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

niwrap_freesurfer/freesurfer/mris_thickness.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_THICKNESS_METADATA = Metadata(
-    id="219cc09086fcb3e40767c96cbad6d1655bbeeb34.boutiques",
+    id="397bfb25dc63ff852ee3fe26678b12f0512990ef.boutiques",
     name="mris_thickness",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRIS_THICKNESS_METADATA = Metadata(
 
 
 MrisThicknessParameters = typing.TypedDict('MrisThicknessParameters', {
-    "__STYXTYPE__": typing.Literal["mris_thickness"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_thickness"]],
+    "subject_name": str,
+    "hemi": str,
+    "thickness_file": str,
+    "max_threshold": typing.NotRequired[float | None],
+    "fill_holes": typing.NotRequired[list[str] | None],
+    "thickness_from_seg": typing.NotRequired[list[str] | None],
+    "vector": bool,
+})
+MrisThicknessParametersTagged = typing.TypedDict('MrisThicknessParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_thickness"],
     "subject_name": str,
     "hemi": str,
     "thickness_file": str,
@@ -23,43 +33,11 @@ MrisThicknessParameters = typing.TypedDict('MrisThicknessParameters', {
     "thickness_from_seg": typing.NotRequired[list[str] | None],
     "vector": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_thickness": mris_thickness_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 {
-        "mris_thickness": mris_thickness_outputs,
-    }.get(t)
 
 
 class MrisThicknessOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_thickness(...)`.
+    Output object returned when calling `MrisThicknessParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mris_thickness_params(
     fill_holes: list[str] | None = None,
     thickness_from_seg: list[str] | None = None,
     vector: bool = False,
-) -> MrisThicknessParameters:
+) -> MrisThicknessParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +73,7 @@ def mris_thickness_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_thickness",
+        "@type": "freesurfer/mris_thickness",
         "subject_name": subject_name,
         "hemi": hemi,
         "thickness_file": thickness_file,
@@ -125,25 +103,25 @@ def mris_thickness_cargs(
     """
     cargs = []
     cargs.append("mris_thickness")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("thickness_file"))
-    if params.get("max_threshold") is not None:
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("thickness_file", None))
+    if params.get("max_threshold", None) is not None:
         cargs.extend([
             "-max",
-            str(params.get("max_threshold"))
+            str(params.get("max_threshold", None))
         ])
-    if params.get("fill_holes") is not None:
+    if params.get("fill_holes", None) is not None:
         cargs.extend([
             "-fill_holes",
-            *params.get("fill_holes")
+            *params.get("fill_holes", None)
         ])
-    if params.get("thickness_from_seg") is not None:
+    if params.get("thickness_from_seg", None) is not None:
         cargs.extend([
             "-thickness-from-seg",
-            *params.get("thickness_from_seg")
+            *params.get("thickness_from_seg", None)
         ])
-    if params.get("vector"):
+    if params.get("vector", False):
         cargs.append("-vector")
     return cargs
 
@@ -163,16 +141,18 @@ def mris_thickness_outputs(
     """
     ret = MrisThicknessOutputs(
         root=execution.output_file("."),
-        output_thickness_file=execution.output_file(params.get("thickness_file")),
+        output_thickness_file=execution.output_file(params.get("thickness_file", None)),
     )
     return ret
 
 
 def mris_thickness_execute(
     params: MrisThicknessParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisThicknessOutputs:
     """
+    mris_thickness
+    
     Measures the thickness of the cortical surface.
     
     Author: FreeSurfer Developers
@@ -181,10 +161,12 @@ def mris_thickness_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisThicknessOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_THICKNESS_METADATA)
     params = execution.params(params)
     cargs = mris_thickness_cargs(params, execution)
     ret = mris_thickness_outputs(params, execution)
@@ -203,6 +185,8 @@ def mris_thickness(
     runner: Runner | None = None,
 ) -> MrisThicknessOutputs:
     """
+    mris_thickness
+    
     Measures the thickness of the cortical surface.
     
