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

niwrap_freesurfer/freesurfer/fvcompare.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FVCOMPARE_METADATA = Metadata(
-    id="a1051daa28d455cf970ddfd61d853128a3adffe9.boutiques",
+    id="2e45e84a88f675a13ba473420447ab26c018ea25.boutiques",
     name="fvcompare",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,35 @@ FVCOMPARE_METADATA = Metadata(
 
 
 FvcompareParameters = typing.TypedDict('FvcompareParameters', {
-    "__STYXTYPE__": typing.Literal["fvcompare"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fvcompare"]],
+    "subject1": str,
+    "subject2": str,
+    "subject_dir1": typing.NotRequired[str | None],
+    "subject_dir2": typing.NotRequired[str | None],
+    "name1": typing.NotRequired[str | None],
+    "name2": typing.NotRequired[str | None],
+    "color1": typing.NotRequired[str | None],
+    "volume": typing.NotRequired[str | None],
+    "segmentation": typing.NotRequired[str | None],
+    "aseg": bool,
+    "no_seg": bool,
+    "left_hemi": bool,
+    "right_hemi": bool,
+    "no_surf": bool,
+    "gray_levels": typing.NotRequired[list[float] | None],
+    "cursor_position": typing.NotRequired[list[float] | None],
+    "zoom_level": typing.NotRequired[float | None],
+    "annotation": typing.NotRequired[str | None],
+    "aparc": bool,
+    "inflated": bool,
+    "white": bool,
+    "orig": bool,
+    "surf_name": typing.NotRequired[str | None],
+    "pointset": typing.NotRequired[InputPathType | None],
+    "wot2": bool,
+})
+FvcompareParametersTagged = typing.TypedDict('FvcompareParametersTagged', {
+    "@type": typing.Literal["freesurfer/fvcompare"],
     "subject1": str,
     "subject2": str,
     "subject_dir1": typing.NotRequired[str | None],
@@ -41,42 +69,11 @@ FvcompareParameters = typing.TypedDict('FvcompareParameters', {
     "pointset": typing.NotRequired[InputPathType | None],
     "wot2": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fvcompare": fvcompare_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 FvcompareOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fvcompare(...)`.
+    Output object returned when calling `FvcompareParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -108,7 +105,7 @@ def fvcompare_params(
     surf_name: str | None = None,
     pointset: InputPathType | None = None,
     wot2: bool = False,
-) -> FvcompareParameters:
+) -> FvcompareParametersTagged:
     """
     Build parameters.
     
