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

niwrap_freesurfer/freesurfer/dmri_pathstats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_PATHSTATS_METADATA = Metadata(
-    id="cb81526efe537cf7caf98d78502615f10aa882e1.boutiques",
+    id="0ba9a6e5794aa140c5435b0e83e325e12bfdcdf8.boutiques",
     name="dmri_pathstats",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,29 @@ DMRI_PATHSTATS_METADATA = Metadata(
 
 
 DmriPathstatsParameters = typing.TypedDict('DmriPathstatsParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_pathstats"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_pathstats"]],
+    "intrk": InputPathType,
+    "rois": typing.NotRequired[list[InputPathType] | None],
+    "intrc": InputPathType,
+    "meas": typing.NotRequired[list[InputPathType] | None],
+    "measname": typing.NotRequired[list[str] | None],
+    "dtbase": typing.NotRequired[str | None],
+    "path": typing.NotRequired[str | None],
+    "subj": typing.NotRequired[str | None],
+    "out": typing.NotRequired[str | None],
+    "outvox": typing.NotRequired[str | None],
+    "median": typing.NotRequired[InputPathType | None],
+    "ends": typing.NotRequired[str | None],
+    "ref": typing.NotRequired[InputPathType | None],
+    "pthr": typing.NotRequired[float | None],
+    "fthr": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": bool,
+    "help": bool,
+    "version": bool,
+})
+DmriPathstatsParametersTagged = typing.TypedDict('DmriPathstatsParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_pathstats"],
     "intrk": InputPathType,
     "rois": typing.NotRequired[list[InputPathType] | None],
     "intrc": InputPathType,
@@ -35,43 +57,11 @@ DmriPathstatsParameters = typing.TypedDict('DmriPathstatsParameters', {
     "help": 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 {
-        "dmri_pathstats": dmri_pathstats_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 {
-        "dmri_pathstats": dmri_pathstats_outputs,
-    }.get(t)
 
 
 class DmriPathstatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_pathstats(...)`.
+    Output object returned when calling `DmriPathstatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +93,7 @@ def dmri_pathstats_params(
     checkopts: bool = False,
     help_: bool = False,
     version: bool = False,
-) -> DmriPathstatsParameters:
+) -> DmriPathstatsParametersTagged:
     """
     Build parameters.
     
@@ -133,7 +123,7 @@ def dmri_pathstats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_pathstats",
+        "@type": "freesurfer/dmri_pathstats",
         "intrk": intrk,
         "intrc": intrc,
         "debug": debug,
@@ -187,84 +177,84 @@ def dmri_pathstats_cargs(
     cargs.append("dmri_pathstats")
     cargs.extend([
         "--intrk",
-        execution.input_file(params.get("intrk"))
+        execution.input_file(params.get("intrk", None))
     ])
-    if params.get("rois") is not None:
+    if params.get("rois", None) is not None:
         cargs.extend([
             "--rois",
-            *[execution.input_file(f) for f in params.get("rois")]
+            *[execution.input_file(f) for f in params.get("rois", None)]
         ])
     cargs.extend([
         "--intrc",
-        execution.input_file(params.get("intrc"))
+        execution.input_file(params.get("intrc", None))
     ])
-    if params.get("meas") is not None:
+    if params.get("meas", None) is not None:
         cargs.extend([
             "--meas",
-            *[execution.input_file(f) for f in params.get("meas")]
+            *[execution.input_file(f) for f in params.get("meas", None)]
         ])
-    if params.get("measname") is not None:
+    if params.get("measname", None) is not None:
         cargs.extend([
             "--measname",
-            *params.get("measname")
+            *params.get("measname", None)
         ])
-    if params.get("dtbase") is not None:
+    if params.get("dtbase", None) is not None:
         cargs.extend([
             "--dtbase",
-            params.get("dtbase")
+            params.get("dtbase", None)
         ])
-    if params.get("path") is not None:
+    if params.get("path", None) is not None:
         cargs.extend([
             "--path",
-            params.get("path")
+            params.get("path", None)
         ])
-    if params.get("subj") is not None:
+    if params.get("subj", None) is not None:
         cargs.extend([
             "--subj",
-            params.get("subj")
+            params.get("subj", None)
         ])
-    if params.get("out") is not None:
+    if params.get("out", None) is not None:
         cargs.extend([
             "--out",
-            params.get("out")
+            params.get("out", 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("median") is not None:
+    if params.get("median", None) is not None:
         cargs.extend([
             "--median",
-            execution.input_file(params.get("median"))
+            execution.input_file(params.get("median", None))
         ])
-    if params.get("ends") is not None:
+    if params.get("ends", None) is not None:
         cargs.extend([
             "--ends",
-            params.get("ends")
+            params.get("ends", None)
         ])
-    if params.get("ref") is not None:
+    if params.get("ref", None) is not None:
         cargs.extend([
             "--ref",
-            execution.input_file(params.get("ref"))
+            execution.input_file(params.get("ref", None))
         ])
-    if params.get("pthr") is not None:
+    if params.get("pthr", None) is not None:
         cargs.extend([
             "--pthr",
-            str(params.get("pthr"))
+            str(params.get("pthr", None))
         ])
-    if params.get("fthr") is not None:
+    if params.get("fthr", None) is not None:
         cargs.extend([
             "--fthr",
-            str(params.get("fthr"))
+            str(params.get("fthr", None))
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -284,18 +274,20 @@ def dmri_pathstats_outputs(
     """
     ret = DmriPathstatsOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("out")) if (params.get("out") is not None) else None,
-        out_vox_file=execution.output_file(params.get("outvox")) if (params.get("outvox") is not None) else None,
-        median_file=execution.output_file(pathlib.Path(params.get("median")).name) if (params.get("median") is not None) else None,
+        out_file=execution.output_file(params.get("out", None)) if (params.get("out") is not None) else None,
+        out_vox_file=execution.output_file(params.get("outvox", None)) if (params.get("outvox") is not None) else None,
+        median_file=execution.output_file(pathlib.Path(params.get("median", None)).name) if (params.get("median") is not None) else None,
     )
     return ret
 
