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

niwrap_freesurfer/freesurfer/mri_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_DIFF_METADATA = Metadata(
-    id="5fa5d903b07503901e91b56443e403edfb88973b.boutiques",
+    id="04d8f2770358c1c25968bbc9ef6b94a393fa2346.boutiques",
     name="mri_diff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,41 @@ MRI_DIFF_METADATA = Metadata(
 
 
 MriDiffParameters = typing.TypedDict('MriDiffParameters', {
-    "__STYXTYPE__": typing.Literal["mri_diff"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_diff"]],
+    "vol1file": InputPathType,
+    "vol2file": InputPathType,
+    "resolution_check": bool,
+    "acquisition_param_check": bool,
+    "geometry_check": bool,
+    "precision_check": bool,
+    "pixel_check": bool,
+    "orientation_check": bool,
+    "file_type_diff_check": bool,
+    "no_exit_on_diff": bool,
+    "quality_assurance": bool,
+    "pixel_only": bool,
+    "abs_difference": bool,
+    "no_abs_difference": bool,
+    "difference_abs": bool,
+    "percentage_difference": bool,
+    "rss_save": bool,
+    "ssd_print": bool,
+    "rms_print": bool,
+    "count_diff_voxels": bool,
+    "pixel_threshold": typing.NotRequired[float | None],
+    "count_thresh_voxels": typing.NotRequired[float | None],
+    "log_file": typing.NotRequired[str | None],
+    "difference_image": typing.NotRequired[InputPathType | None],
+    "suspicious_diff_volume": typing.NotRequired[InputPathType | None],
+    "segmentation_diff": typing.NotRequired[str | None],
+    "merge_edits": typing.NotRequired[str | None],
+    "average_difference": typing.NotRequired[str | None],
+    "debug_mode": bool,
+    "verbose_mode": bool,
+    "check_options": bool,
+})
+MriDiffParametersTagged = typing.TypedDict('MriDiffParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_diff"],
     "vol1file": InputPathType,
     "vol2file": InputPathType,
     "resolution_check": bool,
@@ -47,43 +81,11 @@ MriDiffParameters = typing.TypedDict('MriDiffParameters', {
     "verbose_mode": bool,
     "check_options": 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_diff": mri_diff_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_diff": mri_diff_outputs,
-    }.get(t)
 
 
 class MriDiffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_diff(...)`.
+    Output object returned when calling `MriDiffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -127,7 +129,7 @@ def mri_diff_params(
     debug_mode: bool = False,
     verbose_mode: bool = False,
     check_options: bool = False,
-) -> MriDiffParameters:
+) -> MriDiffParametersTagged:
     """
     Build parameters.
     
