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

niwrap_freesurfer/freesurfer/mri_annotation2label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_ANNOTATION2LABEL_METADATA = Metadata(
-    id="55fc21182a781a7f38a958280013700685656b3a.boutiques",
+    id="dfb4132e393a73bf703ddc3d078e6fb732dd4241.boutiques",
     name="mri_annotation2label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,29 @@ MRI_ANNOTATION2LABEL_METADATA = Metadata(
 
 
 MriAnnotation2labelParameters = typing.TypedDict('MriAnnotation2labelParameters', {
-    "__STYXTYPE__": typing.Literal["mri_annotation2label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_annotation2label"]],
+    "subject": str,
+    "hemi": str,
+    "lobes": typing.NotRequired[InputPathType | None],
+    "lobes_strict": typing.NotRequired[InputPathType | None],
+    "lobes_strict_phcg": typing.NotRequired[InputPathType | None],
+    "label": typing.NotRequired[float | None],
+    "labelbase": typing.NotRequired[str | None],
+    "outdir": typing.NotRequired[str | None],
+    "seg": typing.NotRequired[InputPathType | None],
+    "segbase": typing.NotRequired[float | None],
+    "ctab": typing.NotRequired[InputPathType | None],
+    "border": typing.NotRequired[InputPathType | None],
+    "border_annot": typing.NotRequired[str | None],
+    "annotation": typing.NotRequired[str | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "surface": typing.NotRequired[str | None],
+    "stat": typing.NotRequired[InputPathType | None],
+    "help": bool,
+    "version": bool,
+})
+MriAnnotation2labelParametersTagged = typing.TypedDict('MriAnnotation2labelParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_annotation2label"],
     "subject": str,
     "hemi": str,
     "lobes": typing.NotRequired[InputPathType | None],
@@ -35,42 +57,11 @@ MriAnnotation2labelParameters = typing.TypedDict('MriAnnotation2labelParameters'
     "help": bool,
     "version": 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_annotation2label": mri_annotation2label_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 MriAnnotation2labelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_annotation2label(...)`.
+    Output object returned when calling `MriAnnotation2labelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -96,7 +87,7 @@ def mri_annotation2label_params(
     stat_: InputPathType | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MriAnnotation2labelParameters:
+) -> MriAnnotation2labelParametersTagged:
     """
     Build parameters.
     
@@ -127,7 +118,7 @@ def mri_annotation2label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_annotation2label",
+        "@type": "freesurfer/mri_annotation2label",
         "subject": subject,
         "hemi": hemi,
         "help": help_,
@@ -183,90 +174,90 @@ def mri_annotation2label_cargs(
     cargs.append("mri_annotation2label")
     cargs.extend([
         "--subject",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "--hemi",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
-    if params.get("lobes") is not None:
+    if params.get("lobes", None) is not None:
         cargs.extend([
             "--lobes",
-            execution.input_file(params.get("lobes"))
+            execution.input_file(params.get("lobes", None))
         ])
-    if params.get("lobes_strict") is not None:
+    if params.get("lobes_strict", None) is not None:
         cargs.extend([
             "--lobesStrict",
-            execution.input_file(params.get("lobes_strict"))
+            execution.input_file(params.get("lobes_strict", None))
         ])
-    if params.get("lobes_strict_phcg") is not None:
+    if params.get("lobes_strict_phcg", None) is not None:
         cargs.extend([
             "--lobesStrictPHCG",
-            execution.input_file(params.get("lobes_strict_phcg"))
+            execution.input_file(params.get("lobes_strict_phcg", None))
         ])
-    if params.get("label") is not None:
+    if params.get("label", None) is not None:
         cargs.extend([
             "--label",
-            str(params.get("label"))
+            str(params.get("label", None))
         ])
-    if params.get("labelbase") is not None:
+    if params.get("labelbase", None) is not None:
         cargs.extend([
             "--labelbase",
-            params.get("labelbase")
+            params.get("labelbase", None)
         ])
-    if params.get("outdir") is not None:
+    if params.get("outdir", None) is not None:
         cargs.extend([
             "--outdir",
-            params.get("outdir")
+            params.get("outdir", None)
         ])
-    if params.get("seg") is not None:
+    if params.get("seg", None) is not None:
         cargs.extend([
             "--seg",
-            execution.input_file(params.get("seg"))
+            execution.input_file(params.get("seg", None))
         ])
-    if params.get("segbase") is not None:
+    if params.get("segbase", None) is not None:
         cargs.extend([
             "--segbase",
-            str(params.get("segbase"))
+            str(params.get("segbase", None))
         ])
-    if params.get("ctab") is not None:
+    if params.get("ctab", None) is not None:
         cargs.extend([
             "--ctab",
-            execution.input_file(params.get("ctab"))
+            execution.input_file(params.get("ctab", None))
         ])
-    if params.get("border") is not None:
+    if params.get("border", None) is not None:
         cargs.extend([
             "--border",
-            execution.input_file(params.get("border"))
+            execution.input_file(params.get("border", None))
         ])
-    if params.get("border_annot") is not None:
+    if params.get("border_annot", None) is not None:
         cargs.extend([
             "--border-annot",
-            params.get("border_annot")
+            params.get("border_annot", None)
         ])
-    if params.get("annotation") is not None:
+    if params.get("annotation", None) is not None:
         cargs.extend([
             "--annotation",
-            params.get("annotation")
+            params.get("annotation", None)
         ])
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("surface") is not None:
+    if params.get("surface", None) is not None:
         cargs.extend([
             "--surface",
-            params.get("surface")
+            params.get("surface", None)
         ])
-    if params.get("stat") is not None:
+    if params.get("stat", None) is not None:
         cargs.extend([
             "--stat",
-            execution.input_file(params.get("stat"))
+            execution.input_file(params.get("stat", None))
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -292,10 +283,13 @@ def mri_annotation2label_outputs(
 
