None))
         ])
-    if params.get("bonferroni_correction"):
+    if params.get("bonferroni_correction", False):
         cargs.append("-b")
     return cargs
 
@@ -149,16 +127,18 @@ def mri_twoclass_outputs(
     """
     ret = MriTwoclassOutputs(
         root=execution.output_file("."),
-        result_volume=execution.output_file(params.get("output_volume")),
+        result_volume=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_twoclass_execute(
     params: MriTwoclassParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriTwoclassOutputs:
     """
+    mri_twoclass
+    
     Compute cross-subject statistics of two sets of labels.
     
     Author: FreeSurfer Developers
@@ -167,10 +147,12 @@ def mri_twoclass_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriTwoclassOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_TWOCLASS_METADATA)
     params = execution.params(params)
     cargs = mri_twoclass_cargs(params, execution)
     ret = mri_twoclass_outputs(params, execution)
@@ -189,6 +171,8 @@ def mri_twoclass(
     runner: Runner | None = None,
 ) -> MriTwoclassOutputs:
     """
+    mri_twoclass
+    
     Compute cross-subject statistics of two sets of labels.
     
     Author: FreeSurfer Developers
@@ -207,8 +191,6 @@ def mri_twoclass(
     Returns:
         NamedTuple of outputs (described in `MriTwoclassOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_TWOCLASS_METADATA)
     params = mri_twoclass_params(
         segmentation_volume=segmentation_volume,
         output_subject=output_subject,
@@ -218,13 +200,13 @@ def mri_twoclass(
         f_threshold=f_threshold,
         bonferroni_correction=bonferroni_correction,
     )
-    return mri_twoclass_execute(params, execution)
+    return mri_twoclass_execute(params, runner)
 
 
 __all__ = [
     "MRI_TWOCLASS_METADATA",
     "MriTwoclassOutputs",
-    "MriTwoclassParameters",
     "mri_twoclass",
+    "mri_twoclass_execute",
     "mri_twoclass_params",
 ]

niwrap_freesurfer/freesurfer/mri_validate_skull_stripped.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_VALIDATE_SKULL_STRIPPED_METADATA = Metadata(
-    id="0de0265b82e5cc83b346cf1e1de5cade0f9128b2.boutiques",
+    id="66a7a4466fdb7b810c88a24d0012d9b6303845fb.boutiques",
     name="mri_validate_skull_stripped",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ MRI_VALIDATE_SKULL_STRIPPED_METADATA = Metadata(
 
 
 MriValidateSkullStrippedParameters = typing.TypedDict('MriValidateSkullStrippedParameters', {
-    "__STYXTYPE__": typing.Literal["mri_validate_skull_stripped"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_validate_skull_stripped"]],
+    "mri_reference": InputPathType,
+    "mri_test": InputPathType,
+    "weight": float,
+})
+MriValidateSkullStrippedParametersTagged = typing.TypedDict('MriValidateSkullStrippedParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_validate_skull_stripped"],
     "mri_reference": InputPathType,
     "mri_test": InputPathType,
     "weight": float,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_validate_skull_stripped": mri_validate_skull_stripped_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 MriValidateSkullStrippedOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_validate_skull_stripped(...)`.
+    Output object returned when calling `MriValidateSkullStrippedParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def mri_validate_skull_stripped_params(
     mri_reference: InputPathType,
     mri_test: InputPathType,
     weight: float,
-) -> MriValidateSkullStrippedParameters:
+) -> MriValidateSkullStrippedParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def mri_validate_skull_stripped_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_validate_skull_stripped",
+        "@type": "freesurfer/mri_validate_skull_stripped",
         "mri_reference": mri_reference,
         "mri_test": mri_test,
         "weight": weight,
@@ -99,9 +74,9 @@ def mri_validate_skull_stripped_cargs(
     """
     cargs = []
     cargs.append("mri_validate_skull_stripped")
-    cargs.append(execution.input_file(params.get("mri_reference")))
-    cargs.append(execution.input_file(params.get("mri_test")))
-    cargs.append(str(params.get("weight")))
+    cargs.append(execution.input_file(params.get("mri_reference", None)))
+    cargs.append(execution.input_file(params.get("mri_test", None)))
+    cargs.append(str(params.get("weight", None)))
     return cargs
 
 
@@ -126,9 +101,11 @@ def mri_validate_skull_stripped_outputs(
 
 def mri_validate_skull_stripped_execute(
     params: MriValidateSkullStrippedParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriValidateSkullStrippedOutputs:
     """
+    mri_validate_skull_stripped
+    
     Tool to validate skull stripped MRI images.
     
     Author: FreeSurfer Developers
@@ -137,10 +114,12 @@ def mri_validate_skull_stripped_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriValidateSkullStrippedOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_VALIDATE_SKULL_STRIPPED_METADATA)
     params = execution.params(params)
     cargs = mri_validate_skull_stripped_cargs(params, execution)
     ret = mri_validate_skull_stripped_outputs(params, execution)
@@ -155,6 +134,8 @@ def mri_validate_skull_stripped(
     runner: Runner | None = None,
 ) -> MriValidateSkullStrippedOutputs:
     """
+    mri_validate_skull_stripped
+    
     Tool to validate skull stripped MRI images.
     
