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

niwrap_freesurfer/freesurfer/feat2segstats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FEAT2SEGSTATS_METADATA = Metadata(
-    id="8d158acb040bff5a288c837ac949fc84e362a83b.boutiques",
+    id="a6f479bd29c683d988da8503ff21408d0b0077e7.boutiques",
     name="feat2segstats",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,30 @@ FEAT2SEGSTATS_METADATA = Metadata(
 
 
 Feat2segstatsParameters = typing.TypedDict('Feat2segstatsParameters', {
-    "__STYXTYPE__": typing.Literal["feat2segstats"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/feat2segstats"]],
+    "feat_dir": str,
+    "featdirfile": typing.NotRequired[InputPathType | None],
+    "seg_vol": typing.NotRequired[str | None],
+    "aseg_flag": bool,
+    "aparc_aseg_flag": bool,
+    "ctab": typing.NotRequired[InputPathType | None],
+    "all_segs_flag": bool,
+    "copes_flag": bool,
+    "varcopes_flag": bool,
+    "zstats_flag": bool,
+    "pes_flag": bool,
+    "rvar": typing.NotRequired[str | None],
+    "example_func": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[str | None],
+    "mean_func": typing.NotRequired[str | None],
+    "stat": str,
+    "version_flag": bool,
+    "help_flag": bool,
+    "debug_flag": bool,
+    "nolog_flag": bool,
+})
+Feat2segstatsParametersTagged = typing.TypedDict('Feat2segstatsParametersTagged', {
+    "@type": typing.Literal["freesurfer/feat2segstats"],
     "feat_dir": str,
     "featdirfile": typing.NotRequired[InputPathType | None],
     "seg_vol": typing.NotRequired[str | None],
@@ -36,43 +59,11 @@ Feat2segstatsParameters = typing.TypedDict('Feat2segstatsParameters', {
     "debug_flag": bool,
     "nolog_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 {
-        "feat2segstats": feat2segstats_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 {
-        "feat2segstats": feat2segstats_outputs,
-    }.get(t)
 
 
 class Feat2segstatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `feat2segstats(...)`.
+    Output object returned when calling `Feat2segstatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +92,7 @@ def feat2segstats_params(
     help_flag: bool = False,
     debug_flag: bool = False,
     nolog_flag: bool = False,
-) -> Feat2segstatsParameters:
+) -> Feat2segstatsParametersTagged:
     """
     Build parameters.
     
@@ -131,7 +122,7 @@ def feat2segstats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "feat2segstats",
+        "@type": "freesurfer/feat2segstats",
         "feat_dir": feat_dir,
         "aseg_flag": aseg_flag,
         "aparc_aseg_flag": aparc_aseg_flag,
@@ -180,68 +171,68 @@ def feat2segstats_cargs(
     cargs.append("feat2segstats")
     cargs.extend([
         "--feat",
-        params.get("feat_dir")
+        params.get("feat_dir", None)
     ])
-    if params.get("featdirfile") is not None:
+    if params.get("featdirfile", None) is not None:
         cargs.extend([
             "--featdirfile",
-            execution.input_file(params.get("featdirfile"))
+            execution.input_file(params.get("featdirfile", None))
         ])
-    if params.get("seg_vol") is not None:
+    if params.get("seg_vol", None) is not None:
         cargs.extend([
             "--seg",
-            params.get("seg_vol")
+            params.get("seg_vol", None)
         ])
-    if params.get("aseg_flag"):
+    if params.get("aseg_flag", False):
         cargs.append("--aseg")
-    if params.get("aparc_aseg_flag"):
+    if params.get("aparc_aseg_flag", False):
         cargs.append("--aparc+aseg")
-    if params.get("ctab") is not None:
+    if params.get("ctab", None) is not None:
         cargs.extend([
             "--ctab",
-            execution.input_file(params.get("ctab"))
+            execution.input_file(params.get("ctab", None))
         ])
-    if params.get("all_segs_flag"):
+    if params.get("all_segs_flag", False):
         cargs.append("--all-segs")
-    if params.get("copes_flag"):
+    if params.get("copes_flag", False):
         cargs.append("--copes")
-    if params.get("varcopes_flag"):
+    if params.get("varcopes_flag", False):
         cargs.append("--varcopes")
-    if params.get("zstats_flag"):
+    if params.get("zstats_flag", False):
         cargs.append("--zstats")
-    if params.get("pes_flag"):
+    if params.get("pes_flag", False):
         cargs.append("--pes")
-    if params.get("rvar") is not None:
+    if params.get("rvar", None) is not None:
         cargs.extend([
             "--rvar",
-            params.get("rvar")
+            params.get("rvar", None)
         ])
-    if params.get("example_func") is not None:
+    if params.get("example_func", None) is not None:
         cargs.extend([
             "--exf",
-            params.get("example_func")
+            params.get("example_func", None)
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "--mask",
-            params.get("mask")
+            params.get("mask", None)
         ])
-    if params.get("mean_func") is not None:
+    if params.get("mean_func", None) is not None:
         cargs.extend([
             "--mean_func",
-            params.get("mean_func")
+            params.get("mean_func", None)
         ])
     cargs.extend([
         "--stat",
-        params.get("stat")
+        params.get("stat", None)
     ])
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("--version")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("--help")
-    if params.get("debug_flag"):
+    if params.get("debug_flag", False):
         cargs.append("--debug")
-    if params.get("nolog_flag"):
+    if params.get("nolog_flag", False):
         cargs.append("--nolog")
     return cargs
 
