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

niwrap_freesurfer/freesurfer/segment_thalamic_nuclei_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_THALAMIC_NUCLEI_SH_METADATA = Metadata(
-    id="69ea92310c993122b1f5d2cde1689310a297d670.boutiques",
+    id="84a6eb3421d82b05e58b49ad9846e7c894e8a995.boutiques",
     name="segmentThalamicNuclei.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ SEGMENT_THALAMIC_NUCLEI_SH_METADATA = Metadata(
 
 
 SegmentThalamicNucleiShParameters = typing.TypedDict('SegmentThalamicNucleiShParameters', {
-    "__STYXTYPE__": typing.Literal["segmentThalamicNuclei.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segmentThalamicNuclei.sh"]],
+    "subject_id": str,
+    "output_dir": str,
+})
+SegmentThalamicNucleiShParametersTagged = typing.TypedDict('SegmentThalamicNucleiShParametersTagged', {
+    "@type": typing.Literal["freesurfer/segmentThalamicNuclei.sh"],
     "subject_id": str,
     "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 {
-        "segmentThalamicNuclei.sh": segment_thalamic_nuclei_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 {
-        "segmentThalamicNuclei.sh": segment_thalamic_nuclei_sh_outputs,
-    }.get(t)
 
 
 class SegmentThalamicNucleiShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_thalamic_nuclei_sh(...)`.
+    Output object returned when calling `SegmentThalamicNucleiShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class SegmentThalamicNucleiShOutputs(typing.NamedTuple):
 def segment_thalamic_nuclei_sh_params(
     subject_id: str,
     output_dir: str,
-) -> SegmentThalamicNucleiShParameters:
+) -> SegmentThalamicNucleiShParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def segment_thalamic_nuclei_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segmentThalamicNuclei.sh",
+        "@type": "freesurfer/segmentThalamicNuclei.sh",
         "subject_id": subject_id,
         "output_dir": output_dir,
     }
@@ -98,8 +71,8 @@ def segment_thalamic_nuclei_sh_cargs(
     """
     cargs = []
     cargs.append("segmentThalamicNuclei.sh")
-    cargs.append(params.get("subject_id"))
-    cargs.append(params.get("output_dir"))
+    cargs.append(params.get("subject_id", None))
+    cargs.append(params.get("output_dir", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def segment_thalamic_nuclei_sh_outputs(
     """
     ret = SegmentThalamicNucleiShOutputs(
         root=execution.output_file("."),
-        thalamic_nuclei_output=execution.output_file(params.get("output_dir") + "/" + params.get("subject_id") + "_thalamic_nuclei.mgz"),
+        thalamic_nuclei_output=execution.output_file(params.get("output_dir", None) + "/" + params.get("subject_id", None) + "_thalamic_nuclei.mgz"),
     )
     return ret
 
 
 def segment_thalamic_nuclei_sh_execute(
     params: SegmentThalamicNucleiShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentThalamicNucleiShOutputs:
     """
+    segmentThalamicNuclei.sh
+    
     Segment the thalamic nuclei using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def segment_thalamic_nuclei_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentThalamicNucleiShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_THALAMIC_NUCLEI_SH_METADATA)
     params = execution.params(params)
     cargs = segment_thalamic_nuclei_sh_cargs(params, execution)
     ret = segment_thalamic_nuclei_sh_outputs(params, execution)
@@ -153,6 +130,8 @@ def segment_thalamic_nuclei_sh(
     runner: Runner | None = None,
 ) -> SegmentThalamicNucleiShOutputs:
     """
+    segmentThalamicNuclei.sh
+    
     Segment the thalamic nuclei using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def segment_thalamic_nuclei_sh(
     Returns:
         NamedTuple of outputs (described in `SegmentThalamicNucleiShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_THALAMIC_NUCLEI_SH_METADATA)
     params = segment_thalamic_nuclei_sh_params(
         subject_id=subject_id,
         output_dir=output_dir,
     )
-    return segment_thalamic_nuclei_sh_execute(params, execution)
+    return segment_thalamic_nuclei_sh_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_THALAMIC_NUCLEI_SH_METADATA",
     "SegmentThalamicNucleiShOutputs",
-    "SegmentThalamicNucleiShParameters",
     "segment_thalamic_nuclei_sh",
+    "segment_thalamic_nuclei_sh_execute",
     "segment_thalamic_nuclei_sh_params",
 ]

niwrap_freesurfer/freesurfer/segpons.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGPONS_METADATA = Metadata(
-    id="e29fa1741fe938f5df90815d585a62e246835aa3.boutiques",
+    id="0748589a85ef4978fe8a7a00b012391ca7336bae.boutiques",
     name="segpons",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ SEGPONS_METADATA = Metadata(
 
