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

niwrap_freesurfer/freesurfer/tkmeditfv.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TKMEDITFV_METADATA = Metadata(
-    id="cbd5f4cf7541f87238cd68202cdafa6b3a7ee7d0.boutiques",
+    id="db0a4cf2357c61dd60a035ba237f0f978f736592.boutiques",
     name="tkmeditfv",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,42 @@ TKMEDITFV_METADATA = Metadata(
 
 
 TkmeditfvParameters = typing.TypedDict('TkmeditfvParameters', {
-    "__STYXTYPE__": typing.Literal["tkmeditfv"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/tkmeditfv"]],
+    "subject": typing.NotRequired[str | None],
+    "mainvol": InputPathType,
+    "aux_volume": typing.NotRequired[InputPathType | None],
+    "seg_volume": typing.NotRequired[InputPathType | None],
+    "overlay": typing.NotRequired[InputPathType | None],
+    "timecourse": typing.NotRequired[InputPathType | None],
+    "overlay_registration": typing.NotRequired[InputPathType | None],
+    "surface": typing.NotRequired[list[str] | None],
+    "extra_volumes": typing.NotRequired[list[InputPathType] | None],
+    "crs_location": typing.NotRequired[list[float] | None],
+    "zoom_level": typing.NotRequired[float | None],
+    "additional_segments": typing.NotRequired[list[InputPathType] | None],
+    "load_white": bool,
+    "load_pial": bool,
+    "load_orig": bool,
+    "load_orig_nofix": bool,
+    "load_smoothwm_nofix": bool,
+    "load_white_preaparc": bool,
+    "load_inflated": bool,
+    "annot": typing.NotRequired[str | None],
+    "load_aparc": bool,
+    "surfext": typing.NotRequired[str | None],
+    "seg_outline": bool,
+    "intensity_minmax": typing.NotRequired[list[float] | None],
+    "load_defects": bool,
+    "load_defect_pointset": bool,
+    "trilin_interpolation": bool,
+    "neurological_orientation": bool,
+    "rotate_around_cursor": bool,
+    "vgl_display": bool,
+    "use_tkmedit": bool,
+    "load_aparc_aseg": bool,
+})
+TkmeditfvParametersTagged = typing.TypedDict('TkmeditfvParametersTagged', {
+    "@type": typing.Literal["freesurfer/tkmeditfv"],
     "subject": typing.NotRequired[str | None],
     "mainvol": InputPathType,
     "aux_volume": typing.NotRequired[InputPathType | None],
@@ -48,42 +83,11 @@ TkmeditfvParameters = typing.TypedDict('TkmeditfvParameters', {
     "use_tkmedit": bool,
     "load_aparc_aseg": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "tkmeditfv": tkmeditfv_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 TkmeditfvOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tkmeditfv(...)`.
+    Output object returned when calling `TkmeditfvParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -122,7 +126,7 @@ def tkmeditfv_params(
     vgl_display: bool = False,
     use_tkmedit: bool = False,
     load_aparc_aseg: bool = False,
-) -> TkmeditfvParameters:
+) -> TkmeditfvParametersTagged:
     """
     Build parameters.
     