@@ -174,7 +176,7 @@ def mri_diff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_diff",
+        "@type": "freesurfer/mri_diff",
         "vol1file": vol1file,
         "vol2file": vol2file,
         "resolution_check": resolution_check,
@@ -233,89 +235,89 @@ def mri_diff_cargs(
     """
     cargs = []
     cargs.append("mri_diff")
-    cargs.append(execution.input_file(params.get("vol1file")))
-    cargs.append(execution.input_file(params.get("vol2file")))
-    if params.get("resolution_check"):
+    cargs.append(execution.input_file(params.get("vol1file", None)))
+    cargs.append(execution.input_file(params.get("vol2file", None)))
+    if params.get("resolution_check", False):
         cargs.append("--notallow-res")
-    if params.get("acquisition_param_check"):
+    if params.get("acquisition_param_check", False):
         cargs.append("--notallow-acq")
-    if params.get("geometry_check"):
+    if params.get("geometry_check", False):
         cargs.append("--notallow-geo")
-    if params.get("precision_check"):
+    if params.get("precision_check", False):
         cargs.append("--notallow-prec")
-    if params.get("pixel_check"):
+    if params.get("pixel_check", False):
         cargs.append("--notallow-pix")
-    if params.get("orientation_check"):
+    if params.get("orientation_check", False):
         cargs.append("--notallow-ori")
-    if params.get("file_type_diff_check"):
+    if params.get("file_type_diff_check", False):
         cargs.append("--notallow-type")
-    if params.get("no_exit_on_diff"):
+    if params.get("no_exit_on_diff", False):
         cargs.append("--no-exit-on-diff")
-    if params.get("quality_assurance"):
+    if params.get("quality_assurance", False):
         cargs.append("--qa")
-    if params.get("pixel_only"):
+    if params.get("pixel_only", False):
         cargs.append("--pix-only")
-    if params.get("abs_difference"):
+    if params.get("abs_difference", False):
         cargs.append("--absdiff")
-    if params.get("no_abs_difference"):
+    if params.get("no_abs_difference", False):
         cargs.append("--no-absdiff")
-    if params.get("difference_abs"):
+    if params.get("difference_abs", False):
         cargs.append("--diffabs")
-    if params.get("percentage_difference"):
+    if params.get("percentage_difference", False):
         cargs.append("--diffpct")
-    if params.get("rss_save"):
+    if params.get("rss_save", False):
         cargs.append("--rss")
-    if params.get("ssd_print"):
+    if params.get("ssd_print", False):
         cargs.append("--ssd")
-    if params.get("rms_print"):
+    if params.get("rms_print", False):
         cargs.append("--rms")
-    if params.get("count_diff_voxels"):
+    if params.get("count_diff_voxels", False):
         cargs.append("--count")
-    if params.get("pixel_threshold") is not None:
+    if params.get("pixel_threshold", None) is not None:
         cargs.extend([
             "--thresh",
-            str(params.get("pixel_threshold"))
+            str(params.get("pixel_threshold", None))
         ])
-    if params.get("count_thresh_voxels") is not None:
+    if params.get("count_thresh_voxels", None) is not None:
         cargs.extend([
             "--count-thresh",
-            str(params.get("count_thresh_voxels"))
+            str(params.get("count_thresh_voxels", None))
         ])
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "--log",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("difference_image") is not None:
+    if params.get("difference_image", None) is not None:
         cargs.extend([
             "--diff",
-            execution.input_file(params.get("difference_image"))
+            execution.input_file(params.get("difference_image", None))
         ])
-    if params.get("suspicious_diff_volume") is not None:
+    if params.get("suspicious_diff_volume", None) is not None:
         cargs.extend([
             "--diff_label_suspicious",
-            execution.input_file(params.get("suspicious_diff_volume"))
+            execution.input_file(params.get("suspicious_diff_volume", None))
         ])
-    if params.get("segmentation_diff") is not None:
+    if params.get("segmentation_diff", None) is not None:
         cargs.extend([
             "--segdiff",
-            params.get("segmentation_diff")
+            params.get("segmentation_diff", None)
         ])
-    if params.get("merge_edits") is not None:
+    if params.get("merge_edits", None) is not None:
         cargs.extend([
             "--merge-edits",
-            params.get("merge_edits")
+            params.get("merge_edits", None)
         ])
-    if params.get("average_difference") is not None:
+    if params.get("average_difference", None) is not None:
         cargs.extend([
             "--avg-diff",
-            params.get("average_difference")
+            params.get("average_difference", None)
         ])
-    if params.get("debug_mode"):
+    if params.get("debug_mode", False):
         cargs.append("--debug")
-    if params.get("verbose_mode"):
+    if params.get("verbose_mode", False):
         cargs.append("--verbose")
-    if params.get("check_options"):
+    if params.get("check_options", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -335,18 +337,20 @@ def mri_diff_outputs(
     """
     ret = MriDiffOutputs(
         root=execution.output_file("."),
-        log_output=execution.output_file(params.get("log_file")) if (params.get("log_file") is not None) else None,
-        difference_image_output=execution.output_file(pathlib.Path(params.get("difference_image")).name) if (params.get("difference_image") is not None) else None,
-        suspicious_difference_output=execution.output_file(pathlib.Path(params.get("suspicious_diff_volume")).name) if (params.get("suspicious_diff_volume") is not None) else None,
+        log_output=execution.output_file(params.get("log_file", None)) if (params.get("log_file") is not None) else None,
+        difference_image_output=execution.output_file(pathlib.Path(params.get("difference_image", None)).name) if (params.get("difference_image") is not None) else None,
+        suspicious_difference_output=execution.output_file(pathlib.Path(params.get("suspicious_diff_volume", None)).name) if (params.get("suspicious_diff_volume") is not None) else None,
     )
     return ret
 
 
 def mri_diff_execute(
     params: MriDiffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriDiffOutputs:
     """
+    mri_diff
+    
     Determines whether two volumes differ based on dimensions, resolutions,
     acquisition parameters, geometry, precision, and pixel data.
     
