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

niwrap_freesurfer/freesurfer/gtmseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GTMSEG_METADATA = Metadata(
-    id="4ab9659e70272d979f39dad258eeff58c22157fc.boutiques",
+    id="905804c42add9b579f3d1f9170baa87421e1e8da.boutiques",
     name="gtmseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,28 @@ GTMSEG_METADATA = Metadata(
 
 
 GtmsegParameters = typing.TypedDict('GtmsegParameters', {
-    "__STYXTYPE__": typing.Literal["gtmseg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/gtmseg"]],
+    "subject": str,
+    "outvol": typing.NotRequired[str | None],
+    "usf": typing.NotRequired[float | None],
+    "subsegwm": bool,
+    "keep_hypo": bool,
+    "keep_cc": bool,
+    "dmax": typing.NotRequired[float | None],
+    "ctx_annot": typing.NotRequired[str | None],
+    "wm_annot": typing.NotRequired[str | None],
+    "output_usf": typing.NotRequired[float | None],
+    "head": typing.NotRequired[str | None],
+    "subseg_cbwm": bool,
+    "no_pons": bool,
+    "no_vermis": bool,
+    "ctab": typing.NotRequired[InputPathType | None],
+    "no_seg_stats": bool,
+    "xcerseg": bool,
+    "debug": bool,
+})
+GtmsegParametersTagged = typing.TypedDict('GtmsegParametersTagged', {
+    "@type": typing.Literal["freesurfer/gtmseg"],
     "subject": str,
     "outvol": typing.NotRequired[str | None],
     "usf": typing.NotRequired[float | None],
@@ -34,43 +55,11 @@ GtmsegParameters = typing.TypedDict('GtmsegParameters', {
     "xcerseg": bool,
     "debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "gtmseg": gtmseg_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 {
-        "gtmseg": gtmseg_outputs,
-    }.get(t)
 
 
 class GtmsegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `gtmseg(...)`.
+    Output object returned when calling `GtmsegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -82,14 +71,14 @@ class GtmsegOutputs(typing.NamedTuple):
 
 def gtmseg_params(
     subject: str,
-    outvol: str | None = "gtmseg.mgz",
-    usf: float | None = 2,
+    outvol: str | None = None,
+    usf: float | None = None,
     subsegwm: bool = False,
     keep_hypo: bool = False,
     keep_cc: bool = False,
-    dmax: float | None = 5,
-    ctx_annot: str | None = "aparc 1000 2000",
-    wm_annot: str | None = "lobes 3200 4200",
+    dmax: float | None = None,
+    ctx_annot: str | None = None,
+    wm_annot: str | None = None,
     output_usf: float | None = None,
     head: str | None = None,
     subseg_cbwm: bool = False,
@@ -99,7 +88,7 @@ def gtmseg_params(
     no_seg_stats: bool = False,
     xcerseg: bool = False,
     debug: bool = False,
-) -> GtmsegParameters:
+) -> GtmsegParametersTagged:
     """
     Build parameters.
     