     Author: FreeSurfer Developers
@@ -225,8 +209,6 @@ def mris_thickness(
     Returns:
         NamedTuple of outputs (described in `MrisThicknessOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_THICKNESS_METADATA)
     params = mris_thickness_params(
         subject_name=subject_name,
         hemi=hemi,
@@ -236,13 +218,13 @@ def mris_thickness(
         thickness_from_seg=thickness_from_seg,
         vector=vector,
     )
-    return mris_thickness_execute(params, execution)
+    return mris_thickness_execute(params, runner)
 
 
 __all__ = [
     "MRIS_THICKNESS_METADATA",
     "MrisThicknessOutputs",
-    "MrisThicknessParameters",
     "mris_thickness",
+    "mris_thickness_execute",
     "mris_thickness_params",
 ]

niwrap_freesurfer/freesurfer/mris_thickness_comparison.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_THICKNESS_COMPARISON_METADATA = Metadata(
-    id="7af273460a46de42cbe519e79fb65ca38e3c1fff.boutiques",
+    id="9a9492d13f619bbb85ad0c50c62520e3b045a025.boutiques",
     name="mris_thickness_comparison",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,26 @@ MRIS_THICKNESS_COMPARISON_METADATA = Metadata(
 
 
 MrisThicknessComparisonParameters = typing.TypedDict('MrisThicknessComparisonParameters', {
-    "__STYXTYPE__": typing.Literal["mris_thickness_comparison"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_thickness_comparison"]],
+    "subject": str,
+    "hemi": str,
+    "thickness_file": InputPathType,
+    "w_file": InputPathType,
+    "labels": list[str],
+})
+MrisThicknessComparisonParametersTagged = typing.TypedDict('MrisThicknessComparisonParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_thickness_comparison"],
     "subject": str,
     "hemi": str,
     "thickness_file": InputPathType,
     "w_file": InputPathType,
     "labels": list[str],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_thickness_comparison": mris_thickness_comparison_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 MrisThicknessComparisonOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_thickness_comparison(...)`.
+    Output object returned when calling `MrisThicknessComparisonParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,7 +45,7 @@ def mris_thickness_comparison_params(
     thickness_file: InputPathType,
     w_file: InputPathType,
     labels: list[str],
-) -> MrisThicknessComparisonParameters:
+) -> MrisThicknessComparisonParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +59,7 @@ def mris_thickness_comparison_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_thickness_comparison",
+        "@type": "freesurfer/mris_thickness_comparison",
         "subject": subject,
         "hemi": hemi,
         "thickness_file": thickness_file,
@@ -107,11 +84,11 @@ def mris_thickness_comparison_cargs(
     """
     cargs = []
     cargs.append("mris_thickness_comparison")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("thickness_file")))
-    cargs.append(execution.input_file(params.get("w_file")))
-    cargs.extend(params.get("labels"))
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("thickness_file", None)))
+    cargs.append(execution.input_file(params.get("w_file", None)))
+    cargs.extend(params.get("labels", None))
     return cargs
 
 
@@ -136,11 +113,13 @@ def mris_thickness_comparison_outputs(
 
 def mris_thickness_comparison_execute(
     params: MrisThicknessComparisonParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisThicknessComparisonOutputs:
     """
-    Tool to compare cortical thickness measurements between two or more specified
-    labels.
+    mris_thickness_comparison
+    
+    Tool to compare cortical thickness measurements between two or more
+    specified labels.
     
     Author: FreeSurfer Developers
     
@@ -148,10 +127,12 @@ def mris_thickness_comparison_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisThicknessComparisonOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_THICKNESS_COMPARISON_METADATA)
     params = execution.params(params)
     cargs = mris_thickness_comparison_cargs(params, execution)
     ret = mris_thickness_comparison_outputs(params, execution)
@@ -168,8 +149,10 @@ def mris_thickness_comparison(
     runner: Runner | None = None,
 ) -> MrisThicknessComparisonOutputs:
     """
-    Tool to compare cortical thickness measurements between two or more specified
-    labels.
+    mris_thickness_comparison
+    
+    Tool to compare cortical thickness measurements between two or more
+    specified labels.
     
