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

niwrap_freesurfer/freesurfer/segment_ha_t1_long_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_HA_T1_LONG_SH_METADATA = Metadata(
-    id="4b45b675654faa4685dd58c821b0fe49807c0e5d.boutiques",
+    id="a1f9c93161c055366f2333e5725968d68fd10303.boutiques",
     name="segmentHA_T1_long.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ SEGMENT_HA_T1_LONG_SH_METADATA = Metadata(
 
 
 SegmentHaT1LongShParameters = typing.TypedDict('SegmentHaT1LongShParameters', {
-    "__STYXTYPE__": typing.Literal["segmentHA_T1_long.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segmentHA_T1_long.sh"]],
+    "subject_dir": str,
+    "subject_id": str,
+})
+SegmentHaT1LongShParametersTagged = typing.TypedDict('SegmentHaT1LongShParametersTagged', {
+    "@type": typing.Literal["freesurfer/segmentHA_T1_long.sh"],
     "subject_dir": str,
     "subject_id": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "segmentHA_T1_long.sh": segment_ha_t1_long_sh_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 {
-        "segmentHA_T1_long.sh": segment_ha_t1_long_sh_outputs,
-    }.get(t)
 
 
 class SegmentHaT1LongShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_ha_t1_long_sh(...)`.
+    Output object returned when calling `SegmentHaT1LongShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class SegmentHaT1LongShOutputs(typing.NamedTuple):
 def segment_ha_t1_long_sh_params(
     subject_dir: str,
     subject_id: str,
-) -> SegmentHaT1LongShParameters:
+) -> SegmentHaT1LongShParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def segment_ha_t1_long_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segmentHA_T1_long.sh",
+        "@type": "freesurfer/segmentHA_T1_long.sh",
         "subject_dir": subject_dir,
         "subject_id": subject_id,
     }
@@ -98,8 +71,8 @@ def segment_ha_t1_long_sh_cargs(
     """
     cargs = []
     cargs.append("segmentHA_T1_long.sh")
-    cargs.append(params.get("subject_dir"))
-    cargs.append(params.get("subject_id"))
+    cargs.append(params.get("subject_dir", None))
+    cargs.append(params.get("subject_id", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def segment_ha_t1_long_sh_outputs(
     """
     ret = SegmentHaT1LongShOutputs(
         root=execution.output_file("."),
-        output_dir=execution.output_file(params.get("subject_dir") + "/" + params.get("subject_id") + "_long_segment/output"),
+        output_dir=execution.output_file(params.get("subject_dir", None) + "/" + params.get("subject_id", None) + "_long_segment/output"),
     )
     return ret
 
 
 def segment_ha_t1_long_sh_execute(
     params: SegmentHaT1LongShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentHaT1LongShOutputs:
     """
+    segmentHA_T1_long.sh
+    
     A script for longitudinal segmentation of the hippocampal/amygdala regions.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def segment_ha_t1_long_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentHaT1LongShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_HA_T1_LONG_SH_METADATA)
     params = execution.params(params)
     cargs = segment_ha_t1_long_sh_cargs(params, execution)
     ret = segment_ha_t1_long_sh_outputs(params, execution)
@@ -153,6 +130,8 @@ def segment_ha_t1_long_sh(
     runner: Runner | None = None,
 ) -> SegmentHaT1LongShOutputs:
     """
+    segmentHA_T1_long.sh
+    
     A script for longitudinal segmentation of the hippocampal/amygdala regions.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def segment_ha_t1_long_sh(
     Returns:
         NamedTuple of outputs (described in `SegmentHaT1LongShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_HA_T1_LONG_SH_METADATA)
     params = segment_ha_t1_long_sh_params(
         subject_dir=subject_dir,
         subject_id=subject_id,
     )
-    return segment_ha_t1_long_sh_execute(params, execution)
+    return segment_ha_t1_long_sh_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_HA_T1_LONG_SH_METADATA",
     "SegmentHaT1LongShOutputs",
-    "SegmentHaT1LongShParameters",
     "segment_ha_t1_long_sh",
+    "segment_ha_t1_long_sh_execute",
     "segment_ha_t1_long_sh_params",
 ]

niwrap_freesurfer/freesurfer/segment_ha_t1_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_HA_T1_SH_METADATA = Metadata(
-    id="10e5f048c0c96d580fd404286652db4a21db113f.boutiques",
+    id="96a2a5ca75f950d41aea74cab73b87ddeb7a4ae3.boutiques",
     name="segmentHA_T1.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ SEGMENT_HA_T1_SH_METADATA = Metadata(
 