@@ -128,7 +117,7 @@ def gtmseg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "gtmseg",
+        "@type": "freesurfer/gtmseg",
         "subject": subject,
         "subsegwm": subsegwm,
         "keep_hypo": keep_hypo,
@@ -176,65 +165,65 @@ def gtmseg_cargs(
     cargs.append("gtmseg")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("outvol") is not None:
+    if params.get("outvol", None) is not None:
         cargs.extend([
             "--o",
-            params.get("outvol")
+            params.get("outvol", None)
         ])
-    if params.get("usf") is not None:
+    if params.get("usf", None) is not None:
         cargs.extend([
             "--usf",
-            str(params.get("usf"))
+            str(params.get("usf", None))
         ])
-    if params.get("subsegwm"):
+    if params.get("subsegwm", False):
         cargs.append("--subsegwm")
-    if params.get("keep_hypo"):
+    if params.get("keep_hypo", False):
         cargs.append("--keep-hypo")
-    if params.get("keep_cc"):
+    if params.get("keep_cc", False):
         cargs.append("--keep-cc")
-    if params.get("dmax") is not None:
+    if params.get("dmax", None) is not None:
         cargs.extend([
             "--dmax",
-            str(params.get("dmax"))
+            str(params.get("dmax", None))
         ])
-    if params.get("ctx_annot") is not None:
+    if params.get("ctx_annot", None) is not None:
         cargs.extend([
             "--ctx-annot",
-            params.get("ctx_annot")
+            params.get("ctx_annot", None)
         ])
-    if params.get("wm_annot") is not None:
+    if params.get("wm_annot", None) is not None:
         cargs.extend([
             "--wm-annot",
-            params.get("wm_annot")
+            params.get("wm_annot", None)
         ])
-    if params.get("output_usf") is not None:
+    if params.get("output_usf", None) is not None:
         cargs.extend([
             "--output-usf",
-            str(params.get("output_usf"))
+            str(params.get("output_usf", None))
         ])
-    if params.get("head") is not None:
+    if params.get("head", None) is not None:
         cargs.extend([
             "--head",
-            params.get("head")
+            params.get("head", None)
         ])
-    if params.get("subseg_cbwm"):
+    if params.get("subseg_cbwm", False):
         cargs.append("--subseg-cblum-wm")
-    if params.get("no_pons"):
+    if params.get("no_pons", False):
         cargs.append("--no-pons")
-    if params.get("no_vermis"):
+    if params.get("no_vermis", False):
         cargs.append("--no-vermis")
-    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("no_seg_stats"):
+    if params.get("no_seg_stats", False):
         cargs.append("--no-seg-stats")
-    if params.get("xcerseg"):
+    if params.get("xcerseg", False):
         cargs.append("--xcerseg")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
     return cargs
 
@@ -254,19 +243,21 @@ def gtmseg_outputs(
     """
     ret = GtmsegOutputs(
         root=execution.output_file("."),
-        output_volume=execution.output_file("$SUBJECTS_DIR/" + params.get("subject") + "/mri/" + params.get("outvol")) if (params.get("outvol") is not None) else None,
-        output_ctab=execution.output_file("$SUBJECTS_DIR/" + params.get("subject") + "/mri/gtmseg+myseg.ctab"),
+        output_volume=execution.output_file("$SUBJECTS_DIR/" + params.get("subject", None) + "/mri/" + params.get("outvol", None)) if (params.get("outvol") is not None) else None,
+        output_ctab=execution.output_file("$SUBJECTS_DIR/" + params.get("subject", None) + "/mri/gtmseg+myseg.ctab"),
     )
     return ret
 
 
 def gtmseg_execute(
     params: GtmsegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> GtmsegOutputs:
     """
-    Creates an anatomical segmentation for the geometric transfer matrix (GTM) used
-    in PET partial volume correction.
+    gtmseg
+    
+    Creates an anatomical segmentation for the geometric transfer matrix (GTM)
+    used in PET partial volume correction.
     
     Author: FreeSurfer Developers
     
@@ -274,10 +265,12 @@ def gtmseg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `GtmsegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GTMSEG_METADATA)
     params = execution.params(params)
     cargs = gtmseg_cargs(params, execution)
     ret = gtmseg_outputs(params, execution)
@@ -287,14 +280,14 @@ def gtmseg_execute(
 
 def gtmseg(
     subject: str,
-    outvol: str | None = "gtmseg.mgz",
-    usf: float | None = 2,
+    outvol: str | None = None,
+    usf: float | None = None,
     subsegwm: bool = False,
     keep_hypo: bool = False,
     keep_cc: bool = False,
-    dmax: float | None = 5,
-    ctx_annot: str | None = "aparc 1000 2000",
-    wm_annot: str | None = "lobes 3200 4200",
+    dmax: float | None = None,
+    ctx_annot: str | None = None,
+    wm_annot: str | None = None,
     output_usf: float | None = None,
     head: str | None = None,
     subseg_cbwm: bool = False,
@@ -307,8 +300,10 @@ def gtmseg(
     runner: Runner | None = None,
 ) -> GtmsegOutputs:
     """
-    Creates an anatomical segmentation for the geometric transfer matrix (GTM) used
-    in PET partial volume correction.
+    gtmseg
+    
+    Creates an anatomical segmentation for the geometric transfer matrix (GTM)
+    used in PET partial volume correction.
     
