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

niwrap_freesurfer/freesurfer/lta_convert.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LTA_CONVERT_METADATA = Metadata(
-    id="a3b2792635fe5446b685eda0b330b46970fccdd8.boutiques",
+    id="5d533d57fb19c18ab0c45cf5d4519ca8b87f7ba3.boutiques",
     name="lta_convert",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,31 @@ LTA_CONVERT_METADATA = Metadata(
 
 
 LtaConvertParameters = typing.TypedDict('LtaConvertParameters', {
-    "__STYXTYPE__": typing.Literal["lta_convert"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/lta_convert"]],
+    "in_lta": typing.NotRequired[InputPathType | None],
+    "in_fsl": typing.NotRequired[InputPathType | None],
+    "in_mni": typing.NotRequired[InputPathType | None],
+    "in_reg": typing.NotRequired[InputPathType | None],
+    "in_niftyreg": typing.NotRequired[InputPathType | None],
+    "in_itk": typing.NotRequired[InputPathType | None],
+    "in_vox": typing.NotRequired[InputPathType | None],
+    "out_lta": typing.NotRequired[str | None],
+    "out_fsl": typing.NotRequired[str | None],
+    "out_mni": typing.NotRequired[str | None],
+    "out_reg": typing.NotRequired[str | None],
+    "out_niftyreg": typing.NotRequired[str | None],
+    "out_itk": typing.NotRequired[str | None],
+    "out_vox": typing.NotRequired[str | None],
+    "invert": bool,
+    "ltavox2vox": bool,
+    "ltatkreg": bool,
+    "src_geometry": typing.NotRequired[InputPathType | None],
+    "trg_geometry": typing.NotRequired[InputPathType | None],
+    "trg_conform": bool,
+    "subject_name": typing.NotRequired[str | None],
+})
+LtaConvertParametersTagged = typing.TypedDict('LtaConvertParametersTagged', {
+    "@type": typing.Literal["freesurfer/lta_convert"],
     "in_lta": typing.NotRequired[InputPathType | None],
     "in_fsl": typing.NotRequired[InputPathType | None],
     "in_mni": typing.NotRequired[InputPathType | None],
@@ -37,43 +61,11 @@ LtaConvertParameters = typing.TypedDict('LtaConvertParameters', {
     "trg_conform": bool,
     "subject_name": 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 {
-        "lta_convert": lta_convert_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 {
-        "lta_convert": lta_convert_outputs,
-    }.get(t)
 
 
 class LtaConvertOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `lta_convert(...)`.
+    Output object returned when calling `LtaConvertParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +95,7 @@ def lta_convert_params(
     trg_geometry: InputPathType | None = None,
     trg_conform: bool = False,
     subject_name: str | None = None,
-) -> LtaConvertParameters:
+) -> LtaConvertParametersTagged:
     """
     Build parameters.
     