 def mri_annotation2label_execute(
     params: MriAnnotation2labelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriAnnotation2labelOutputs:
     """
-    Convert an annotation into multiple label files or into a segmentation volume.
+    mri_annotation2label
+    
+    Convert an annotation into multiple label files or into a segmentation
+    volume.
     
     Author: FreeSurfer Developers
     
@@ -303,10 +297,12 @@ def mri_annotation2label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriAnnotation2labelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_ANNOTATION2LABEL_METADATA)
     params = execution.params(params)
     cargs = mri_annotation2label_cargs(params, execution)
     ret = mri_annotation2label_outputs(params, execution)
@@ -337,7 +333,10 @@ def mri_annotation2label(
     runner: Runner | None = None,
 ) -> MriAnnotation2labelOutputs:
     """
-    Convert an annotation into multiple label files or into a segmentation volume.
+    mri_annotation2label
+    
+    Convert an annotation into multiple label files or into a segmentation
+    volume.
     
     Author: FreeSurfer Developers
     
@@ -370,8 +369,6 @@ def mri_annotation2label(
     Returns:
         NamedTuple of outputs (described in `MriAnnotation2labelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_ANNOTATION2LABEL_METADATA)
     params = mri_annotation2label_params(
         subject=subject,
         hemi=hemi,
@@ -393,13 +390,13 @@ def mri_annotation2label(
         help_=help_,
         version=version,
     )
-    return mri_annotation2label_execute(params, execution)
+    return mri_annotation2label_execute(params, runner)
 
 
 __all__ = [
     "MRI_ANNOTATION2LABEL_METADATA",
     "MriAnnotation2labelOutputs",
-    "MriAnnotation2labelParameters",
     "mri_annotation2label",
+    "mri_annotation2label_execute",
     "mri_annotation2label_params",
 ]

niwrap_freesurfer/freesurfer/mri_aparc2aseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_APARC2ASEG_METADATA = Metadata(
-    id="0b4fa72d59bc4736773c396ee961d7d9070c06da.boutiques",
+    id="dc941a2089f873008413fb964e54b8f35532e9b7.boutiques",
     name="mri_aparc2aseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,31 @@ MRI_APARC2ASEG_METADATA = Metadata(
 
 
 MriAparc2asegParameters = typing.TypedDict('MriAparc2asegParameters', {
-    "__STYXTYPE__": typing.Literal["mri_aparc2aseg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_aparc2aseg"]],
+    "subject": typing.NotRequired[str | None],
+    "output_volfile": typing.NotRequired[str | None],
+    "old_ribbon": bool,
+    "new_ribbon": bool,
+    "a2005s": bool,
+    "a2009s": bool,
+    "annot_name": typing.NotRequired[str | None],
+    "annot_table": typing.NotRequired[str | None],
+    "base_offset": typing.NotRequired[float | None],
+    "label_wm": bool,
+    "wmparc_dmax": typing.NotRequired[float | None],
+    "rip_unknown": bool,
+    "hypo_as_wm": bool,
+    "no_fix_parahip": bool,
+    "smooth_normals": typing.NotRequired[float | None],
+    "crs_test": typing.NotRequired[str | None],
+    "left_hemisphere": bool,
+    "right_hemisphere": bool,
+    "threads": typing.NotRequired[float | None],
+    "help": bool,
+    "version": bool,
+})
+MriAparc2asegParametersTagged = typing.TypedDict('MriAparc2asegParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_aparc2aseg"],
     "subject": typing.NotRequired[str | None],
     "output_volfile": typing.NotRequired[str | None],
     "old_ribbon": bool,
@@ -37,43 +61,11 @@ MriAparc2asegParameters = typing.TypedDict('MriAparc2asegParameters', {
     "help": bool,
     "version": 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_aparc2aseg": mri_aparc2aseg_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_aparc2aseg": mri_aparc2aseg_outputs,
-    }.get(t)
 
 
 class MriAparc2asegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_aparc2aseg(...)`.
+    Output object returned when calling `MriAparc2asegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +95,7 @@ def mri_aparc2aseg_params(
     threads: float | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MriAparc2asegParameters:
+) -> MriAparc2asegParametersTagged:
     """
     Build parameters.
     