     Author: FreeSurfer Developers
     
@@ -339,8 +334,6 @@ def gtmseg(
     Returns:
         NamedTuple of outputs (described in `GtmsegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(GTMSEG_METADATA)
     params = gtmseg_params(
         subject=subject,
         outvol=outvol,
@@ -361,13 +354,13 @@ def gtmseg(
         xcerseg=xcerseg,
         debug=debug,
     )
-    return gtmseg_execute(params, execution)
+    return gtmseg_execute(params, runner)
 
 
 __all__ = [
     "GTMSEG_METADATA",
     "GtmsegOutputs",
-    "GtmsegParameters",
     "gtmseg",
+    "gtmseg_execute",
     "gtmseg_params",
 ]

niwrap_freesurfer/freesurfer/hiam_make_surfaces.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 HIAM_MAKE_SURFACES_METADATA = Metadata(
-    id="1b161d9791e99b79bc12c2e006b7a1a47156fb9f.boutiques",
+    id="82017efb059d0d3b2c38801127d8932b282aaa78.boutiques",
     name="hiam_make_surfaces",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ HIAM_MAKE_SURFACES_METADATA = Metadata(
 
 
 HiamMakeSurfacesParameters = typing.TypedDict('HiamMakeSurfacesParameters', {
-    "__STYXTYPE__": typing.Literal["hiam_make_surfaces"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/hiam_make_surfaces"]],
+    "subject_name": str,
+    "structure": typing.Literal["RA", "LA", "RH", "LH"],
+})
+HiamMakeSurfacesParametersTagged = typing.TypedDict('HiamMakeSurfacesParametersTagged', {
+    "@type": typing.Literal["freesurfer/hiam_make_surfaces"],
     "subject_name": str,
     "structure": typing.Literal["RA", "LA", "RH", "LH"],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "hiam_make_surfaces": hiam_make_surfaces_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 HiamMakeSurfacesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `hiam_make_surfaces(...)`.
+    Output object returned when calling `HiamMakeSurfacesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class HiamMakeSurfacesOutputs(typing.NamedTuple):
 def hiam_make_surfaces_params(
     subject_name: str,
     structure: typing.Literal["RA", "LA", "RH", "LH"],
-) -> HiamMakeSurfacesParameters:
+) -> HiamMakeSurfacesParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +48,7 @@ def hiam_make_surfaces_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "hiam_make_surfaces",
+        "@type": "freesurfer/hiam_make_surfaces",
         "subject_name": subject_name,
         "structure": structure,
     }
@@ -96,8 +70,8 @@ def hiam_make_surfaces_cargs(
     """
     cargs = []
     cargs.append("hiam_make_surfaces")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("structure"))
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("structure", None))
     return cargs
 
 
@@ -122,9 +96,11 @@ def hiam_make_surfaces_outputs(
 
 def hiam_make_surfaces_execute(
     params: HiamMakeSurfacesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> HiamMakeSurfacesOutputs:
     """
+    hiam_make_surfaces
+    
     Surface creation tool for specified brain structures.
     
     Author: FreeSurfer Developers
@@ -133,10 +109,12 @@ def hiam_make_surfaces_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `HiamMakeSurfacesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(HIAM_MAKE_SURFACES_METADATA)
     params = execution.params(params)
     cargs = hiam_make_surfaces_cargs(params, execution)
     ret = hiam_make_surfaces_outputs(params, execution)
@@ -150,6 +128,8 @@ def hiam_make_surfaces(
     runner: Runner | None = None,
 ) -> HiamMakeSurfacesOutputs:
     """
+    hiam_make_surfaces
+    
     Surface creation tool for specified brain structures.
     
