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

niwrap_freesurfer/freesurfer/mri_sph2surf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_SPH2SURF_METADATA = Metadata(
-    id="dd6b3e285073d710fdf923d6ed2c4a5936c19c32.boutiques",
+    id="fad10a451d940d898534a28baa19b86063f2955b.boutiques",
     name="mri-sph2surf",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ MRI_SPH2SURF_METADATA = Metadata(
 
 
 MriSph2surfParameters = typing.TypedDict('MriSph2surfParameters', {
-    "__STYXTYPE__": typing.Literal["mri-sph2surf"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri-sph2surf"]],
+    "instem": str,
+    "outstem": str,
+    "hemi": str,
+    "subject": str,
+    "offset": typing.NotRequired[float | None],
+    "svitdir": typing.NotRequired[str | None],
+    "umask": typing.NotRequired[str | None],
+    "verbose": bool,
+    "version": bool,
+})
+MriSph2surfParametersTagged = typing.TypedDict('MriSph2surfParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri-sph2surf"],
     "instem": str,
     "outstem": str,
     "hemi": str,
@@ -25,43 +37,11 @@ MriSph2surfParameters = typing.TypedDict('MriSph2surfParameters', {
     "verbose": 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 {
-        "mri-sph2surf": mri_sph2surf_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-sph2surf": mri_sph2surf_outputs,
-    }.get(t)
 
 
 class MriSph2surfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_sph2surf(...)`.
+    Output object returned when calling `MriSph2surfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,12 +54,12 @@ def mri_sph2surf_params(
     outstem: str,
     hemi: str,
     subject: str,
-    offset: float | None = 0,
-    svitdir: str | None = "/usr/local/freesurfer/subjects/subject/svit",
+    offset: float | None = None,
+    svitdir: str | None = None,
     umask: str | None = None,
     verbose: bool = False,
     version: bool = False,
-) -> MriSph2surfParameters:
+) -> MriSph2surfParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +82,7 @@ def mri_sph2surf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri-sph2surf",
+        "@type": "freesurfer/mri-sph2surf",
         "instem": instem,
         "outstem": outstem,
         "hemi": hemi,
@@ -136,38 +116,38 @@ def mri_sph2surf_cargs(
     cargs.append("mri-sph2surf")
     cargs.extend([
         "-i",
-        params.get("instem")
+        params.get("instem", None)
     ])
     cargs.extend([
         "-o",
-        params.get("outstem")
+        params.get("outstem", None)
     ])
     cargs.extend([
         "-hemi",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
     cargs.extend([
         "-s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("offset") is not None:
+    if params.get("offset", None) is not None:
         cargs.extend([
             "-offset",
-            str(params.get("offset"))
+            str(params.get("offset", None))
         ])
-    if params.get("svitdir") is not None:
+    if params.get("svitdir", None) is not None:
         cargs.extend([
             "-svitdir",
-            params.get("svitdir")
+            params.get("svitdir", None)
         ])
-    if params.get("umask") is not None:
+    if params.get("umask", None) is not None:
         cargs.extend([
             "-umask",
-            params.get("umask")
+            params.get("umask", None)
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verbose")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
     return cargs
 
@@ -187,18 +167,20 @@ def mri_sph2surf_outputs(
     """
     ret = MriSph2surfOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("outstem") + "-" + params.get("hemi") + ".w"),
+        output_file=execution.output_file(params.get("outstem", None) + "-" + params.get("hemi", None) + ".w"),
     )
     return ret
 
 
 def mri_sph2surf_execute(
     params: MriSph2surfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriSph2surfOutputs:
     """
-    Converts spherical functional data to surface data in the FreeSurfer processing
-    pipeline.
+    mri-sph2surf
+    
+    Converts spherical functional data to surface data in the FreeSurfer
+    processing pipeline.
     
