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

niwrap_freesurfer/freesurfer/mris_intensity_profile.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_INTENSITY_PROFILE_METADATA = Metadata(
-    id="beda2c859ac2d0a2d1258f38cd59663f80ffddd8.boutiques",
+    id="d58b3194aa71d0a5e48772263475e5074d2737f0.boutiques",
     name="mris_intensity_profile",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ MRIS_INTENSITY_PROFILE_METADATA = Metadata(
 
 
 MrisIntensityProfileParameters = typing.TypedDict('MrisIntensityProfileParameters', {
-    "__STYXTYPE__": typing.Literal["mris_intensity_profile"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_intensity_profile"]],
+    "subject_name": str,
+    "hemi": str,
+    "volume": InputPathType,
+    "output_file": str,
+    "write_surf": typing.NotRequired[str | None],
+    "sdir": typing.NotRequired[str | None],
+    "white": typing.NotRequired[str | None],
+    "pial": typing.NotRequired[str | None],
+    "normalize_flag": bool,
+    "mean": typing.NotRequired[str | None],
+    "xform": typing.NotRequired[InputPathType | None],
+    "src": typing.NotRequired[InputPathType | None],
+    "dst": typing.NotRequired[InputPathType | None],
+    "invert_flag": bool,
+})
+MrisIntensityProfileParametersTagged = typing.TypedDict('MrisIntensityProfileParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_intensity_profile"],
     "subject_name": str,
     "hemi": str,
     "volume": InputPathType,
@@ -30,43 +47,11 @@ MrisIntensityProfileParameters = typing.TypedDict('MrisIntensityProfileParameter
     "dst": typing.NotRequired[InputPathType | None],
     "invert_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 {
-        "mris_intensity_profile": mris_intensity_profile_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 {
-        "mris_intensity_profile": mris_intensity_profile_outputs,
-    }.get(t)
 
 
 class MrisIntensityProfileOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_intensity_profile(...)`.
+    Output object returned when calling `MrisIntensityProfileParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +76,7 @@ def mris_intensity_profile_params(
     src: InputPathType | None = None,
     dst: InputPathType | None = None,
     invert_flag: bool = False,
-) -> MrisIntensityProfileParameters:
+) -> MrisIntensityProfileParametersTagged:
     """
     Build parameters.
     
@@ -117,7 +102,7 @@ def mris_intensity_profile_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_intensity_profile",
+        "@type": "freesurfer/mris_intensity_profile",
         "subject_name": subject_name,
         "hemi": hemi,
         "volume": volume,
@@ -159,53 +144,53 @@ def mris_intensity_profile_cargs(
     """
     cargs = []
     cargs.append("mris_intensity_profile")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("volume")))
-    cargs.append(params.get("output_file"))
-    if params.get("write_surf") is not None:
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("volume", None)))
+    cargs.append(params.get("output_file", None))
+    if params.get("write_surf", None) is not None:
         cargs.extend([
             "-write_surf",
-            params.get("write_surf")
+            params.get("write_surf", None)
         ])
-    if params.get("sdir") is not None:
+    if params.get("sdir", None) is not None:
         cargs.extend([
             "-sdir",
-            params.get("sdir")
+            params.get("sdir", None)
         ])
-    if params.get("white") is not None:
+    if params.get("white", None) is not None:
         cargs.extend([
             "-white",
-            params.get("white")
+            params.get("white", None)
         ])
-    if params.get("pial") is not None:
+    if params.get("pial", None) is not None:
         cargs.extend([
             "-pial",
-            params.get("pial")
+            params.get("pial", None)
         ])
-    if params.get("normalize_flag"):
+    if params.get("normalize_flag", False):
         cargs.append("-normalize")
-    if params.get("mean") is not None:
+    if params.get("mean", None) is not None:
         cargs.extend([
             "-mean",
-            params.get("mean")
+            params.get("mean", None)
         ])
-    if params.get("xform") is not None:
+    if params.get("xform", None) is not None:
         cargs.extend([
             "-xform",
-            execution.input_file(params.get("xform"))
+            execution.input_file(params.get("xform", None))
         ])
-    if params.get("src") is not None:
+    if params.get("src", None) is not None:
         cargs.extend([
             "-src",
-            execution.input_file(params.get("src"))
+            execution.input_file(params.get("src", None))
         ])
-    if params.get("dst") is not None:
+    if params.get("dst", None) is not None:
         cargs.extend([
             "-dst",
-            execution.input_file(params.get("dst"))
+            execution.input_file(params.get("dst", None))
         ])
-    if params.get("invert_flag"):
+    if params.get("invert_flag", False):
         cargs.append("-invert")
     return cargs
 
