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

niwrap_freesurfer/freesurfer/segment_subfields_t1_longitudinal.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBFIELDS_T1_LONGITUDINAL_METADATA = Metadata(
-    id="d4b7ee18b602b1f48ca05e9e3df4480075dcd782.boutiques",
+    id="25d3ff2dd663985a3d9ab2f5f1e43c7c4863d5fc.boutiques",
     name="SegmentSubfieldsT1Longitudinal",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ SEGMENT_SUBFIELDS_T1_LONGITUDINAL_METADATA = Metadata(
 
 
 SegmentSubfieldsT1LongitudinalParameters = typing.TypedDict('SegmentSubfieldsT1LongitudinalParameters', {
-    "__STYXTYPE__": typing.Literal["SegmentSubfieldsT1Longitudinal"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/SegmentSubfieldsT1Longitudinal"]],
+    "subject_id": str,
+    "input_image": InputPathType,
+    "output_dir": str,
+})
+SegmentSubfieldsT1LongitudinalParametersTagged = typing.TypedDict('SegmentSubfieldsT1LongitudinalParametersTagged', {
+    "@type": typing.Literal["freesurfer/SegmentSubfieldsT1Longitudinal"],
     "subject_id": str,
     "input_image": InputPathType,
     "output_dir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "SegmentSubfieldsT1Longitudinal": segment_subfields_t1_longitudinal_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 {
-        "SegmentSubfieldsT1Longitudinal": segment_subfields_t1_longitudinal_outputs,
-    }.get(t)
 
 
 class SegmentSubfieldsT1LongitudinalOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_subfields_t1_longitudinal(...)`.
+    Output object returned when calling `SegmentSubfieldsT1LongitudinalParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def segment_subfields_t1_longitudinal_params(
     subject_id: str,
     input_image: InputPathType,
     output_dir: str,
-) -> SegmentSubfieldsT1LongitudinalParameters:
+) -> SegmentSubfieldsT1LongitudinalParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def segment_subfields_t1_longitudinal_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SegmentSubfieldsT1Longitudinal",
+        "@type": "freesurfer/SegmentSubfieldsT1Longitudinal",
         "subject_id": subject_id,
         "input_image": input_image,
         "output_dir": output_dir,
@@ -102,9 +76,9 @@ def segment_subfields_t1_longitudinal_cargs(
     """
     cargs = []
     cargs.append("SegmentSubfieldsT1Longitudinal")
-    cargs.append(params.get("subject_id"))
-    cargs.append(execution.input_file(params.get("input_image")))
-    cargs.append(params.get("output_dir"))
+    cargs.append(params.get("subject_id", None))
+    cargs.append(execution.input_file(params.get("input_image", None)))
+    cargs.append(params.get("output_dir", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def segment_subfields_t1_longitudinal_outputs(
     """
     ret = SegmentSubfieldsT1LongitudinalOutputs(
         root=execution.output_file("."),
-        segmentation_output=execution.output_file(params.get("output_dir") + "/subfields_segmentation.nii.gz"),
+        segmentation_output=execution.output_file(params.get("output_dir", None) + "/subfields_segmentation.nii.gz"),
     )
     return ret
 
 
 def segment_subfields_t1_longitudinal_execute(
     params: SegmentSubfieldsT1LongitudinalParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentSubfieldsT1LongitudinalOutputs:
     """
+    SegmentSubfieldsT1Longitudinal
+    
     FreeSurfer tool for segmenting subfields in longitudinal T1-weighted images.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def segment_subfields_t1_longitudinal_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubfieldsT1LongitudinalOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_SUBFIELDS_T1_LONGITUDINAL_METADATA)
     params = execution.params(params)
     cargs = segment_subfields_t1_longitudinal_cargs(params, execution)
     ret = segment_subfields_t1_longitudinal_outputs(params, execution)
@@ -159,6 +137,8 @@ def segment_subfields_t1_longitudinal(
     runner: Runner | None = None,
 ) -> SegmentSubfieldsT1LongitudinalOutputs:
     """
+    SegmentSubfieldsT1Longitudinal
+    
     FreeSurfer tool for segmenting subfields in longitudinal T1-weighted images.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def segment_subfields_t1_longitudinal(
     Returns:
         NamedTuple of outputs (described in `SegmentSubfieldsT1LongitudinalOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_SUBFIELDS_T1_LONGITUDINAL_METADATA)
     params = segment_subfields_t1_longitudinal_params(
         subject_id=subject_id,
         input_image=input_image,
         output_dir=output_dir,
     )
-    return segment_subfields_t1_longitudinal_execute(params, execution)
+    return segment_subfields_t1_longitudinal_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_SUBFIELDS_T1_LONGITUDINAL_METADATA",
     "SegmentSubfieldsT1LongitudinalOutputs",
-    "SegmentSubfieldsT1LongitudinalParameters",
     "segment_subfields_t1_longitudinal",
+    "segment_subfields_t1_longitudinal_execute",
     "segment_subfields_t1_longitudinal_params",
 ]

niwrap_freesurfer/freesurfer/segment_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_METADATA = Metadata(
-    id="679ed4c91cc788d07b10afeeceb1fe2dc1fec124.boutiques",
+    id="b0ec4ee6f04e6bda46019b21c2f772b846913353.boutiques",
     name="segment_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ SEGMENT_SUBJECT_METADATA = Metadata(
 
