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

niwrap_freesurfer/freesurfer/mri_probedicom.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_PROBEDICOM_METADATA = Metadata(
-    id="7f1797c009bba5f7f144df962f6ea7dfb90ac510.boutiques",
+    id="e1b3bdc72222d3578b3efc72f9534b11ca6f6261.boutiques",
     name="mri_probedicom",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_PROBEDICOM_METADATA = Metadata(
 
 
 MriProbedicomParameters = typing.TypedDict('MriProbedicomParameters', {
-    "__STYXTYPE__": typing.Literal["mri_probedicom"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_probedicom"]],
+    "dicom_file": InputPathType,
+    "option1": typing.NotRequired[str | None],
+    "option2": typing.NotRequired[str | None],
+})
+MriProbedicomParametersTagged = typing.TypedDict('MriProbedicomParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_probedicom"],
     "dicom_file": InputPathType,
     "option1": typing.NotRequired[str | None],
     "option2": 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_probedicom": mri_probedicom_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_probedicom": mri_probedicom_outputs,
-    }.get(t)
 
 
 class MriProbedicomOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_probedicom(...)`.
+    Output object returned when calling `MriProbedicomParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_probedicom_params(
     dicom_file: InputPathType,
     option1: str | None = None,
     option2: str | None = None,
-) -> MriProbedicomParameters:
+) -> MriProbedicomParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mri_probedicom_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_probedicom",
+        "@type": "freesurfer/mri_probedicom",
         "dicom_file": dicom_file,
     }
     if option1 is not None:
@@ -104,16 +78,16 @@ def mri_probedicom_cargs(
     """
     cargs = []
     cargs.append("mri_probedicom")
-    cargs.append(execution.input_file(params.get("dicom_file")))
-    if params.get("option1") is not None:
+    cargs.append(execution.input_file(params.get("dicom_file", None)))
+    if params.get("option1", None) is not None:
         cargs.extend([
             "-option1",
-            params.get("option1")
+            params.get("option1", None)
         ])
-    if params.get("option2") is not None:
+    if params.get("option2", None) is not None:
         cargs.extend([
             "-option2",
-            params.get("option2")
+            params.get("option2", None)
         ])
     return cargs
 
@@ -140,9 +114,11 @@ def mri_probedicom_outputs(
 
 def mri_probedicom_execute(
     params: MriProbedicomParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriProbedicomOutputs:
     """
+    mri_probedicom
+    
     Utility to probe DICOM files for information.
     
     Author: FreeSurfer Developers
@@ -151,10 +127,12 @@ def mri_probedicom_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriProbedicomOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_PROBEDICOM_METADATA)
     params = execution.params(params)
     cargs = mri_probedicom_cargs(params, execution)
     ret = mri_probedicom_outputs(params, execution)
@@ -169,6 +147,8 @@ def mri_probedicom(
     runner: Runner | None = None,
 ) -> MriProbedicomOutputs:
     """
+    mri_probedicom
+    
     Utility to probe DICOM files for information.
     
     Author: FreeSurfer Developers
@@ -183,20 +163,18 @@ def mri_probedicom(
     Returns:
         NamedTuple of outputs (described in `MriProbedicomOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_PROBEDICOM_METADATA)
     params = mri_probedicom_params(
         dicom_file=dicom_file,
         option1=option1,
         option2=option2,
     )
-    return mri_probedicom_execute(params, execution)
+    return mri_probedicom_execute(params, runner)
 
 
 __all__ = [
     "MRI_PROBEDICOM_METADATA",
     "MriProbedicomOutputs",
-    "MriProbedicomParameters",
     "mri_probedicom",
+    "mri_probedicom_execute",
     "mri_probedicom_params",
 ]

niwrap_freesurfer/freesurfer/mri_reduce.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_REDUCE_METADATA = Metadata(
-    id="807357c72ac3fdc63a77f2607e6a6eb21658b2e9.boutiques",
+    id="98b0cda9a9dd474327f34e0a75f5de64b98979da.boutiques",
     name="mri_reduce",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRI_REDUCE_METADATA = Metadata(
 