@@ -135,7 +127,7 @@ def lta_convert_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "lta_convert",
+        "@type": "freesurfer/lta_convert",
         "invert": invert,
         "ltavox2vox": ltavox2vox,
         "ltatkreg": ltatkreg,
@@ -193,98 +185,98 @@ def lta_convert_cargs(
     """
     cargs = []
     cargs.append("lta_convert")
-    if params.get("in_lta") is not None:
+    if params.get("in_lta", None) is not None:
         cargs.extend([
             "--inlta",
-            execution.input_file(params.get("in_lta"))
+            execution.input_file(params.get("in_lta", None))
         ])
-    if params.get("in_fsl") is not None:
+    if params.get("in_fsl", None) is not None:
         cargs.extend([
             "--infsl",
-            execution.input_file(params.get("in_fsl"))
+            execution.input_file(params.get("in_fsl", None))
         ])
-    if params.get("in_mni") is not None:
+    if params.get("in_mni", None) is not None:
         cargs.extend([
             "--inmni",
-            execution.input_file(params.get("in_mni"))
+            execution.input_file(params.get("in_mni", None))
         ])
-    if params.get("in_reg") is not None:
+    if params.get("in_reg", None) is not None:
         cargs.extend([
             "--inreg",
-            execution.input_file(params.get("in_reg"))
+            execution.input_file(params.get("in_reg", None))
         ])
-    if params.get("in_niftyreg") is not None:
+    if params.get("in_niftyreg", None) is not None:
         cargs.extend([
             "--inniftyreg",
-            execution.input_file(params.get("in_niftyreg"))
+            execution.input_file(params.get("in_niftyreg", None))
         ])
-    if params.get("in_itk") is not None:
+    if params.get("in_itk", None) is not None:
         cargs.extend([
             "--initk",
-            execution.input_file(params.get("in_itk"))
+            execution.input_file(params.get("in_itk", None))
         ])
-    if params.get("in_vox") is not None:
+    if params.get("in_vox", None) is not None:
         cargs.extend([
             "--invox",
-            execution.input_file(params.get("in_vox"))
+            execution.input_file(params.get("in_vox", None))
         ])
-    if params.get("out_lta") is not None:
+    if params.get("out_lta", None) is not None:
         cargs.extend([
             "--outlta",
-            params.get("out_lta")
+            params.get("out_lta", None)
         ])
-    if params.get("out_fsl") is not None:
+    if params.get("out_fsl", None) is not None:
         cargs.extend([
             "--outfsl",
-            params.get("out_fsl")
+            params.get("out_fsl", None)
         ])
-    if params.get("out_mni") is not None:
+    if params.get("out_mni", None) is not None:
         cargs.extend([
             "--outmni",
-            params.get("out_mni")
+            params.get("out_mni", None)
         ])
-    if params.get("out_reg") is not None:
+    if params.get("out_reg", None) is not None:
         cargs.extend([
             "--outreg",
-            params.get("out_reg")
+            params.get("out_reg", None)
         ])
-    if params.get("out_niftyreg") is not None:
+    if params.get("out_niftyreg", None) is not None:
         cargs.extend([
             "--outniftyreg",
-            params.get("out_niftyreg")
+            params.get("out_niftyreg", None)
         ])
-    if params.get("out_itk") is not None:
+    if params.get("out_itk", None) is not None:
         cargs.extend([
             "--outitk",
-            params.get("out_itk")
+            params.get("out_itk", None)
         ])
-    if params.get("out_vox") is not None:
+    if params.get("out_vox", None) is not None:
         cargs.extend([
             "--outvox",
-            params.get("out_vox")
+            params.get("out_vox", None)
         ])
-    if params.get("invert"):
+    if params.get("invert", False):
         cargs.append("--invert")
-    if params.get("ltavox2vox"):
+    if params.get("ltavox2vox", False):
         cargs.append("--ltavox2vox")
-    if params.get("ltatkreg"):
+    if params.get("ltatkreg", False):
         cargs.append("--ltatkreg")
-    if params.get("src_geometry") is not None:
+    if params.get("src_geometry", None) is not None:
         cargs.extend([
             "--src",
-            execution.input_file(params.get("src_geometry"))
+            execution.input_file(params.get("src_geometry", None))
         ])
-    if params.get("trg_geometry") is not None:
+    if params.get("trg_geometry", None) is not None:
         cargs.extend([
             "--trg",
-            execution.input_file(params.get("trg_geometry"))
+            execution.input_file(params.get("trg_geometry", None))
         ])
-    if params.get("trg_conform"):
+    if params.get("trg_conform", False):
         cargs.append("--trgconform")
-    if params.get("subject_name") is not None:
+    if params.get("subject_name", None) is not None:
         cargs.extend([
             "--subject",
-            params.get("subject_name")
+            params.get("subject_name", None)
         ])
     return cargs
 
@@ -304,16 +296,18 @@ def lta_convert_outputs(
     """
     ret = LtaConvertOutputs(
         root=execution.output_file("."),
-        output_transform_file=execution.output_file(params.get("out_vox")) if (params.get("out_vox") is not None) else None,
+        output_transform_file=execution.output_file(params.get("out_vox", None)) if (params.get("out_vox") is not None) else None,
     )
     return ret
 
 
 def lta_convert_execute(
     params: LtaConvertParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LtaConvertOutputs:
     """
+    lta_convert
+    
     This program converts between different linear transform formats.
     
     Author: FreeSurfer Developers
@@ -322,10 +316,12 @@ def lta_convert_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LtaConvertOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LTA_CONVERT_METADATA)
     params = execution.params(params)
     cargs = lta_convert_cargs(params, execution)
     ret = lta_convert_outputs(params, execution)
@@ -358,6 +354,8 @@ def lta_convert(
     runner: Runner | None = None,
 ) -> LtaConvertOutputs:
     """
+    lta_convert
+    
     This program converts between different linear transform formats.
     