@@ -141,7 +133,7 @@ def mri_aparc2aseg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_aparc2aseg",
+        "@type": "freesurfer/mri_aparc2aseg",
         "old_ribbon": old_ribbon,
         "new_ribbon": new_ribbon,
         "a2005s": a2005s,
@@ -191,74 +183,74 @@ def mri_aparc2aseg_cargs(
     """
     cargs = []
     cargs.append("mri_aparc2aseg")
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "--s",
-            params.get("subject")
+            params.get("subject", None)
         ])
-    if params.get("output_volfile") is not None:
+    if params.get("output_volfile", None) is not None:
         cargs.extend([
             "--o",
-            params.get("output_volfile")
+            params.get("output_volfile", None)
         ])
-    if params.get("old_ribbon"):
+    if params.get("old_ribbon", False):
         cargs.append("--old-ribbon")
-    if params.get("new_ribbon"):
+    if params.get("new_ribbon", False):
         cargs.append("--new-ribbon")
-    if params.get("a2005s"):
+    if params.get("a2005s", False):
         cargs.append("--a2005s")
-    if params.get("a2009s"):
+    if params.get("a2009s", False):
         cargs.append("--a2009s")
-    if params.get("annot_name") is not None:
+    if params.get("annot_name", None) is not None:
         cargs.extend([
             "--annot",
-            params.get("annot_name")
+            params.get("annot_name", None)
         ])
-    if params.get("annot_table") is not None:
+    if params.get("annot_table", None) is not None:
         cargs.extend([
             "--annot-table",
-            params.get("annot_table")
+            params.get("annot_table", None)
         ])
-    if params.get("base_offset") is not None:
+    if params.get("base_offset", None) is not None:
         cargs.extend([
             "--base-offset",
-            str(params.get("base_offset"))
+            str(params.get("base_offset", None))
         ])
-    if params.get("label_wm"):
+    if params.get("label_wm", False):
         cargs.append("--labelwm")
-    if params.get("wmparc_dmax") is not None:
+    if params.get("wmparc_dmax", None) is not None:
         cargs.extend([
             "--wmparc-dmax",
-            str(params.get("wmparc_dmax"))
+            str(params.get("wmparc_dmax", None))
         ])
-    if params.get("rip_unknown"):
+    if params.get("rip_unknown", False):
         cargs.append("--rip-unknown")
-    if params.get("hypo_as_wm"):
+    if params.get("hypo_as_wm", False):
         cargs.append("--hypo-as-wm")
-    if params.get("no_fix_parahip"):
+    if params.get("no_fix_parahip", False):
         cargs.append("--no-fix-parahip")
-    if params.get("smooth_normals") is not None:
+    if params.get("smooth_normals", None) is not None:
         cargs.extend([
             "--smooth_normals",
-            str(params.get("smooth_normals"))
+            str(params.get("smooth_normals", None))
         ])
-    if params.get("crs_test") is not None:
+    if params.get("crs_test", None) is not None:
         cargs.extend([
             "--crs-test",
-            params.get("crs_test")
+            params.get("crs_test", None)
         ])
-    if params.get("left_hemisphere"):
+    if params.get("left_hemisphere", False):
         cargs.append("--lh")
-    if params.get("right_hemisphere"):
+    if params.get("right_hemisphere", False):
         cargs.append("--rh")
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -285,9 +277,11 @@ def mri_aparc2aseg_outputs(
 
 def mri_aparc2aseg_execute(
     params: MriAparc2asegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriAparc2asegOutputs:
     """
+    mri_aparc2aseg
+    
     Maps the cortical labels from the automatic cortical parcellation to the
     automatic segmentation volume.
     
@@ -297,10 +291,12 @@ def mri_aparc2aseg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriAparc2asegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_APARC2ASEG_METADATA)
     params = execution.params(params)
     cargs = mri_aparc2aseg_cargs(params, execution)
     ret = mri_aparc2aseg_outputs(params, execution)
@@ -333,6 +329,8 @@ def mri_aparc2aseg(
     runner: Runner | None = None,
 ) -> MriAparc2asegOutputs:
     """
+    mri_aparc2aseg
+    
     Maps the cortical labels from the automatic cortical parcellation to the
     automatic segmentation volume.
     
@@ -374,8 +372,6 @@ def mri_aparc2aseg(
     Returns:
         NamedTuple of outputs (described in `MriAparc2asegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_APARC2ASEG_METADATA)
     params = mri_aparc2aseg_params(
         subject=subject,
         output_volfile=output_volfile,
@@ -399,13 +395,13 @@ def mri_aparc2aseg(
         help_=help_,
         version=version,
     )
-    return mri_aparc2aseg_execute(params, execution)
+    return mri_aparc2aseg_execute(params, runner)
 
 
 __all__ = [
     "MRI_APARC2ASEG_METADATA",
     "MriAparc2asegOutputs",
-    "MriAparc2asegParameters",
     "mri_aparc2aseg",
+    "mri_aparc2aseg_execute",
     "mri_aparc2aseg_params",
 ]