@@ -164,7 +168,7 @@ def tkmeditfv_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tkmeditfv",
+        "@type": "freesurfer/tkmeditfv",
         "mainvol": mainvol,
         "load_white": load_white,
         "load_pial": load_pial,
@@ -230,107 +234,107 @@ def tkmeditfv_cargs(
     """
     cargs = []
     cargs.append("tkmeditfv")
-    if params.get("subject") is not None:
-        cargs.append(params.get("subject"))
-    cargs.append(execution.input_file(params.get("mainvol")))
-    if params.get("aux_volume") is not None:
+    if params.get("subject", None) is not None:
+        cargs.append(params.get("subject", None))
+    cargs.append(execution.input_file(params.get("mainvol", None)))
+    if params.get("aux_volume", None) is not None:
         cargs.extend([
             "-aux",
-            execution.input_file(params.get("aux_volume"))
+            execution.input_file(params.get("aux_volume", None))
         ])
-    if params.get("seg_volume") is not None:
+    if params.get("seg_volume", None) is not None:
         cargs.extend([
             "-seg",
-            execution.input_file(params.get("seg_volume"))
+            execution.input_file(params.get("seg_volume", None))
         ])
-    if params.get("overlay") is not None:
+    if params.get("overlay", None) is not None:
         cargs.extend([
             "-ov",
-            execution.input_file(params.get("overlay"))
+            execution.input_file(params.get("overlay", None))
         ])
-    if params.get("timecourse") is not None:
+    if params.get("timecourse", None) is not None:
         cargs.extend([
             "-t",
-            execution.input_file(params.get("timecourse"))
+            execution.input_file(params.get("timecourse", None))
         ])
-    if params.get("overlay_registration") is not None:
+    if params.get("overlay_registration", None) is not None:
         cargs.extend([
             "-reg",
-            execution.input_file(params.get("overlay_registration"))
+            execution.input_file(params.get("overlay_registration", None))
         ])
-    if params.get("surface") is not None:
+    if params.get("surface", None) is not None:
         cargs.extend([
             "-surf",
-            *params.get("surface")
+            *params.get("surface", None)
         ])
-    if params.get("extra_volumes") is not None:
+    if params.get("extra_volumes", None) is not None:
         cargs.extend([
             "-vol",
-            *[execution.input_file(f) for f in params.get("extra_volumes")]
+            *[execution.input_file(f) for f in params.get("extra_volumes", None)]
         ])
-    if params.get("crs_location") is not None:
+    if params.get("crs_location", None) is not None:
         cargs.extend([
             "-crs",
-            *map(str, params.get("crs_location"))
+            *map(str, params.get("crs_location", 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("additional_segments") is not None:
+    if params.get("additional_segments", None) is not None:
         cargs.extend([
             "-seg2",
-            *[execution.input_file(f) for f in params.get("additional_segments")]
+            *[execution.input_file(f) for f in params.get("additional_segments", None)]
         ])
-    if params.get("load_white"):
+    if params.get("load_white", False):
         cargs.append("-white")
-    if params.get("load_pial"):
+    if params.get("load_pial", False):
         cargs.append("-pial")
-    if params.get("load_orig"):
+    if params.get("load_orig", False):
         cargs.append("-orig")
-    if params.get("load_orig_nofix"):
+    if params.get("load_orig_nofix", False):
         cargs.append("-orig.nofix")
-    if params.get("load_smoothwm_nofix"):
+    if params.get("load_smoothwm_nofix", False):
         cargs.append("-smoothwm.nofix")
-    if params.get("load_white_preaparc"):
+    if params.get("load_white_preaparc", False):
         cargs.append("-white.preaparc")
-    if params.get("load_inflated"):
+    if params.get("load_inflated", False):
         cargs.append("-inflated")
-    if params.get("annot") is not None:
+    if params.get("annot", None) is not None:
         cargs.extend([
             "-annot",
-            params.get("annot")
+            params.get("annot", None)
         ])
-    if params.get("load_aparc"):
+    if params.get("load_aparc", False):
         cargs.append("-aparc")
-    if params.get("surfext") is not None:
+    if params.get("surfext", None) is not None:
         cargs.extend([
             "-surfext",
-            params.get("surfext")
+            params.get("surfext", None)
         ])
-    if params.get("seg_outline"):
+    if params.get("seg_outline", False):
         cargs.append("-seg-outline")
-    if params.get("intensity_minmax") is not None:
+    if params.get("intensity_minmax", None) is not None:
         cargs.extend([
             "-main-minmax",
-            *map(str, params.get("intensity_minmax"))
+            *map(str, params.get("intensity_minmax", None))
         ])
-    if params.get("load_defects"):
+    if params.get("load_defects", False):
         cargs.append("-defects")
-    if params.get("load_defect_pointset"):
+    if params.get("load_defect_pointset", False):
         cargs.append("-defectps")
-    if params.get("trilin_interpolation"):
+    if params.get("trilin_interpolation", False):
         cargs.append("-trilin")
-    if params.get("neurological_orientation"):
+    if params.get("neurological_orientation", False):
         cargs.append("-neuro")
-    if params.get("rotate_around_cursor"):
+    if params.get("rotate_around_cursor", False):
         cargs.append("-rotate-around-cursor")
-    if params.get("vgl_display"):
+    if params.get("vgl_display", False):
         cargs.append("-vgl")
-    if params.get("use_tkmedit"):
+    if params.get("use_tkmedit", False):
         cargs.append("-tkmedit")
-    if params.get("load_aparc_aseg"):
+    if params.get("load_aparc_aseg", False):
         cargs.append("-aparc+aseg")
     return cargs
 