 
 def dmri_pathstats_execute(
     params: DmriPathstatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriPathstatsOutputs:
     """
+    dmri_pathstats
+    
     Compute path statistics for diffusion MRI data based on input .trk file and
     optional various measures.
     
@@ -305,10 +297,12 @@ def dmri_pathstats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriPathstatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_PATHSTATS_METADATA)
     params = execution.params(params)
     cargs = dmri_pathstats_cargs(params, execution)
     ret = dmri_pathstats_outputs(params, execution)
@@ -339,6 +333,8 @@ def dmri_pathstats(
     runner: Runner | None = None,
 ) -> DmriPathstatsOutputs:
     """
+    dmri_pathstats
+    
     Compute path statistics for diffusion MRI data based on input .trk file and
     optional various measures.
     
@@ -372,8 +368,6 @@ def dmri_pathstats(
     Returns:
         NamedTuple of outputs (described in `DmriPathstatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_PATHSTATS_METADATA)
     params = dmri_pathstats_params(
         intrk=intrk,
         rois=rois,
@@ -395,13 +389,13 @@ def dmri_pathstats(
         help_=help_,
         version=version,
     )
-    return dmri_pathstats_execute(params, execution)
+    return dmri_pathstats_execute(params, runner)
 
 
 __all__ = [
     "DMRI_PATHSTATS_METADATA",
     "DmriPathstatsOutputs",
-    "DmriPathstatsParameters",
     "dmri_pathstats",
+    "dmri_pathstats_execute",
     "dmri_pathstats_params",
 ]

niwrap_freesurfer/freesurfer/dmri_project_end_points.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_PROJECT_END_POINTS_METADATA = Metadata(
-    id="6838065064c721570c8651a29b3d26a7eb70f5f9.boutiques",
+    id="61111b40c648f169944bf98b5918d4561840f813.boutiques",
     name="dmri_projectEndPoints",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ DMRI_PROJECT_END_POINTS_METADATA = Metadata(
 
 
 DmriProjectEndPointsParameters = typing.TypedDict('DmriProjectEndPointsParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_projectEndPoints"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_projectEndPoints"]],
+    "streamline_file": InputPathType,
+    "left_surface_file": InputPathType,
+    "right_surface_file": InputPathType,
+    "left_overlay_file": str,
+    "right_overlay_file": str,
+    "reference_image": InputPathType,
+})
+DmriProjectEndPointsParametersTagged = typing.TypedDict('DmriProjectEndPointsParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_projectEndPoints"],
     "streamline_file": InputPathType,
     "left_surface_file": InputPathType,
     "right_surface_file": InputPathType,
@@ -22,43 +31,11 @@ DmriProjectEndPointsParameters = typing.TypedDict('DmriProjectEndPointsParameter
     "right_overlay_file": str,
     "reference_image": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "dmri_projectEndPoints": dmri_project_end_points_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 {
-        "dmri_projectEndPoints": dmri_project_end_points_outputs,
-    }.get(t)
 