     Author: FreeSurfer Developers
@@ -169,20 +150,18 @@ def mri_validate_skull_stripped(
     Returns:
         NamedTuple of outputs (described in `MriValidateSkullStrippedOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_VALIDATE_SKULL_STRIPPED_METADATA)
     params = mri_validate_skull_stripped_params(
         mri_reference=mri_reference,
         mri_test=mri_test,
         weight=weight,
     )
-    return mri_validate_skull_stripped_execute(params, execution)
+    return mri_validate_skull_stripped_execute(params, runner)
 
 
 __all__ = [
     "MRI_VALIDATE_SKULL_STRIPPED_METADATA",
     "MriValidateSkullStrippedOutputs",
-    "MriValidateSkullStrippedParameters",
     "mri_validate_skull_stripped",
+    "mri_validate_skull_stripped_execute",
     "mri_validate_skull_stripped_params",
 ]

niwrap_freesurfer/freesurfer/mri_vessel_segment.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_VESSEL_SEGMENT_METADATA = Metadata(
-    id="b79f0f0834cfb829127887556ded00ae35e155ae.boutiques",
+    id="3f2cffef406b09dc6bd4cbd76379913f53ca676c.boutiques",
     name="mri_vessel_segment",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRI_VESSEL_SEGMENT_METADATA = Metadata(
 
 
 MriVesselSegmentParameters = typing.TypedDict('MriVesselSegmentParameters', {
-    "__STYXTYPE__": typing.Literal["mri_vessel_segment"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_vessel_segment"]],
+    "t1_image": InputPathType,
+    "t2_image": InputPathType,
+    "aseg_file": InputPathType,
+    "output_file": str,
+    "shape_flag": bool,
+})
+MriVesselSegmentParametersTagged = typing.TypedDict('MriVesselSegmentParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_vessel_segment"],
     "t1_image": InputPathType,
     "t2_image": InputPathType,
     "aseg_file": InputPathType,
     "output_file": str,
     "shape_flag": 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_vessel_segment": mri_vessel_segment_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_vessel_segment": mri_vessel_segment_outputs,
-    }.get(t)
 
 
 class MriVesselSegmentOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_vessel_segment(...)`.
+    Output object returned when calling `MriVesselSegmentParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mri_vessel_segment_params(
     aseg_file: InputPathType,
     output_file: str,
     shape_flag: bool = False,
-) -> MriVesselSegmentParameters:
+) -> MriVesselSegmentParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def mri_vessel_segment_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_vessel_segment",
+        "@type": "freesurfer/mri_vessel_segment",
         "t1_image": t1_image,
         "t2_image": t2_image,
         "aseg_file": aseg_file,
@@ -112,21 +88,21 @@ def mri_vessel_segment_cargs(
     cargs.append("mri_vessel_segment")
     cargs.extend([
         "-t1",
-        execution.input_file(params.get("t1_image"))
+        execution.input_file(params.get("t1_image", None))
     ])
     cargs.extend([
         "-t2",
-        execution.input_file(params.get("t2_image"))
+        execution.input_file(params.get("t2_image", None))
     ])
     cargs.extend([
         "-aseg",
-        execution.input_file(params.get("aseg_file"))
+        execution.input_file(params.get("aseg_file", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("shape_flag"):
+    if params.get("shape_flag", False):
         cargs.append("--shape")
     return cargs
 
@@ -146,16 +122,18 @@ def mri_vessel_segment_outputs(
     """
     ret = MriVesselSegmentOutputs(
         root=execution.output_file("."),
-        segmented_output=execution.output_file(params.get("output_file")),
+        segmented_output=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mri_vessel_segment_execute(
     params: MriVesselSegmentParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriVesselSegmentOutputs:
     """
+    mri_vessel_segment
+    
     MRI vessel segmentation tool.
     
     Author: FreeSurfer Developers
@@ -164,10 +142,12 @@ def mri_vessel_segment_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriVesselSegmentOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_VESSEL_SEGMENT_METADATA)
     params = execution.params(params)
     cargs = mri_vessel_segment_cargs(params, execution)
     ret = mri_vessel_segment_outputs(params, execution)
@@ -184,6 +164,8 @@ def mri_vessel_segment(
     runner: Runner | None = None,
 ) -> MriVesselSegmentOutputs:
     """
+    mri_vessel_segment
+    
     MRI vessel segmentation tool.
     
     Author: FreeSurfer Developers
@@ -200,8 +182,6 @@ def mri_vessel_segment(
     Returns:
         NamedTuple of outputs (described in `MriVesselSegmentOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_VESSEL_SEGMENT_METADATA)
     params = mri_vessel_segment_params(
         t1_image=t1_image,
         t2_image=t2_image,
@@ -209,13 +189,13 @@ def mri_vessel_segment(
         output_file=output_file,
         shape_flag=shape_flag,
     )
-    return mri_vessel_segment_execute(params, execution)
+    return mri_vessel_segment_execute(params, runner)
 
 
 __all__ = [
     "MRI_VESSEL_SEGMENT_METADATA",
     "MriVesselSegmentOutputs",
-    "MriVesselSegmentParameters",
     "mri_vessel_segment",
+    "mri_vessel_segment_execute",
     "mri_vessel_segment_params",
 ]