 
 SegponsParameters = typing.TypedDict('SegponsParameters', {
-    "__STYXTYPE__": typing.Literal["segpons"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segpons"]],
+    "subject": str,
+    "aseg": bool,
+    "apas": bool,
+    "seg": typing.NotRequired[InputPathType | None],
+    "no_refine": bool,
+    "pons152_mask": typing.NotRequired[InputPathType | None],
+})
+SegponsParametersTagged = typing.TypedDict('SegponsParametersTagged', {
+    "@type": typing.Literal["freesurfer/segpons"],
     "subject": str,
     "aseg": bool,
     "apas": bool,
@@ -22,43 +31,11 @@ SegponsParameters = typing.TypedDict('SegponsParameters', {
     "no_refine": bool,
     "pons152_mask": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "segpons": segpons_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 {
-        "segpons": segpons_outputs,
-    }.get(t)
 
 
 class SegponsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segpons(...)`.
+    Output object returned when calling `SegponsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def segpons_params(
     seg: InputPathType | None = None,
     no_refine: bool = False,
     pons152_mask: InputPathType | None = None,
-) -> SegponsParameters:
+) -> SegponsParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def segpons_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segpons",
+        "@type": "freesurfer/segpons",
         "subject": subject,
         "aseg": aseg,
         "apas": apas,
@@ -118,23 +95,23 @@ def segpons_cargs(
     cargs.append("segpons")
     cargs.extend([
         "-s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("aseg"):
+    if params.get("aseg", False):
         cargs.append("--aseg")
-    if params.get("apas"):
+    if params.get("apas", False):
         cargs.append("--apas")
-    if params.get("seg") is not None:
+    if params.get("seg", None) is not None:
         cargs.extend([
             "--seg",
-            execution.input_file(params.get("seg"))
+            execution.input_file(params.get("seg", None))
         ])
-    if params.get("no_refine"):
+    if params.get("no_refine", False):
         cargs.append("--no-refine")
-    if params.get("pons152_mask") is not None:
+    if params.get("pons152_mask", None) is not None:
         cargs.extend([
             "--pons152",
-            execution.input_file(params.get("pons152_mask"))
+            execution.input_file(params.get("pons152_mask", None))
         ])
     return cargs
 
@@ -154,16 +131,18 @@ def segpons_outputs(
     """
     ret = SegponsOutputs(
         root=execution.output_file("."),
-        pons_output=execution.output_file(params.get("subject") + "+pons.mgz"),
+        pons_output=execution.output_file(params.get("subject", None) + "+pons.mgz"),
     )
     return ret
 
 
 def segpons_execute(
     params: SegponsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegponsOutputs:
     """
+    segpons
+    
     Approximate segmentation of pons using MNI152 space registration.
     
     Author: FreeSurfer Developers
@@ -172,10 +151,12 @@ def segpons_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegponsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGPONS_METADATA)
     params = execution.params(params)
     cargs = segpons_cargs(params, execution)
     ret = segpons_outputs(params, execution)
@@ -193,6 +174,8 @@ def segpons(
     runner: Runner | None = None,
 ) -> SegponsOutputs:
     """
+    segpons
+    
     Approximate segmentation of pons using MNI152 space registration.
     