     Author: FreeSurfer Developers
     
@@ -206,10 +188,12 @@ def mri_sph2surf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriSph2surfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SPH2SURF_METADATA)
     params = execution.params(params)
     cargs = mri_sph2surf_cargs(params, execution)
     ret = mri_sph2surf_outputs(params, execution)
@@ -222,16 +206,18 @@ def mri_sph2surf(
     outstem: str,
     hemi: str,
     subject: str,
-    offset: float | None = 0,
-    svitdir: str | None = "/usr/local/freesurfer/subjects/subject/svit",
+    offset: float | None = None,
+    svitdir: str | None = None,
     umask: str | None = None,
     verbose: bool = False,
     version: bool = False,
     runner: Runner | None = None,
 ) -> MriSph2surfOutputs:
     """
-    Converts spherical functional data to surface data in the FreeSurfer processing
-    pipeline.
+    mri-sph2surf
+    
+    Converts spherical functional data to surface data in the FreeSurfer
+    processing pipeline.
     
     Author: FreeSurfer Developers
     
@@ -256,8 +242,6 @@ def mri_sph2surf(
     Returns:
         NamedTuple of outputs (described in `MriSph2surfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_SPH2SURF_METADATA)
     params = mri_sph2surf_params(
         instem=instem,
         outstem=outstem,
@@ -269,13 +253,13 @@ def mri_sph2surf(
         verbose=verbose,
         version=version,
     )
-    return mri_sph2surf_execute(params, execution)
+    return mri_sph2surf_execute(params, runner)
 
 
 __all__ = [
     "MRI_SPH2SURF_METADATA",
     "MriSph2surfOutputs",
-    "MriSph2surfParameters",
     "mri_sph2surf",
+    "mri_sph2surf_execute",
     "mri_sph2surf_params",
 ]

niwrap_freesurfer/freesurfer/mri_stats2seg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_STATS2SEG_METADATA = Metadata(
-    id="22103812fe530207b1cd1d156d97602a5bfbe12c.boutiques",
+    id="7e0c5f5d6a788384f4579ed9b9699dd6dad8dac7.boutiques",
     name="mri_stats2seg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRI_STATS2SEG_METADATA = Metadata(
 
 
 MriStats2segParameters = typing.TypedDict('MriStats2segParameters', {
-    "__STYXTYPE__": typing.Literal["mri_stats2seg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_stats2seg"]],
+    "stat_file": InputPathType,
+    "segmentation_volume": InputPathType,
+    "output_file": str,
+    "debug": bool,
+    "check_opts": bool,
+})
+MriStats2segParametersTagged = typing.TypedDict('MriStats2segParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_stats2seg"],
     "stat_file": InputPathType,
     "segmentation_volume": InputPathType,
     "output_file": str,
     "debug": bool,
     "check_opts": 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_stats2seg": mri_stats2seg_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_stats2seg": mri_stats2seg_outputs,
-    }.get(t)
 
 
 class MriStats2segOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_stats2seg(...)`.
+    Output object returned when calling `MriStats2segParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mri_stats2seg_params(
     output_file: str,
     debug: bool = False,
     check_opts: bool = False,
-) -> MriStats2segParameters:
+) -> MriStats2segParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def mri_stats2seg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_stats2seg",
+        "@type": "freesurfer/mri_stats2seg",
         "stat_file": stat_file,
         "segmentation_volume": segmentation_volume,
         "output_file": output_file,
@@ -112,19 +88,19 @@ def mri_stats2seg_cargs(
     cargs.append("mri_stats2seg")
     cargs.extend([
         "--stat",
-        execution.input_file(params.get("stat_file"))
+        execution.input_file(params.get("stat_file", None))
     ])
     cargs.extend([
         "--seg",
-        execution.input_file(params.get("segmentation_volume"))
+        execution.input_file(params.get("segmentation_volume", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("check_opts"):
+    if params.get("check_opts", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -144,16 +120,18 @@ def mri_stats2seg_outputs(
     """
     ret = MriStats2segOutputs(
         root=execution.output_file("."),
-        segmented_output=execution.output_file(params.get("output_file")),
+        segmented_output=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mri_stats2seg_execute(
     params: MriStats2segParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriStats2segOutputs:
     """
+    mri_stats2seg
+    
     A command-line tool for converting MRI statistical maps to segmented volume.
     
