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

niwrap_freesurfer/freesurfer/mrisp_write.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRISP_WRITE_METADATA = Metadata(
-    id="0ef5a849bb5e74469b12a33ed174cd4f7396c2f1.boutiques",
+    id="81011c1d707f5b750cc6ca9c5a5dc0fa621b36db.boutiques",
     name="mrisp_write",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,21 @@ MRISP_WRITE_METADATA = Metadata(
 
 
 MrispWriteParameters = typing.TypedDict('MrispWriteParameters', {
-    "__STYXTYPE__": typing.Literal["mrisp_write"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mrisp_write"]],
+    "input_surface": InputPathType,
+    "overlay_filename": InputPathType,
+    "output_name": str,
+    "subjects_dir": typing.NotRequired[str | None],
+    "coords": typing.NotRequired[str | None],
+    "average_curvature": typing.NotRequired[float | None],
+    "correlation_matrix": typing.NotRequired[InputPathType | None],
+    "scale_factor": typing.NotRequired[float | None],
+    "normalize_curvature": bool,
+    "verbose_vertex": typing.NotRequired[float | None],
+    "write_diagnostics": bool,
+})
+MrispWriteParametersTagged = typing.TypedDict('MrispWriteParametersTagged', {
+    "@type": typing.Literal["freesurfer/mrisp_write"],
     "input_surface": InputPathType,
     "overlay_filename": InputPathType,
     "output_name": str,
@@ -27,43 +41,11 @@ MrispWriteParameters = typing.TypedDict('MrispWriteParameters', {
     "verbose_vertex": typing.NotRequired[float | None],
     "write_diagnostics": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mrisp_write": mrisp_write_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 {
-        "mrisp_write": mrisp_write_outputs,
-    }.get(t)
 
 
 class MrispWriteOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrisp_write(...)`.
+    Output object returned when calling `MrispWriteParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +66,7 @@ def mrisp_write_params(
     normalize_curvature: bool = False,
     verbose_vertex: float | None = None,
     write_diagnostics: bool = False,
-) -> MrispWriteParameters:
+) -> MrispWriteParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +88,7 @@ def mrisp_write_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrisp_write",
+        "@type": "freesurfer/mrisp_write",
         "input_surface": input_surface,
         "overlay_filename": overlay_filename,
         "output_name": output_name,
@@ -143,42 +125,42 @@ def mrisp_write_cargs(
     """
     cargs = []
     cargs.append("mrisp_write")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("overlay_filename")))
-    cargs.append(params.get("output_name"))
-    if params.get("subjects_dir") is not None:
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("overlay_filename", None)))
+    cargs.append(params.get("output_name", None))
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "-SDIR",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("coords") is not None:
+    if params.get("coords", None) is not None:
         cargs.extend([
             "-coords",
-            params.get("coords")
+            params.get("coords", None)
         ])
-    if params.get("average_curvature") is not None:
+    if params.get("average_curvature", None) is not None:
         cargs.extend([
             "-A",
-            str(params.get("average_curvature"))
+            str(params.get("average_curvature", None))
         ])
-    if params.get("correlation_matrix") is not None:
+    if params.get("correlation_matrix", None) is not None:
         cargs.extend([
             "-CORR",
-            execution.input_file(params.get("correlation_matrix"))
+            execution.input_file(params.get("correlation_matrix", None))
         ])
-    if params.get("scale_factor") is not None:
+    if params.get("scale_factor", None) is not None:
         cargs.extend([
             "-SCALE",
-            str(params.get("scale_factor"))
+            str(params.get("scale_factor", None))
         ])
-    if params.get("normalize_curvature"):
+    if params.get("normalize_curvature", False):
         cargs.append("-N")
-    if params.get("verbose_vertex") is not None:
+    if params.get("verbose_vertex", None) is not None:
         cargs.extend([
             "-V",
-            str(params.get("verbose_vertex"))
+            str(params.get("verbose_vertex", None))
         ])
-    if params.get("write_diagnostics"):
+    if params.get("write_diagnostics", False):
         cargs.append("-W")
     return cargs
 
@@ -198,16 +180,18 @@ def mrisp_write_outputs(
     """
     ret = MrispWriteOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_name")),
+        output_file=execution.output_file(params.get("output_name", None)),
     )
     return ret
 
 
 def mrisp_write_execute(
     params: MrispWriteParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrispWriteOutputs:
     """
+    mrisp_write
+    
     This tool converts a surface overlay on a sphere into spherical coordinates.
     
