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

niwrap_freesurfer/freesurfer/analyzeto4dfp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ANALYZETO4DFP_METADATA = Metadata(
-    id="991ffef88bef8e5d81444f5958c1c7d3e22644f0.boutiques",
+    id="3f5d3d809a30ecb597d74082f936e1be4e243840.boutiques",
     name="analyzeto4dfp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ ANALYZETO4DFP_METADATA = Metadata(
 
 
 Analyzeto4dfpParameters = typing.TypedDict('Analyzeto4dfpParameters', {
-    "__STYXTYPE__": typing.Literal["analyzeto4dfp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/analyzeto4dfp"]],
+    "analyze_image": InputPathType,
+    "rois_scale": bool,
+    "flip_x": bool,
+    "flip_y": bool,
+    "flip_z": bool,
+    "endian": typing.NotRequired[str | None],
+    "orientation": typing.NotRequired[int | None],
+})
+Analyzeto4dfpParametersTagged = typing.TypedDict('Analyzeto4dfpParametersTagged', {
+    "@type": typing.Literal["freesurfer/analyzeto4dfp"],
     "analyze_image": InputPathType,
     "rois_scale": bool,
     "flip_x": bool,
@@ -23,42 +33,11 @@ Analyzeto4dfpParameters = typing.TypedDict('Analyzeto4dfpParameters', {
     "endian": typing.NotRequired[str | None],
     "orientation": typing.NotRequired[int | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "analyzeto4dfp": analyzeto4dfp_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 Analyzeto4dfpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `analyzeto4dfp(...)`.
+    Output object returned when calling `Analyzeto4dfpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def analyzeto4dfp_params(
     flip_z: bool = False,
     endian: str | None = None,
     orientation: int | None = None,
-) -> Analyzeto4dfpParameters:
+) -> Analyzeto4dfpParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +67,7 @@ def analyzeto4dfp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "analyzeto4dfp",
+        "@type": "freesurfer/analyzeto4dfp",
         "analyze_image": analyze_image,
         "rois_scale": rois_scale,
         "flip_x": flip_x,
@@ -117,24 +96,24 @@ def analyzeto4dfp_cargs(
     """
     cargs = []
     cargs.append("analyzeto4dfp")
-    cargs.append(execution.input_file(params.get("analyze_image")))
-    if params.get("rois_scale"):
+    cargs.append(execution.input_file(params.get("analyze_image", None)))
+    if params.get("rois_scale", False):
         cargs.append("-s")
-    if params.get("flip_x"):
+    if params.get("flip_x", False):
         cargs.append("-x")
-    if params.get("flip_y"):
+    if params.get("flip_y", False):
         cargs.append("-y")
-    if params.get("flip_z"):
+    if params.get("flip_z", False):
         cargs.append("-z")
-    if params.get("endian") is not None:
+    if params.get("endian", None) is not None:
         cargs.extend([
             "-@",
-            params.get("endian")
+            params.get("endian", None)
         ])
-    if params.get("orientation") is not None:
+    if params.get("orientation", None) is not None:
         cargs.extend([
             "-O",
-            str(params.get("orientation"))
+            str(params.get("orientation", None))
         ])
     return cargs
 
@@ -160,9 +139,11 @@ def analyzeto4dfp_outputs(
 
 def analyzeto4dfp_execute(
     params: Analyzeto4dfpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Analyzeto4dfpOutputs:
     """
+    analyzeto4dfp
+    
     Convert ANALYZE image format to 4dfp format with various options.
     
     Author: FreeSurfer Developers
@@ -171,10 +152,12 @@ def analyzeto4dfp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Analyzeto4dfpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ANALYZETO4DFP_METADATA)
     params = execution.params(params)
     cargs = analyzeto4dfp_cargs(params, execution)
     ret = analyzeto4dfp_outputs(params, execution)
@@ -193,6 +176,8 @@ def analyzeto4dfp(
     runner: Runner | None = None,
 ) -> Analyzeto4dfpOutputs:
     """
+    analyzeto4dfp
+    
     Convert ANALYZE image format to 4dfp format with various options.
     
