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

niwrap_freesurfer/freesurfer/defect2seg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DEFECT2SEG_METADATA = Metadata(
-    id="ee34539fd2b9014ec765deedfc67dab265d637bf.boutiques",
+    id="12ffaaea46cdc5d96ba3f6b4833570361e61f73d.boutiques",
     name="defect2seg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ DEFECT2SEG_METADATA = Metadata(
 
 
 Defect2segParameters = typing.TypedDict('Defect2segParameters', {
-    "__STYXTYPE__": typing.Literal["defect2seg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/defect2seg"]],
+    "output_seg": str,
+    "template": InputPathType,
+    "left_hemisphere": typing.NotRequired[list[str] | None],
+    "right_hemisphere": typing.NotRequired[list[str] | None],
+    "subject": typing.NotRequired[str | None],
+    "lh_only": bool,
+    "rh_only": bool,
+    "cortex": bool,
+    "no_cortex": bool,
+})
+Defect2segParametersTagged = typing.TypedDict('Defect2segParametersTagged', {
+    "@type": typing.Literal["freesurfer/defect2seg"],
     "output_seg": str,
     "template": InputPathType,
     "left_hemisphere": typing.NotRequired[list[str] | None],
@@ -25,43 +37,11 @@ Defect2segParameters = typing.TypedDict('Defect2segParameters', {
     "cortex": bool,
     "no_cortex": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "defect2seg": defect2seg_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 {
-        "defect2seg": defect2seg_outputs,
-    }.get(t)
 
 
 class Defect2segOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `defect2seg(...)`.
+    Output object returned when calling `Defect2segParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def defect2seg_params(
     rh_only: bool = False,
     cortex: bool = False,
     no_cortex: bool = False,
-) -> Defect2segParameters:
+) -> Defect2segParametersTagged:
     """
     Build parameters.
     
@@ -99,7 +79,7 @@ def defect2seg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "defect2seg",
+        "@type": "freesurfer/defect2seg",
         "output_seg": output_seg,
         "template": template,
         "lh_only": lh_only,
@@ -133,34 +113,34 @@ def defect2seg_cargs(
     cargs.append("defect2seg")
     cargs.extend([
         "--o",
-        params.get("output_seg")
+        params.get("output_seg", None)
     ])
     cargs.extend([
         "--t",
-        execution.input_file(params.get("template"))
+        execution.input_file(params.get("template", None))
     ])
-    if params.get("left_hemisphere") is not None:
+    if params.get("left_hemisphere", None) is not None:
         cargs.extend([
             "--lh",
-            *params.get("left_hemisphere")
+            *params.get("left_hemisphere", None)
         ])
-    if params.get("right_hemisphere") is not None:
+    if params.get("right_hemisphere", None) is not None:
         cargs.extend([
             "--rh",
-            *params.get("right_hemisphere")
+            *params.get("right_hemisphere", None)
         ])
-    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("lh_only"):
+    if params.get("lh_only", False):
         cargs.append("--lh-only")
-    if params.get("rh_only"):
+    if params.get("rh_only", False):
         cargs.append("--rh-only")
-    if params.get("cortex"):
+    if params.get("cortex", False):
         cargs.append("--cortex")
-    if params.get("no_cortex"):
+    if params.get("no_cortex", False):
         cargs.append("--no-cortex")
     return cargs
 
@@ -180,16 +160,18 @@ def defect2seg_outputs(
     """
     ret = Defect2segOutputs(
         root=execution.output_file("."),
-        output_segmentation=execution.output_file(params.get("output_seg")),
+        output_segmentation=execution.output_file(params.get("output_seg", None)),
     )
     return ret
 
 
 def defect2seg_execute(
     params: Defect2segParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Defect2segOutputs:
     """
+    defect2seg
+    
     Converts surface defect labels into a segmentation volume and pointsets.
     
     Author: FreeSurfer Developers
@@ -198,10 +180,12 @@ def defect2seg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Defect2segOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DEFECT2SEG_METADATA)
     params = execution.params(params)
     cargs = defect2seg_cargs(params, execution)
     ret = defect2seg_outputs(params, execution)
@@ -222,6 +206,8 @@ def defect2seg(
     runner: Runner | None = None,
 ) -> Defect2segOutputs:
     """
+    defect2seg
+    
     Converts surface defect labels into a segmentation volume and pointsets.
     
