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

niwrap_freesurfer/freesurfer/run_samseg_long.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RUN_SAMSEG_LONG_METADATA = Metadata(
-    id="281cafde4435543fa9734d7698891e798550c9ed.boutiques",
+    id="099916b21f2e46fd8082ecf1726ddb1c04fbe330.boutiques",
     name="run_samseg_long",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,32 @@ RUN_SAMSEG_LONG_METADATA = Metadata(
 
 
 RunSamsegLongParameters = typing.TypedDict('RunSamsegLongParameters', {
-    "__STYXTYPE__": typing.Literal["run_samseg_long"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/run_samseg_long"]],
+    "timepoint": list[InputPathType],
+    "output": str,
+    "lesion": bool,
+    "threshold": typing.NotRequired[float | None],
+    "samples": typing.NotRequired[float | None],
+    "burnin": typing.NotRequired[float | None],
+    "lesion_mask_structure": typing.NotRequired[str | None],
+    "lesion_mask_pattern": typing.NotRequired[list[float] | None],
+    "mode": typing.NotRequired[list[str] | None],
+    "atlas": typing.NotRequired[str | None],
+    "deformation_hyperprior": typing.NotRequired[float | None],
+    "gmm_hyperprior": typing.NotRequired[float | None],
+    "save_warp": bool,
+    "save_mesh": bool,
+    "save_posteriors": typing.NotRequired[list[str] | None],
+    "pallidum_separate": bool,
+    "threads": typing.NotRequired[float | None],
+    "tp_to_base_transform": typing.NotRequired[list[InputPathType] | None],
+    "force_different_resolutions": bool,
+    "history": bool,
+    "showfigs": bool,
+    "movie": bool,
+})
+RunSamsegLongParametersTagged = typing.TypedDict('RunSamsegLongParametersTagged', {
+    "@type": typing.Literal["freesurfer/run_samseg_long"],
     "timepoint": list[InputPathType],
     "output": str,
     "lesion": bool,
@@ -38,42 +63,11 @@ RunSamsegLongParameters = typing.TypedDict('RunSamsegLongParameters', {
     "showfigs": bool,
     "movie": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "run_samseg_long": run_samseg_long_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 RunSamsegLongOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `run_samseg_long(...)`.
+    Output object returned when calling `RunSamsegLongParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -102,7 +96,7 @@ def run_samseg_long_params(
     history: bool = False,
     showfigs: bool = False,
     movie: bool = False,
-) -> RunSamsegLongParameters:
+) -> RunSamsegLongParametersTagged:
     """
     Build parameters.
     