@@ -261,16 +252,18 @@ def feat2segstats_outputs(
     """
     ret = Feat2segstatsOutputs(
         root=execution.output_file("."),
-        segstats_output=execution.output_file(params.get("feat_dir") + "/freesurfer/segstats/" + params.get("seg_vol") + "/" + params.get("stat") + ".dat") if (params.get("seg_vol") is not None) else None,
+        segstats_output=execution.output_file(params.get("feat_dir", None) + "/freesurfer/segstats/" + params.get("seg_vol", None) + "/" + params.get("stat", None) + ".dat") if (params.get("seg_vol") is not None) else None,
     )
     return ret
 
 
 def feat2segstats_execute(
     params: Feat2segstatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Feat2segstatsOutputs:
     """
+    feat2segstats
+    
     Computes segmentation summaries and stores output in
     featdir/freesurfer/segstats/segvol/statname.dat.
     
@@ -280,10 +273,12 @@ def feat2segstats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Feat2segstatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FEAT2SEGSTATS_METADATA)
     params = execution.params(params)
     cargs = feat2segstats_cargs(params, execution)
     ret = feat2segstats_outputs(params, execution)
@@ -315,6 +310,8 @@ def feat2segstats(
     runner: Runner | None = None,
 ) -> Feat2segstatsOutputs:
     """
+    feat2segstats
+    
     Computes segmentation summaries and stores output in
     featdir/freesurfer/segstats/segvol/statname.dat.
     
@@ -348,8 +345,6 @@ def feat2segstats(
     Returns:
         NamedTuple of outputs (described in `Feat2segstatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FEAT2SEGSTATS_METADATA)
     params = feat2segstats_params(
         feat_dir=feat_dir,
         featdirfile=featdirfile,
@@ -372,13 +367,13 @@ def feat2segstats(
         debug_flag=debug_flag,
         nolog_flag=nolog_flag,
     )
-    return feat2segstats_execute(params, execution)
+    return feat2segstats_execute(params, runner)
 
 
 __all__ = [
     "FEAT2SEGSTATS_METADATA",
     "Feat2segstatsOutputs",
-    "Feat2segstatsParameters",
     "feat2segstats",
+    "feat2segstats_execute",
     "feat2segstats_params",
 ]

niwrap_freesurfer/freesurfer/feat2surf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FEAT2SURF_METADATA = Metadata(
-    id="079e8361241b52495efdfd5864147688324111e9.boutiques",
+    id="ea388f80ec52b33d4652831d3f9adda30df03731.boutiques",
     name="feat2surf",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ FEAT2SURF_METADATA = Metadata(
 
 
 Feat2surfParameters = typing.TypedDict('Feat2surfParameters', {
-    "__STYXTYPE__": typing.Literal["feat2surf"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/feat2surf"]],
+    "feat_dirs": list[str],
+    "feat_dirfile": typing.NotRequired[InputPathType | None],
+    "proj_frac": typing.NotRequired[float | None],
+    "hemi": typing.NotRequired[str | None],
+    "target": typing.NotRequired[str | None],
+    "surf": typing.NotRequired[str | None],
+    "cope_only": bool,
+    "debug_flag": bool,
+    "nolog_flag": bool,
+    "out_dir": typing.NotRequired[str | None],
+})
+Feat2surfParametersTagged = typing.TypedDict('Feat2surfParametersTagged', {
+    "@type": typing.Literal["freesurfer/feat2surf"],
     "feat_dirs": list[str],
     "feat_dirfile": typing.NotRequired[InputPathType | None],
     "proj_frac": typing.NotRequired[float | None],
@@ -26,43 +39,11 @@ Feat2surfParameters = typing.TypedDict('Feat2surfParameters', {
     "nolog_flag": bool,
     "out_dir": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "feat2surf": feat2surf_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 {
-        "feat2surf": feat2surf_outputs,
-    }.get(t)
 
 
 class Feat2surfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `feat2surf(...)`.
+    Output object returned when calling `Feat2surfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +68,7 @@ def feat2surf_params(
     debug_flag: bool = False,
     nolog_flag: bool = False,
     out_dir: str | None = None,
-) -> Feat2surfParameters:
+) -> Feat2surfParametersTagged:
     """
     Build parameters.
     