     Author: FreeSurfer Developers
@@ -244,8 +230,6 @@ def defect2seg(
     Returns:
         NamedTuple of outputs (described in `Defect2segOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DEFECT2SEG_METADATA)
     params = defect2seg_params(
         output_seg=output_seg,
         template=template,
@@ -257,13 +241,13 @@ def defect2seg(
         cortex=cortex,
         no_cortex=no_cortex,
     )
-    return defect2seg_execute(params, execution)
+    return defect2seg_execute(params, runner)
 
 
 __all__ = [
     "DEFECT2SEG_METADATA",
     "Defect2segOutputs",
-    "Defect2segParameters",
     "defect2seg",
+    "defect2seg_execute",
     "defect2seg_params",
 ]

niwrap_freesurfer/freesurfer/defect_seg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DEFECT_SEG_METADATA = Metadata(
-    id="9b31a7d103732cf28fbea5f8fb3d389448877d3a.boutiques",
+    id="1583927f622eec1fc55a57cf0a70382ea0e8f31c.boutiques",
     name="defect-seg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,72 +14,60 @@ DEFECT_SEG_METADATA = Metadata(
 
 
 DefectSegParameters = typing.TypedDict('DefectSegParameters', {
-    "__STYXTYPE__": typing.Literal["defect-seg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/defect-seg"]],
+    "subject": str,
+    "lh_only": bool,
+    "rh_only": bool,
+})
+DefectSegParametersTagged = typing.TypedDict('DefectSegParametersTagged', {
+    "@type": typing.Literal["freesurfer/defect-seg"],
     "subject": str,
     "lh_only": bool,
     "rh_only": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "defect-seg": defect_seg_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 {
-        "defect-seg": defect_seg_outputs,
-    }.get(t)
 
 
 class DefectSegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `defect_seg(...)`.
+    Output object returned when calling `DefectSegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
     surface_defects: OutputPathType
     """Surface defects volume."""
-    defects_summary: OutputPathType
-    """Summary of defects indicating numerical ID and number of vertices."""
-    defect_labels_fix: OutputPathType
-    """Fixed defect labels on the surface."""
-    defect_labels_fix_bin: OutputPathType
-    """Binary labels for fixed defects."""
-    defects_nofix_annot: OutputPathType
-    """Annotation file for defects without fixes."""
-    defects_fix_annot: OutputPathType
-    """Annotation file for defects with fixes."""
-    defects_stats: OutputPathType
-    """Statistics summary of defects indicating area and average thickness."""
+    lh_defects_summary: OutputPathType
+    """Defects summary with ID and number of vertices for left hemisphere."""
+    lh_defect_labels_fix: OutputPathType
+    """Fixed defect labels on the left hemisphere surface."""
+    lh_defect_labels_fix_bin: OutputPathType
+    """Binary labels for fixed defects on the left hemisphere."""
+    lh_defects_nofix_annot: OutputPathType
+    """Annotation file for defects without fixes on the left hemisphere."""
+    lh_defects_fix_annot: OutputPathType
+    """Annotation file for defects with fixes on the left hemisphere."""
+    lh_defects_stats: OutputPathType
+    """Statistics summary of defects indicating area and average thickness on
+    the left hemisphere."""
+    rh_defects_summary: OutputPathType
+    """Defects summary with ID and number of vertices for right hemisphere."""
+    rh_defect_labels_fix: OutputPathType
+    """Fixed defect labels on the Right hemisphere surface."""
+    rh_defect_labels_fix_bin: OutputPathType
+    """Binary labels for fixed defects on the right hemisphere."""
+    rh_defects_nofix_annot: OutputPathType
+    """Annotation file for defects without fixes on the right hemisphere."""
+    rh_defects_fix_annot: OutputPathType
+    """Annotation file for defects with fixes on the right hemisphere."""
+    rh_defects_stats: OutputPathType
+    """Statistics summary of defects indicating area and average thickness on
+    the right hemisphere."""
 
