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

niwrap_freesurfer/freesurfer/mri_warp_convert.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_WARP_CONVERT_METADATA = Metadata(
-    id="88f6767747c349aa6e8d0167d32cd39374ba05cc.boutiques",
+    id="3533ec1320189a9f8557b0a301115068a3b5f02e.boutiques",
     name="mri_warp_convert",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ MRI_WARP_CONVERT_METADATA = Metadata(
 
 
 MriWarpConvertParameters = typing.TypedDict('MriWarpConvertParameters', {
-    "__STYXTYPE__": typing.Literal["mri_warp_convert"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_warp_convert"]],
+    "inm3z": typing.NotRequired[InputPathType | None],
+    "infsl": typing.NotRequired[InputPathType | None],
+    "inlps": typing.NotRequired[InputPathType | None],
+    "initk": typing.NotRequired[InputPathType | None],
+    "inras": typing.NotRequired[InputPathType | None],
+    "invox": typing.NotRequired[InputPathType | None],
+    "outm3z": typing.NotRequired[str | None],
+    "outfsl": typing.NotRequired[str | None],
+    "outlps": typing.NotRequired[str | None],
+    "outitk": typing.NotRequired[str | None],
+    "outras": typing.NotRequired[str | None],
+    "outvox": typing.NotRequired[str | None],
+    "insrcgeom": typing.NotRequired[InputPathType | None],
+    "downsample": bool,
+})
+MriWarpConvertParametersTagged = typing.TypedDict('MriWarpConvertParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_warp_convert"],
     "inm3z": typing.NotRequired[InputPathType | None],
     "infsl": typing.NotRequired[InputPathType | None],
     "inlps": typing.NotRequired[InputPathType | None],
@@ -30,43 +47,11 @@ MriWarpConvertParameters = typing.TypedDict('MriWarpConvertParameters', {
     "insrcgeom": typing.NotRequired[InputPathType | None],
     "downsample": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_warp_convert": mri_warp_convert_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 {
-        "mri_warp_convert": mri_warp_convert_outputs,
-    }.get(t)
 
 
 class MriWarpConvertOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_warp_convert(...)`.
+    Output object returned when calling `MriWarpConvertParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +74,7 @@ def mri_warp_convert_params(
     outvox: str | None = None,
     insrcgeom: InputPathType | None = None,
     downsample: bool = False,
-) -> MriWarpConvertParameters:
+) -> MriWarpConvertParametersTagged:
     """
     Build parameters.
     
@@ -112,7 +97,7 @@ def mri_warp_convert_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_warp_convert",
+        "@type": "freesurfer/mri_warp_convert",
         "downsample": downsample,
     }
     if inm3z is not None:
@@ -159,72 +144,72 @@ def mri_warp_convert_cargs(
     """
     cargs = []
     cargs.append("mri_warp_convert")
-    if params.get("inm3z") is not None:
+    if params.get("inm3z", None) is not None:
         cargs.extend([
             "--inm3z",
-            execution.input_file(params.get("inm3z"))
+            execution.input_file(params.get("inm3z", None))
         ])
-    if params.get("infsl") is not None:
+    if params.get("infsl", None) is not None:
         cargs.extend([
             "--infsl",
-            execution.input_file(params.get("infsl"))
+            execution.input_file(params.get("infsl", None))
         ])
-    if params.get("inlps") is not None:
+    if params.get("inlps", None) is not None:
         cargs.extend([
             "--inlps",
-            execution.input_file(params.get("inlps"))
+            execution.input_file(params.get("inlps", None))
         ])
-    if params.get("initk") is not None:
+    if params.get("initk", None) is not None:
         cargs.extend([
             "--initk",
-            execution.input_file(params.get("initk"))
+            execution.input_file(params.get("initk", None))
         ])
-    if params.get("inras") is not None:
+    if params.get("inras", None) is not None:
         cargs.extend([
             "--inras",
-            execution.input_file(params.get("inras"))
+            execution.input_file(params.get("inras", None))
         ])
-    if params.get("invox") is not None:
+    if params.get("invox", None) is not None:
         cargs.extend([
             "--invox",
-            execution.input_file(params.get("invox"))
+            execution.input_file(params.get("invox", None))
         ])
-    if params.get("outm3z") is not None:
+    if params.get("outm3z", None) is not None:
         cargs.extend([
             "--outm3z",
-            params.get("outm3z")
+            params.get("outm3z", None)
         ])
-    if params.get("outfsl") is not None:
+    if params.get("outfsl", None) is not None:
         cargs.extend([
             "--outfsl",
-            params.get("outfsl")
+            params.get("outfsl", None)
         ])
-    if params.get("outlps") is not None:
+    if params.get("outlps", None) is not None:
         cargs.extend([
             "--outlps",
-            params.get("outlps")
+            params.get("outlps", None)
         ])
-    if params.get("outitk") is not None:
+    if params.get("outitk", None) is not None:
         cargs.extend([
             "--outitk",
-            params.get("outitk")
+            params.get("outitk", None)
         ])
-    if params.get("outras") is not None:
+    if params.get("outras", None) is not None:
         cargs.extend([
             "--outras",
-            params.get("outras")
+            params.get("outras", None)
         ])
-    if params.get("outvox") is not None:
+    if params.get("outvox", None) is not None:
         cargs.extend([
             "--outvox",
-            params.get("outvox")
+            params.get("outvox", None)
         ])
-    if params.get("insrcgeom") is not None:
+    if params.get("insrcgeom", None) is not None:
         cargs.extend([
             "--insrcgeom",
-            execution.input_file(params.get("insrcgeom"))
+            execution.input_file(params.get("insrcgeom", None))
         ])
-    if params.get("downsample"):
+    if params.get("downsample", False):
         cargs.append("--downsample")
     return cargs
 