     Author: FreeSurfer Developers
@@ -162,10 +140,12 @@ def mri_stats2seg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriStats2segOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_STATS2SEG_METADATA)
     params = execution.params(params)
     cargs = mri_stats2seg_cargs(params, execution)
     ret = mri_stats2seg_outputs(params, execution)
@@ -182,6 +162,8 @@ def mri_stats2seg(
     runner: Runner | None = None,
 ) -> MriStats2segOutputs:
     """
+    mri_stats2seg
+    
     A command-line tool for converting MRI statistical maps to segmented volume.
     
     Author: FreeSurfer Developers
@@ -198,8 +180,6 @@ def mri_stats2seg(
     Returns:
         NamedTuple of outputs (described in `MriStats2segOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_STATS2SEG_METADATA)
     params = mri_stats2seg_params(
         stat_file=stat_file,
         segmentation_volume=segmentation_volume,
@@ -207,13 +187,13 @@ def mri_stats2seg(
         debug=debug,
         check_opts=check_opts,
     )
-    return mri_stats2seg_execute(params, execution)
+    return mri_stats2seg_execute(params, runner)
 
 
 __all__ = [
     "MRI_STATS2SEG_METADATA",
     "MriStats2segOutputs",
-    "MriStats2segParameters",
     "mri_stats2seg",
+    "mri_stats2seg_execute",
     "mri_stats2seg_params",
 ]

niwrap_freesurfer/freesurfer/mri_stopmask.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_STOPMASK_METADATA = Metadata(
-    id="38e7fa2abd35271883a0f65f5dbaff1fc083659f.boutiques",
+    id="1c9df873427ea33c04be53852a0c8cd2cc7265c8.boutiques",
     name="mri_stopmask",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ MRI_STOPMASK_METADATA = Metadata(
 
 
 MriStopmaskParameters = typing.TypedDict('MriStopmaskParameters', {
-    "__STYXTYPE__": typing.Literal["mri_stopmask"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_stopmask"]],
+    "output_mask": str,
+    "filled": list[InputPathType],
+    "aseg_presurf": InputPathType,
+    "lateral_ventricles": bool,
+    "wmsa": typing.NotRequired[float | None],
+    "wm_voxels": typing.NotRequired[InputPathType | None],
+    "brain_final_surfs": typing.NotRequired[InputPathType | None],
+    "no_filled": bool,
+    "no_lv": bool,
+    "no_wmsa": bool,
+    "no_wm": bool,
+    "no_bfs": bool,
+})
+MriStopmaskParametersTagged = typing.TypedDict('MriStopmaskParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_stopmask"],
     "output_mask": str,
     "filled": list[InputPathType],
     "aseg_presurf": InputPathType,
@@ -28,43 +43,11 @@ MriStopmaskParameters = typing.TypedDict('MriStopmaskParameters', {
     "no_wm": bool,
     "no_bfs": 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_stopmask": mri_stopmask_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_stopmask": mri_stopmask_outputs,
-    }.get(t)
 
 
 class MriStopmaskOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_stopmask(...)`.
+    Output object returned when calling `MriStopmaskParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +68,7 @@ def mri_stopmask_params(
     no_wmsa: bool = False,
     no_wm: bool = False,
     no_bfs: bool = False,
-) -> MriStopmaskParameters:
+) -> MriStopmaskParametersTagged:
     """
     Build parameters.
     