     Author: FreeSurfer Developers
     
@@ -185,8 +168,6 @@ def mris_thickness_comparison(
     Returns:
         NamedTuple of outputs (described in `MrisThicknessComparisonOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_THICKNESS_COMPARISON_METADATA)
     params = mris_thickness_comparison_params(
         subject=subject,
         hemi=hemi,
@@ -194,13 +175,13 @@ def mris_thickness_comparison(
         w_file=w_file,
         labels=labels,
     )
-    return mris_thickness_comparison_execute(params, execution)
+    return mris_thickness_comparison_execute(params, runner)
 
 
 __all__ = [
     "MRIS_THICKNESS_COMPARISON_METADATA",
     "MrisThicknessComparisonOutputs",
-    "MrisThicknessComparisonParameters",
     "mris_thickness_comparison",
+    "mris_thickness_comparison_execute",
     "mris_thickness_comparison_params",
 ]

niwrap_freesurfer/freesurfer/mris_thickness_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_THICKNESS_DIFF_METADATA = Metadata(
-    id="95efc622125bf8bcd42b0208effbdbe434d5b062.boutiques",
+    id="a3ec581547cad53689b40c2404afc383dac2983f.boutiques",
     name="mris_thickness_diff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ MRIS_THICKNESS_DIFF_METADATA = Metadata(
 
 
 MrisThicknessDiffParameters = typing.TypedDict('MrisThicknessDiffParameters', {
-    "__STYXTYPE__": typing.Literal["mris_thickness_diff"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_thickness_diff"]],
+    "src_type": typing.NotRequired[str | None],
+    "trg_type": typing.NotRequired[str | None],
+    "out_file": str,
+    "out_resampled": typing.NotRequired[str | None],
+    "nsmooth": typing.NotRequired[float | None],
+    "register": bool,
+    "xform": typing.NotRequired[InputPathType | None],
+    "invert": bool,
+    "src_volume": typing.NotRequired[InputPathType | None],
+    "dst_volume": typing.NotRequired[InputPathType | None],
+    "abs": bool,
+    "log_file": typing.NotRequired[InputPathType | None],
+    "subject_name": typing.NotRequired[str | None],
+})
+MrisThicknessDiffParametersTagged = typing.TypedDict('MrisThicknessDiffParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_thickness_diff"],
     "src_type": typing.NotRequired[str | None],
     "trg_type": typing.NotRequired[str | None],
     "out_file": str,
@@ -29,43 +45,11 @@ MrisThicknessDiffParameters = typing.TypedDict('MrisThicknessDiffParameters', {
     "log_file": typing.NotRequired[InputPathType | None],
     "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 {
-        "mris_thickness_diff": mris_thickness_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 {
-        "mris_thickness_diff": mris_thickness_diff_outputs,
-    }.get(t)
 
 
 class MrisThicknessDiffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_thickness_diff(...)`.
+    Output object returned when calling `MrisThicknessDiffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +73,7 @@ def mris_thickness_diff_params(
     abs_: bool = False,
     log_file: InputPathType | None = None,
     subject_name: str | None = None,
-) -> MrisThicknessDiffParameters:
+) -> MrisThicknessDiffParametersTagged:
     """
     Build parameters.
     