     Author: FreeSurfer Developers
@@ -392,8 +390,6 @@ def lta_convert(
     Returns:
         NamedTuple of outputs (described in `LtaConvertOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LTA_CONVERT_METADATA)
     params = lta_convert_params(
         in_lta=in_lta,
         in_fsl=in_fsl,
@@ -417,13 +413,13 @@ def lta_convert(
         trg_conform=trg_conform,
         subject_name=subject_name,
     )
-    return lta_convert_execute(params, execution)
+    return lta_convert_execute(params, runner)
 
 
 __all__ = [
     "LTA_CONVERT_METADATA",
     "LtaConvertOutputs",
-    "LtaConvertParameters",
     "lta_convert",
+    "lta_convert_execute",
     "lta_convert_params",
 ]

niwrap_freesurfer/freesurfer/lta_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LTA_DIFF_METADATA = Metadata(
-    id="a8aaf9dc5936d4d700e770a1244924798ec88c42.boutiques",
+    id="906aee152c43f9cde4cae26d9c792fbdde016349.boutiques",
     name="lta_diff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ LTA_DIFF_METADATA = Metadata(
 
 
 LtaDiffParameters = typing.TypedDict('LtaDiffParameters', {
-    "__STYXTYPE__": typing.Literal["lta_diff"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/lta_diff"]],
+    "transform1": InputPathType,
+    "transform2": typing.NotRequired[InputPathType | None],
+    "dist_type": typing.NotRequired[int | None],
+    "invert1": bool,
+    "invert2": bool,
+    "vox": bool,
+    "normdiv": typing.NotRequired[float | None],
+    "radius": typing.NotRequired[float | None],
+})
+LtaDiffParametersTagged = typing.TypedDict('LtaDiffParametersTagged', {
+    "@type": typing.Literal["freesurfer/lta_diff"],
     "transform1": InputPathType,
     "transform2": typing.NotRequired[InputPathType | None],
     "dist_type": typing.NotRequired[int | None],
@@ -24,42 +35,11 @@ LtaDiffParameters = typing.TypedDict('LtaDiffParameters', {
     "normdiv": typing.NotRequired[float | None],
     "radius": 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 {
-        "lta_diff": lta_diff_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 LtaDiffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `lta_diff(...)`.
+    Output object returned when calling `LtaDiffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def lta_diff_params(
     vox: bool = False,
     normdiv: float | None = None,
     radius: float | None = None,
-) -> LtaDiffParameters:
+) -> LtaDiffParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +76,7 @@ def lta_diff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "lta_diff",
+        "@type": "freesurfer/lta_diff",
         "transform1": transform1,
         "invert1": invert1,
         "invert2": invert2,
@@ -128,29 +108,29 @@ def lta_diff_cargs(
     """
     cargs = []
     cargs.append("lta_diff")
-    cargs.append(execution.input_file(params.get("transform1")))
-    if params.get("transform2") is not None:
-        cargs.append(execution.input_file(params.get("transform2")))
-    if params.get("dist_type") is not None:
+    cargs.append(execution.input_file(params.get("transform1", None)))
+    if params.get("transform2", None) is not None:
+        cargs.append(execution.input_file(params.get("transform2", None)))
+    if params.get("dist_type", None) is not None:
         cargs.extend([
             "--dist",
-            str(params.get("dist_type"))
+            str(params.get("dist_type", None))
         ])
-    if params.get("invert1"):
+    if params.get("invert1", False):
         cargs.append("--invert1")
-    if params.get("invert2"):
+    if params.get("invert2", False):
         cargs.append("--invert2")
-    if params.get("vox"):
+    if params.get("vox", False):
         cargs.append("--vox")
-    if params.get("normdiv") is not None:
+    if params.get("normdiv", None) is not None:
         cargs.extend([
             "--normdiv",
-            str(params.get("normdiv"))
+            str(params.get("normdiv", None))
         ])
-    if params.get("radius") is not None:
+    if params.get("radius", None) is not None:
         cargs.extend([
             "--radius",
-            str(params.get("radius"))
+            str(params.get("radius", None))
         ])
     return cargs
 
@@ -176,9 +156,11 @@ def lta_diff_outputs(
 
 def lta_diff_execute(
     params: LtaDiffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LtaDiffOutputs:
     """
+    lta_diff
+    
     A tool to compute different distance norms for a single transform or for the
     difference between two transforms.
     
@@ -188,10 +170,12 @@ def lta_diff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LtaDiffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LTA_DIFF_METADATA)
     params = execution.params(params)
     cargs = lta_diff_cargs(params, execution)
     ret = lta_diff_outputs(params, execution)
@@ -211,6 +195,8 @@ def lta_diff(
     runner: Runner | None = None,
 ) -> LtaDiffOutputs:
     """
+    lta_diff
+    
     A tool to compute different distance norms for a single transform or for the
     difference between two transforms.
     