 
 SegmentHaT1ShParameters = typing.TypedDict('SegmentHaT1ShParameters', {
-    "__STYXTYPE__": typing.Literal["segmentHA_T1.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segmentHA_T1.sh"]],
+    "input_image": InputPathType,
+    "output_directory": str,
+    "brain_mask": typing.NotRequired[InputPathType | None],
+    "verbose": bool,
+    "debug": bool,
+})
+SegmentHaT1ShParametersTagged = typing.TypedDict('SegmentHaT1ShParametersTagged', {
+    "@type": typing.Literal["freesurfer/segmentHA_T1.sh"],
     "input_image": InputPathType,
     "output_directory": str,
     "brain_mask": typing.NotRequired[InputPathType | None],
     "verbose": bool,
     "debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "segmentHA_T1.sh": segment_ha_t1_sh_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 {
-        "segmentHA_T1.sh": segment_ha_t1_sh_outputs,
-    }.get(t)
 
 
 class SegmentHaT1ShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_ha_t1_sh(...)`.
+    Output object returned when calling `SegmentHaT1ShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +49,7 @@ def segment_ha_t1_sh_params(
     brain_mask: InputPathType | None = None,
     verbose: bool = False,
     debug: bool = False,
-) -> SegmentHaT1ShParameters:
+) -> SegmentHaT1ShParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +64,7 @@ def segment_ha_t1_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segmentHA_T1.sh",
+        "@type": "freesurfer/segmentHA_T1.sh",
         "input_image": input_image,
         "output_directory": output_directory,
         "verbose": verbose,
@@ -114,16 +90,16 @@ def segment_ha_t1_sh_cargs(
     """
     cargs = []
     cargs.append("segmentHA_T1.sh")
-    cargs.append(execution.input_file(params.get("input_image")))
-    cargs.append(params.get("output_directory"))
-    if params.get("brain_mask") is not None:
+    cargs.append(execution.input_file(params.get("input_image", None)))
+    cargs.append(params.get("output_directory", None))
+    if params.get("brain_mask", None) is not None:
         cargs.extend([
             "--brainmask",
-            execution.input_file(params.get("brain_mask"))
+            execution.input_file(params.get("brain_mask", None))
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("--verbose")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
     return cargs
 
@@ -143,17 +119,19 @@ def segment_ha_t1_sh_outputs(
     """
     ret = SegmentHaT1ShOutputs(
         root=execution.output_file("."),
-        hippocampus_aseg=execution.output_file(params.get("output_directory") + "/hippocampus_aseg.mgz"),
-        amygdala_aseg=execution.output_file(params.get("output_directory") + "/amygdala_aseg.mgz"),
+        hippocampus_aseg=execution.output_file(params.get("output_directory", None) + "/hippocampus_aseg.mgz"),
+        amygdala_aseg=execution.output_file(params.get("output_directory", None) + "/amygdala_aseg.mgz"),
     )
     return ret
 
 
 def segment_ha_t1_sh_execute(
     params: SegmentHaT1ShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentHaT1ShOutputs:
     """
+    segmentHA_T1.sh
+    
     Tool for hippocampal/amygdalar subfield segmentation.
     
     Author: FreeSurfer Developers
@@ -162,10 +140,12 @@ def segment_ha_t1_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentHaT1ShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_HA_T1_SH_METADATA)
     params = execution.params(params)
     cargs = segment_ha_t1_sh_cargs(params, execution)
     ret = segment_ha_t1_sh_outputs(params, execution)
@@ -182,6 +162,8 @@ def segment_ha_t1_sh(
     runner: Runner | None = None,
 ) -> SegmentHaT1ShOutputs:
     """
+    segmentHA_T1.sh
+    
     Tool for hippocampal/amygdalar subfield segmentation.
     