     Author: FreeSurfer Developers
@@ -211,8 +196,6 @@ def analyzeto4dfp(
     Returns:
         NamedTuple of outputs (described in `Analyzeto4dfpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ANALYZETO4DFP_METADATA)
     params = analyzeto4dfp_params(
         analyze_image=analyze_image,
         rois_scale=rois_scale,
@@ -222,13 +205,13 @@ def analyzeto4dfp(
         endian=endian,
         orientation=orientation,
     )
-    return analyzeto4dfp_execute(params, execution)
+    return analyzeto4dfp_execute(params, runner)
 
 
 __all__ = [
     "ANALYZETO4DFP_METADATA",
     "Analyzeto4dfpOutputs",
-    "Analyzeto4dfpParameters",
     "analyzeto4dfp",
+    "analyzeto4dfp_execute",
     "analyzeto4dfp_params",
 ]

niwrap_freesurfer/freesurfer/anatomi_cuts_utils.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ANATOMI_CUTS_UTILS_METADATA = Metadata(
-    id="5b8fc2fbd044825ca8524543fcf4b4b3d56cb1f7.boutiques",
+    id="5b69d917d40aa2d42c8485fb374b3003d3556d0b.boutiques",
     name="anatomiCutsUtils",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ ANATOMI_CUTS_UTILS_METADATA = Metadata(
 
 
 AnatomiCutsUtilsParameters = typing.TypedDict('AnatomiCutsUtilsParameters', {
-    "__STYXTYPE__": typing.Literal["anatomiCutsUtils"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/anatomiCutsUtils"]],
+    "modules": typing.NotRequired[list[str] | None],
+})
+AnatomiCutsUtilsParametersTagged = typing.TypedDict('AnatomiCutsUtilsParametersTagged', {
+    "@type": typing.Literal["freesurfer/anatomiCutsUtils"],
     "modules": typing.NotRequired[list[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 {
-        "anatomiCutsUtils": anatomi_cuts_utils_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 AnatomiCutsUtilsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `anatomi_cuts_utils(...)`.
+    Output object returned when calling `AnatomiCutsUtilsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class AnatomiCutsUtilsOutputs(typing.NamedTuple):
 
 def anatomi_cuts_utils_params(
     modules: list[str] | None = None,
-) -> AnatomiCutsUtilsParameters:
+) -> AnatomiCutsUtilsParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def anatomi_cuts_utils_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "anatomiCutsUtils",
+        "@type": "freesurfer/anatomiCutsUtils",
     }
     if modules is not None:
         params["modules"] = modules
@@ -93,8 +66,8 @@ def anatomi_cuts_utils_cargs(
     """
     cargs = []
     cargs.append("anatomiCutsUtils")
-    if params.get("modules") is not None:
-        cargs.extend(params.get("modules"))
+    if params.get("modules", None) is not None:
+        cargs.extend(params.get("modules", None))
     return cargs
 
 
@@ -119,9 +92,11 @@ def anatomi_cuts_utils_outputs(
 
 def anatomi_cuts_utils_execute(
     params: AnatomiCutsUtilsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AnatomiCutsUtilsOutputs:
     """
+    anatomiCutsUtils
+    
     A tool for anatomical segmentation using graph-based methods.
     
     Author: FreeSurfer Developers
@@ -130,10 +105,12 @@ def anatomi_cuts_utils_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AnatomiCutsUtilsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ANATOMI_CUTS_UTILS_METADATA)
     params = execution.params(params)
     cargs = anatomi_cuts_utils_cargs(params, execution)
     ret = anatomi_cuts_utils_outputs(params, execution)
@@ -146,6 +123,8 @@ def anatomi_cuts_utils(
     runner: Runner | None = None,
 ) -> AnatomiCutsUtilsOutputs:
     """
+    anatomiCutsUtils
+    
     A tool for anatomical segmentation using graph-based methods.
     