@@ -356,10 +360,12 @@ def mri_diff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriDiffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_DIFF_METADATA)
     params = execution.params(params)
     cargs = mri_diff_cargs(params, execution)
     ret = mri_diff_outputs(params, execution)
@@ -402,6 +408,8 @@ def mri_diff(
     runner: Runner | None = None,
 ) -> MriDiffOutputs:
     """
+    mri_diff
+    
     Determines whether two volumes differ based on dimensions, resolutions,
     acquisition parameters, geometry, precision, and pixel data.
     
@@ -452,8 +460,6 @@ def mri_diff(
     Returns:
         NamedTuple of outputs (described in `MriDiffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_DIFF_METADATA)
     params = mri_diff_params(
         vol1file=vol1file,
         vol2file=vol2file,
@@ -487,13 +493,13 @@ def mri_diff(
         verbose_mode=verbose_mode,
         check_options=check_options,
     )
-    return mri_diff_execute(params, execution)
+    return mri_diff_execute(params, runner)
 
 
 __all__ = [
     "MRI_DIFF_METADATA",
     "MriDiffOutputs",
-    "MriDiffParameters",
     "mri_diff",
+    "mri_diff_execute",
     "mri_diff_params",
 ]

niwrap_freesurfer/freesurfer/mri_dist_surf_label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_DIST_SURF_LABEL_METADATA = Metadata(
-    id="72b4cdbb35a27d1559099cff0310255f2417fec4.boutiques",
+    id="b8f1d994fbc14161f2a911f59853d731de46cac1.boutiques",
     name="mri_dist_surf_label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_DIST_SURF_LABEL_METADATA = Metadata(
 
 
 MriDistSurfLabelParameters = typing.TypedDict('MriDistSurfLabelParameters', {
-    "__STYXTYPE__": typing.Literal["mri_dist_surf_label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_dist_surf_label"]],
+    "surface": InputPathType,
+    "label_file": InputPathType,
+    "output": str,
+})
+MriDistSurfLabelParametersTagged = typing.TypedDict('MriDistSurfLabelParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_dist_surf_label"],
     "surface": InputPathType,
     "label_file": InputPathType,
     "output": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_dist_surf_label": mri_dist_surf_label_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_dist_surf_label": mri_dist_surf_label_outputs,
-    }.get(t)
 
 
 class MriDistSurfLabelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_dist_surf_label(...)`.
+    Output object returned when calling `MriDistSurfLabelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_dist_surf_label_params(
     surface: InputPathType,
     label_file: InputPathType,
     output: str,
-) -> MriDistSurfLabelParameters:
+) -> MriDistSurfLabelParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mri_dist_surf_label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_dist_surf_label",
+        "@type": "freesurfer/mri_dist_surf_label",
         "surface": surface,
         "label_file": label_file,
         "output": output,
@@ -102,9 +76,9 @@ def mri_dist_surf_label_cargs(
     """
     cargs = []
     cargs.append("mri_dist_surf_label")
-    cargs.append(execution.input_file(params.get("surface")))
-    cargs.append(execution.input_file(params.get("label_file")))
-    cargs.append(params.get("output"))
+    cargs.append(execution.input_file(params.get("surface", None)))
+    cargs.append(execution.input_file(params.get("label_file", None)))
+    cargs.append(params.get("output", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def mri_dist_surf_label_outputs(
     """
     ret = MriDistSurfLabelOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("output")),
+        output=execution.output_file(params.get("output", None)),
     )
     return ret
 
 
 def mri_dist_surf_label_execute(
     params: MriDistSurfLabelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriDistSurfLabelOutputs:
     """
+    mri_dist_surf_label
+    
     Computes distances from input surface to label points or waypoints.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def mri_dist_surf_label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriDistSurfLabelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_DIST_SURF_LABEL_METADATA)
     params = execution.params(params)
     cargs = mri_dist_surf_label_cargs(params, execution)
     ret = mri_dist_surf_label_outputs(params, execution)
@@ -159,6 +137,8 @@ def mri_dist_surf_label(
     runner: Runner | None = None,
 ) -> MriDistSurfLabelOutputs:
     """
+    mri_dist_surf_label
+    
     Computes distances from input surface to label points or waypoints.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def mri_dist_surf_label(
     Returns:
         NamedTuple of outputs (described in `MriDistSurfLabelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_DIST_SURF_LABEL_METADATA)
     params = mri_dist_surf_label_params(
         surface=surface,
         label_file=label_file,
         output=output,
     )
-    return mri_dist_surf_label_execute(params, execution)
+    return mri_dist_surf_label_execute(params, runner)
 