     Author: FreeSurfer Developers
@@ -216,10 +200,12 @@ def mrisp_write_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrispWriteOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRISP_WRITE_METADATA)
     params = execution.params(params)
     cargs = mrisp_write_cargs(params, execution)
     ret = mrisp_write_outputs(params, execution)
@@ -242,6 +228,8 @@ def mrisp_write(
     runner: Runner | None = None,
 ) -> MrispWriteOutputs:
     """
+    mrisp_write
+    
     This tool converts a surface overlay on a sphere into spherical coordinates.
     
     Author: FreeSurfer Developers
@@ -266,8 +254,6 @@ def mrisp_write(
     Returns:
         NamedTuple of outputs (described in `MrispWriteOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRISP_WRITE_METADATA)
     params = mrisp_write_params(
         input_surface=input_surface,
         overlay_filename=overlay_filename,
@@ -281,13 +267,13 @@ def mrisp_write(
         verbose_vertex=verbose_vertex,
         write_diagnostics=write_diagnostics,
     )
-    return mrisp_write_execute(params, execution)
+    return mrisp_write_execute(params, runner)
 
 
 __all__ = [
     "MRISP_WRITE_METADATA",
     "MrispWriteOutputs",
-    "MrispWriteParameters",
     "mrisp_write",
+    "mrisp_write_execute",
     "mrisp_write_params",
 ]

niwrap_freesurfer/freesurfer/ms_refine_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MS_REFINE_SUBJECT_METADATA = Metadata(
-    id="f721290b4f615b29593a88005b00f64f24e7ebf7.boutiques",
+    id="f46e11b66b6a0cb3bedcbb0f473efee7620b5570.boutiques",
     name="ms_refine_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MS_REFINE_SUBJECT_METADATA = Metadata(
 
 
 MsRefineSubjectParameters = typing.TypedDict('MsRefineSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["ms_refine_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/ms_refine_subject"]],
+    "subjects_dir": str,
+})
+MsRefineSubjectParametersTagged = typing.TypedDict('MsRefineSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/ms_refine_subject"],
     "subjects_dir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "ms_refine_subject": ms_refine_subject_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 MsRefineSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `ms_refine_subject(...)`.
+    Output object returned when calling `MsRefineSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class MsRefineSubjectOutputs(typing.NamedTuple):
 
 def ms_refine_subject_params(
     subjects_dir: str,
-) -> MsRefineSubjectParameters:
+) -> MsRefineSubjectParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def ms_refine_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ms_refine_subject",
+        "@type": "freesurfer/ms_refine_subject",
         "subjects_dir": subjects_dir,
     }
     return params
@@ -92,7 +65,7 @@ def ms_refine_subject_cargs(
     """
     cargs = []
     cargs.append("ms_refine_subject")
-    cargs.append(params.get("subjects_dir"))
+    cargs.append(params.get("subjects_dir", None))
     return cargs
 
 
@@ -117,9 +90,11 @@ def ms_refine_subject_outputs(
 
 def ms_refine_subject_execute(
     params: MsRefineSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MsRefineSubjectOutputs:
     """
+    ms_refine_subject
+    
     Unknown.
     
     Author: FreeSurfer Developers
@@ -128,10 +103,12 @@ def ms_refine_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MsRefineSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MS_REFINE_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = ms_refine_subject_cargs(params, execution)
     ret = ms_refine_subject_outputs(params, execution)
@@ -144,6 +121,8 @@ def ms_refine_subject(
     runner: Runner | None = None,
 ) -> MsRefineSubjectOutputs:
     """
+    ms_refine_subject
+    
     Unknown.
     