@@ -145,7 +142,7 @@ def fvcompare_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fvcompare",
+        "@type": "freesurfer/fvcompare",
         "subject1": subject1,
         "subject2": subject2,
         "aseg": aseg,
@@ -205,96 +202,96 @@ def fvcompare_cargs(
     cargs.append("fvcompare")
     cargs.extend([
         "--s1",
-        params.get("subject1")
+        params.get("subject1", None)
     ])
     cargs.extend([
         "--s2",
-        params.get("subject2")
+        params.get("subject2", None)
     ])
-    if params.get("subject_dir1") is not None:
+    if params.get("subject_dir1", None) is not None:
         cargs.extend([
             "--sd1",
-            params.get("subject_dir1")
+            params.get("subject_dir1", None)
         ])
-    if params.get("subject_dir2") is not None:
+    if params.get("subject_dir2", None) is not None:
         cargs.extend([
             "--sd2",
-            params.get("subject_dir2")
+            params.get("subject_dir2", None)
         ])
-    if params.get("name1") is not None:
+    if params.get("name1", None) is not None:
         cargs.extend([
             "--n1",
-            params.get("name1")
+            params.get("name1", None)
         ])
-    if params.get("name2") is not None:
+    if params.get("name2", None) is not None:
         cargs.extend([
             "--n2",
-            params.get("name2")
+            params.get("name2", None)
         ])
-    if params.get("color1") is not None:
+    if params.get("color1", None) is not None:
         cargs.extend([
             "--c1",
-            params.get("color1")
+            params.get("color1", None)
         ])
-    if params.get("volume") is not None:
+    if params.get("volume", None) is not None:
         cargs.extend([
             "--vol",
-            params.get("volume")
+            params.get("volume", None)
         ])
-    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("aseg"):
+    if params.get("aseg", False):
         cargs.append("--aseg")
-    if params.get("no_seg"):
+    if params.get("no_seg", False):
         cargs.append("--no-seg")
-    if params.get("left_hemi"):
+    if params.get("left_hemi", False):
         cargs.append("--lh")
-    if params.get("right_hemi"):
+    if params.get("right_hemi", False):
         cargs.append("--rh")
-    if params.get("no_surf"):
+    if params.get("no_surf", False):
         cargs.append("--no-surf")
-    if params.get("gray_levels") is not None:
+    if params.get("gray_levels", None) is not None:
         cargs.extend([
             "--gray",
-            *map(str, params.get("gray_levels"))
+            *map(str, params.get("gray_levels", None))
         ])
-    if params.get("cursor_position") is not None:
+    if params.get("cursor_position", None) is not None:
         cargs.extend([
             "--crs",
-            *map(str, params.get("cursor_position"))
+            *map(str, params.get("cursor_position", None))
         ])
-    if params.get("zoom_level") is not None:
+    if params.get("zoom_level", None) is not None:
         cargs.extend([
             "--zoom",
-            str(params.get("zoom_level"))
+            str(params.get("zoom_level", None))
         ])
-    if params.get("annotation") is not None:
+    if params.get("annotation", None) is not None:
         cargs.extend([
             "--annot",
-            params.get("annotation")
+            params.get("annotation", None)
         ])
-    if params.get("aparc"):
+    if params.get("aparc", False):
         cargs.append("--aparc")
-    if params.get("inflated"):
+    if params.get("inflated", False):
         cargs.append("--inflated")
-    if params.get("white"):
+    if params.get("white", False):
         cargs.append("--white")
-    if params.get("orig"):
+    if params.get("orig", False):
         cargs.append("--orig")
-    if params.get("surf_name") is not None:
+    if params.get("surf_name", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf_name")
+            params.get("surf_name", None)
         ])
-    if params.get("pointset") is not None:
+    if params.get("pointset", None) is not None:
         cargs.extend([
             "--p",
-            execution.input_file(params.get("pointset"))
+            execution.input_file(params.get("pointset", None))
         ])
-    if params.get("wot2"):
+    if params.get("wot2", False):
         cargs.append("--wot2")
     return cargs
 
@@ -320,11 +317,14 @@ def fvcompare_outputs(
 
 def fvcompare_execute(
     params: FvcompareParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FvcompareOutputs:
     """
-    Simultaneously loads volume, segmentation, and surface data from two subjects in
-    freeview, for comparing across time or different analysis methods.
+    fvcompare
+    
+    Simultaneously loads volume, segmentation, and surface data from two
+    subjects in freeview, for comparing across time or different analysis
+    methods.
     
     Author: FreeSurfer Developers
     
@@ -332,10 +332,12 @@ def fvcompare_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FvcompareOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FVCOMPARE_METADATA)
     params = execution.params(params)
     cargs = fvcompare_cargs(params, execution)
     ret = fvcompare_outputs(params, execution)
@@ -372,8 +374,11 @@ def fvcompare(
     runner: Runner | None = None,
 ) -> FvcompareOutputs:
     """
-    Simultaneously loads volume, segmentation, and surface data from two subjects in
-    freeview, for comparing across time or different analysis methods.
+    fvcompare
+    
+    Simultaneously loads volume, segmentation, and surface data from two
+    subjects in freeview, for comparing across time or different analysis
+    methods.
     
     Author: FreeSurfer Developers
     
@@ -412,8 +417,6 @@ def fvcompare(
     Returns:
         NamedTuple of outputs (described in `FvcompareOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FVCOMPARE_METADATA)
     params = fvcompare_params(
         subject1=subject1,
         subject2=subject2,
@@ -441,13 +444,13 @@ def fvcompare(
         pointset=pointset,
         wot2=wot2,
     )
-    return fvcompare_execute(params, execution)
+    return fvcompare_execute(params, runner)
 
 
 __all__ = [
     "FVCOMPARE_METADATA",
     "FvcompareOutputs",
-    "FvcompareParameters",
     "fvcompare",
+    "fvcompare_execute",
     "fvcompare_params",
 ]

niwrap_freesurfer/freesurfer/gauss_4dfp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GAUSS_4DFP_METADATA = Metadata(
-    id="1b33166dfa5b19856253a99beba28cbf386876d7.boutiques",
+    id="6d11d8425528912df342c19328cabab937d18ae5.boutiques",
     name="gauss_4dfp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ GAUSS_4DFP_METADATA = Metadata(
 