@@ -236,8 +222,6 @@ def lta_diff(
     Returns:
         NamedTuple of outputs (described in `LtaDiffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LTA_DIFF_METADATA)
     params = lta_diff_params(
         transform1=transform1,
         transform2=transform2,
@@ -248,13 +232,13 @@ def lta_diff(
         normdiv=normdiv,
         radius=radius,
     )
-    return lta_diff_execute(params, execution)
+    return lta_diff_execute(params, runner)
 
 
 __all__ = [
     "LTA_DIFF_METADATA",
     "LtaDiffOutputs",
-    "LtaDiffParameters",
     "lta_diff",
+    "lta_diff_execute",
     "lta_diff_params",
 ]

niwrap_freesurfer/freesurfer/make_average_subcort.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_AVERAGE_SUBCORT_METADATA = Metadata(
-    id="b17b1c4b76255506a8adefa172c0d0695e88aa4d.boutiques",
+    id="a9d2af7caad7bc6f8a3561a2a0b6e179fcad642a.boutiques",
     name="make_average_subcort",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MAKE_AVERAGE_SUBCORT_METADATA = Metadata(
 
 
 MakeAverageSubcortParameters = typing.TypedDict('MakeAverageSubcortParameters', {
-    "__STYXTYPE__": typing.Literal["make_average_subcort"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/make_average_subcort"]],
+    "subjects": list[str],
+    "output_volume": str,
+})
+MakeAverageSubcortParametersTagged = typing.TypedDict('MakeAverageSubcortParametersTagged', {
+    "@type": typing.Literal["freesurfer/make_average_subcort"],
     "subjects": list[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 {
-        "make_average_subcort": make_average_subcort_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 {
-        "make_average_subcort": make_average_subcort_outputs,
-    }.get(t)
 
 
 class MakeAverageSubcortOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_average_subcort(...)`.
+    Output object returned when calling `MakeAverageSubcortParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MakeAverageSubcortOutputs(typing.NamedTuple):
 def make_average_subcort_params(
     subjects: list[str],
     output_volume: str,
-) -> MakeAverageSubcortParameters:
+) -> MakeAverageSubcortParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def make_average_subcort_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "make_average_subcort",
+        "@type": "freesurfer/make_average_subcort",
         "subjects": subjects,
         "output_volume": output_volume,
     }
@@ -98,10 +71,10 @@ def make_average_subcort_cargs(
     """
     cargs = []
     cargs.append("make_average_subcort")
-    cargs.extend(params.get("subjects"))
+    cargs.extend(params.get("subjects", None))
     cargs.extend([
         "--o",
-        params.get("output_volume")
+        params.get("output_volume", None)
     ])
     return cargs
 
@@ -121,18 +94,21 @@ def make_average_subcort_outputs(
     """
     ret = MakeAverageSubcortOutputs(
         root=execution.output_file("."),
-        output_mask_file=execution.output_file(params.get("output_volume")),
+        output_mask_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def make_average_subcort_execute(
     params: MakeAverageSubcortParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakeAverageSubcortOutputs:
     """
-    This creates an average subcortical mask for the given input subjects, intended
-    for use in subcortical analysis in FSFAST to exclude cortical voxels.
+    make_average_subcort
+    
+    This creates an average subcortical mask for the given input subjects,
+    intended for use in subcortical analysis in FSFAST to exclude cortical
+    voxels.
     
     Author: FreeSurfer Developers
     
@@ -140,10 +116,12 @@ def make_average_subcort_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakeAverageSubcortOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_AVERAGE_SUBCORT_METADATA)
     params = execution.params(params)
     cargs = make_average_subcort_cargs(params, execution)
     ret = make_average_subcort_outputs(params, execution)
@@ -157,8 +135,11 @@ def make_average_subcort(
     runner: Runner | None = None,
 ) -> MakeAverageSubcortOutputs:
     """
-    This creates an average subcortical mask for the given input subjects, intended
-    for use in subcortical analysis in FSFAST to exclude cortical voxels.
+    make_average_subcort
+    
+    This creates an average subcortical mask for the given input subjects,
+    intended for use in subcortical analysis in FSFAST to exclude cortical
+    voxels.
     
     Author: FreeSurfer Developers
     
@@ -171,19 +152,17 @@ def make_average_subcort(
     Returns:
         NamedTuple of outputs (described in `MakeAverageSubcortOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_AVERAGE_SUBCORT_METADATA)
     params = make_average_subcort_params(
         subjects=subjects,
         output_volume=output_volume,
     )
-    return make_average_subcort_execute(params, execution)
+    return make_average_subcort_execute(params, runner)
 
 
 __all__ = [
     "MAKE_AVERAGE_SUBCORT_METADATA",
     "MakeAverageSubcortOutputs",
-    "MakeAverageSubcortParameters",
     "make_average_subcort",
+    "make_average_subcort_execute",
     "make_average_subcort_params",
 ]