     Author: FreeSurfer Developers
@@ -164,19 +144,17 @@ def hiam_make_surfaces(
     Returns:
         NamedTuple of outputs (described in `HiamMakeSurfacesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(HIAM_MAKE_SURFACES_METADATA)
     params = hiam_make_surfaces_params(
         subject_name=subject_name,
         structure=structure,
     )
-    return hiam_make_surfaces_execute(params, execution)
+    return hiam_make_surfaces_execute(params, runner)
 
 
 __all__ = [
     "HIAM_MAKE_SURFACES_METADATA",
     "HiamMakeSurfacesOutputs",
-    "HiamMakeSurfacesParameters",
     "hiam_make_surfaces",
+    "hiam_make_surfaces_execute",
     "hiam_make_surfaces_params",
 ]

niwrap_freesurfer/freesurfer/hiam_make_template.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 HIAM_MAKE_TEMPLATE_METADATA = Metadata(
-    id="8c48bbfd46c7f8da62fb53ac9c94dd28311f4d1a.boutiques",
+    id="cff63861cbf29cdcfe129e4757475ee25b7add49.boutiques",
     name="hiam_make_template",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ HIAM_MAKE_TEMPLATE_METADATA = Metadata(
 
 
 HiamMakeTemplateParameters = typing.TypedDict('HiamMakeTemplateParameters', {
-    "__STYXTYPE__": typing.Literal["hiam_make_template"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/hiam_make_template"]],
+    "hemi": str,
+    "surface_name": str,
+    "subjects": list[str],
+    "output_name": str,
+})
+HiamMakeTemplateParametersTagged = typing.TypedDict('HiamMakeTemplateParametersTagged', {
+    "@type": typing.Literal["freesurfer/hiam_make_template"],
     "hemi": str,
     "surface_name": str,
     "subjects": list[str],
     "output_name": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "hiam_make_template": hiam_make_template_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 HiamMakeTemplateOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `hiam_make_template(...)`.
+    Output object returned when calling `HiamMakeTemplateParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def hiam_make_template_params(
     surface_name: str,
     subjects: list[str],
     output_name: str,
-) -> HiamMakeTemplateParameters:
+) -> HiamMakeTemplateParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def hiam_make_template_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "hiam_make_template",
+        "@type": "freesurfer/hiam_make_template",
         "hemi": hemi,
         "surface_name": surface_name,
         "subjects": subjects,
@@ -103,10 +79,10 @@ def hiam_make_template_cargs(
     """
     cargs = []
     cargs.append("hiam_make_template")
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("surface_name"))
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_name"))
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("surface_name", None))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_name", None))
     return cargs
 
 
@@ -131,9 +107,11 @@ def hiam_make_template_outputs(
 
 def hiam_make_template_execute(
     params: HiamMakeTemplateParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> HiamMakeTemplateOutputs:
     """
+    hiam_make_template
+    
     This program adds a template into an average surface using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -142,10 +120,12 @@ def hiam_make_template_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `HiamMakeTemplateOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(HIAM_MAKE_TEMPLATE_METADATA)
     params = execution.params(params)
     cargs = hiam_make_template_cargs(params, execution)
     ret = hiam_make_template_outputs(params, execution)
@@ -161,6 +141,8 @@ def hiam_make_template(
     runner: Runner | None = None,
 ) -> HiamMakeTemplateOutputs:
     """
+    hiam_make_template
+    
     This program adds a template into an average surface using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -176,21 +158,19 @@ def hiam_make_template(
     Returns:
         NamedTuple of outputs (described in `HiamMakeTemplateOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(HIAM_MAKE_TEMPLATE_METADATA)
     params = hiam_make_template_params(
         hemi=hemi,
         surface_name=surface_name,
         subjects=subjects,
         output_name=output_name,
     )
-    return hiam_make_template_execute(params, execution)
+    return hiam_make_template_execute(params, runner)
 
 
 __all__ = [
     "HIAM_MAKE_TEMPLATE_METADATA",
     "HiamMakeTemplateOutputs",
-    "HiamMakeTemplateParameters",
     "hiam_make_template",
+    "hiam_make_template_execute",
     "hiam_make_template_params",
 ]