@@ -225,19 +210,21 @@ def mris_intensity_profile_outputs(
     """
     ret = MrisIntensityProfileOutputs(
         root=execution.output_file("."),
-        output_curvature_file=execution.output_file(params.get("output_file")),
-        output_mean_profile_integral=execution.output_file(params.get("mean")) if (params.get("mean") is not None) else None,
+        output_curvature_file=execution.output_file(params.get("output_file", None)),
+        output_mean_profile_integral=execution.output_file(params.get("mean", None)) if (params.get("mean") is not None) else None,
     )
     return ret
 
 
 def mris_intensity_profile_execute(
     params: MrisIntensityProfileParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisIntensityProfileOutputs:
     """
-    This program computes the intensity profile of the cortical ribbon and writes
-    the resulting measurement into a 'curvature' file.
+    mris_intensity_profile
+    
+    This program computes the intensity profile of the cortical ribbon and
+    writes the resulting measurement into a 'curvature' file.
     
     Author: FreeSurfer Developers
     
@@ -245,10 +232,12 @@ def mris_intensity_profile_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisIntensityProfileOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_INTENSITY_PROFILE_METADATA)
     params = execution.params(params)
     cargs = mris_intensity_profile_cargs(params, execution)
     ret = mris_intensity_profile_outputs(params, execution)
@@ -274,8 +263,10 @@ def mris_intensity_profile(
     runner: Runner | None = None,
 ) -> MrisIntensityProfileOutputs:
     """
-    This program computes the intensity profile of the cortical ribbon and writes
-    the resulting measurement into a 'curvature' file.
+    mris_intensity_profile
+    
+    This program computes the intensity profile of the cortical ribbon and
+    writes the resulting measurement into a 'curvature' file.
     
     Author: FreeSurfer Developers
     
@@ -303,8 +294,6 @@ def mris_intensity_profile(
     Returns:
         NamedTuple of outputs (described in `MrisIntensityProfileOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_INTENSITY_PROFILE_METADATA)
     params = mris_intensity_profile_params(
         subject_name=subject_name,
         hemi=hemi,
@@ -321,13 +310,13 @@ def mris_intensity_profile(
         dst=dst,
         invert_flag=invert_flag,
     )
-    return mris_intensity_profile_execute(params, execution)
+    return mris_intensity_profile_execute(params, runner)
 
 
 __all__ = [
     "MRIS_INTENSITY_PROFILE_METADATA",
     "MrisIntensityProfileOutputs",
-    "MrisIntensityProfileParameters",
     "mris_intensity_profile",
+    "mris_intensity_profile_execute",
     "mris_intensity_profile_params",
 ]

niwrap_freesurfer/freesurfer/mris_interpolate_warp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_INTERPOLATE_WARP_METADATA = Metadata(
-    id="4c3b574c8d475695ef29da0c89214dc574282c1e.boutiques",
+    id="d38045240e9b32965a96154d194af130972c37bd.boutiques",
     name="mris_interpolate_warp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ MRIS_INTERPOLATE_WARP_METADATA = Metadata(
 