@@ -110,7 +93,7 @@ def mri_stopmask_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_stopmask",
+        "@type": "freesurfer/mri_stopmask",
         "output_mask": output_mask,
         "filled": filled,
         "aseg_presurf": aseg_presurf,
@@ -147,42 +130,42 @@ def mri_stopmask_cargs(
     cargs.append("mri_stopmask")
     cargs.extend([
         "--o",
-        params.get("output_mask")
+        params.get("output_mask", None)
     ])
     cargs.extend([
         "--filled",
-        *[execution.input_file(f) for f in params.get("filled")]
+        *[execution.input_file(f) for f in params.get("filled", None)]
     ])
     cargs.extend([
         "--aseg",
-        execution.input_file(params.get("aseg_presurf"))
+        execution.input_file(params.get("aseg_presurf", None))
     ])
-    if params.get("lateral_ventricles"):
+    if params.get("lateral_ventricles", False):
         cargs.append("--lv")
-    if params.get("wmsa") is not None:
+    if params.get("wmsa", None) is not None:
         cargs.extend([
             "--wmsa",
-            str(params.get("wmsa"))
+            str(params.get("wmsa", None))
         ])
-    if params.get("wm_voxels") is not None:
+    if params.get("wm_voxels", None) is not None:
         cargs.extend([
             "--wm",
-            execution.input_file(params.get("wm_voxels"))
+            execution.input_file(params.get("wm_voxels", None))
         ])
-    if params.get("brain_final_surfs") is not None:
+    if params.get("brain_final_surfs", None) is not None:
         cargs.extend([
             "--bfs",
-            execution.input_file(params.get("brain_final_surfs"))
+            execution.input_file(params.get("brain_final_surfs", None))
         ])
-    if params.get("no_filled"):
+    if params.get("no_filled", False):
         cargs.append("--no-filled")
-    if params.get("no_lv"):
+    if params.get("no_lv", False):
         cargs.append("--no-lv")
-    if params.get("no_wmsa"):
+    if params.get("no_wmsa", False):
         cargs.append("--no-wmsa")
-    if params.get("no_wm"):
+    if params.get("no_wm", False):
         cargs.append("--no-wm")
-    if params.get("no_bfs"):
+    if params.get("no_bfs", False):
         cargs.append("--no-bfs")
     return cargs
 
@@ -202,19 +185,21 @@ def mri_stopmask_outputs(
     """
     ret = MriStopmaskOutputs(
         root=execution.output_file("."),
-        generated_mask=execution.output_file(params.get("output_mask")),
+        generated_mask=execution.output_file(params.get("output_mask", None)),
     )
     return ret
 
 
 def mri_stopmask_execute(
     params: MriStopmaskParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriStopmaskOutputs:
     """
-    This program creates a mask used to stop the search for the maximum gradient in
-    mris_place_surface, preventing the surface from wandering into areas it should
-    not.
+    mri_stopmask
+    
+    This program creates a mask used to stop the search for the maximum gradient
+    in mris_place_surface, preventing the surface from wandering into areas it
+    should not.
     
     Author: FreeSurfer Developers
     
@@ -222,10 +207,12 @@ def mri_stopmask_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriStopmaskOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_STOPMASK_METADATA)
     params = execution.params(params)
     cargs = mri_stopmask_cargs(params, execution)
     ret = mri_stopmask_outputs(params, execution)
@@ -249,9 +236,11 @@ def mri_stopmask(
     runner: Runner | None = None,
 ) -> MriStopmaskOutputs:
     """
-    This program creates a mask used to stop the search for the maximum gradient in
-    mris_place_surface, preventing the surface from wandering into areas it should
-    not.
+    mri_stopmask
+    
+    This program creates a mask used to stop the search for the maximum gradient
+    in mris_place_surface, preventing the surface from wandering into areas it
+    should not.
     
     Author: FreeSurfer Developers
     
@@ -278,8 +267,6 @@ def mri_stopmask(
     Returns:
         NamedTuple of outputs (described in `MriStopmaskOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_STOPMASK_METADATA)
     params = mri_stopmask_params(
         output_mask=output_mask,
         filled=filled,
@@ -294,13 +281,13 @@ def mri_stopmask(
         no_wm=no_wm,
         no_bfs=no_bfs,
     )
-    return mri_stopmask_execute(params, execution)
+    return mri_stopmask_execute(params, runner)
 
 
 __all__ = [
     "MRI_STOPMASK_METADATA",
     "MriStopmaskOutputs",
-    "MriStopmaskParameters",
     "mri_stopmask",
+    "mri_stopmask_execute",
     "mri_stopmask_params",
 ]