 
 MriReduceParameters = typing.TypedDict('MriReduceParameters', {
-    "__STYXTYPE__": typing.Literal["mri_reduce"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_reduce"]],
+    "input_file": InputPathType,
+    "output_file": str,
+})
+MriReduceParametersTagged = typing.TypedDict('MriReduceParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_reduce"],
     "input_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_reduce": mri_reduce_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_reduce": mri_reduce_outputs,
-    }.get(t)
 
 
 class MriReduceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_reduce(...)`.
+    Output object returned when calling `MriReduceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MriReduceOutputs(typing.NamedTuple):
 def mri_reduce_params(
     input_file: InputPathType,
     output_file: str,
-) -> MriReduceParameters:
+) -> MriReduceParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mri_reduce_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_reduce",
+        "@type": "freesurfer/mri_reduce",
         "input_file": input_file,
         "output_file": output_file,
     }
@@ -98,8 +71,8 @@ def mri_reduce_cargs(
     """
     cargs = []
     cargs.append("mri_reduce")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def mri_reduce_outputs(
     """
     ret = MriReduceOutputs(
         root=execution.output_file("."),
-        reduced_output=execution.output_file(params.get("output_file")),
+        reduced_output=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mri_reduce_execute(
     params: MriReduceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriReduceOutputs:
     """
+    mri_reduce
+    
     A tool to reduce MRI file dimensions.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def mri_reduce_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriReduceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_REDUCE_METADATA)
     params = execution.params(params)
     cargs = mri_reduce_cargs(params, execution)
     ret = mri_reduce_outputs(params, execution)
@@ -153,6 +130,8 @@ def mri_reduce(
     runner: Runner | None = None,
 ) -> MriReduceOutputs:
     """
+    mri_reduce
+    
     A tool to reduce MRI file dimensions.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def mri_reduce(
     Returns:
         NamedTuple of outputs (described in `MriReduceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_REDUCE_METADATA)
     params = mri_reduce_params(
         input_file=input_file,
         output_file=output_file,
     )
-    return mri_reduce_execute(params, execution)
+    return mri_reduce_execute(params, runner)
 
 
 __all__ = [
     "MRI_REDUCE_METADATA",
     "MriReduceOutputs",
-    "MriReduceParameters",
     "mri_reduce",
+    "mri_reduce_execute",
     "mri_reduce_params",
 ]

niwrap_freesurfer/freesurfer/mri_refine_seg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_REFINE_SEG_METADATA = Metadata(
-    id="3fd4469d4b5b46b051a686f52cb055d8d5026a72.boutiques",
+    id="fedbb56a7b39cb49e4a0e963f96d90e569f37745.boutiques",
     name="mri_refine_seg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_REFINE_SEG_METADATA = Metadata(
 
 
 MriRefineSegParameters = typing.TypedDict('MriRefineSegParameters', {
-    "__STYXTYPE__": typing.Literal["mri_refine_seg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_refine_seg"]],
+    "input_segmentation": InputPathType,
+    "output_segmentation": str,
+    "debug": bool,
+})
+MriRefineSegParametersTagged = typing.TypedDict('MriRefineSegParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_refine_seg"],
     "input_segmentation": InputPathType,
     "output_segmentation": str,
     "debug": 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_refine_seg": mri_refine_seg_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_refine_seg": mri_refine_seg_outputs,
-    }.get(t)
 
 
 class MriRefineSegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_refine_seg(...)`.
+    Output object returned when calling `MriRefineSegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_refine_seg_params(
     input_segmentation: InputPathType,
     output_segmentation: str,
     debug: bool = False,
-) -> MriRefineSegParameters:
+) -> MriRefineSegParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def mri_refine_seg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_refine_seg",
+        "@type": "freesurfer/mri_refine_seg",
         "input_segmentation": input_segmentation,
         "output_segmentation": output_segmentation,
         "debug": debug,
@@ -105,13 +79,13 @@ def mri_refine_seg_cargs(
     cargs.append("mri_refine_seg")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_segmentation"))
+        execution.input_file(params.get("input_segmentation", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_segmentation")
+        params.get("output_segmentation", None)
     ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
     return cargs
 
@@ -131,16 +105,18 @@ def mri_refine_seg_outputs(
     """
     ret = MriRefineSegOutputs(
         root=execution.output_file("."),
-        refined_output=execution.output_file(params.get("output_segmentation")),
+        refined_output=execution.output_file(params.get("output_segmentation", None)),
     )
     return ret
 
 
 def mri_refine_seg_execute(
     params: MriRefineSegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriRefineSegOutputs:
     """
+    mri_refine_seg
+    
     Refines a messy segmentation by recoding stray voxels.
     
     Author: FreeSurfer Developers
@@ -149,10 +125,12 @@ def mri_refine_seg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriRefineSegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_REFINE_SEG_METADATA)
     params = execution.params(params)
     cargs = mri_refine_seg_cargs(params, execution)
     ret = mri_refine_seg_outputs(params, execution)
@@ -167,6 +145,8 @@ def mri_refine_seg(
     runner: Runner | None = None,
 ) -> MriRefineSegOutputs:
     """
+    mri_refine_seg
+    
     Refines a messy segmentation by recoding stray voxels.
     