 
 MrisInterpolateWarpParameters = typing.TypedDict('MrisInterpolateWarpParameters', {
-    "__STYXTYPE__": typing.Literal["mris_interpolate_warp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_interpolate_warp"]],
+    "start_surface": InputPathType,
+    "end_surface": InputPathType,
+    "warp_field": InputPathType,
+})
+MrisInterpolateWarpParametersTagged = typing.TypedDict('MrisInterpolateWarpParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_interpolate_warp"],
     "start_surface": InputPathType,
     "end_surface": InputPathType,
     "warp_field": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_interpolate_warp": mris_interpolate_warp_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 MrisInterpolateWarpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_interpolate_warp(...)`.
+    Output object returned when calling `MrisInterpolateWarpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def mris_interpolate_warp_params(
     start_surface: InputPathType,
     end_surface: InputPathType,
     warp_field: InputPathType,
-) -> MrisInterpolateWarpParameters:
+) -> MrisInterpolateWarpParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def mris_interpolate_warp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_interpolate_warp",
+        "@type": "freesurfer/mris_interpolate_warp",
         "start_surface": start_surface,
         "end_surface": end_surface,
         "warp_field": warp_field,
@@ -99,9 +74,9 @@ def mris_interpolate_warp_cargs(
     """
     cargs = []
     cargs.append("mris_interpolate_warp")
-    cargs.append(execution.input_file(params.get("start_surface")))
-    cargs.append(execution.input_file(params.get("end_surface")))
-    cargs.append(execution.input_file(params.get("warp_field")))
+    cargs.append(execution.input_file(params.get("start_surface", None)))
+    cargs.append(execution.input_file(params.get("end_surface", None)))
+    cargs.append(execution.input_file(params.get("warp_field", None)))
     return cargs
 
 
@@ -126,9 +101,11 @@ def mris_interpolate_warp_outputs(
 
 def mris_interpolate_warp_execute(
     params: MrisInterpolateWarpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisInterpolateWarpOutputs:
     """
+    mris_interpolate_warp
+    
     Interpolate warp on cortical surfaces.
     
     Author: FreeSurfer Developers
@@ -137,10 +114,12 @@ def mris_interpolate_warp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisInterpolateWarpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_INTERPOLATE_WARP_METADATA)
     params = execution.params(params)
     cargs = mris_interpolate_warp_cargs(params, execution)
     ret = mris_interpolate_warp_outputs(params, execution)
@@ -155,6 +134,8 @@ def mris_interpolate_warp(
     runner: Runner | None = None,
 ) -> MrisInterpolateWarpOutputs:
     """
+    mris_interpolate_warp
+    
     Interpolate warp on cortical surfaces.
     
     Author: FreeSurfer Developers
@@ -169,20 +150,18 @@ def mris_interpolate_warp(
     Returns:
         NamedTuple of outputs (described in `MrisInterpolateWarpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_INTERPOLATE_WARP_METADATA)
     params = mris_interpolate_warp_params(
         start_surface=start_surface,
         end_surface=end_surface,
         warp_field=warp_field,
     )
-    return mris_interpolate_warp_execute(params, execution)
+    return mris_interpolate_warp_execute(params, runner)
 
 
 __all__ = [
     "MRIS_INTERPOLATE_WARP_METADATA",
     "MrisInterpolateWarpOutputs",
-    "MrisInterpolateWarpParameters",
     "mris_interpolate_warp",
+    "mris_interpolate_warp_execute",
     "mris_interpolate_warp_params",
 ]

niwrap_freesurfer/freesurfer/mris_jacobian.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_JACOBIAN_METADATA = Metadata(
-    id="8c5f11cbc9fae8ad16d28449a9a0520092d3d47d.boutiques",
+    id="c86d79feae349e7fe21b17a4ef927e93ff05549c.boutiques",
     name="mris_jacobian",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_JACOBIAN_METADATA = Metadata(
 