     Author: FreeSurfer Developers
@@ -199,8 +181,6 @@ def segment_ha_t1_sh(
     Returns:
         NamedTuple of outputs (described in `SegmentHaT1ShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_HA_T1_SH_METADATA)
     params = segment_ha_t1_sh_params(
         input_image=input_image,
         output_directory=output_directory,
@@ -208,13 +188,13 @@ def segment_ha_t1_sh(
         verbose=verbose,
         debug=debug,
     )
-    return segment_ha_t1_sh_execute(params, execution)
+    return segment_ha_t1_sh_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_HA_T1_SH_METADATA",
     "SegmentHaT1ShOutputs",
-    "SegmentHaT1ShParameters",
     "segment_ha_t1_sh",
+    "segment_ha_t1_sh_execute",
     "segment_ha_t1_sh_params",
 ]

niwrap_freesurfer/freesurfer/segment_ha_t2_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_HA_T2_SH_METADATA = Metadata(
-    id="03e4bc097925711fe0a6c4bb76cfba6f0420d3f6.boutiques",
+    id="88bb3b2933ae836a2808334930bcf6abb07e6253.boutiques",
     name="segmentHA_T2.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ SEGMENT_HA_T2_SH_METADATA = Metadata(
 
 
 SegmentHaT2ShParameters = typing.TypedDict('SegmentHaT2ShParameters', {
-    "__STYXTYPE__": typing.Literal["segmentHA_T2.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segmentHA_T2.sh"]],
+    "input_image": InputPathType,
+    "output_directory": str,
+})
+SegmentHaT2ShParametersTagged = typing.TypedDict('SegmentHaT2ShParametersTagged', {
+    "@type": typing.Literal["freesurfer/segmentHA_T2.sh"],
     "input_image": InputPathType,
     "output_directory": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "segmentHA_T2.sh": segment_ha_t2_sh_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 {
-        "segmentHA_T2.sh": segment_ha_t2_sh_outputs,
-    }.get(t)
 
 
 class SegmentHaT2ShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_ha_t2_sh(...)`.
+    Output object returned when calling `SegmentHaT2ShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +40,7 @@ class SegmentHaT2ShOutputs(typing.NamedTuple):
 def segment_ha_t2_sh_params(
     input_image: InputPathType,
     output_directory: str,
-) -> SegmentHaT2ShParameters:
+) -> SegmentHaT2ShParametersTagged:
     """
     Build parameters.
     
@@ -78,7 +51,7 @@ def segment_ha_t2_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segmentHA_T2.sh",
+        "@type": "freesurfer/segmentHA_T2.sh",
         "input_image": input_image,
         "output_directory": output_directory,
     }
@@ -100,8 +73,8 @@ def segment_ha_t2_sh_cargs(
     """
     cargs = []
     cargs.append("segmentHA_T2.sh")
-    cargs.append(execution.input_file(params.get("input_image")))
-    cargs.append(params.get("output_directory"))
+    cargs.append(execution.input_file(params.get("input_image", None)))
+    cargs.append(params.get("output_directory", None))
     return cargs
 
 
@@ -120,19 +93,21 @@ def segment_ha_t2_sh_outputs(
     """
     ret = SegmentHaT2ShOutputs(
         root=execution.output_file("."),
-        left_hemisphere_labels=execution.output_file(params.get("output_directory") + "/lh.hippoAmygLabels-T2.v21.mgz"),
-        right_hemisphere_labels=execution.output_file(params.get("output_directory") + "/rh.hippoAmygLabels-T2.v21.mgz"),
+        left_hemisphere_labels=execution.output_file(params.get("output_directory", None) + "/lh.hippoAmygLabels-T2.v21.mgz"),
+        right_hemisphere_labels=execution.output_file(params.get("output_directory", None) + "/rh.hippoAmygLabels-T2.v21.mgz"),
     )
     return ret
 
 
 def segment_ha_t2_sh_execute(
     params: SegmentHaT2ShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentHaT2ShOutputs:
     """
-    Segments hippocampal and amygdala structures from T2-weighted MRI images using
-    the FreeSurfer suite.
+    segmentHA_T2.sh
+    
+    Segments hippocampal and amygdala structures from T2-weighted MRI images
+    using the FreeSurfer suite.
     