     Author: FreeSurfer Developers
@@ -210,8 +193,6 @@ def segpons(
     Returns:
         NamedTuple of outputs (described in `SegponsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGPONS_METADATA)
     params = segpons_params(
         subject=subject,
         aseg=aseg,
@@ -220,13 +201,13 @@ def segpons(
         no_refine=no_refine,
         pons152_mask=pons152_mask,
     )
-    return segpons_execute(params, execution)
+    return segpons_execute(params, runner)
 
 
 __all__ = [
     "SEGPONS_METADATA",
     "SegponsOutputs",
-    "SegponsParameters",
     "segpons",
+    "segpons_execute",
     "segpons_params",
 ]

niwrap_freesurfer/freesurfer/setlabelstat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SETLABELSTAT_METADATA = Metadata(
-    id="d596ef8de99453ef4bca6fe2470b698bdc0cefea.boutiques",
+    id="d8aed72783cf5237b35f2a0127e5b23567df7704.boutiques",
     name="setlabelstat",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ SETLABELSTAT_METADATA = Metadata(
 
 
 SetlabelstatParameters = typing.TypedDict('SetlabelstatParameters', {
-    "__STYXTYPE__": typing.Literal["setlabelstat"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/setlabelstat"]],
+    "inlabelfile": InputPathType,
+    "outlabelfile": InputPathType,
+    "statval": float,
+    "help": bool,
+})
+SetlabelstatParametersTagged = typing.TypedDict('SetlabelstatParametersTagged', {
+    "@type": typing.Literal["freesurfer/setlabelstat"],
     "inlabelfile": InputPathType,
     "outlabelfile": InputPathType,
     "statval": float,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "setlabelstat": setlabelstat_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 {
-        "setlabelstat": setlabelstat_outputs,
-    }.get(t)
 
 
 class SetlabelstatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `setlabelstat(...)`.
+    Output object returned when calling `SetlabelstatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def setlabelstat_params(
     outlabelfile: InputPathType,
     statval: float,
     help_: bool = False,
-) -> SetlabelstatParameters:
+) -> SetlabelstatParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def setlabelstat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "setlabelstat",
+        "@type": "freesurfer/setlabelstat",
         "inlabelfile": inlabelfile,
         "outlabelfile": outlabelfile,
         "statval": statval,
@@ -108,17 +83,17 @@ def setlabelstat_cargs(
     cargs.append("setlabelstat")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("inlabelfile"))
+        execution.input_file(params.get("inlabelfile", None))
     ])
     cargs.extend([
         "-o",
-        execution.input_file(params.get("outlabelfile"))
+        execution.input_file(params.get("outlabelfile", None))
     ])
     cargs.extend([
         "-s",
-        str(params.get("statval"))
+        str(params.get("statval", None))
     ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -138,18 +113,20 @@ def setlabelstat_outputs(
     """
     ret = SetlabelstatOutputs(
         root=execution.output_file("."),
-        output_label_file=execution.output_file(pathlib.Path(params.get("outlabelfile")).name),
+        output_label_file=execution.output_file(pathlib.Path(params.get("outlabelfile", None)).name),
     )
     return ret
 
 
 def setlabelstat_execute(
     params: SetlabelstatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SetlabelstatOutputs:
     """
-    Replaces the stat values in a label file with the single stat value supplied on
-    the command-line.
+    setlabelstat
+    
+    Replaces the stat values in a label file with the single stat value supplied
+    on the command-line.
     
     Author: FreeSurfer Developers
     
@@ -157,10 +134,12 @@ def setlabelstat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SetlabelstatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SETLABELSTAT_METADATA)
     params = execution.params(params)
     cargs = setlabelstat_cargs(params, execution)
     ret = setlabelstat_outputs(params, execution)
@@ -176,8 +155,10 @@ def setlabelstat(
     runner: Runner | None = None,
 ) -> SetlabelstatOutputs:
     """
-    Replaces the stat values in a label file with the single stat value supplied on
-    the command-line.
+    setlabelstat
+    
+    Replaces the stat values in a label file with the single stat value supplied
+    on the command-line.
     
     Author: FreeSurfer Developers
     
@@ -192,21 +173,19 @@ def setlabelstat(
     Returns:
         NamedTuple of outputs (described in `SetlabelstatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SETLABELSTAT_METADATA)
     params = setlabelstat_params(
         inlabelfile=inlabelfile,
         outlabelfile=outlabelfile,
         statval=statval,
         help_=help_,
     )
-    return setlabelstat_execute(params, execution)
+    return setlabelstat_execute(params, runner)
 
 
 __all__ = [
     "SETLABELSTAT_METADATA",
     "SetlabelstatOutputs",
-    "SetlabelstatParameters",
     "setlabelstat",
+    "setlabelstat_execute",
     "setlabelstat_params",
 ]