 
 def defect_seg_params(
     subject: str,
     lh_only: bool = False,
     rh_only: bool = False,
-) -> DefectSegParameters:
+) -> DefectSegParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +79,7 @@ def defect_seg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "defect-seg",
+        "@type": "freesurfer/defect-seg",
         "subject": subject,
         "lh_only": lh_only,
         "rh_only": rh_only,
@@ -116,11 +104,11 @@ def defect_seg_cargs(
     cargs.append("defect-seg")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("lh_only"):
+    if params.get("lh_only", False):
         cargs.append("--lh-only")
-    if params.get("rh_only"):
+    if params.get("rh_only", False):
         cargs.append("--rh-only")
     return cargs
 
@@ -141,24 +129,32 @@ def defect_seg_outputs(
     ret = DefectSegOutputs(
         root=execution.output_file("."),
         surface_defects=execution.output_file("mri/surface.defects.mgz"),
-        defects_summary=execution.output_file("scripts/?h.defects.summary"),
-        defect_labels_fix=execution.output_file("surf/?h.defect_labels.fix.mgz"),
-        defect_labels_fix_bin=execution.output_file("surf/?h.defect_labels.fix.bin.mgz"),
-        defects_nofix_annot=execution.output_file("label/?h.defects.nofix.annot"),
-        defects_fix_annot=execution.output_file("label/?h.defects.fix.annot"),
-        defects_stats=execution.output_file("stats/?h.defects.stats"),
+        lh_defects_summary=execution.output_file("scripts/lh.defects.summary"),
+        lh_defect_labels_fix=execution.output_file("surf/lh.defect_labels.fix.mgz"),
+        lh_defect_labels_fix_bin=execution.output_file("surf/lh.defect_labels.fix.bin.mgz"),
+        lh_defects_nofix_annot=execution.output_file("label/lh.defects.nofix.annot"),
+        lh_defects_fix_annot=execution.output_file("label/lh.defects.fix.annot"),
+        lh_defects_stats=execution.output_file("stats/lh.defects.stats"),
+        rh_defects_summary=execution.output_file("scripts/rh.defects.summary"),
+        rh_defect_labels_fix=execution.output_file("surf/rh.defect_labels.fix.mgz"),
+        rh_defect_labels_fix_bin=execution.output_file("surf/rh.defect_labels.fix.bin.mgz"),
+        rh_defects_nofix_annot=execution.output_file("label/rh.defects.nofix.annot"),
+        rh_defects_fix_annot=execution.output_file("label/rh.defects.fix.annot"),
+        rh_defects_stats=execution.output_file("stats/rh.defects.stats"),
     )
     return ret
 
 
 def defect_seg_execute(
     params: DefectSegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DefectSegOutputs:
     """
-    This program creates some files that allows the user to visualize and evaluate
-    the surface defects that were automatically detected and fixed by the topology
-    correction program.
+    defect-seg
+    
+    This program creates some files that allows the user to visualize and
+    evaluate the surface defects that were automatically detected and fixed by
+    the topology correction program.
     
     Author: FreeSurfer Developers
     
@@ -166,10 +162,12 @@ def defect_seg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DefectSegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DEFECT_SEG_METADATA)
     params = execution.params(params)
     cargs = defect_seg_cargs(params, execution)
     ret = defect_seg_outputs(params, execution)
@@ -184,9 +182,11 @@ def defect_seg(
     runner: Runner | None = None,
 ) -> DefectSegOutputs:
     """
-    This program creates some files that allows the user to visualize and evaluate
-    the surface defects that were automatically detected and fixed by the topology
-    correction program.
+    defect-seg
+    
+    This program creates some files that allows the user to visualize and
+    evaluate the surface defects that were automatically detected and fixed by
+    the topology correction program.
     