     Author: FreeSurfer Developers
@@ -157,18 +136,16 @@ def ms_refine_subject(
     Returns:
         NamedTuple of outputs (described in `MsRefineSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MS_REFINE_SUBJECT_METADATA)
     params = ms_refine_subject_params(
         subjects_dir=subjects_dir,
     )
-    return ms_refine_subject_execute(params, execution)
+    return ms_refine_subject_execute(params, runner)
 
 
 __all__ = [
     "MS_REFINE_SUBJECT_METADATA",
     "MsRefineSubjectOutputs",
-    "MsRefineSubjectParameters",
     "ms_refine_subject",
+    "ms_refine_subject_execute",
     "ms_refine_subject_params",
 ]

niwrap_freesurfer/freesurfer/nmovie_qt.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 NMOVIE_QT_METADATA = Metadata(
-    id="40a52c883b6ef1eabbaca98341ef5cfeff36ee79.boutiques",
+    id="3c4302c8f4835c6715ec211ff9b02ab82b8e6b5b.boutiques",
     name="nmovie_qt",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ NMOVIE_QT_METADATA = Metadata(
 
 
 NmovieQtParameters = typing.TypedDict('NmovieQtParameters', {
-    "__STYXTYPE__": typing.Literal["nmovie_qt"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/nmovie_qt"]],
+    "images": list[InputPathType],
+})
+NmovieQtParametersTagged = typing.TypedDict('NmovieQtParametersTagged', {
+    "@type": typing.Literal["freesurfer/nmovie_qt"],
     "images": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "nmovie_qt": nmovie_qt_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 NmovieQtOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `nmovie_qt(...)`.
+    Output object returned when calling `NmovieQtParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class NmovieQtOutputs(typing.NamedTuple):
 
 def nmovie_qt_params(
     images: list[InputPathType],
-) -> NmovieQtParameters:
+) -> NmovieQtParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def nmovie_qt_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "nmovie_qt",
+        "@type": "freesurfer/nmovie_qt",
         "images": images,
     }
     return params
@@ -92,7 +65,7 @@ def nmovie_qt_cargs(
     """
     cargs = []
     cargs.append("nmovie_qt")
-    cargs.extend([execution.input_file(f) for f in params.get("images")])
+    cargs.extend([execution.input_file(f) for f in params.get("images", None)])
     return cargs
 
 
@@ -117,9 +90,11 @@ def nmovie_qt_outputs(
 
 def nmovie_qt_execute(
     params: NmovieQtParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> NmovieQtOutputs:
     """
+    nmovie_qt
+    
     An image viewer using Qt for displaying images in sequence.
     
     Author: FreeSurfer Developers
@@ -128,10 +103,12 @@ def nmovie_qt_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `NmovieQtOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NMOVIE_QT_METADATA)
     params = execution.params(params)
     cargs = nmovie_qt_cargs(params, execution)
     ret = nmovie_qt_outputs(params, execution)
@@ -144,6 +121,8 @@ def nmovie_qt(
     runner: Runner | None = None,
 ) -> NmovieQtOutputs:
     """
+    nmovie_qt
+    
     An image viewer using Qt for displaying images in sequence.
     
     Author: FreeSurfer Developers
@@ -157,18 +136,16 @@ def nmovie_qt(
     Returns:
         NamedTuple of outputs (described in `NmovieQtOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(NMOVIE_QT_METADATA)
     params = nmovie_qt_params(
         images=images,
     )
-    return nmovie_qt_execute(params, execution)
+    return nmovie_qt_execute(params, runner)
 
 
 __all__ = [
     "NMOVIE_QT_METADATA",
     "NmovieQtOutputs",
-    "NmovieQtParameters",
     "nmovie_qt",
+    "nmovie_qt_execute",
     "nmovie_qt_params",
 ]

niwrap_freesurfer/freesurfer/oct_register_mosaic.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 OCT_REGISTER_MOSAIC_METADATA = Metadata(
-    id="2b546a9d749a673358ff3e012b68d84d7dcd2c19.boutiques",
+    id="8de23bd673cf55ea10f2de41e3f5ce24d0006860.boutiques",
     name="oct_register_mosaic",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ OCT_REGISTER_MOSAIC_METADATA = Metadata(
 
