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

niwrap_freesurfer/freesurfer/mri_vol2label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_VOL2LABEL_METADATA = Metadata(
-    id="e96f5a0ae21d22dfa1a0424a0ee90b67c8953101.boutiques",
+    id="7cc861ed2ff3c722e750dd4fbdaf8ecac68a4778.boutiques",
     name="mri_vol2label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ MRI_VOL2LABEL_METADATA = Metadata(
 
 
 MriVol2labelParameters = typing.TypedDict('MriVol2labelParameters', {
-    "__STYXTYPE__": typing.Literal["mri_vol2label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_vol2label"]],
+    "input": InputPathType,
+    "label_id": typing.NotRequired[float | None],
+    "threshold": typing.NotRequired[float | None],
+    "label_file": str,
+    "vol_file": typing.NotRequired[str | None],
+    "surf_subject_hemi": typing.NotRequired[str | None],
+    "surf_path": typing.NotRequired[str | None],
+    "opt_params": typing.NotRequired[str | None],
+    "remove_holes": bool,
+    "dilations": typing.NotRequired[float | None],
+    "erosions": typing.NotRequired[float | None],
+    "help": bool,
+})
+MriVol2labelParametersTagged = typing.TypedDict('MriVol2labelParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_vol2label"],
     "input": InputPathType,
     "label_id": typing.NotRequired[float | None],
     "threshold": typing.NotRequired[float | None],
@@ -28,43 +43,11 @@ MriVol2labelParameters = typing.TypedDict('MriVol2labelParameters', {
     "erosions": typing.NotRequired[float | None],
     "help": 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_vol2label": mri_vol2label_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_vol2label": mri_vol2label_outputs,
-    }.get(t)
 
 
 class MriVol2labelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_vol2label(...)`.
+    Output object returned when calling `MriVol2labelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +70,7 @@ def mri_vol2label_params(
     dilations: float | None = None,
     erosions: float | None = None,
     help_: bool = False,
-) -> MriVol2labelParameters:
+) -> MriVol2labelParametersTagged:
     """
     Build parameters.
     
@@ -111,7 +94,7 @@ def mri_vol2label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_vol2label",
+        "@type": "freesurfer/mri_vol2label",
         "input": input_,
         "label_file": label_file,
         "remove_holes": remove_holes,
@@ -153,55 +136,55 @@ def mri_vol2label_cargs(
     cargs.append("mri_vol2label")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input"))
+        execution.input_file(params.get("input", None))
     ])
-    if params.get("label_id") is not None:
+    if params.get("label_id", None) is not None:
         cargs.extend([
             "--id",
-            str(params.get("label_id"))
+            str(params.get("label_id", None))
         ])
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "--thresh",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
     cargs.extend([
         "--l",
-        params.get("label_file")
+        params.get("label_file", None)
     ])
-    if params.get("vol_file") is not None:
+    if params.get("vol_file", None) is not None:
         cargs.extend([
             "--v",
-            params.get("vol_file")
+            params.get("vol_file", None)
         ])
-    if params.get("surf_subject_hemi") is not None:
+    if params.get("surf_subject_hemi", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf_subject_hemi")
+            params.get("surf_subject_hemi", None)
         ])
-    if params.get("surf_path") is not None:
+    if params.get("surf_path", None) is not None:
         cargs.extend([
             "--surf-path",
-            params.get("surf_path")
+            params.get("surf_path", None)
         ])
-    if params.get("opt_params") is not None:
+    if params.get("opt_params", None) is not None:
         cargs.extend([
             "--opt",
-            params.get("opt_params")
+            params.get("opt_params", None)
         ])
-    if params.get("remove_holes"):
+    if params.get("remove_holes", False):
         cargs.append("--remove-holes-islands")
-    if params.get("dilations") is not None:
+    if params.get("dilations", None) is not None:
         cargs.extend([
             "--dilate",
-            str(params.get("dilations"))
+            str(params.get("dilations", None))
         ])
-    if params.get("erosions") is not None:
+    if params.get("erosions", None) is not None:
         cargs.extend([
             "--erode",
-            str(params.get("erosions"))
+            str(params.get("erosions", None))
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -221,17 +204,19 @@ def mri_vol2label_outputs(
     """
     ret = MriVol2labelOutputs(
         root=execution.output_file("."),
-        output_label_file=execution.output_file(params.get("label_file")),
-        output_volume_file=execution.output_file(params.get("vol_file")) if (params.get("vol_file") is not None) else None,
+        output_label_file=execution.output_file(params.get("label_file", None)),
+        output_volume_file=execution.output_file(params.get("vol_file", None)) if (params.get("vol_file") is not None) else None,
     )
     return ret
 