 
 SegmentSubjectParameters = typing.TypedDict('SegmentSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["segment_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segment_subject"]],
+    "input_volume": InputPathType,
+    "output_xfm": str,
+    "log_file": typing.NotRequired[str | None],
+    "help_flag": bool,
+    "debug_flag": bool,
+    "version_flag": bool,
+})
+SegmentSubjectParametersTagged = typing.TypedDict('SegmentSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/segment_subject"],
     "input_volume": InputPathType,
     "output_xfm": str,
     "log_file": typing.NotRequired[str | None],
@@ -22,43 +31,11 @@ SegmentSubjectParameters = typing.TypedDict('SegmentSubjectParameters', {
     "debug_flag": bool,
     "version_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 {
-        "segment_subject": segment_subject_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 {
-        "segment_subject": segment_subject_outputs,
-    }.get(t)
 
 
 class SegmentSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_subject(...)`.
+    Output object returned when calling `SegmentSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def segment_subject_params(
     help_flag: bool = False,
     debug_flag: bool = False,
     version_flag: bool = False,
-) -> SegmentSubjectParameters:
+) -> SegmentSubjectParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def segment_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segment_subject",
+        "@type": "freesurfer/segment_subject",
         "input_volume": input_volume,
         "output_xfm": output_xfm,
         "help_flag": help_flag,
@@ -117,22 +94,22 @@ def segment_subject_cargs(
     cargs.append("segment_subject")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "--xfm",
-        params.get("output_xfm")
+        params.get("output_xfm", 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("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("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("--version")
     return cargs
 
@@ -152,18 +129,20 @@ def segment_subject_outputs(
     """
     ret = SegmentSubjectOutputs(
         root=execution.output_file("."),
-        output_xfm_file=execution.output_file(params.get("output_xfm")),
+        output_xfm_file=execution.output_file(params.get("output_xfm", None)),
     )
     return ret
 
 
 def segment_subject_execute(
     params: SegmentSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentSubjectOutputs:
     """
-    Front-end for MINCs mritotal to compute the Talairach transform that maps the
-    input volume to the MNI305 space.
+    segment_subject
+    
+    Front-end for MINCs mritotal to compute the Talairach transform that maps
+    the input volume to the MNI305 space.
     
     Author: FreeSurfer Developers
     
@@ -171,10 +150,12 @@ def segment_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = segment_subject_cargs(params, execution)
     ret = segment_subject_outputs(params, execution)
@@ -192,8 +173,10 @@ def segment_subject(
     runner: Runner | None = None,
 ) -> SegmentSubjectOutputs:
     """
-    Front-end for MINCs mritotal to compute the Talairach transform that maps the
-    input volume to the MNI305 space.
+    segment_subject
+    
+    Front-end for MINCs mritotal to compute the Talairach transform that maps
+    the input volume to the MNI305 space.
     
     Author: FreeSurfer Developers
     
@@ -210,8 +193,6 @@ def segment_subject(
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_SUBJECT_METADATA)
     params = segment_subject_params(
         input_volume=input_volume,
         output_xfm=output_xfm,
@@ -220,13 +201,13 @@ def segment_subject(
         debug_flag=debug_flag,
         version_flag=version_flag,
     )
-    return segment_subject_execute(params, execution)
+    return segment_subject_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_SUBJECT_METADATA",
     "SegmentSubjectOutputs",
-    "SegmentSubjectParameters",
     "segment_subject",
+    "segment_subject_execute",
     "segment_subject_params",
 ]

niwrap_freesurfer/freesurfer/segment_subject_notal.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_NOTAL_METADATA = Metadata(
-    id="a7a96a3826fdc962ee75d09bc6629b89ee8c17d9.boutiques",
+    id="2cc454d43b3f94b2bc424f0960f6cbaa1eee9ce0.boutiques",
     name="segment_subject_notal",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ SEGMENT_SUBJECT_NOTAL_METADATA = Metadata(
 
 
 SegmentSubjectNotalParameters = typing.TypedDict('SegmentSubjectNotalParameters', {
-    "__STYXTYPE__": typing.Literal["segment_subject_notal"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segment_subject_notal"]],
+    "subject_path": str,
+})
+SegmentSubjectNotalParametersTagged = typing.TypedDict('SegmentSubjectNotalParametersTagged', {
+    "@type": typing.Literal["freesurfer/segment_subject_notal"],
     "subject_path": 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_subject_notal": segment_subject_notal_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 SegmentSubjectNotalOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_subject_notal(...)`.
+    Output object returned when calling `SegmentSubjectNotalParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class SegmentSubjectNotalOutputs(typing.NamedTuple):
 
 def segment_subject_notal_params(
     subject_path: str,
-) -> SegmentSubjectNotalParameters:
+) -> SegmentSubjectNotalParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def segment_subject_notal_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segment_subject_notal",
+        "@type": "freesurfer/segment_subject_notal",
         "subject_path": subject_path,
     }
     return params
@@ -91,7 +64,7 @@ def segment_subject_notal_cargs(
     """
     cargs = []
     cargs.append("segment_subject_notal")
-    cargs.append(params.get("subject_path"))
+    cargs.append(params.get("subject_path", None))
     return cargs
 
