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

niwrap_freesurfer/freesurfer/mris_watershed.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_WATERSHED_METADATA = Metadata(
-    id="00a449a8a6f51c196100ff275164c3c37acfd4fd.boutiques",
+    id="76d3ef836a20a8e86fdcebbcd4bd4d6de67216e2.boutiques",
     name="mris_watershed",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRIS_WATERSHED_METADATA = Metadata(
 
 
 MrisWatershedParameters = typing.TypedDict('MrisWatershedParameters', {
-    "__STYXTYPE__": typing.Literal["mris_watershed"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_watershed"]],
+    "input_surface": InputPathType,
+    "input_gradient_field": InputPathType,
+    "output_annotation": str,
+    "max_clusters": typing.NotRequired[float | None],
+    "mask_label": typing.NotRequired[str | None],
+})
+MrisWatershedParametersTagged = typing.TypedDict('MrisWatershedParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_watershed"],
     "input_surface": InputPathType,
     "input_gradient_field": InputPathType,
     "output_annotation": str,
     "max_clusters": typing.NotRequired[float | None],
     "mask_label": 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_watershed": mris_watershed_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_watershed": mris_watershed_outputs,
-    }.get(t)
 
 
 class MrisWatershedOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_watershed(...)`.
+    Output object returned when calling `MrisWatershedParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mris_watershed_params(
     output_annotation: str,
     max_clusters: float | None = None,
     mask_label: str | None = None,
-) -> MrisWatershedParameters:
+) -> MrisWatershedParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +62,7 @@ def mris_watershed_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_watershed",
+        "@type": "freesurfer/mris_watershed",
         "input_surface": input_surface,
         "input_gradient_field": input_gradient_field,
         "output_annotation": output_annotation,
@@ -113,18 +89,18 @@ def mris_watershed_cargs(
     """
     cargs = []
     cargs.append("mris_watershed")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("input_gradient_field")))
-    cargs.append(params.get("output_annotation"))
-    if params.get("max_clusters") is not None:
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("input_gradient_field", None)))
+    cargs.append(params.get("output_annotation", None))
+    if params.get("max_clusters", None) is not None:
         cargs.extend([
             "-M",
-            str(params.get("max_clusters"))
+            str(params.get("max_clusters", None))
         ])
-    if params.get("mask_label") is not None:
+    if params.get("mask_label", None) is not None:
         cargs.extend([
             "-mask_label",
-            params.get("mask_label")
+            params.get("mask_label", None)
         ])
     return cargs
 
@@ -144,16 +120,18 @@ def mris_watershed_outputs(
     """
     ret = MrisWatershedOutputs(
         root=execution.output_file("."),
-        output_annotation_file=execution.output_file(params.get("output_annotation")),
+        output_annotation_file=execution.output_file(params.get("output_annotation", None)),
     )
     return ret
 
 
 def mris_watershed_execute(
     params: MrisWatershedParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisWatershedOutputs:
     """
+    mris_watershed
+    
     This program computes the watershed transform on the surface of an intensity
     gradient and writes the resulting measurement into a .annot file.
     
@@ -163,10 +141,12 @@ def mris_watershed_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisWatershedOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_WATERSHED_METADATA)
     params = execution.params(params)
     cargs = mris_watershed_cargs(params, execution)
     ret = mris_watershed_outputs(params, execution)
@@ -183,6 +163,8 @@ def mris_watershed(
     runner: Runner | None = None,
 ) -> MrisWatershedOutputs:
     """
+    mris_watershed
+    
     This program computes the watershed transform on the surface of an intensity
     gradient and writes the resulting measurement into a .annot file.
     
@@ -201,8 +183,6 @@ def mris_watershed(
     Returns:
         NamedTuple of outputs (described in `MrisWatershedOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_WATERSHED_METADATA)
     params = mris_watershed_params(
         input_surface=input_surface,
         input_gradient_field=input_gradient_field,
@@ -210,13 +190,13 @@ def mris_watershed(
         max_clusters=max_clusters,
         mask_label=mask_label,
     )
-    return mris_watershed_execute(params, execution)
+    return mris_watershed_execute(params, runner)
 
 
 __all__ = [
     "MRIS_WATERSHED_METADATA",
     "MrisWatershedOutputs",
-    "MrisWatershedParameters",
     "mris_watershed",
+    "mris_watershed_execute",
     "mris_watershed_params",
 ]

niwrap_freesurfer/freesurfer/mris_wm_volume.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_WM_VOLUME_METADATA = Metadata(
-    id="587eff884475c51ca4db98e3c82ac79329b0686d.boutiques",
+    id="7a262143473871cbee9cc9dc098e5db8119e8932.boutiques",
     name="mris_wm_volume",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_WM_VOLUME_METADATA = Metadata(
 