@@ -111,7 +92,7 @@ def feat2surf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "feat2surf",
+        "@type": "freesurfer/feat2surf",
         "feat_dirs": feat_dirs,
         "cope_only": cope_only,
         "debug_flag": debug_flag,
@@ -149,43 +130,43 @@ def feat2surf_cargs(
     cargs.append("feat2surf")
     cargs.extend([
         "--feat",
-        *params.get("feat_dirs")
+        *params.get("feat_dirs", None)
     ])
-    if params.get("feat_dirfile") is not None:
+    if params.get("feat_dirfile", None) is not None:
         cargs.extend([
             "--featdirfile",
-            execution.input_file(params.get("feat_dirfile"))
+            execution.input_file(params.get("feat_dirfile", None))
         ])
-    if params.get("proj_frac") is not None:
+    if params.get("proj_frac", None) is not None:
         cargs.extend([
             "--projfrac",
-            str(params.get("proj_frac"))
+            str(params.get("proj_frac", None))
         ])
-    if params.get("hemi") is not None:
+    if params.get("hemi", None) is not None:
         cargs.extend([
             "--hemi",
-            params.get("hemi")
+            params.get("hemi", None)
         ])
-    if params.get("target") is not None:
+    if params.get("target", None) is not None:
         cargs.extend([
             "--target",
-            params.get("target")
+            params.get("target", None)
         ])
-    if params.get("surf") is not None:
+    if params.get("surf", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf")
+            params.get("surf", None)
         ])
-    if params.get("cope_only"):
+    if params.get("cope_only", False):
         cargs.append("--cope-only")
-    if params.get("debug_flag"):
+    if params.get("debug_flag", False):
         cargs.append("--debug")
-    if params.get("nolog_flag"):
+    if params.get("nolog_flag", False):
         cargs.append("--nolog")
-    if params.get("out_dir") is not None:
+    if params.get("out_dir", None) is not None:
         cargs.extend([
             "--out",
-            params.get("out_dir")
+            params.get("out_dir", None)
         ])
     return cargs
 
@@ -205,19 +186,21 @@ def feat2surf_outputs(
     """
     ret = Feat2surfOutputs(
         root=execution.output_file("."),
-        lh_output=execution.output_file(params.get("out_dir") + "/reg_surf-lh-Subject/stats") if (params.get("out_dir") is not None) else None,
-        rh_output=execution.output_file(params.get("out_dir") + "/reg_surf-rh-Subject/stats") if (params.get("out_dir") is not None) else None,
-        lh_target_output=execution.output_file(params.get("out_dir") + "/reg_surf-lh-targid/stats") if (params.get("out_dir") is not None) else None,
-        rh_target_output=execution.output_file(params.get("out_dir") + "/reg_surf-rh-targid/stats") if (params.get("out_dir") is not None) else None,
+        lh_output=execution.output_file(params.get("out_dir", None) + "/reg_surf-lh-Subject/stats") if (params.get("out_dir") is not None) else None,
+        rh_output=execution.output_file(params.get("out_dir", None) + "/reg_surf-rh-Subject/stats") if (params.get("out_dir") is not None) else None,
+        lh_target_output=execution.output_file(params.get("out_dir", None) + "/reg_surf-lh-targid/stats") if (params.get("out_dir") is not None) else None,
+        rh_target_output=execution.output_file(params.get("out_dir", None) + "/reg_surf-rh-targid/stats") if (params.get("out_dir") is not None) else None,
     )
     return ret
 
 
 def feat2surf_execute(
     params: Feat2surfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Feat2surfOutputs:
     """
+    feat2surf
+    
     Resamples Feat statistics onto the surface of the subject and onto a
     stereo-taxic surface atlas.
     
@@ -227,10 +210,12 @@ def feat2surf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Feat2surfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FEAT2SURF_METADATA)
     params = execution.params(params)
     cargs = feat2surf_cargs(params, execution)
     ret = feat2surf_outputs(params, execution)
@@ -252,6 +237,8 @@ def feat2surf(
     runner: Runner | None = None,
 ) -> Feat2surfOutputs:
     """
+    feat2surf
+    
     Resamples Feat statistics onto the surface of the subject and onto a
     stereo-taxic surface atlas.
     