@@ -141,7 +135,7 @@ def run_samseg_long_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "run_samseg_long",
+        "@type": "freesurfer/run_samseg_long",
         "timepoint": timepoint,
         "output": output,
         "lesion": lesion,
@@ -197,87 +191,87 @@ def run_samseg_long_cargs(
     cargs.append("run_samseg_long")
     cargs.extend([
         "-t",
-        *[execution.input_file(f) for f in params.get("timepoint")]
+        *[execution.input_file(f) for f in params.get("timepoint", None)]
     ])
     cargs.extend([
         "-o",
-        params.get("output")
+        params.get("output", None)
     ])
-    if params.get("lesion"):
+    if params.get("lesion", False):
         cargs.append("--lesion")
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "--threshold",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("samples") is not None:
+    if params.get("samples", None) is not None:
         cargs.extend([
             "--samples",
-            str(params.get("samples"))
+            str(params.get("samples", None))
         ])
-    if params.get("burnin") is not None:
+    if params.get("burnin", None) is not None:
         cargs.extend([
             "--burnin",
-            str(params.get("burnin"))
+            str(params.get("burnin", None))
         ])
-    if params.get("lesion_mask_structure") is not None:
+    if params.get("lesion_mask_structure", None) is not None:
         cargs.extend([
             "--lesion-mask-structure",
-            params.get("lesion_mask_structure")
+            params.get("lesion_mask_structure", None)
         ])
-    if params.get("lesion_mask_pattern") is not None:
+    if params.get("lesion_mask_pattern", None) is not None:
         cargs.extend([
             "--lesion-mask-pattern",
-            *map(str, params.get("lesion_mask_pattern"))
+            *map(str, params.get("lesion_mask_pattern", None))
         ])
-    if params.get("mode") is not None:
+    if params.get("mode", None) is not None:
         cargs.extend([
             "-m",
-            *params.get("mode")
+            *params.get("mode", None)
         ])
-    if params.get("atlas") is not None:
+    if params.get("atlas", None) is not None:
         cargs.extend([
             "-a",
-            params.get("atlas")
+            params.get("atlas", None)
         ])
-    if params.get("deformation_hyperprior") is not None:
+    if params.get("deformation_hyperprior", None) is not None:
         cargs.extend([
             "--deformation-hyperprior",
-            str(params.get("deformation_hyperprior"))
+            str(params.get("deformation_hyperprior", None))
         ])
-    if params.get("gmm_hyperprior") is not None:
+    if params.get("gmm_hyperprior", None) is not None:
         cargs.extend([
             "--gmm-hyperprior",
-            str(params.get("gmm_hyperprior"))
+            str(params.get("gmm_hyperprior", None))
         ])
-    if params.get("save_warp"):
+    if params.get("save_warp", False):
         cargs.append("--save-warp")
-    if params.get("save_mesh"):
+    if params.get("save_mesh", False):
         cargs.append("--save-mesh")
-    if params.get("save_posteriors") is not None:
+    if params.get("save_posteriors", None) is not None:
         cargs.extend([
             "--save-posteriors",
-            *params.get("save_posteriors")
+            *params.get("save_posteriors", None)
         ])
-    if params.get("pallidum_separate"):
+    if params.get("pallidum_separate", False):
         cargs.append("--pallidum-separate")
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
-    if params.get("tp_to_base_transform") is not None:
+    if params.get("tp_to_base_transform", None) is not None:
         cargs.extend([
             "--tp-to-base-transform",
-            *[execution.input_file(f) for f in params.get("tp_to_base_transform")]
+            *[execution.input_file(f) for f in params.get("tp_to_base_transform", None)]
         ])
-    if params.get("force_different_resolutions"):
+    if params.get("force_different_resolutions", False):
         cargs.append("--force-different-resolutions")
-    if params.get("history"):
+    if params.get("history", False):
         cargs.append("--history")
-    if params.get("showfigs"):
+    if params.get("showfigs", False):
         cargs.append("--showfigs")
-    if params.get("movie"):
+    if params.get("movie", False):
         cargs.append("--movie")
     return cargs
 
@@ -303,9 +297,11 @@ def run_samseg_long_outputs(
 
 def run_samseg_long_execute(
     params: RunSamsegLongParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RunSamsegLongOutputs:
     """
+    run_samseg_long
+    
     Longitudinal image segmentation using SAMSEG.
     
     Author: FreeSurfer Developers
@@ -314,10 +310,12 @@ def run_samseg_long_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RunSamsegLongOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RUN_SAMSEG_LONG_METADATA)
     params = execution.params(params)
     cargs = run_samseg_long_cargs(params, execution)
     ret = run_samseg_long_outputs(params, execution)
@@ -351,6 +349,8 @@ def run_samseg_long(
     runner: Runner | None = None,
 ) -> RunSamsegLongOutputs:
     """
+    run_samseg_long
+    
     Longitudinal image segmentation using SAMSEG.
     
     Author: FreeSurfer Developers
@@ -392,8 +392,6 @@ def run_samseg_long(
     Returns:
         NamedTuple of outputs (described in `RunSamsegLongOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RUN_SAMSEG_LONG_METADATA)
     params = run_samseg_long_params(
         timepoint=timepoint,
         output=output,
@@ -418,13 +416,13 @@ def run_samseg_long(
         showfigs=showfigs,
         movie=movie,
     )
-    return run_samseg_long_execute(params, execution)
+    return run_samseg_long_execute(params, runner)
 
 
 __all__ = [
     "RUN_SAMSEG_LONG_METADATA",
     "RunSamsegLongOutputs",
-    "RunSamsegLongParameters",
     "run_samseg_long",
+    "run_samseg_long_execute",
     "run_samseg_long_params",
 ]

niwrap_freesurfer/freesurfer/run_segment_subfields_t1_longitudinal_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RUN_SEGMENT_SUBFIELDS_T1_LONGITUDINAL_SH_METADATA = Metadata(
-    id="06a7bfba6231f999f1b4d6fa26f1a22c4fe4eb12.boutiques",
+    id="352a5bd10fe62a4f02d962f741d26ee74a14ef5c.boutiques",
     name="run_SegmentSubfieldsT1Longitudinal.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ RUN_SEGMENT_SUBFIELDS_T1_LONGITUDINAL_SH_METADATA = Metadata(
 