 
 MrisJacobianParameters = typing.TypedDict('MrisJacobianParameters', {
-    "__STYXTYPE__": typing.Literal["mris_jacobian"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_jacobian"]],
+    "original_surface": InputPathType,
+    "mapped_surface": InputPathType,
+    "jacobian_file": str,
+    "log": bool,
+    "noscale": bool,
+    "invert": bool,
+})
+MrisJacobianParametersTagged = typing.TypedDict('MrisJacobianParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_jacobian"],
     "original_surface": InputPathType,
     "mapped_surface": InputPathType,
     "jacobian_file": str,
@@ -22,43 +31,11 @@ MrisJacobianParameters = typing.TypedDict('MrisJacobianParameters', {
     "noscale": bool,
     "invert": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_jacobian": mris_jacobian_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 {
-        "mris_jacobian": mris_jacobian_outputs,
-    }.get(t)
 
 
 class MrisJacobianOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_jacobian(...)`.
+    Output object returned when calling `MrisJacobianParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mris_jacobian_params(
     log: bool = False,
     noscale: bool = False,
     invert: bool = False,
-) -> MrisJacobianParameters:
+) -> MrisJacobianParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def mris_jacobian_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_jacobian",
+        "@type": "freesurfer/mris_jacobian",
         "original_surface": original_surface,
         "mapped_surface": mapped_surface,
         "jacobian_file": jacobian_file,
@@ -114,14 +91,14 @@ def mris_jacobian_cargs(
     """
     cargs = []
     cargs.append("mris_jacobian")
-    cargs.append(execution.input_file(params.get("original_surface")))
-    cargs.append(execution.input_file(params.get("mapped_surface")))
-    cargs.append(params.get("jacobian_file"))
-    if params.get("log"):
+    cargs.append(execution.input_file(params.get("original_surface", None)))
+    cargs.append(execution.input_file(params.get("mapped_surface", None)))
+    cargs.append(params.get("jacobian_file", None))
+    if params.get("log", False):
         cargs.append("-log")
-    if params.get("noscale"):
+    if params.get("noscale", False):
         cargs.append("-noscale")
-    if params.get("invert"):
+    if params.get("invert", False):
         cargs.append("-invert")
     return cargs
 
@@ -141,16 +118,18 @@ def mris_jacobian_outputs(
     """
     ret = MrisJacobianOutputs(
         root=execution.output_file("."),
-        output_jacobian_file=execution.output_file(params.get("jacobian_file")),
+        output_jacobian_file=execution.output_file(params.get("jacobian_file", None)),
     )
     return ret
 
 
 def mris_jacobian_execute(
     params: MrisJacobianParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisJacobianOutputs:
     """
+    mris_jacobian
+    
     This program computes the Jacobian of a surface mapping.
     
     Author: FreeSurfer Developers
@@ -159,10 +138,12 @@ def mris_jacobian_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisJacobianOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_JACOBIAN_METADATA)
     params = execution.params(params)
     cargs = mris_jacobian_cargs(params, execution)
     ret = mris_jacobian_outputs(params, execution)
@@ -180,6 +161,8 @@ def mris_jacobian(
     runner: Runner | None = None,
 ) -> MrisJacobianOutputs:
     """
+    mris_jacobian
+    
     This program computes the Jacobian of a surface mapping.
     
     Author: FreeSurfer Developers
@@ -197,8 +180,6 @@ def mris_jacobian(
     Returns:
         NamedTuple of outputs (described in `MrisJacobianOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_JACOBIAN_METADATA)
     params = mris_jacobian_params(
         original_surface=original_surface,
         mapped_surface=mapped_surface,
@@ -207,13 +188,13 @@ def mris_jacobian(
         noscale=noscale,
         invert=invert,
     )
-    return mris_jacobian_execute(params, execution)
+    return mris_jacobian_execute(params, runner)
 
 
 __all__ = [
     "MRIS_JACOBIAN_METADATA",
     "MrisJacobianOutputs",
-    "MrisJacobianParameters",
     "mris_jacobian",
+    "mris_jacobian_execute",
     "mris_jacobian_params",
 ]