@@ -244,16 +229,18 @@ def mri_warp_convert_outputs(
     """
     ret = MriWarpConvertOutputs(
         root=execution.output_file("."),
-        outwarp=execution.output_file(params.get("outvox")) if (params.get("outvox") is not None) else None,
+        outwarp=execution.output_file(params.get("outvox", None)) if (params.get("outvox") is not None) else None,
     )
     return ret
 
 
 def mri_warp_convert_execute(
     params: MriWarpConvertParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriWarpConvertOutputs:
     """
+    mri_warp_convert
+    
     This program converts non-linear deformation field warp file formats.
     
     Author: FreeSurfer Developers
@@ -262,10 +249,12 @@ def mri_warp_convert_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriWarpConvertOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_WARP_CONVERT_METADATA)
     params = execution.params(params)
     cargs = mri_warp_convert_cargs(params, execution)
     ret = mri_warp_convert_outputs(params, execution)
@@ -291,6 +280,8 @@ def mri_warp_convert(
     runner: Runner | None = None,
 ) -> MriWarpConvertOutputs:
     """
+    mri_warp_convert
+    
     This program converts non-linear deformation field warp file formats.
     
     Author: FreeSurfer Developers
@@ -316,8 +307,6 @@ def mri_warp_convert(
     Returns:
         NamedTuple of outputs (described in `MriWarpConvertOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_WARP_CONVERT_METADATA)
     params = mri_warp_convert_params(
         inm3z=inm3z,
         infsl=infsl,
@@ -334,13 +323,13 @@ def mri_warp_convert(
         insrcgeom=insrcgeom,
         downsample=downsample,
     )
-    return mri_warp_convert_execute(params, execution)
+    return mri_warp_convert_execute(params, runner)
 
 
 __all__ = [
     "MRI_WARP_CONVERT_METADATA",
     "MriWarpConvertOutputs",
-    "MriWarpConvertParameters",
     "mri_warp_convert",
+    "mri_warp_convert_execute",
     "mri_warp_convert_params",
 ]

niwrap_freesurfer/freesurfer/mri_watershed.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_WATERSHED_METADATA = Metadata(
-    id="354efa340bc804305241e0c76919e7c308f1c870.boutiques",
+    id="9bb7e9db1af91a3ea8abfd151b5e5e53143c30fe.boutiques",
     name="mri_watershed",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,41 @@ MRI_WATERSHED_METADATA = Metadata(
 