 
 RunSegmentSubfieldsT1LongitudinalShParameters = typing.TypedDict('RunSegmentSubfieldsT1LongitudinalShParameters', {
-    "__STYXTYPE__": typing.Literal["run_SegmentSubfieldsT1Longitudinal.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/run_SegmentSubfieldsT1Longitudinal.sh"]],
+    "deployed_mcr_root": str,
+    "additional_args": typing.NotRequired[str | None],
+})
+RunSegmentSubfieldsT1LongitudinalShParametersTagged = typing.TypedDict('RunSegmentSubfieldsT1LongitudinalShParametersTagged', {
+    "@type": typing.Literal["freesurfer/run_SegmentSubfieldsT1Longitudinal.sh"],
     "deployed_mcr_root": str,
     "additional_args": 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 {
-        "run_SegmentSubfieldsT1Longitudinal.sh": run_segment_subfields_t1_longitudinal_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 {
-    }.get(t)
 
 
 class RunSegmentSubfieldsT1LongitudinalShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `run_segment_subfields_t1_longitudinal_sh(...)`.
+    Output object returned when calling `RunSegmentSubfieldsT1LongitudinalShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class RunSegmentSubfieldsT1LongitudinalShOutputs(typing.NamedTuple):
 def run_segment_subfields_t1_longitudinal_sh_params(
     deployed_mcr_root: str,
     additional_args: str | None = None,
-) -> RunSegmentSubfieldsT1LongitudinalShParameters:
+) -> RunSegmentSubfieldsT1LongitudinalShParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +48,7 @@ def run_segment_subfields_t1_longitudinal_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "run_SegmentSubfieldsT1Longitudinal.sh",
+        "@type": "freesurfer/run_SegmentSubfieldsT1Longitudinal.sh",
         "deployed_mcr_root": deployed_mcr_root,
     }
     if additional_args is not None:
@@ -97,9 +71,9 @@ def run_segment_subfields_t1_longitudinal_sh_cargs(
     """
     cargs = []
     cargs.append("run_SegmentSubfieldsT1Longitudinal.sh")
-    cargs.append(params.get("deployed_mcr_root"))
-    if params.get("additional_args") is not None:
-        cargs.append(params.get("additional_args"))
+    cargs.append(params.get("deployed_mcr_root", None))
+    if params.get("additional_args", None) is not None:
+        cargs.append(params.get("additional_args", None))
     return cargs
 
 
@@ -124,9 +98,11 @@ def run_segment_subfields_t1_longitudinal_sh_outputs(
 
 def run_segment_subfields_t1_longitudinal_sh_execute(
     params: RunSegmentSubfieldsT1LongitudinalShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RunSegmentSubfieldsT1LongitudinalShOutputs:
     """
+    run_SegmentSubfieldsT1Longitudinal.sh
+    
     Script for segmenting subfields from T1-weighted longitudinal data using
     FreeSurfer.
     
@@ -136,10 +112,12 @@ def run_segment_subfields_t1_longitudinal_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RunSegmentSubfieldsT1LongitudinalShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RUN_SEGMENT_SUBFIELDS_T1_LONGITUDINAL_SH_METADATA)
     params = execution.params(params)
     cargs = run_segment_subfields_t1_longitudinal_sh_cargs(params, execution)
     ret = run_segment_subfields_t1_longitudinal_sh_outputs(params, execution)
@@ -153,6 +131,8 @@ def run_segment_subfields_t1_longitudinal_sh(
     runner: Runner | None = None,
 ) -> RunSegmentSubfieldsT1LongitudinalShOutputs:
     """
+    run_SegmentSubfieldsT1Longitudinal.sh
+    
     Script for segmenting subfields from T1-weighted longitudinal data using
     FreeSurfer.
     
@@ -168,19 +148,17 @@ def run_segment_subfields_t1_longitudinal_sh(
     Returns:
         NamedTuple of outputs (described in `RunSegmentSubfieldsT1LongitudinalShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RUN_SEGMENT_SUBFIELDS_T1_LONGITUDINAL_SH_METADATA)
     params = run_segment_subfields_t1_longitudinal_sh_params(
         deployed_mcr_root=deployed_mcr_root,
         additional_args=additional_args,
     )
-    return run_segment_subfields_t1_longitudinal_sh_execute(params, execution)
+    return run_segment_subfields_t1_longitudinal_sh_execute(params, runner)
 