 
 Gauss4dfpParameters = typing.TypedDict('Gauss4dfpParameters', {
-    "__STYXTYPE__": typing.Literal["gauss_4dfp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/gauss_4dfp"]],
+    "input_file": str,
+    "f_half": float,
+    "output_root": typing.NotRequired[str | None],
+    "endian_flag": typing.NotRequired[str | None],
+    "wrap_flag": bool,
+    "differentiate_flag": bool,
+})
+Gauss4dfpParametersTagged = typing.TypedDict('Gauss4dfpParametersTagged', {
+    "@type": typing.Literal["freesurfer/gauss_4dfp"],
     "input_file": str,
     "f_half": float,
     "output_root": typing.NotRequired[str | None],
@@ -22,43 +31,11 @@ Gauss4dfpParameters = typing.TypedDict('Gauss4dfpParameters', {
     "wrap_flag": bool,
     "differentiate_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 {
-        "gauss_4dfp": gauss_4dfp_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 {
-        "gauss_4dfp": gauss_4dfp_outputs,
-    }.get(t)
 
 
 class Gauss4dfpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `gauss_4dfp(...)`.
+    Output object returned when calling `Gauss4dfpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def gauss_4dfp_params(
     endian_flag: str | None = None,
     wrap_flag: bool = False,
     differentiate_flag: bool = False,
-) -> Gauss4dfpParameters:
+) -> Gauss4dfpParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +68,7 @@ def gauss_4dfp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "gauss_4dfp",
+        "@type": "freesurfer/gauss_4dfp",
         "input_file": input_file,
         "f_half": f_half,
         "wrap_flag": wrap_flag,
@@ -119,18 +96,18 @@ def gauss_4dfp_cargs(
     """
     cargs = []
     cargs.append("gauss_4dfp")
-    cargs.append(params.get("input_file"))
-    cargs.append(str(params.get("f_half")))
-    if params.get("output_root") is not None:
-        cargs.append(params.get("output_root"))
-    if params.get("endian_flag") is not None:
+    cargs.append(params.get("input_file", None))
+    cargs.append(str(params.get("f_half", None)))
+    if params.get("output_root", None) is not None:
+        cargs.append(params.get("output_root", None))
+    if params.get("endian_flag", None) is not None:
         cargs.extend([
             "-@",
-            params.get("endian_flag")
+            params.get("endian_flag", None)
         ])
-    if params.get("wrap_flag"):
+    if params.get("wrap_flag", False):
         cargs.append("-w")
-    if params.get("differentiate_flag"):
+    if params.get("differentiate_flag", False):
         cargs.append("-d")
     return cargs
 
@@ -150,16 +127,18 @@ def gauss_4dfp_outputs(
     """
     ret = Gauss4dfpOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_root") + ".4dfp.ifh") if (params.get("output_root") is not None) else None,
+        output_file=execution.output_file(params.get("output_root", None) + ".4dfp.ifh") if (params.get("output_root") is not None) else None,
     )
     return ret
 
 
 def gauss_4dfp_execute(
     params: Gauss4dfpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Gauss4dfpOutputs:
     """
+    gauss_4dfp
+    
     Applies a Gaussian filter to 4dfp or conc input files.
     
     Author: FreeSurfer Developers
@@ -168,10 +147,12 @@ def gauss_4dfp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Gauss4dfpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GAUSS_4DFP_METADATA)
     params = execution.params(params)
     cargs = gauss_4dfp_cargs(params, execution)
     ret = gauss_4dfp_outputs(params, execution)
@@ -189,6 +170,8 @@ def gauss_4dfp(
     runner: Runner | None = None,
 ) -> Gauss4dfpOutputs:
     """
+    gauss_4dfp
+    
     Applies a Gaussian filter to 4dfp or conc input files.
     
     Author: FreeSurfer Developers
@@ -209,8 +192,6 @@ def gauss_4dfp(
     Returns:
         NamedTuple of outputs (described in `Gauss4dfpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(GAUSS_4DFP_METADATA)
     params = gauss_4dfp_params(
         input_file=input_file,
         f_half=f_half,
@@ -219,13 +200,13 @@ def gauss_4dfp(
         wrap_flag=wrap_flag,
         differentiate_flag=differentiate_flag,
     )
-    return gauss_4dfp_execute(params, execution)
+    return gauss_4dfp_execute(params, runner)
 
 
 __all__ = [
     "GAUSS_4DFP_METADATA",
     "Gauss4dfpOutputs",
-    "Gauss4dfpParameters",
     "gauss_4dfp",
+    "gauss_4dfp_execute",
     "gauss_4dfp_params",
 ]