 
 def mri_vol2label_execute(
     params: MriVol2labelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriVol2labelOutputs:
     """
+    mri_vol2label
+    
     Converts values in a volume or surface overlay to a label using specified
     parameters.
     
@@ -241,10 +226,12 @@ def mri_vol2label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriVol2labelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_VOL2LABEL_METADATA)
     params = execution.params(params)
     cargs = mri_vol2label_cargs(params, execution)
     ret = mri_vol2label_outputs(params, execution)
@@ -268,6 +255,8 @@ def mri_vol2label(
     runner: Runner | None = None,
 ) -> MriVol2labelOutputs:
     """
+    mri_vol2label
+    
     Converts values in a volume or surface overlay to a label using specified
     parameters.
     
@@ -295,8 +284,6 @@ def mri_vol2label(
     Returns:
         NamedTuple of outputs (described in `MriVol2labelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_VOL2LABEL_METADATA)
     params = mri_vol2label_params(
         input_=input_,
         label_id=label_id,
@@ -311,13 +298,13 @@ def mri_vol2label(
         erosions=erosions,
         help_=help_,
     )
-    return mri_vol2label_execute(params, execution)
+    return mri_vol2label_execute(params, runner)
 
 
 __all__ = [
     "MRI_VOL2LABEL_METADATA",
     "MriVol2labelOutputs",
-    "MriVol2labelParameters",
     "mri_vol2label",
+    "mri_vol2label_execute",
     "mri_vol2label_params",
 ]

niwrap_freesurfer/freesurfer/mri_vol2surf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_VOL2SURF_METADATA = Metadata(
-    id="fcc05ec3c34c8382bd7c4cb2eeaa9d46a8804f41.boutiques",
+    id="2503c379fe63f85fc425451e4ccde489c206dce9.boutiques",
     name="mri_vol2surf",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ MRI_VOL2SURF_METADATA = Metadata(
 
 
 MriVol2surfParameters = typing.TypedDict('MriVol2surfParameters', {
-    "__STYXTYPE__": typing.Literal["mri_vol2surf"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_vol2surf"]],
+    "input_volume": InputPathType,
+    "registration_file": InputPathType,
+    "output_path": str,
+    "reference_volume": typing.NotRequired[str | None],
+    "regheader_subject": typing.NotRequired[str | None],
+    "mni152reg_flag": bool,
+    "target_subject": typing.NotRequired[str | None],
+    "hemisphere": typing.NotRequired[typing.Literal["lh", "rh"] | None],
+    "surface": typing.NotRequired[str | None],
+})
+MriVol2surfParametersTagged = typing.TypedDict('MriVol2surfParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_vol2surf"],
     "input_volume": InputPathType,
     "registration_file": InputPathType,
     "output_path": str,
@@ -25,43 +37,11 @@ MriVol2surfParameters = typing.TypedDict('MriVol2surfParameters', {
     "hemisphere": typing.NotRequired[typing.Literal["lh", "rh"] | None],
     "surface": 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_vol2surf": mri_vol2surf_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_vol2surf": mri_vol2surf_outputs,
-    }.get(t)
 