     Author: FreeSurfer Developers
     
@@ -140,10 +115,12 @@ def segment_ha_t2_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentHaT2ShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_HA_T2_SH_METADATA)
     params = execution.params(params)
     cargs = segment_ha_t2_sh_cargs(params, execution)
     ret = segment_ha_t2_sh_outputs(params, execution)
@@ -157,8 +134,10 @@ def segment_ha_t2_sh(
     runner: Runner | None = None,
 ) -> SegmentHaT2ShOutputs:
     """
-    Segments hippocampal and amygdala structures from T2-weighted MRI images using
-    the FreeSurfer suite.
+    segmentHA_T2.sh
+    
+    Segments hippocampal and amygdala structures from T2-weighted MRI images
+    using the FreeSurfer suite.
     
     Author: FreeSurfer Developers
     
@@ -171,19 +150,17 @@ def segment_ha_t2_sh(
     Returns:
         NamedTuple of outputs (described in `SegmentHaT2ShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_HA_T2_SH_METADATA)
     params = segment_ha_t2_sh_params(
         input_image=input_image,
         output_directory=output_directory,
     )
-    return segment_ha_t2_sh_execute(params, execution)
+    return segment_ha_t2_sh_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_HA_T2_SH_METADATA",
     "SegmentHaT2ShOutputs",
-    "SegmentHaT2ShParameters",
     "segment_ha_t2_sh",
+    "segment_ha_t2_sh_execute",
     "segment_ha_t2_sh_params",
 ]

niwrap_freesurfer/freesurfer/segment_monkey.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_MONKEY_METADATA = Metadata(
-    id="d99648d5897e88948d11ff4132bd5ecfdf37b4ad.boutiques",
+    id="0615d8035d844bed5c1a9ffb83560ac72aa61c4d.boutiques",
     name="segment_monkey",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ SEGMENT_MONKEY_METADATA = Metadata(
 
 
 SegmentMonkeyParameters = typing.TypedDict('SegmentMonkeyParameters', {
-    "__STYXTYPE__": typing.Literal["segment_monkey"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segment_monkey"]],
+    "control_points": list[str],
+})
+SegmentMonkeyParametersTagged = typing.TypedDict('SegmentMonkeyParametersTagged', {
+    "@type": typing.Literal["freesurfer/segment_monkey"],
     "control_points": list[str],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "segment_monkey": segment_monkey_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 SegmentMonkeyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_monkey(...)`.
+    Output object returned when calling `SegmentMonkeyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class SegmentMonkeyOutputs(typing.NamedTuple):
 
 def segment_monkey_params(
     control_points: list[str],
-) -> SegmentMonkeyParameters:
+) -> SegmentMonkeyParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def segment_monkey_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segment_monkey",
+        "@type": "freesurfer/segment_monkey",
         "control_points": control_points,
     }
     return params
@@ -91,7 +64,7 @@ def segment_monkey_cargs(
     """
     cargs = []
     cargs.append("segment_monkey")
-    cargs.extend(params.get("control_points"))
+    cargs.extend(params.get("control_points", None))
     return cargs
 
 
@@ -116,9 +89,11 @@ def segment_monkey_outputs(
 
 def segment_monkey_execute(
     params: SegmentMonkeyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentMonkeyOutputs:
     """
+    segment_monkey
+    
     A tool for segmenting images using specified control points.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def segment_monkey_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentMonkeyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_MONKEY_METADATA)
     params = execution.params(params)
     cargs = segment_monkey_cargs(params, execution)
     ret = segment_monkey_outputs(params, execution)
@@ -143,6 +120,8 @@ def segment_monkey(
     runner: Runner | None = None,
 ) -> SegmentMonkeyOutputs:
     """
+    segment_monkey
+    
     A tool for segmenting images using specified control points.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def segment_monkey(
     Returns:
         NamedTuple of outputs (described in `SegmentMonkeyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_MONKEY_METADATA)
     params = segment_monkey_params(
         control_points=control_points,
     )
-    return segment_monkey_execute(params, execution)
+    return segment_monkey_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_MONKEY_METADATA",
     "SegmentMonkeyOutputs",
-    "SegmentMonkeyParameters",
     "segment_monkey",
+    "segment_monkey_execute",
     "segment_monkey_params",
 ]