 
 class DmriProjectEndPointsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_project_end_points(...)`.
+    Output object returned when calling `DmriProjectEndPointsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def dmri_project_end_points_params(
     left_overlay_file: str,
     right_overlay_file: str,
     reference_image: InputPathType,
-) -> DmriProjectEndPointsParameters:
+) -> DmriProjectEndPointsParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +69,7 @@ def dmri_project_end_points_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_projectEndPoints",
+        "@type": "freesurfer/dmri_projectEndPoints",
         "streamline_file": streamline_file,
         "left_surface_file": left_surface_file,
         "right_surface_file": right_surface_file,
@@ -120,27 +97,27 @@ def dmri_project_end_points_cargs(
     cargs.append("dmri_projectEndPoints")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("streamline_file"))
+        execution.input_file(params.get("streamline_file", None))
     ])
     cargs.extend([
         "-sl",
-        execution.input_file(params.get("left_surface_file"))
+        execution.input_file(params.get("left_surface_file", None))
     ])
     cargs.extend([
         "-sr",
-        execution.input_file(params.get("right_surface_file"))
+        execution.input_file(params.get("right_surface_file", None))
     ])
     cargs.extend([
         "-ol",
-        params.get("left_overlay_file")
+        params.get("left_overlay_file", None)
     ])
     cargs.extend([
         "-or",
-        params.get("right_overlay_file")
+        params.get("right_overlay_file", None)
     ])
     cargs.extend([
         "-ri",
-        execution.input_file(params.get("reference_image"))
+        execution.input_file(params.get("reference_image", None))
     ])
     return cargs
 
@@ -160,17 +137,19 @@ def dmri_project_end_points_outputs(
     """
     ret = DmriProjectEndPointsOutputs(
         root=execution.output_file("."),
-        out_left_overlay=execution.output_file(params.get("left_overlay_file")),
-        out_right_overlay=execution.output_file(params.get("right_overlay_file")),
+        out_left_overlay=execution.output_file(params.get("left_overlay_file", None)),
+        out_right_overlay=execution.output_file(params.get("right_overlay_file", None)),
     )
     return ret
 
 
 def dmri_project_end_points_execute(
     params: DmriProjectEndPointsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriProjectEndPointsOutputs:
     """
+    dmri_projectEndPoints
+    
     A tool for projecting the endpoints of streamlines onto cortical surfaces,
     producing overlay files for visualization.
     
@@ -180,10 +159,12 @@ def dmri_project_end_points_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriProjectEndPointsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_PROJECT_END_POINTS_METADATA)
     params = execution.params(params)
     cargs = dmri_project_end_points_cargs(params, execution)
     ret = dmri_project_end_points_outputs(params, execution)
@@ -201,6 +182,8 @@ def dmri_project_end_points(
     runner: Runner | None = None,
 ) -> DmriProjectEndPointsOutputs:
     """
+    dmri_projectEndPoints
+    
     A tool for projecting the endpoints of streamlines onto cortical surfaces,
     producing overlay files for visualization.
     
@@ -221,8 +204,6 @@ def dmri_project_end_points(
     Returns:
         NamedTuple of outputs (described in `DmriProjectEndPointsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_PROJECT_END_POINTS_METADATA)
     params = dmri_project_end_points_params(
         streamline_file=streamline_file,
         left_surface_file=left_surface_file,
@@ -231,13 +212,13 @@ def dmri_project_end_points(
         right_overlay_file=right_overlay_file,
         reference_image=reference_image,
     )
-    return dmri_project_end_points_execute(params, execution)
+    return dmri_project_end_points_execute(params, runner)
 
 
 __all__ = [
     "DMRI_PROJECT_END_POINTS_METADATA",
     "DmriProjectEndPointsOutputs",
-    "DmriProjectEndPointsParameters",
     "dmri_project_end_points",
+    "dmri_project_end_points_execute",
     "dmri_project_end_points_params",
 ]

niwrap_freesurfer/freesurfer/dmri_save_histograms.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 DMRI_SAVE_HISTOGRAMS_METADATA = Metadata(
-    id="bb194c65a1426660b384fcbf85e8e5301e4425c1.boutiques",
+    id="9c13eb2eb3b781b53fc909106a2b27e609b6ea8f.boutiques",
     name="dmri_saveHistograms",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ DMRI_SAVE_HISTOGRAMS_METADATA = Metadata(
 