     Author: FreeSurfer Developers
     
@@ -200,20 +200,18 @@ def defect_seg(
     Returns:
         NamedTuple of outputs (described in `DefectSegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DEFECT_SEG_METADATA)
     params = defect_seg_params(
         subject=subject,
         lh_only=lh_only,
         rh_only=rh_only,
     )
-    return defect_seg_execute(params, execution)
+    return defect_seg_execute(params, runner)
 
 
 __all__ = [
     "DEFECT_SEG_METADATA",
     "DefectSegOutputs",
-    "DefectSegParameters",
     "defect_seg",
+    "defect_seg_execute",
     "defect_seg_params",
 ]

niwrap_freesurfer/freesurfer/dicom_rename.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DICOM_RENAME_METADATA = Metadata(
-    id="3fa82f4f7cfa0f517393cf4bbd8d9673564b758d.boutiques",
+    id="ca4d93c3e9518d2c158aeb7b4b47f5257f9ce799.boutiques",
     name="dicom-rename",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ DICOM_RENAME_METADATA = Metadata(
 
 
 DicomRenameParameters = typing.TypedDict('DicomRenameParameters', {
-    "__STYXTYPE__": typing.Literal["dicom-rename"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dicom-rename"]],
+    "input_files": list[InputPathType],
+    "output_base": str,
+    "version": bool,
+    "help": bool,
+})
+DicomRenameParametersTagged = typing.TypedDict('DicomRenameParametersTagged', {
+    "@type": typing.Literal["freesurfer/dicom-rename"],
     "input_files": list[InputPathType],
     "output_base": str,
     "version": bool,
     "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 {
-        "dicom-rename": dicom_rename_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 {
-        "dicom-rename": dicom_rename_outputs,
-    }.get(t)
 
 
 class DicomRenameOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dicom_rename(...)`.
+    Output object returned when calling `DicomRenameParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def dicom_rename_params(
     output_base: str,
     version: bool = False,
     help_: bool = False,
-) -> DicomRenameParameters:
+) -> DicomRenameParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def dicom_rename_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dicom-rename",
+        "@type": "freesurfer/dicom-rename",
         "input_files": input_files,
         "output_base": output_base,
         "version": version,
@@ -109,15 +84,15 @@ def dicom_rename_cargs(
     cargs.append("dicom-rename")
     cargs.extend([
         "-rename",
-        *[execution.input_file(f) for f in params.get("input_files")]
+        *[execution.input_file(f) for f in params.get("input_files", None)]
     ])
     cargs.extend([
         "--o",
-        params.get("output_base")
+        params.get("output_base", None)
     ])
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -137,16 +112,18 @@ def dicom_rename_outputs(
     """
     ret = DicomRenameOutputs(
         root=execution.output_file("."),
-        renamed_dicom=execution.output_file(params.get("output_base") + "-SSS-IIIII.dcm"),
+        renamed_dicom=execution.output_file(params.get("output_base", None) + "-SSS-IIIII.dcm"),
     )
     return ret
 
 
 def dicom_rename_execute(
     params: DicomRenameParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DicomRenameOutputs:
     """
+    dicom-rename
+    
     Copies dicom file(s) to new path with more meaningful names.
     
     Author: FreeSurfer Developers
@@ -155,10 +132,12 @@ def dicom_rename_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DicomRenameOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DICOM_RENAME_METADATA)
     params = execution.params(params)
     cargs = dicom_rename_cargs(params, execution)
     ret = dicom_rename_outputs(params, execution)
@@ -174,6 +153,8 @@ def dicom_rename(
     runner: Runner | None = None,
 ) -> DicomRenameOutputs:
     """
+    dicom-rename
+    
     Copies dicom file(s) to new path with more meaningful names.
     
     Author: FreeSurfer Developers
@@ -190,21 +171,19 @@ def dicom_rename(
     Returns:
         NamedTuple of outputs (described in `DicomRenameOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DICOM_RENAME_METADATA)
     params = dicom_rename_params(
         input_files=input_files,
         output_base=output_base,
         version=version,
         help_=help_,
     )
-    return dicom_rename_execute(params, execution)
+    return dicom_rename_execute(params, runner)
 
 
 __all__ = [
     "DICOM_RENAME_METADATA",
     "DicomRenameOutputs",
-    "DicomRenameParameters",
     "dicom_rename",
+    "dicom_rename_execute",
     "dicom_rename_params",
 ]