@@ -356,11 +360,13 @@ def tkmeditfv_outputs(
 
 def tkmeditfv_execute(
     params: TkmeditfvParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TkmeditfvOutputs:
     """
-    A wrapper script to run Freeview with arguments similar to tkmedit, providing
-    both functionalities.
+    tkmeditfv
+    
+    A wrapper script to run Freeview with arguments similar to tkmedit,
+    providing both functionalities.
     
     Author: FreeSurfer Developers
     
@@ -368,10 +374,12 @@ def tkmeditfv_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TkmeditfvOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TKMEDITFV_METADATA)
     params = execution.params(params)
     cargs = tkmeditfv_cargs(params, execution)
     ret = tkmeditfv_outputs(params, execution)
@@ -415,8 +423,10 @@ def tkmeditfv(
     runner: Runner | None = None,
 ) -> TkmeditfvOutputs:
     """
-    A wrapper script to run Freeview with arguments similar to tkmedit, providing
-    both functionalities.
+    tkmeditfv
+    
+    A wrapper script to run Freeview with arguments similar to tkmedit,
+    providing both functionalities.
     
     Author: FreeSurfer Developers
     
@@ -460,8 +470,6 @@ def tkmeditfv(
     Returns:
         NamedTuple of outputs (described in `TkmeditfvOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TKMEDITFV_METADATA)
     params = tkmeditfv_params(
         subject=subject,
         mainvol=mainvol,
@@ -496,13 +504,13 @@ def tkmeditfv(
         use_tkmedit=use_tkmedit,
         load_aparc_aseg=load_aparc_aseg,
     )
-    return tkmeditfv_execute(params, execution)
+    return tkmeditfv_execute(params, runner)
 
 
 __all__ = [
     "TKMEDITFV_METADATA",
     "TkmeditfvOutputs",
-    "TkmeditfvParameters",
     "tkmeditfv",
+    "tkmeditfv_execute",
     "tkmeditfv_params",
 ]

niwrap_freesurfer/freesurfer/tkregister2.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TKREGISTER2_METADATA = Metadata(
-    id="1f24eb8859271e38bd38304bae70f2a0a2fb4f5b.boutiques",
+    id="fd186deebd01873f84736aa493b727a1bdc0a7fd.boutiques",
     name="tkregister2",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ TKREGISTER2_METADATA = Metadata(
 