 
@@ -116,9 +89,11 @@ def segment_subject_notal_outputs(
 
 def segment_subject_notal_execute(
     params: SegmentSubjectNotalParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentSubjectNotalOutputs:
     """
+    segment_subject_notal
+    
     A script to segment subjects (notal).
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def segment_subject_notal_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectNotalOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_SUBJECT_NOTAL_METADATA)
     params = execution.params(params)
     cargs = segment_subject_notal_cargs(params, execution)
     ret = segment_subject_notal_outputs(params, execution)
@@ -143,6 +120,8 @@ def segment_subject_notal(
     runner: Runner | None = None,
 ) -> SegmentSubjectNotalOutputs:
     """
+    segment_subject_notal
+    
     A script to segment subjects (notal).
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def segment_subject_notal(
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectNotalOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_SUBJECT_NOTAL_METADATA)
     params = segment_subject_notal_params(
         subject_path=subject_path,
     )
-    return segment_subject_notal_execute(params, execution)
+    return segment_subject_notal_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_SUBJECT_NOTAL_METADATA",
     "SegmentSubjectNotalOutputs",
-    "SegmentSubjectNotalParameters",
     "segment_subject_notal",
+    "segment_subject_notal_execute",
     "segment_subject_notal_params",
 ]

niwrap_freesurfer/freesurfer/segment_subject_notal2.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_NOTAL2_METADATA = Metadata(
-    id="e868882e2e6641277409761b25a2083cd6437b1c.boutiques",
+    id="ea8149a0016fff9377a069d545e9205addade320.boutiques",
     name="segment_subject_notal2",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ SEGMENT_SUBJECT_NOTAL2_METADATA = Metadata(
 
 
 SegmentSubjectNotal2Parameters = typing.TypedDict('SegmentSubjectNotal2Parameters', {
-    "__STYXTYPE__": typing.Literal["segment_subject_notal2"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segment_subject_notal2"]],
+    "license_file": InputPathType,
+})
+SegmentSubjectNotal2ParametersTagged = typing.TypedDict('SegmentSubjectNotal2ParametersTagged', {
+    "@type": typing.Literal["freesurfer/segment_subject_notal2"],
     "license_file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "segment_subject_notal2": segment_subject_notal2_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 {
-        "segment_subject_notal2": segment_subject_notal2_outputs,
-    }.get(t)
 
 
 class SegmentSubjectNotal2Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_subject_notal2(...)`.
+    Output object returned when calling `SegmentSubjectNotal2Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class SegmentSubjectNotal2Outputs(typing.NamedTuple):
 
 def segment_subject_notal2_params(
     license_file: InputPathType,
-) -> SegmentSubjectNotal2Parameters:
+) -> SegmentSubjectNotal2ParametersTagged:
     """
     Build parameters.
     
@@ -75,7 +47,7 @@ def segment_subject_notal2_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segment_subject_notal2",
+        "@type": "freesurfer/segment_subject_notal2",
         "license_file": license_file,
     }
     return params
@@ -98,7 +70,7 @@ def segment_subject_notal2_cargs(
     cargs.append("segment_subject_notal2")
     cargs.extend([
         "--fs-license-file",
-        execution.input_file(params.get("license_file"))
+        execution.input_file(params.get("license_file", None))
     ])
     return cargs
 
@@ -125,9 +97,11 @@ def segment_subject_notal2_outputs(
 
 def segment_subject_notal2_execute(
     params: SegmentSubjectNotal2Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentSubjectNotal2Outputs:
     """
+    segment_subject_notal2
+    
     FreeSurfer tool for segmenting subject data using notal2 algorithm.
     
     Author: FreeSurfer Developers
@@ -136,10 +110,12 @@ def segment_subject_notal2_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectNotal2Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_SUBJECT_NOTAL2_METADATA)
     params = execution.params(params)
     cargs = segment_subject_notal2_cargs(params, execution)
     ret = segment_subject_notal2_outputs(params, execution)
@@ -152,6 +128,8 @@ def segment_subject_notal2(
     runner: Runner | None = None,
 ) -> SegmentSubjectNotal2Outputs:
     """
+    segment_subject_notal2
+    
     FreeSurfer tool for segmenting subject data using notal2 algorithm.
     
     Author: FreeSurfer Developers
@@ -166,18 +144,16 @@ def segment_subject_notal2(
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectNotal2Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_SUBJECT_NOTAL2_METADATA)
     params = segment_subject_notal2_params(
         license_file=license_file,
     )
-    return segment_subject_notal2_execute(params, execution)
+    return segment_subject_notal2_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_SUBJECT_NOTAL2_METADATA",
     "SegmentSubjectNotal2Outputs",
-    "SegmentSubjectNotal2Parameters",
     "segment_subject_notal2",
+    "segment_subject_notal2_execute",
     "segment_subject_notal2_params",
 ]