 
 class MriVol2surfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_vol2surf(...)`.
+    Output object returned when calling `MriVol2surfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def mri_vol2surf_params(
     target_subject: str | None = None,
     hemisphere: typing.Literal["lh", "rh"] | None = None,
     surface: str | None = None,
-) -> MriVol2surfParameters:
+) -> MriVol2surfParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +82,7 @@ def mri_vol2surf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_vol2surf",
+        "@type": "freesurfer/mri_vol2surf",
         "input_volume": input_volume,
         "registration_file": registration_file,
         "output_path": output_path,
@@ -138,42 +118,42 @@ def mri_vol2surf_cargs(
     cargs.append("mri_vol2surf")
     cargs.extend([
         "--mov",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "--reg",
-        execution.input_file(params.get("registration_file"))
+        execution.input_file(params.get("registration_file", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output_path")
+        params.get("output_path", None)
     ])
-    if params.get("reference_volume") is not None:
+    if params.get("reference_volume", None) is not None:
         cargs.extend([
             "--ref",
-            params.get("reference_volume")
+            params.get("reference_volume", None)
         ])
-    if params.get("regheader_subject") is not None:
+    if params.get("regheader_subject", None) is not None:
         cargs.extend([
             "--regheader",
-            params.get("regheader_subject")
+            params.get("regheader_subject", None)
         ])
-    if params.get("mni152reg_flag"):
+    if params.get("mni152reg_flag", False):
         cargs.append("--mni152reg")
-    if params.get("target_subject") is not None:
+    if params.get("target_subject", None) is not None:
         cargs.extend([
             "--trgsubject",
-            params.get("target_subject")
+            params.get("target_subject", None)
         ])
-    if params.get("hemisphere") is not None:
+    if params.get("hemisphere", None) is not None:
         cargs.extend([
             "--hemi",
-            params.get("hemisphere")
+            params.get("hemisphere", None)
         ])
-    if params.get("surface") is not None:
+    if params.get("surface", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surface")
+            params.get("surface", None)
         ])
     return cargs
 
@@ -193,18 +173,20 @@ def mri_vol2surf_outputs(
     """
     ret = MriVol2surfOutputs(
         root=execution.output_file("."),
-        resampled_volume_output=execution.output_file(params.get("output_path")),
+        resampled_volume_output=execution.output_file(params.get("output_path", None)),
     )
     return ret
 
 
 def mri_vol2surf_execute(
     params: MriVol2surfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriVol2surfOutputs:
     """
-    This program resamples a volume onto a surface of a subject or the sphere. The
-    output can be viewed on the surface (using tksurfer) or can be used for
+    mri_vol2surf
+    
+    This program resamples a volume onto a surface of a subject or the sphere.
+    The output can be viewed on the surface (using tksurfer) or can be used for
     surface-based intersubject averaging.
     
     Author: FreeSurfer Developers
@@ -213,10 +195,12 @@ def mri_vol2surf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriVol2surfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_VOL2SURF_METADATA)
     params = execution.params(params)
     cargs = mri_vol2surf_cargs(params, execution)
     ret = mri_vol2surf_outputs(params, execution)
@@ -237,8 +221,10 @@ def mri_vol2surf(
     runner: Runner | None = None,
 ) -> MriVol2surfOutputs:
     """
-    This program resamples a volume onto a surface of a subject or the sphere. The
-    output can be viewed on the surface (using tksurfer) or can be used for
+    mri_vol2surf
+    
+    This program resamples a volume onto a surface of a subject or the sphere.
+    The output can be viewed on the surface (using tksurfer) or can be used for
     surface-based intersubject averaging.
     
     Author: FreeSurfer Developers
@@ -264,8 +250,6 @@ def mri_vol2surf(
     Returns:
         NamedTuple of outputs (described in `MriVol2surfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_VOL2SURF_METADATA)
     params = mri_vol2surf_params(
         input_volume=input_volume,
         registration_file=registration_file,
@@ -277,13 +261,13 @@ def mri_vol2surf(
         hemisphere=hemisphere,
         surface=surface,
     )
-    return mri_vol2surf_execute(params, execution)
+    return mri_vol2surf_execute(params, runner)
 
 
 __all__ = [
     "MRI_VOL2SURF_METADATA",
     "MriVol2surfOutputs",
-    "MriVol2surfParameters",
     "mri_vol2surf",
+    "mri_vol2surf_execute",
     "mri_vol2surf_params",
 ]