     Author: FreeSurfer Developers
@@ -159,18 +138,16 @@ def anatomi_cuts_utils(
     Returns:
         NamedTuple of outputs (described in `AnatomiCutsUtilsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ANATOMI_CUTS_UTILS_METADATA)
     params = anatomi_cuts_utils_params(
         modules=modules,
     )
-    return anatomi_cuts_utils_execute(params, execution)
+    return anatomi_cuts_utils_execute(params, runner)
 
 
 __all__ = [
     "ANATOMI_CUTS_UTILS_METADATA",
     "AnatomiCutsUtilsOutputs",
-    "AnatomiCutsUtilsParameters",
     "anatomi_cuts_utils",
+    "anatomi_cuts_utils_execute",
     "anatomi_cuts_utils_params",
 ]

niwrap_freesurfer/freesurfer/annot2std.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ANNOT2STD_METADATA = Metadata(
-    id="94260c16cb751cafe61816e78c1cd15d1558bf0f.boutiques",
+    id="45b8175f1d07bf65b5ac1029d277b1f4d1aa942b.boutiques",
     name="annot2std",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,28 @@ ANNOT2STD_METADATA = Metadata(
 
 
 Annot2stdParameters = typing.TypedDict('Annot2stdParameters', {
-    "__STYXTYPE__": typing.Literal["annot2std"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/annot2std"]],
+    "output_annot_path": str,
+    "subjects": list[str],
+    "fsgd_file": typing.NotRequired[InputPathType | None],
+    "subject_list_file": typing.NotRequired[InputPathType | None],
+    "target": typing.NotRequired[str | None],
+    "left_hemisphere": bool,
+    "right_hemisphere": bool,
+    "xhemi": bool,
+    "surfreg": typing.NotRequired[str | None],
+    "srcsurfreg": typing.NotRequired[str | None],
+    "trgsurfreg": typing.NotRequired[str | None],
+    "annotname": typing.NotRequired[str | None],
+    "aparc": bool,
+    "a2009s": bool,
+    "segmentation": typing.NotRequired[str | None],
+    "stack": typing.NotRequired[str | None],
+    "help": bool,
+    "version": bool,
+})
+Annot2stdParametersTagged = typing.TypedDict('Annot2stdParametersTagged', {
+    "@type": typing.Literal["freesurfer/annot2std"],
     "output_annot_path": str,
     "subjects": list[str],
     "fsgd_file": typing.NotRequired[InputPathType | None],
@@ -34,43 +55,11 @@ Annot2stdParameters = typing.TypedDict('Annot2stdParameters', {
     "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 {
-        "annot2std": annot2std_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 {
-        "annot2std": annot2std_outputs,
-    }.get(t)
 
 
 class Annot2stdOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `annot2std(...)`.
+    Output object returned when calling `Annot2stdParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +90,7 @@ def annot2std_params(
     stack: str | None = None,
     help_: bool = False,
     version: bool = False,
-) -> Annot2stdParameters:
+) -> Annot2stdParametersTagged:
     """
     Build parameters.
     