 
 __all__ = [
     "MRI_DIST_SURF_LABEL_METADATA",
     "MriDistSurfLabelOutputs",
-    "MriDistSurfLabelParameters",
     "mri_dist_surf_label",
+    "mri_dist_surf_label_execute",
     "mri_dist_surf_label_params",
 ]

niwrap_freesurfer/freesurfer/mri_distance_transform.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_DISTANCE_TRANSFORM_METADATA = Metadata(
-    id="e70d33e3cab2523df541297c46b2cf585160584b.boutiques",
+    id="2b944b61d2ef9fdb67d3c850d1a11b2da816c066.boutiques",
     name="mri_distance_transform",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRI_DISTANCE_TRANSFORM_METADATA = Metadata(
 
 
 MriDistanceTransformParameters = typing.TypedDict('MriDistanceTransformParameters', {
-    "__STYXTYPE__": typing.Literal["mri_distance_transform"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_distance_transform"]],
+    "input_volume": InputPathType,
+    "label": int,
+    "max_distance": int,
+    "mode": typing.NotRequired[int | None],
+    "output_volume": str,
+})
+MriDistanceTransformParametersTagged = typing.TypedDict('MriDistanceTransformParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_distance_transform"],
     "input_volume": InputPathType,
     "label": int,
     "max_distance": int,
     "mode": typing.NotRequired[int | None],
     "output_volume": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_distance_transform": mri_distance_transform_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_distance_transform": mri_distance_transform_outputs,
-    }.get(t)
 
 
 class MriDistanceTransformOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_distance_transform(...)`.
+    Output object returned when calling `MriDistanceTransformParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,8 +46,8 @@ def mri_distance_transform_params(
     label: int,
     max_distance: int,
     output_volume: str,
-    mode: int | None = 1,
-) -> MriDistanceTransformParameters:
+    mode: int | None = None,
+) -> MriDistanceTransformParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +62,7 @@ def mri_distance_transform_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_distance_transform",
+        "@type": "freesurfer/mri_distance_transform",
         "input_volume": input_volume,
         "label": label,
         "max_distance": max_distance,
@@ -112,12 +88,12 @@ def mri_distance_transform_cargs(
     """
     cargs = []
     cargs.append("mri_distance_transform")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(str(params.get("label")))
-    cargs.append(str(params.get("max_distance")))
-    if params.get("mode") is not None:
-        cargs.append(str(params.get("mode")))
-    cargs.append(params.get("output_volume"))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(str(params.get("label", None)))
+    cargs.append(str(params.get("max_distance", None)))
+    if params.get("mode", None) is not None:
+        cargs.append(str(params.get("mode", None)))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -136,16 +112,18 @@ def mri_distance_transform_outputs(
     """
     ret = MriDistanceTransformOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_volume")),
+        output_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_distance_transform_execute(
     params: MriDistanceTransformParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriDistanceTransformOutputs:
     """
+    mri_distance_transform
+    
     Tool to compute distance transforms on MRI volumes.
     
     Author: FreeSurfer Developers
@@ -154,10 +132,12 @@ def mri_distance_transform_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriDistanceTransformOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_DISTANCE_TRANSFORM_METADATA)
     params = execution.params(params)
     cargs = mri_distance_transform_cargs(params, execution)
     ret = mri_distance_transform_outputs(params, execution)
@@ -170,10 +150,12 @@ def mri_distance_transform(
     label: int,
     max_distance: int,
     output_volume: str,
-    mode: int | None = 1,
+    mode: int | None = None,
     runner: Runner | None = None,
 ) -> MriDistanceTransformOutputs:
     """
+    mri_distance_transform
+    
     Tool to compute distance transforms on MRI volumes.
     
     Author: FreeSurfer Developers
@@ -191,8 +173,6 @@ def mri_distance_transform(
     Returns:
         NamedTuple of outputs (described in `MriDistanceTransformOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_DISTANCE_TRANSFORM_METADATA)
     params = mri_distance_transform_params(
         input_volume=input_volume,
         label=label,
@@ -200,13 +180,13 @@ def mri_distance_transform(
         mode=mode,
         output_volume=output_volume,
     )
-    return mri_distance_transform_execute(params, execution)
+    return mri_distance_transform_execute(params, runner)
 
 
 __all__ = [
     "MRI_DISTANCE_TRANSFORM_METADATA",
     "MriDistanceTransformOutputs",
-    "MriDistanceTransformParameters",
     "mri_distance_transform",
+    "mri_distance_transform_execute",
     "mri_distance_transform_params",
 ]