@@ -279,8 +266,6 @@ def feat2surf(
     Returns:
         NamedTuple of outputs (described in `Feat2surfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FEAT2SURF_METADATA)
     params = feat2surf_params(
         feat_dirs=feat_dirs,
         feat_dirfile=feat_dirfile,
@@ -293,13 +278,13 @@ def feat2surf(
         nolog_flag=nolog_flag,
         out_dir=out_dir,
     )
-    return feat2surf_execute(params, execution)
+    return feat2surf_execute(params, runner)
 
 
 __all__ = [
     "FEAT2SURF_METADATA",
     "Feat2surfOutputs",
-    "Feat2surfParameters",
     "feat2surf",
+    "feat2surf_execute",
     "feat2surf_params",
 ]

niwrap_freesurfer/freesurfer/fiducials_calibration.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIDUCIALS_CALIBRATION_METADATA = Metadata(
-    id="b87cb0a61e77503c416b5bd15c7cec1c1ef97456.boutiques",
+    id="2fbae70c4a6a0306f48287ffefda752f7458bd36.boutiques",
     name="fiducials_calibration",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,53 +14,26 @@ FIDUCIALS_CALIBRATION_METADATA = Metadata(
 
 
 FiducialsCalibrationParameters = typing.TypedDict('FiducialsCalibrationParameters', {
-    "__STYXTYPE__": typing.Literal["fiducials_calibration"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fiducials_calibration"]],
+    "qt_plugin_installation": typing.NotRequired[str | None],
+})
+FiducialsCalibrationParametersTagged = typing.TypedDict('FiducialsCalibrationParametersTagged', {
+    "@type": typing.Literal["freesurfer/fiducials_calibration"],
     "qt_plugin_installation": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fiducials_calibration": fiducials_calibration_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 FiducialsCalibrationOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fiducials_calibration(...)`.
+    Output object returned when calling `FiducialsCalibrationParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
 
 
 def fiducials_calibration_params(
-    qt_plugin_installation: str | None = "Check Qt installation and platform plugin availability",
-) -> FiducialsCalibrationParameters:
+    qt_plugin_installation: str | None = None,
+) -> FiducialsCalibrationParametersTagged:
     """
     Build parameters.
     
@@ -72,7 +45,7 @@ def fiducials_calibration_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fiducials_calibration",
+        "@type": "freesurfer/fiducials_calibration",
     }
     if qt_plugin_installation is not None:
         params["qt_plugin_installation"] = qt_plugin_installation
@@ -94,8 +67,8 @@ def fiducials_calibration_cargs(
     """
     cargs = []
     cargs.append("fiducials_calibration")
-    if params.get("qt_plugin_installation") is not None:
-        cargs.append(params.get("qt_plugin_installation"))
+    if params.get("qt_plugin_installation", None) is not None:
+        cargs.append(params.get("qt_plugin_installation", None))
     return cargs
 
 
@@ -120,9 +93,11 @@ def fiducials_calibration_outputs(
 
 def fiducials_calibration_execute(
     params: FiducialsCalibrationParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FiducialsCalibrationOutputs:
     """
+    fiducials_calibration
+    
     A tool used for calibrating fiducials.
     
     Author: FreeSurfer Developers
@@ -131,10 +106,12 @@ def fiducials_calibration_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FiducialsCalibrationOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIDUCIALS_CALIBRATION_METADATA)
     params = execution.params(params)
     cargs = fiducials_calibration_cargs(params, execution)
     ret = fiducials_calibration_outputs(params, execution)
@@ -143,10 +120,12 @@ def fiducials_calibration_execute(
 
 
 def fiducials_calibration(
-    qt_plugin_installation: str | None = "Check Qt installation and platform plugin availability",
+    qt_plugin_installation: str | None = None,
     runner: Runner | None = None,
 ) -> FiducialsCalibrationOutputs:
     """
+    fiducials_calibration
+    
     A tool used for calibrating fiducials.
     
     Author: FreeSurfer Developers
@@ -161,18 +140,16 @@ def fiducials_calibration(
     Returns:
         NamedTuple of outputs (described in `FiducialsCalibrationOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIDUCIALS_CALIBRATION_METADATA)
     params = fiducials_calibration_params(
         qt_plugin_installation=qt_plugin_installation,
     )
-    return fiducials_calibration_execute(params, execution)
+    return fiducials_calibration_execute(params, runner)
 
 
 __all__ = [
     "FIDUCIALS_CALIBRATION_METADATA",
     "FiducialsCalibrationOutputs",
-    "FiducialsCalibrationParameters",
     "fiducials_calibration",
+    "fiducials_calibration_execute",
     "fiducials_calibration_params",
 ]