@@ -130,7 +119,7 @@ def annot2std_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "annot2std",
+        "@type": "freesurfer/annot2std",
         "output_annot_path": output_annot_path,
         "subjects": subjects,
         "left_hemisphere": left_hemisphere,
@@ -179,70 +168,70 @@ def annot2std_cargs(
     cargs.append("annot2std")
     cargs.extend([
         "--o",
-        params.get("output_annot_path")
+        params.get("output_annot_path", None)
     ])
     cargs.extend([
         "--s",
-        *params.get("subjects")
+        *params.get("subjects", None)
     ])
-    if params.get("fsgd_file") is not None:
+    if params.get("fsgd_file", None) is not None:
         cargs.extend([
             "--fsgd",
-            execution.input_file(params.get("fsgd_file"))
+            execution.input_file(params.get("fsgd_file", None))
         ])
-    if params.get("subject_list_file") is not None:
+    if params.get("subject_list_file", None) is not None:
         cargs.extend([
             "--f",
-            execution.input_file(params.get("subject_list_file"))
+            execution.input_file(params.get("subject_list_file", None))
         ])
-    if params.get("target") is not None:
+    if params.get("target", None) is not None:
         cargs.extend([
             "--t",
-            params.get("target")
+            params.get("target", 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("xhemi"):
+    if params.get("xhemi", False):
         cargs.append("--xhemi")
-    if params.get("surfreg") is not None:
+    if params.get("surfreg", None) is not None:
         cargs.extend([
             "--surfreg",
-            params.get("surfreg")
+            params.get("surfreg", None)
         ])
-    if params.get("srcsurfreg") is not None:
+    if params.get("srcsurfreg", None) is not None:
         cargs.extend([
             "--srcsurfreg",
-            params.get("srcsurfreg")
+            params.get("srcsurfreg", None)
         ])
-    if params.get("trgsurfreg") is not None:
+    if params.get("trgsurfreg", None) is not None:
         cargs.extend([
             "--trgsurfreg",
-            params.get("trgsurfreg")
+            params.get("trgsurfreg", None)
         ])
-    if params.get("annotname") is not None:
+    if params.get("annotname", None) is not None:
         cargs.extend([
             "--a",
-            params.get("annotname")
+            params.get("annotname", None)
         ])
-    if params.get("aparc"):
+    if params.get("aparc", False):
         cargs.append("--aparc")
-    if params.get("a2009s"):
+    if params.get("a2009s", False):
         cargs.append("--a2009s")
-    if params.get("segmentation") is not None:
+    if params.get("segmentation", None) is not None:
         cargs.extend([
             "--seg",
-            params.get("segmentation")
+            params.get("segmentation", None)
         ])
-    if params.get("stack") is not None:
+    if params.get("stack", None) is not None:
         cargs.extend([
             "--stack",
-            params.get("stack")
+            params.get("stack", 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
 
@@ -262,21 +251,23 @@ def annot2std_outputs(
     """
     ret = Annot2stdOutputs(
         root=execution.output_file("."),
-        out_annot_file=execution.output_file(params.get("output_annot_path")),
-        out_prob_map_file=execution.output_file(params.get("output_annot_path") + ".p.mgh"),
-        output_surface_segmentation=execution.output_file(params.get("segmentation")) if (params.get("segmentation") is not None) else None,
+        out_annot_file=execution.output_file(params.get("output_annot_path", None)),
+        out_prob_map_file=execution.output_file(params.get("output_annot_path", None) + ".p.mgh"),
+        output_surface_segmentation=execution.output_file(params.get("segmentation", None)) if (params.get("segmentation") is not None) else None,
     )
     return ret
 
 
 def annot2std_execute(
     params: Annot2stdParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Annot2stdOutputs:
     """
+    annot2std
+    
     Creates an average annotation in a standard space based on transforming the
-    annotations of the individual subjects to the standard space through the surface
-    registration.
+    annotations of the individual subjects to the standard space through the
+    surface registration.
     
     Author: FreeSurfer Developers
     
@@ -284,10 +275,12 @@ def annot2std_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Annot2stdOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ANNOT2STD_METADATA)
     params = execution.params(params)
     cargs = annot2std_cargs(params, execution)
     ret = annot2std_outputs(params, execution)
@@ -317,9 +310,11 @@ def annot2std(
     runner: Runner | None = None,
 ) -> Annot2stdOutputs:
     """
+    annot2std
+    
     Creates an average annotation in a standard space based on transforming the
-    annotations of the individual subjects to the standard space through the surface
-    registration.
+    annotations of the individual subjects to the standard space through the
+    surface registration.
     
     Author: FreeSurfer Developers
     
@@ -350,8 +345,6 @@ def annot2std(
     Returns:
         NamedTuple of outputs (described in `Annot2stdOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ANNOT2STD_METADATA)
     params = annot2std_params(
         output_annot_path=output_annot_path,
         subjects=subjects,
@@ -372,13 +365,13 @@ def annot2std(
         help_=help_,
         version=version,
     )
-    return annot2std_execute(params, execution)
+    return annot2std_execute(params, runner)
 
 
 __all__ = [
     "ANNOT2STD_METADATA",
     "Annot2stdOutputs",
-    "Annot2stdParameters",
     "annot2std",
+    "annot2std_execute",
     "annot2std_params",
 ]