@@ -111,7 +95,7 @@ def mris_thickness_diff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_thickness_diff",
+        "@type": "freesurfer/mris_thickness_diff",
         "out_file": out_file,
         "register": register,
         "invert": invert,
@@ -153,60 +137,60 @@ def mris_thickness_diff_cargs(
     """
     cargs = []
     cargs.append("mris_thickness_diff")
-    if params.get("src_type") is not None:
+    if params.get("src_type", None) is not None:
         cargs.extend([
             "-src_type",
-            params.get("src_type")
+            params.get("src_type", None)
         ])
-    if params.get("trg_type") is not None:
+    if params.get("trg_type", None) is not None:
         cargs.extend([
             "-trg_type",
-            params.get("trg_type")
+            params.get("trg_type", None)
         ])
     cargs.extend([
         "-out",
-        params.get("out_file")
+        params.get("out_file", None)
     ])
-    if params.get("out_resampled") is not None:
+    if params.get("out_resampled", None) is not None:
         cargs.extend([
             "-out_resampled",
-            params.get("out_resampled")
+            params.get("out_resampled", None)
         ])
-    if params.get("nsmooth") is not None:
+    if params.get("nsmooth", None) is not None:
         cargs.extend([
             "-nsmooth",
-            str(params.get("nsmooth"))
+            str(params.get("nsmooth", None))
         ])
-    if params.get("register"):
+    if params.get("register", False):
         cargs.append("-register")
-    if params.get("xform") is not None:
+    if params.get("xform", None) is not None:
         cargs.extend([
             "-xform",
-            execution.input_file(params.get("xform"))
+            execution.input_file(params.get("xform", None))
         ])
-    if params.get("invert"):
+    if params.get("invert", False):
         cargs.append("-invert")
-    if params.get("src_volume") is not None:
+    if params.get("src_volume", None) is not None:
         cargs.extend([
             "-src",
-            execution.input_file(params.get("src_volume"))
+            execution.input_file(params.get("src_volume", None))
         ])
-    if params.get("dst_volume") is not None:
+    if params.get("dst_volume", None) is not None:
         cargs.extend([
             "-dst",
-            execution.input_file(params.get("dst_volume"))
+            execution.input_file(params.get("dst_volume", None))
         ])
-    if params.get("abs"):
+    if params.get("abs", False):
         cargs.append("-abs")
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "-L",
-            execution.input_file(params.get("log_file"))
+            execution.input_file(params.get("log_file", None))
         ])
-    if params.get("subject_name") is not None:
+    if params.get("subject_name", None) is not None:
         cargs.extend([
             "-S",
-            params.get("subject_name")
+            params.get("subject_name", None)
         ])
     return cargs
 
@@ -226,18 +210,21 @@ def mris_thickness_diff_outputs(
     """
     ret = MrisThicknessDiffOutputs(
         root=execution.output_file("."),
-        output_difference=execution.output_file(params.get("out_file")),
-        output_resampled=execution.output_file(params.get("out_resampled")) if (params.get("out_resampled") is not None) else None,
+        output_difference=execution.output_file(params.get("out_file", None)),
+        output_resampled=execution.output_file(params.get("out_resampled", None)) if (params.get("out_resampled") is not None) else None,
     )
     return ret
 
 
 def mris_thickness_diff_execute(
     params: MrisThicknessDiffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisThicknessDiffOutputs:
     """
-    Computes the difference of two surface data sets defined on two surface meshes.
+    mris_thickness_diff
+    
+    Computes the difference of two surface data sets defined on two surface
+    meshes.
     
     Author: FreeSurfer Developers
     
@@ -245,10 +232,12 @@ def mris_thickness_diff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisThicknessDiffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_THICKNESS_DIFF_METADATA)
     params = execution.params(params)
     cargs = mris_thickness_diff_cargs(params, execution)
     ret = mris_thickness_diff_outputs(params, execution)
@@ -273,7 +262,10 @@ def mris_thickness_diff(
     runner: Runner | None = None,
 ) -> MrisThicknessDiffOutputs:
     """
-    Computes the difference of two surface data sets defined on two surface meshes.
+    mris_thickness_diff
+    
+    Computes the difference of two surface data sets defined on two surface
+    meshes.
     
     Author: FreeSurfer Developers
     
@@ -297,8 +289,6 @@ def mris_thickness_diff(
     Returns:
         NamedTuple of outputs (described in `MrisThicknessDiffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_THICKNESS_DIFF_METADATA)
     params = mris_thickness_diff_params(
         src_type=src_type,
         trg_type=trg_type,
@@ -314,13 +304,13 @@ def mris_thickness_diff(
         log_file=log_file,
         subject_name=subject_name,
     )
-    return mris_thickness_diff_execute(params, execution)
+    return mris_thickness_diff_execute(params, runner)
 
 
 __all__ = [
     "MRIS_THICKNESS_DIFF_METADATA",
     "MrisThicknessDiffOutputs",
-    "MrisThicknessDiffParameters",
     "mris_thickness_diff",
+    "mris_thickness_diff_execute",
     "mris_thickness_diff_params",
 ]