 
 MriWatershedParameters = typing.TypedDict('MriWatershedParameters', {
-    "__STYXTYPE__": typing.Literal["mri_watershed"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_watershed"]],
+    "input_volume": InputPathType,
+    "output_volume": str,
+    "weight": typing.NotRequired[float | None],
+    "no_wta_flag": bool,
+    "proba_merging": typing.NotRequired[float | None],
+    "preflooding_height": typing.NotRequired[float | None],
+    "no_seedpt_flag": bool,
+    "no_ta_flag": bool,
+    "copy_flag": bool,
+    "atlas_flag": bool,
+    "surf_name": typing.NotRequired[str | None],
+    "usesurf_ras_flag": bool,
+    "no_t1_analysis_flag": bool,
+    "shrink_surface_flag": bool,
+    "expand_surface_flag": bool,
+    "use_watershed_flag": bool,
+    "t1_volume": typing.NotRequired[InputPathType | None],
+    "wat_temp_flag": bool,
+    "first_temp_flag": bool,
+    "surf_debug_flag": bool,
+    "brain_surf_name": typing.NotRequired[str | None],
+    "shrink_brain_surf": typing.NotRequired[str | None],
+    "seed_point": typing.NotRequired[list[float] | None],
+    "center_brain": typing.NotRequired[list[float] | None],
+    "brain_radius": typing.NotRequired[float | None],
+    "watershed_threshold": typing.NotRequired[float | None],
+    "no_watershed_analysis_flag": bool,
+    "label_flag": bool,
+    "manual_params": typing.NotRequired[list[float] | None],
+    "xthresh": typing.NotRequired[float | None],
+    "mask_flag": bool,
+})
+MriWatershedParametersTagged = typing.TypedDict('MriWatershedParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_watershed"],
     "input_volume": InputPathType,
     "output_volume": str,
     "weight": typing.NotRequired[float | None],
@@ -47,43 +81,11 @@ MriWatershedParameters = typing.TypedDict('MriWatershedParameters', {
     "xthresh": typing.NotRequired[float | None],
     "mask_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 {
-        "mri_watershed": mri_watershed_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 {
-        "mri_watershed": mri_watershed_outputs,
-    }.get(t)
 
 
 class MriWatershedOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_watershed(...)`.
+    Output object returned when calling `MriWatershedParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -125,7 +127,7 @@ def mri_watershed_params(
     manual_params: list[float] | None = None,
     xthresh: float | None = None,
     mask_flag: bool = False,
-) -> MriWatershedParameters:
+) -> MriWatershedParametersTagged:
     """
     Build parameters.
     
@@ -170,7 +172,7 @@ def mri_watershed_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_watershed",
+        "@type": "freesurfer/mri_watershed",
         "input_volume": input_volume,
         "output_volume": output_volume,
         "no_wta_flag": no_wta_flag,
@@ -234,104 +236,104 @@ def mri_watershed_cargs(
     """
     cargs = []
     cargs.append("mri_watershed")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(params.get("output_volume"))
-    if params.get("weight") is not None:
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(params.get("output_volume", None))
+    if params.get("weight", None) is not None:
         cargs.extend([
             "-w",
-            str(params.get("weight"))
+            str(params.get("weight", None))
         ])
-    if params.get("no_wta_flag"):
+    if params.get("no_wta_flag", False):
         cargs.append("-no_wta")
-    if params.get("proba_merging") is not None:
+    if params.get("proba_merging", None) is not None:
         cargs.extend([
             "-b",
-            str(params.get("proba_merging"))
+            str(params.get("proba_merging", None))
         ])
-    if params.get("preflooding_height") is not None:
+    if params.get("preflooding_height", None) is not None:
         cargs.extend([
             "-h",
-            str(params.get("preflooding_height"))
+            str(params.get("preflooding_height", None))
         ])
-    if params.get("no_seedpt_flag"):
+    if params.get("no_seedpt_flag", False):
         cargs.append("-no_seedpt")
-    if params.get("no_ta_flag"):
+    if params.get("no_ta_flag", False):
         cargs.append("-no-ta")
-    if params.get("copy_flag"):
+    if params.get("copy_flag", False):
         cargs.append("-copy")
-    if params.get("atlas_flag"):
+    if params.get("atlas_flag", False):
         cargs.append("-atlas")
-    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("usesurf_ras_flag"):
+    if params.get("usesurf_ras_flag", False):
         cargs.append("-useSRAS")
-    if params.get("no_t1_analysis_flag"):
+    if params.get("no_t1_analysis_flag", False):
         cargs.append("-noT1")
-    if params.get("shrink_surface_flag"):
+    if params.get("shrink_surface_flag", False):
         cargs.append("-less")
-    if params.get("expand_surface_flag"):
+    if params.get("expand_surface_flag", False):
         cargs.append("-more")
-    if params.get("use_watershed_flag"):
+    if params.get("use_watershed_flag", False):
         cargs.append("-wat")
-    if params.get("t1_volume") is not None:
+    if params.get("t1_volume", None) is not None:
         cargs.extend([
             "-T1",
-            execution.input_file(params.get("t1_volume"))
+            execution.input_file(params.get("t1_volume", None))
         ])
-    if params.get("wat_temp_flag"):
+    if params.get("wat_temp_flag", False):
         cargs.append("-wat+temp")
-    if params.get("first_temp_flag"):
+    if params.get("first_temp_flag", False):
         cargs.append("-first_temp")
-    if params.get("surf_debug_flag"):
+    if params.get("surf_debug_flag", False):
         cargs.append("-surf_debug")
-    if params.get("brain_surf_name") is not None:
+    if params.get("brain_surf_name", None) is not None:
         cargs.extend([
             "-brainsurf",
-            params.get("brain_surf_name")
+            params.get("brain_surf_name", None)
         ])
-    if params.get("shrink_brain_surf") is not None:
+    if params.get("shrink_brain_surf", None) is not None:
         cargs.extend([
             "-shk_br_surf",
-            params.get("shrink_brain_surf")
+            params.get("shrink_brain_surf", None)
         ])
-    if params.get("seed_point") is not None:
+    if params.get("seed_point", None) is not None:
         cargs.extend([
             "-s",
-            *map(str, params.get("seed_point"))
+            *map(str, params.get("seed_point", None))
         ])
-    if params.get("center_brain") is not None:
+    if params.get("center_brain", None) is not None:
         cargs.extend([
             "-c",
-            *map(str, params.get("center_brain"))
+            *map(str, params.get("center_brain", None))
         ])
-    if params.get("brain_radius") is not None:
+    if params.get("brain_radius", None) is not None:
         cargs.extend([
             "-r",
-            str(params.get("brain_radius"))
+            str(params.get("brain_radius", None))
         ])
-    if params.get("watershed_threshold") is not None:
+    if params.get("watershed_threshold", None) is not None:
         cargs.extend([
             "-t",
-            str(params.get("watershed_threshold"))
+            str(params.get("watershed_threshold", None))
         ])
-    if params.get("no_watershed_analysis_flag"):
+    if params.get("no_watershed_analysis_flag", False):
         cargs.append("-n")
-    if params.get("label_flag"):
+    if params.get("label_flag", False):
         cargs.append("-LABEL")
-    if params.get("manual_params") is not None:
+    if params.get("manual_params", None) is not None:
         cargs.extend([
             "-man",
-            *map(str, params.get("manual_params"))
+            *map(str, params.get("manual_params", None))
         ])
-    if params.get("xthresh") is not None:
+    if params.get("xthresh", None) is not None:
         cargs.extend([
             "-xthresh",
-            str(params.get("xthresh"))
+            str(params.get("xthresh", None))
         ])
-    if params.get("mask_flag"):
+    if params.get("mask_flag", False):
         cargs.append("-mask")
     return cargs
 