 
 OctRegisterMosaicParameters = typing.TypedDict('OctRegisterMosaicParameters', {
-    "__STYXTYPE__": typing.Literal["oct_register_mosaic"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/oct_register_mosaic"]],
+    "tiles_or_mosaic_list": list[str],
+    "output_volume": str,
+    "downsample": typing.NotRequired[float | None],
+    "weight_file": typing.NotRequired[InputPathType | None],
+})
+OctRegisterMosaicParametersTagged = typing.TypedDict('OctRegisterMosaicParametersTagged', {
+    "@type": typing.Literal["freesurfer/oct_register_mosaic"],
     "tiles_or_mosaic_list": list[str],
     "output_volume": str,
     "downsample": typing.NotRequired[float | None],
     "weight_file": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "oct_register_mosaic": oct_register_mosaic_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 {
-        "oct_register_mosaic": oct_register_mosaic_outputs,
-    }.get(t)
 
 
 class OctRegisterMosaicOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `oct_register_mosaic(...)`.
+    Output object returned when calling `OctRegisterMosaicParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def oct_register_mosaic_params(
     output_volume: str,
     downsample: float | None = None,
     weight_file: InputPathType | None = None,
-) -> OctRegisterMosaicParameters:
+) -> OctRegisterMosaicParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def oct_register_mosaic_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "oct_register_mosaic",
+        "@type": "freesurfer/oct_register_mosaic",
         "tiles_or_mosaic_list": tiles_or_mosaic_list,
         "output_volume": output_volume,
     }
@@ -109,17 +84,17 @@ def oct_register_mosaic_cargs(
     """
     cargs = []
     cargs.append("oct_register_mosaic")
-    cargs.extend(params.get("tiles_or_mosaic_list"))
-    cargs.append(params.get("output_volume"))
-    if params.get("downsample") is not None:
+    cargs.extend(params.get("tiles_or_mosaic_list", None))
+    cargs.append(params.get("output_volume", None))
+    if params.get("downsample", None) is not None:
         cargs.extend([
             "-D",
-            str(params.get("downsample"))
+            str(params.get("downsample", None))
         ])
-    if params.get("weight_file") is not None:
+    if params.get("weight_file", None) is not None:
         cargs.extend([
             "-W",
-            execution.input_file(params.get("weight_file"))
+            execution.input_file(params.get("weight_file", None))
         ])
     return cargs
 
@@ -139,16 +114,18 @@ def oct_register_mosaic_outputs(
     """
     ret = OctRegisterMosaicOutputs(
         root=execution.output_file("."),
-        registered_output=execution.output_file(params.get("output_volume")),
+        registered_output=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def oct_register_mosaic_execute(
     params: OctRegisterMosaicParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> OctRegisterMosaicOutputs:
     """
+    oct_register_mosaic
+    
     Tool for registering multiple OCT (Optical Coherence Tomography) tiles or a
     mosaic list into a single output volume.
     
@@ -158,10 +135,12 @@ def oct_register_mosaic_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `OctRegisterMosaicOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(OCT_REGISTER_MOSAIC_METADATA)
     params = execution.params(params)
     cargs = oct_register_mosaic_cargs(params, execution)
     ret = oct_register_mosaic_outputs(params, execution)
@@ -177,6 +156,8 @@ def oct_register_mosaic(
     runner: Runner | None = None,
 ) -> OctRegisterMosaicOutputs:
     """
+    oct_register_mosaic
+    
     Tool for registering multiple OCT (Optical Coherence Tomography) tiles or a
     mosaic list into a single output volume.
     
@@ -194,21 +175,19 @@ def oct_register_mosaic(
     Returns:
         NamedTuple of outputs (described in `OctRegisterMosaicOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(OCT_REGISTER_MOSAIC_METADATA)
     params = oct_register_mosaic_params(
         tiles_or_mosaic_list=tiles_or_mosaic_list,
         output_volume=output_volume,
         downsample=downsample,
         weight_file=weight_file,
     )
-    return oct_register_mosaic_execute(params, execution)
+    return oct_register_mosaic_execute(params, runner)
 
 
 __all__ = [
     "OCT_REGISTER_MOSAIC_METADATA",
     "OctRegisterMosaicOutputs",
-    "OctRegisterMosaicParameters",
     "oct_register_mosaic",
+    "oct_register_mosaic_execute",
     "oct_register_mosaic_params",
 ]