 
 Tkregister2Parameters = typing.TypedDict('Tkregister2Parameters', {
-    "__STYXTYPE__": typing.Literal["tkregister2"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/tkregister2"]],
+    "fixed_volume": InputPathType,
+    "moving_volume": InputPathType,
+    "reg_file": InputPathType,
+    "noedit": bool,
+    "lta": bool,
+    "surf_reg": bool,
+    "reg_only": bool,
+    "help": bool,
+})
+Tkregister2ParametersTagged = typing.TypedDict('Tkregister2ParametersTagged', {
+    "@type": typing.Literal["freesurfer/tkregister2"],
     "fixed_volume": InputPathType,
     "moving_volume": InputPathType,
     "reg_file": InputPathType,
@@ -24,43 +35,11 @@ Tkregister2Parameters = typing.TypedDict('Tkregister2Parameters', {
     "reg_only": 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 {
-        "tkregister2": tkregister2_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 {
-        "tkregister2": tkregister2_outputs,
-    }.get(t)
 
 
 class Tkregister2Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `tkregister2(...)`.
+    Output object returned when calling `Tkregister2Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def tkregister2_params(
     surf_reg: bool = False,
     reg_only: bool = False,
     help_: bool = False,
-) -> Tkregister2Parameters:
+) -> Tkregister2ParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +73,7 @@ def tkregister2_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tkregister2",
+        "@type": "freesurfer/tkregister2",
         "fixed_volume": fixed_volume,
         "moving_volume": moving_volume,
         "reg_file": reg_file,
@@ -122,18 +101,18 @@ def tkregister2_cargs(
     """
     cargs = []
     cargs.append("tkregister2")
-    cargs.append(execution.input_file(params.get("fixed_volume")))
-    cargs.append(execution.input_file(params.get("moving_volume")))
-    cargs.append(execution.input_file(params.get("reg_file")))
-    if params.get("noedit"):
+    cargs.append(execution.input_file(params.get("fixed_volume", None)))
+    cargs.append(execution.input_file(params.get("moving_volume", None)))
+    cargs.append(execution.input_file(params.get("reg_file", None)))
+    if params.get("noedit", False):
         cargs.append("--noedit")
-    if params.get("lta"):
+    if params.get("lta", False):
         cargs.append("--lta")
-    if params.get("surf_reg"):
+    if params.get("surf_reg", False):
         cargs.append("--surf")
-    if params.get("reg_only"):
+    if params.get("reg_only", False):
         cargs.append("--regonly")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -153,16 +132,18 @@ def tkregister2_outputs(
     """
     ret = Tkregister2Outputs(
         root=execution.output_file("."),
-        output_reg_file=execution.output_file(pathlib.Path(params.get("reg_file")).name),
+        output_reg_file=execution.output_file(pathlib.Path(params.get("reg_file", None)).name),
     )
     return ret
 
 
 def tkregister2_execute(
     params: Tkregister2Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Tkregister2Outputs:
     """
+    tkregister2
+    
     tkregister2 is a tool from FreeSurfer used for registration of MRI images.
     
     Author: FreeSurfer Developers
@@ -171,10 +152,12 @@ def tkregister2_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Tkregister2Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TKREGISTER2_METADATA)
     params = execution.params(params)
     cargs = tkregister2_cargs(params, execution)
     ret = tkregister2_outputs(params, execution)
@@ -194,6 +177,8 @@ def tkregister2(
     runner: Runner | None = None,
 ) -> Tkregister2Outputs:
     """
+    tkregister2
+    
     tkregister2 is a tool from FreeSurfer used for registration of MRI images.
     
     Author: FreeSurfer Developers
@@ -213,8 +198,6 @@ def tkregister2(
     Returns:
         NamedTuple of outputs (described in `Tkregister2Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TKREGISTER2_METADATA)
     params = tkregister2_params(
         fixed_volume=fixed_volume,
         moving_volume=moving_volume,
@@ -225,13 +208,13 @@ def tkregister2(
         reg_only=reg_only,
         help_=help_,
     )
-    return tkregister2_execute(params, execution)
+    return tkregister2_execute(params, runner)
 
 
 __all__ = [
     "TKREGISTER2_METADATA",
     "Tkregister2Outputs",
-    "Tkregister2Parameters",
     "tkregister2",
+    "tkregister2_execute",
     "tkregister2_params",
 ]