@@ -351,19 +353,21 @@ def mri_watershed_outputs(
     """
     ret = MriWatershedOutputs(
         root=execution.output_file("."),
-        output_brain_vol=execution.output_file(params.get("output_volume")),
-        output_brain_surf=execution.output_file(params.get("brain_surf_name")) if (params.get("brain_surf_name") is not None) else None,
+        output_brain_vol=execution.output_file(params.get("output_volume", None)),
+        output_brain_surf=execution.output_file(params.get("brain_surf_name", None)) if (params.get("brain_surf_name") is not None) else None,
     )
     return ret
 
 
 def mri_watershed_execute(
     params: MriWatershedParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriWatershedOutputs:
     """
-    A tool for stripping skull and other non-brain tissues to produce brain volume
-    from T1 volume.
+    mri_watershed
+    
+    A tool for stripping skull and other non-brain tissues to produce brain
+    volume from T1 volume.
     
     Author: FreeSurfer Developers
     
@@ -371,10 +375,12 @@ def mri_watershed_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriWatershedOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_WATERSHED_METADATA)
     params = execution.params(params)
     cargs = mri_watershed_cargs(params, execution)
     ret = mri_watershed_outputs(params, execution)
@@ -417,8 +423,10 @@ def mri_watershed(
     runner: Runner | None = None,
 ) -> MriWatershedOutputs:
     """
-    A tool for stripping skull and other non-brain tissues to produce brain volume
-    from T1 volume.
+    mri_watershed
+    
+    A tool for stripping skull and other non-brain tissues to produce brain
+    volume from T1 volume.
     
     Author: FreeSurfer Developers
     
@@ -465,8 +473,6 @@ def mri_watershed(
     Returns:
         NamedTuple of outputs (described in `MriWatershedOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_WATERSHED_METADATA)
     params = mri_watershed_params(
         input_volume=input_volume,
         output_volume=output_volume,
@@ -500,13 +506,13 @@ def mri_watershed(
         xthresh=xthresh,
         mask_flag=mask_flag,
     )
-    return mri_watershed_execute(params, execution)
+    return mri_watershed_execute(params, runner)
 
 
 __all__ = [
     "MRI_WATERSHED_METADATA",
     "MriWatershedOutputs",
-    "MriWatershedParameters",
     "mri_watershed",
+    "mri_watershed_execute",
     "mri_watershed_params",
 ]