 
 __all__ = [
     "RUN_SEGMENT_SUBFIELDS_T1_LONGITUDINAL_SH_METADATA",
     "RunSegmentSubfieldsT1LongitudinalShOutputs",
-    "RunSegmentSubfieldsT1LongitudinalShParameters",
     "run_segment_subfields_t1_longitudinal_sh",
+    "run_segment_subfields_t1_longitudinal_sh_execute",
     "run_segment_subfields_t1_longitudinal_sh_params",
 ]

niwrap_freesurfer/freesurfer/run_segment_subject_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RUN_SEGMENT_SUBJECT_SH_METADATA = Metadata(
-    id="edb09a7dae02cd39d07b26767fc90bc0473bdf53.boutiques",
+    id="deb475696935c383441105407e65cfcf8a1742bd.boutiques",
     name="run_SegmentSubject.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ RUN_SEGMENT_SUBJECT_SH_METADATA = Metadata(
 
 
 RunSegmentSubjectShParameters = typing.TypedDict('RunSegmentSubjectShParameters', {
-    "__STYXTYPE__": typing.Literal["run_SegmentSubject.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/run_SegmentSubject.sh"]],
+    "deployedMCRroot": str,
+    "arguments": typing.NotRequired[str | None],
+})
+RunSegmentSubjectShParametersTagged = typing.TypedDict('RunSegmentSubjectShParametersTagged', {
+    "@type": typing.Literal["freesurfer/run_SegmentSubject.sh"],
     "deployedMCRroot": str,
     "arguments": 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 {
-        "run_SegmentSubject.sh": run_segment_subject_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 {
-        "run_SegmentSubject.sh": run_segment_subject_sh_outputs,
-    }.get(t)
 
 
 class RunSegmentSubjectShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `run_segment_subject_sh(...)`.
+    Output object returned when calling `RunSegmentSubjectShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class RunSegmentSubjectShOutputs(typing.NamedTuple):
 def run_segment_subject_sh_params(
     deployed_mcrroot: str,
     arguments: str | None = None,
-) -> RunSegmentSubjectShParameters:
+) -> RunSegmentSubjectShParametersTagged:
     """
     Build parameters.
     
@@ -78,7 +51,7 @@ def run_segment_subject_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "run_SegmentSubject.sh",
+        "@type": "freesurfer/run_SegmentSubject.sh",
         "deployedMCRroot": deployed_mcrroot,
     }
     if arguments is not None:
@@ -101,9 +74,9 @@ def run_segment_subject_sh_cargs(
     """
     cargs = []
     cargs.append("run_SegmentSubject.sh")
-    cargs.append(params.get("deployedMCRroot"))
-    if params.get("arguments") is not None:
-        cargs.append(params.get("arguments"))
+    cargs.append(params.get("deployedMCRroot", None))
+    if params.get("arguments", None) is not None:
+        cargs.append(params.get("arguments", None))
     return cargs
 
 
@@ -129,9 +102,11 @@ def run_segment_subject_sh_outputs(
 
 def run_segment_subject_sh_execute(
     params: RunSegmentSubjectShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RunSegmentSubjectShOutputs:
     """
+    run_SegmentSubject.sh
+    
     A command-line tool for subject segmentation in Freesurfer.
     
     Author: FreeSurfer Developers
@@ -140,10 +115,12 @@ def run_segment_subject_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RunSegmentSubjectShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RUN_SEGMENT_SUBJECT_SH_METADATA)
     params = execution.params(params)
     cargs = run_segment_subject_sh_cargs(params, execution)
     ret = run_segment_subject_sh_outputs(params, execution)
@@ -157,6 +134,8 @@ def run_segment_subject_sh(
     runner: Runner | None = None,
 ) -> RunSegmentSubjectShOutputs:
     """
+    run_SegmentSubject.sh
+    
     A command-line tool for subject segmentation in Freesurfer.
     
     Author: FreeSurfer Developers
@@ -172,19 +151,17 @@ def run_segment_subject_sh(
     Returns:
         NamedTuple of outputs (described in `RunSegmentSubjectShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RUN_SEGMENT_SUBJECT_SH_METADATA)
     params = run_segment_subject_sh_params(
         deployed_mcrroot=deployed_mcrroot,
         arguments=arguments,
     )
-    return run_segment_subject_sh_execute(params, execution)
+    return run_segment_subject_sh_execute(params, runner)
 
 
 __all__ = [
     "RUN_SEGMENT_SUBJECT_SH_METADATA",
     "RunSegmentSubjectShOutputs",
-    "RunSegmentSubjectShParameters",
     "run_segment_subject_sh",
+    "run_segment_subject_sh_execute",
     "run_segment_subject_sh_params",
 ]