 
 DmriSaveHistogramsParameters = typing.TypedDict('DmriSaveHistogramsParameters', {
-    "__STYXTYPE__": typing.Literal["dmri_saveHistograms"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/dmri_saveHistograms"]],
+    "parcellation": InputPathType,
+    "number_of_bundles": float,
+    "vtk_bundle_list": list[InputPathType],
+    "output_csv": str,
+    "brain_bundle_flag": bool,
+})
+DmriSaveHistogramsParametersTagged = typing.TypedDict('DmriSaveHistogramsParametersTagged', {
+    "@type": typing.Literal["freesurfer/dmri_saveHistograms"],
     "parcellation": InputPathType,
     "number_of_bundles": float,
     "vtk_bundle_list": list[InputPathType],
     "output_csv": str,
     "brain_bundle_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 {
-        "dmri_saveHistograms": dmri_save_histograms_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 {
-        "dmri_saveHistograms": dmri_save_histograms_outputs,
-    }.get(t)
 
 
 class DmriSaveHistogramsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `dmri_save_histograms(...)`.
+    Output object returned when calling `DmriSaveHistogramsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def dmri_save_histograms_params(
     vtk_bundle_list: list[InputPathType],
     output_csv: str,
     brain_bundle_flag: bool = False,
-) -> DmriSaveHistogramsParameters:
+) -> DmriSaveHistogramsParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def dmri_save_histograms_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "dmri_saveHistograms",
+        "@type": "freesurfer/dmri_saveHistograms",
         "parcellation": parcellation,
         "number_of_bundles": number_of_bundles,
         "vtk_bundle_list": vtk_bundle_list,
@@ -112,18 +88,18 @@ def dmri_save_histograms_cargs(
     cargs.append("dmri_saveHistograms")
     cargs.extend([
         "-p",
-        execution.input_file(params.get("parcellation"))
+        execution.input_file(params.get("parcellation", None))
     ])
     cargs.extend([
         "-f",
-        str(params.get("number_of_bundles"))
+        str(params.get("number_of_bundles", None))
     ])
-    cargs.extend([execution.input_file(f) for f in params.get("vtk_bundle_list")])
+    cargs.extend([execution.input_file(f) for f in params.get("vtk_bundle_list", None)])
     cargs.extend([
         "-o",
-        params.get("output_csv")
+        params.get("output_csv", None)
     ])
-    if params.get("brain_bundle_flag"):
+    if params.get("brain_bundle_flag", False):
         cargs.append("-bb")
     return cargs
 
@@ -150,9 +126,11 @@ def dmri_save_histograms_outputs(
 
 def dmri_save_histograms_execute(
     params: DmriSaveHistogramsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> DmriSaveHistogramsOutputs:
     """
+    dmri_saveHistograms
+    
     A tool to save histograms from diffusion MRI tractography data.
     
     Author: FreeSurfer Developers
@@ -161,10 +139,12 @@ def dmri_save_histograms_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `DmriSaveHistogramsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DMRI_SAVE_HISTOGRAMS_METADATA)
     params = execution.params(params)
     cargs = dmri_save_histograms_cargs(params, execution)
     ret = dmri_save_histograms_outputs(params, execution)
@@ -181,6 +161,8 @@ def dmri_save_histograms(
     runner: Runner | None = None,
 ) -> DmriSaveHistogramsOutputs:
     """
+    dmri_saveHistograms
+    
     A tool to save histograms from diffusion MRI tractography data.
     
     Author: FreeSurfer Developers
@@ -197,8 +179,6 @@ def dmri_save_histograms(
     Returns:
         NamedTuple of outputs (described in `DmriSaveHistogramsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(DMRI_SAVE_HISTOGRAMS_METADATA)
     params = dmri_save_histograms_params(
         parcellation=parcellation,
         number_of_bundles=number_of_bundles,
@@ -206,13 +186,13 @@ def dmri_save_histograms(
         output_csv=output_csv,
         brain_bundle_flag=brain_bundle_flag,
     )
-    return dmri_save_histograms_execute(params, execution)
+    return dmri_save_histograms_execute(params, runner)
 
 
 __all__ = [
     "DMRI_SAVE_HISTOGRAMS_METADATA",
     "DmriSaveHistogramsOutputs",
-    "DmriSaveHistogramsParameters",
     "dmri_save_histograms",
+    "dmri_save_histograms_execute",
     "dmri_save_histograms_params",
 ]