     Author: FreeSurfer Developers
@@ -182,20 +162,18 @@ def mri_refine_seg(
     Returns:
         NamedTuple of outputs (described in `MriRefineSegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_REFINE_SEG_METADATA)
     params = mri_refine_seg_params(
         input_segmentation=input_segmentation,
         output_segmentation=output_segmentation,
         debug=debug,
     )
-    return mri_refine_seg_execute(params, execution)
+    return mri_refine_seg_execute(params, runner)
 
 
 __all__ = [
     "MRI_REFINE_SEG_METADATA",
     "MriRefineSegOutputs",
-    "MriRefineSegParameters",
     "mri_refine_seg",
+    "mri_refine_seg_execute",
     "mri_refine_seg_params",
 ]

niwrap_freesurfer/freesurfer/mri_relabel_hypointensities.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_RELABEL_HYPOINTENSITIES_METADATA = Metadata(
-    id="aa3bc866c8f63e117e0cb669962f59b7392d3770.boutiques",
+    id="6c2bbbdd6015ede6590888699f5288643dcd8f7b.boutiques",
     name="mri_relabel_hypointensities",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_RELABEL_HYPOINTENSITIES_METADATA = Metadata(
 
 
 MriRelabelHypointensitiesParameters = typing.TypedDict('MriRelabelHypointensitiesParameters', {
-    "__STYXTYPE__": typing.Literal["mri_relabel_hypointensities"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_relabel_hypointensities"]],
+    "input_aseg": InputPathType,
+    "surface_directory": str,
+    "output_aseg": str,
+})
+MriRelabelHypointensitiesParametersTagged = typing.TypedDict('MriRelabelHypointensitiesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_relabel_hypointensities"],
     "input_aseg": InputPathType,
     "surface_directory": str,
     "output_aseg": 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_relabel_hypointensities": mri_relabel_hypointensities_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_relabel_hypointensities": mri_relabel_hypointensities_outputs,
-    }.get(t)
 
 
 class MriRelabelHypointensitiesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_relabel_hypointensities(...)`.
+    Output object returned when calling `MriRelabelHypointensitiesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_relabel_hypointensities_params(
     input_aseg: InputPathType,
     surface_directory: str,
     output_aseg: str,
-) -> MriRelabelHypointensitiesParameters:
+) -> MriRelabelHypointensitiesParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mri_relabel_hypointensities_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_relabel_hypointensities",
+        "@type": "freesurfer/mri_relabel_hypointensities",
         "input_aseg": input_aseg,
         "surface_directory": surface_directory,
         "output_aseg": output_aseg,
@@ -102,9 +76,9 @@ def mri_relabel_hypointensities_cargs(
     """
     cargs = []
     cargs.append("mri_relabel_hypointensities")
-    cargs.append(execution.input_file(params.get("input_aseg")))
-    cargs.append(params.get("surface_directory"))
-    cargs.append(params.get("output_aseg"))
+    cargs.append(execution.input_file(params.get("input_aseg", None)))
+    cargs.append(params.get("surface_directory", None))
+    cargs.append(params.get("output_aseg", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def mri_relabel_hypointensities_outputs(
     """
     ret = MriRelabelHypointensitiesOutputs(
         root=execution.output_file("."),
-        output_aseg_file=execution.output_file(params.get("output_aseg")),
+        output_aseg_file=execution.output_file(params.get("output_aseg", None)),
     )
     return ret
 
 
 def mri_relabel_hypointensities_execute(
     params: MriRelabelHypointensitiesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriRelabelHypointensitiesOutputs:
     """
+    mri_relabel_hypointensities
+    
     Tool for relabeling hypointensities in FreeSurfer's aseg files.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def mri_relabel_hypointensities_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriRelabelHypointensitiesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_RELABEL_HYPOINTENSITIES_METADATA)
     params = execution.params(params)
     cargs = mri_relabel_hypointensities_cargs(params, execution)
     ret = mri_relabel_hypointensities_outputs(params, execution)
@@ -159,6 +137,8 @@ def mri_relabel_hypointensities(
     runner: Runner | None = None,
 ) -> MriRelabelHypointensitiesOutputs:
     """
+    mri_relabel_hypointensities
+    
     Tool for relabeling hypointensities in FreeSurfer's aseg files.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def mri_relabel_hypointensities(
     Returns:
         NamedTuple of outputs (described in `MriRelabelHypointensitiesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_RELABEL_HYPOINTENSITIES_METADATA)
     params = mri_relabel_hypointensities_params(
         input_aseg=input_aseg,
         surface_directory=surface_directory,
         output_aseg=output_aseg,
     )
-    return mri_relabel_hypointensities_execute(params, execution)
+    return mri_relabel_hypointensities_execute(params, runner)
 
 
 __all__ = [
     "MRI_RELABEL_HYPOINTENSITIES_METADATA",
     "MriRelabelHypointensitiesOutputs",
-    "MriRelabelHypointensitiesParameters",
     "mri_relabel_hypointensities",
+    "mri_relabel_hypointensities_execute",
     "mri_relabel_hypointensities_params",
 ]