 
 MrisWmVolumeParameters = typing.TypedDict('MrisWmVolumeParameters', {
-    "__STYXTYPE__": typing.Literal["mris_wm_volume"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_wm_volume"]],
+    "subject": str,
+    "hemi": str,
+    "subjects_dir": typing.NotRequired[str | None],
+    "whitesurfname": typing.NotRequired[str | None],
+    "asegname": typing.NotRequired[str | None],
+    "verbose": bool,
+})
+MrisWmVolumeParametersTagged = typing.TypedDict('MrisWmVolumeParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_wm_volume"],
     "subject": str,
     "hemi": str,
     "subjects_dir": typing.NotRequired[str | None],
@@ -22,42 +31,11 @@ MrisWmVolumeParameters = typing.TypedDict('MrisWmVolumeParameters', {
     "asegname": typing.NotRequired[str | None],
     "verbose": 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_wm_volume": mris_wm_volume_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 MrisWmVolumeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_wm_volume(...)`.
+    Output object returned when calling `MrisWmVolumeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def mris_wm_volume_params(
     whitesurfname: str | None = None,
     asegname: str | None = None,
     verbose: bool = False,
-) -> MrisWmVolumeParameters:
+) -> MrisWmVolumeParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +63,7 @@ def mris_wm_volume_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_wm_volume",
+        "@type": "freesurfer/mris_wm_volume",
         "subject": subject,
         "hemi": hemi,
         "verbose": verbose,
@@ -114,24 +92,24 @@ def mris_wm_volume_cargs(
     """
     cargs = []
     cargs.append("mris_wm_volume")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("hemi"))
-    if params.get("subjects_dir") is not None:
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("hemi", 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("whitesurfname") is not None:
+    if params.get("whitesurfname", None) is not None:
         cargs.extend([
             "-white",
-            params.get("whitesurfname")
+            params.get("whitesurfname", None)
         ])
-    if params.get("asegname") is not None:
+    if params.get("asegname", None) is not None:
         cargs.extend([
             "-aseg",
-            params.get("asegname")
+            params.get("asegname", None)
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-v")
     return cargs
 
@@ -157,11 +135,13 @@ def mris_wm_volume_outputs(
 
 def mris_wm_volume_execute(
     params: MrisWmVolumeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisWmVolumeOutputs:
     """
-    Computes the volume of the enclosed hemisphere white matter surface, ignoring
-    non-white matter voxels in the aseg.
+    mris_wm_volume
+    
+    Computes the volume of the enclosed hemisphere white matter surface,
+    ignoring non-white matter voxels in the aseg.
     
     Author: FreeSurfer Developers
     
@@ -169,10 +149,12 @@ def mris_wm_volume_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisWmVolumeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_WM_VOLUME_METADATA)
     params = execution.params(params)
     cargs = mris_wm_volume_cargs(params, execution)
     ret = mris_wm_volume_outputs(params, execution)
@@ -190,8 +172,10 @@ def mris_wm_volume(
     runner: Runner | None = None,
 ) -> MrisWmVolumeOutputs:
     """
-    Computes the volume of the enclosed hemisphere white matter surface, ignoring
-    non-white matter voxels in the aseg.
+    mris_wm_volume
+    
+    Computes the volume of the enclosed hemisphere white matter surface,
+    ignoring non-white matter voxels in the aseg.
     
     Author: FreeSurfer Developers
     
@@ -208,8 +192,6 @@ def mris_wm_volume(
     Returns:
         NamedTuple of outputs (described in `MrisWmVolumeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_WM_VOLUME_METADATA)
     params = mris_wm_volume_params(
         subject=subject,
         hemi=hemi,
@@ -218,13 +200,13 @@ def mris_wm_volume(
         asegname=asegname,
         verbose=verbose,
     )
-    return mris_wm_volume_execute(params, execution)
+    return mris_wm_volume_execute(params, runner)
 
 
 __all__ = [
     "MRIS_WM_VOLUME_METADATA",
     "MrisWmVolumeOutputs",
-    "MrisWmVolumeParameters",
     "mris_wm_volume",
+    "mris_wm_volume_execute",
     "mris_wm_volume_params",
 ]

niwrap_freesurfer/freesurfer/mrisp_paint.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRISP_PAINT_METADATA = Metadata(
-    id="d16941ee5e8f63175f830c6357cad0fb5eda9270.boutiques",
+    id="9dec9f7ee526556391d7778d04d28c94dac60651.boutiques",
     name="mrisp_paint",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,26 @@ MRISP_PAINT_METADATA = Metadata(
 
 
 MrispPaintParameters = typing.TypedDict('MrispPaintParameters', {
-    "__STYXTYPE__": typing.Literal["mrisp_paint"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mrisp_paint"]],
+    "template_file": InputPathType,
+    "input_surface": InputPathType,
+    "output_name": str,
+    "subjects_dir": typing.NotRequired[str | None],
+    "vertex_coords": typing.NotRequired[str | None],
+    "average_flag": typing.NotRequired[float | None],
+    "normalize_flag": bool,
+    "frame_number": typing.NotRequired[float | None],
+    "square_root_flag": bool,
+    "variance_params": typing.NotRequired[str | None],
+    "usage_flag": bool,
+    "birn_info_flag": bool,
+    "help_flag": bool,
+    "diag_vertex": typing.NotRequired[float | None],
+    "version_flag": bool,
+    "diag_write_flag": bool,
+})
+MrispPaintParametersTagged = typing.TypedDict('MrispPaintParametersTagged', {
+    "@type": typing.Literal["freesurfer/mrisp_paint"],
     "template_file": InputPathType,
     "input_surface": InputPathType,
     "output_name": str,
@@ -32,43 +51,11 @@ MrispPaintParameters = typing.TypedDict('MrispPaintParameters', {
     "version_flag": bool,
     "diag_write_flag": 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_paint": mrisp_paint_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_paint": mrisp_paint_outputs,
-    }.get(t)
 
 
 class MrispPaintOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mrisp_paint(...)`.
+    Output object returned when calling `MrispPaintParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -94,7 +81,7 @@ def mrisp_paint_params(
     diag_vertex: float | None = None,
     version_flag: bool = False,
     diag_write_flag: bool = False,
-) -> MrispPaintParameters:
+) -> MrispPaintParametersTagged:
     """
     Build parameters.
     
@@ -125,7 +112,7 @@ def mrisp_paint_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mrisp_paint",
+        "@type": "freesurfer/mrisp_paint",
         "template_file": template_file,
         "input_surface": input_surface,
         "output_name": output_name,
@@ -167,52 +154,52 @@ def mrisp_paint_cargs(
     """
     cargs = []
     cargs.append("mrisp_paint")
-    cargs.append(execution.input_file(params.get("template_file")))
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(params.get("output_name"))
-    if params.get("subjects_dir") is not None:
+    cargs.append(execution.input_file(params.get("template_file", None)))
+    cargs.append(execution.input_file(params.get("input_surface", 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("vertex_coords") is not None:
+    if params.get("vertex_coords", None) is not None:
         cargs.extend([
             "-coords",
-            params.get("vertex_coords")
+            params.get("vertex_coords", None)
         ])
-    if params.get("average_flag") is not None:
+    if params.get("average_flag", None) is not None:
         cargs.extend([
             "-A",
-            str(params.get("average_flag"))
+            str(params.get("average_flag", None))
         ])
-    if params.get("normalize_flag"):
+    if params.get("normalize_flag", False):
         cargs.append("-N")
-    if params.get("frame_number") is not None:
+    if params.get("frame_number", None) is not None:
         cargs.extend([
             "-f",
-            str(params.get("frame_number"))
+            str(params.get("frame_number", None))
         ])
-    if params.get("square_root_flag"):
+    if params.get("square_root_flag", False):
         cargs.append("-S")
-    if params.get("variance_params") is not None:
+    if params.get("variance_params", None) is not None:
         cargs.extend([
             "-variance",
-            params.get("variance_params")
+            params.get("variance_params", None)
         ])
-    if params.get("usage_flag"):
+    if params.get("usage_flag", False):
         cargs.append("-?")
-    if params.get("birn_info_flag"):
+    if params.get("birn_info_flag", False):
         cargs.append("--all-info")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("--help")
-    if params.get("diag_vertex") is not None:
+    if params.get("diag_vertex", None) is not None:
         cargs.extend([
             "-V",
-            str(params.get("diag_vertex"))
+            str(params.get("diag_vertex", None))
         ])
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("--version")
-    if params.get("diag_write_flag"):
+    if params.get("diag_write_flag", False):
         cargs.append("-W")
     return cargs
 
@@ -232,16 +219,18 @@ def mrisp_paint_outputs(
     """
     ret = MrispPaintOutputs(
         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_paint_execute(
     params: MrispPaintParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrispPaintOutputs:
     """
+    mrisp_paint
+    
     A tool for extracting arrays from a surface-registration template file and
     sampling them onto a surface mesh.
     
@@ -251,10 +240,12 @@ def mrisp_paint_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrispPaintOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRISP_PAINT_METADATA)
     params = execution.params(params)
     cargs = mrisp_paint_cargs(params, execution)
     ret = mrisp_paint_outputs(params, execution)
@@ -282,6 +273,8 @@ def mrisp_paint(
     runner: Runner | None = None,
 ) -> MrispPaintOutputs:
     """
+    mrisp_paint
+    
     A tool for extracting arrays from a surface-registration template file and
     sampling them onto a surface mesh.
     
@@ -316,8 +309,6 @@ def mrisp_paint(
     Returns:
         NamedTuple of outputs (described in `MrispPaintOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRISP_PAINT_METADATA)
     params = mrisp_paint_params(
         template_file=template_file,
         input_surface=input_surface,
@@ -336,13 +327,13 @@ def mrisp_paint(
         version_flag=version_flag,
         diag_write_flag=diag_write_flag,
     )
-    return mrisp_paint_execute(params, execution)
+    return mrisp_paint_execute(params, runner)
 
 
 __all__ = [
     "MRISP_PAINT_METADATA",
     "MrispPaintOutputs",
-    "MrispPaintParameters",
     "mrisp_paint",
+    "mrisp_paint_execute",
     "mrisp_paint_params",
 ]