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

niwrap_freesurfer/freesurfer/segment_subject_old_skull_strip.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_OLD_SKULL_STRIP_METADATA = Metadata(
-    id="cc92dcb2f7e4bb046baab00eb1150ee3c6a1adae.boutiques",
+    id="529cb84c59822284cc109ff60693dc0ec5b93c42.boutiques",
     name="segment_subject_old_skull_strip",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ SEGMENT_SUBJECT_OLD_SKULL_STRIP_METADATA = Metadata(
 
 
 SegmentSubjectOldSkullStripParameters = typing.TypedDict('SegmentSubjectOldSkullStripParameters', {
-    "__STYXTYPE__": typing.Literal["segment_subject_old_skull_strip"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segment_subject_old_skull_strip"]],
+    "input_volume": InputPathType,
+    "output_xfm": str,
+    "log_file": typing.NotRequired[str | None],
+    "help_flag": bool,
+    "debug_flag": bool,
+    "version_flag": bool,
+})
+SegmentSubjectOldSkullStripParametersTagged = typing.TypedDict('SegmentSubjectOldSkullStripParametersTagged', {
+    "@type": typing.Literal["freesurfer/segment_subject_old_skull_strip"],
     "input_volume": InputPathType,
     "output_xfm": str,
     "log_file": typing.NotRequired[str | None],
@@ -22,43 +31,11 @@ SegmentSubjectOldSkullStripParameters = typing.TypedDict('SegmentSubjectOldSkull
     "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_old_skull_strip": segment_subject_old_skull_strip_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_old_skull_strip": segment_subject_old_skull_strip_outputs,
-    }.get(t)
 
 
 class SegmentSubjectOldSkullStripOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_subject_old_skull_strip(...)`.
+    Output object returned when calling `SegmentSubjectOldSkullStripParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def segment_subject_old_skull_strip_params(
     help_flag: bool = False,
     debug_flag: bool = False,
     version_flag: bool = False,
-) -> SegmentSubjectOldSkullStripParameters:
+) -> SegmentSubjectOldSkullStripParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def segment_subject_old_skull_strip_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segment_subject_old_skull_strip",
+        "@type": "freesurfer/segment_subject_old_skull_strip",
         "input_volume": input_volume,
         "output_xfm": output_xfm,
         "help_flag": help_flag,
@@ -119,22 +96,22 @@ def segment_subject_old_skull_strip_cargs(
     cargs.append("segment_subject_old_skull_strip")
     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
 
@@ -154,19 +131,21 @@ def segment_subject_old_skull_strip_outputs(
     """
     ret = SegmentSubjectOldSkullStripOutputs(
         root=execution.output_file("."),
-        output_xfm_file=execution.output_file(params.get("output_xfm")),
-        log_output_file=execution.output_file(params.get("log_file")) if (params.get("log_file") is not None) else None,
+        output_xfm_file=execution.output_file(params.get("output_xfm", None)),
+        log_output_file=execution.output_file(params.get("log_file", None)) if (params.get("log_file") is not None) else None,
     )
     return ret
 
 
 def segment_subject_old_skull_strip_execute(
     params: SegmentSubjectOldSkullStripParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentSubjectOldSkullStripOutputs:
     """
-    Front-end for MINCs mritotal for computing the talairach transform that maps the
-    input volume to the MNI305.
+    segment_subject_old_skull_strip
+    
+    Front-end for MINCs mritotal for computing the talairach transform that maps
+    the input volume to the MNI305.
     
     Author: FreeSurfer Developers
     
@@ -174,10 +153,12 @@ def segment_subject_old_skull_strip_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectOldSkullStripOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_SUBJECT_OLD_SKULL_STRIP_METADATA)
     params = execution.params(params)
     cargs = segment_subject_old_skull_strip_cargs(params, execution)
     ret = segment_subject_old_skull_strip_outputs(params, execution)
@@ -195,8 +176,10 @@ def segment_subject_old_skull_strip(
     runner: Runner | None = None,
 ) -> SegmentSubjectOldSkullStripOutputs:
     """
-    Front-end for MINCs mritotal for computing the talairach transform that maps the
-    input volume to the MNI305.
+    segment_subject_old_skull_strip
+    
+    Front-end for MINCs mritotal for computing the talairach transform that maps
+    the input volume to the MNI305.
     
     Author: FreeSurfer Developers
     
@@ -213,8 +196,6 @@ def segment_subject_old_skull_strip(
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectOldSkullStripOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_SUBJECT_OLD_SKULL_STRIP_METADATA)
     params = segment_subject_old_skull_strip_params(
         input_volume=input_volume,
         output_xfm=output_xfm,
@@ -223,13 +204,13 @@ def segment_subject_old_skull_strip(
         debug_flag=debug_flag,
         version_flag=version_flag,
     )
-    return segment_subject_old_skull_strip_execute(params, execution)
+    return segment_subject_old_skull_strip_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_SUBJECT_OLD_SKULL_STRIP_METADATA",
     "SegmentSubjectOldSkullStripOutputs",
-    "SegmentSubjectOldSkullStripParameters",
     "segment_subject_old_skull_strip",
+    "segment_subject_old_skull_strip_execute",
     "segment_subject_old_skull_strip_params",
 ]

niwrap_freesurfer/freesurfer/segment_subject_sc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_SC_METADATA = Metadata(
-    id="af3f234535976de2949cc6612aaedde219cc1d8b.boutiques",
+    id="4c2381beb58d56ae886afe592d41221ee611a1c9.boutiques",
     name="segment_subject_sc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ SEGMENT_SUBJECT_SC_METADATA = Metadata(
 
 
 SegmentSubjectScParameters = typing.TypedDict('SegmentSubjectScParameters', {
-    "__STYXTYPE__": typing.Literal["segment_subject_sc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segment_subject_sc"]],
+    "invol": InputPathType,
+    "outxfm": InputPathType,
+    "log": typing.NotRequired[str | None],
+    "debug": bool,
+})
+SegmentSubjectScParametersTagged = typing.TypedDict('SegmentSubjectScParametersTagged', {
+    "@type": typing.Literal["freesurfer/segment_subject_sc"],
     "invol": InputPathType,
     "outxfm": InputPathType,
     "log": typing.NotRequired[str | None],
     "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 {
-        "segment_subject_sc": segment_subject_sc_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_sc": segment_subject_sc_outputs,
-    }.get(t)
 
 
 class SegmentSubjectScOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_subject_sc(...)`.
+    Output object returned when calling `SegmentSubjectScParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,9 +42,9 @@ class SegmentSubjectScOutputs(typing.NamedTuple):
 def segment_subject_sc_params(
     invol: InputPathType,
     outxfm: InputPathType,
-    log: str | None = "outdir/talarach.log",
+    log: str | None = None,
     debug: bool = False,
-) -> SegmentSubjectScParameters:
+) -> SegmentSubjectScParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def segment_subject_sc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segment_subject_sc",
+        "@type": "freesurfer/segment_subject_sc",
         "invol": invol,
         "outxfm": outxfm,
         "debug": debug,
@@ -109,18 +84,18 @@ def segment_subject_sc_cargs(
     cargs.append("segment_subject_sc")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("invol"))
+        execution.input_file(params.get("invol", None))
     ])
     cargs.extend([
         "-xfm",
-        execution.input_file(params.get("outxfm"))
+        execution.input_file(params.get("outxfm", None))
     ])
-    if params.get("log") is not None:
+    if params.get("log", None) is not None:
         cargs.extend([
             "--log",
-            params.get("log")
+            params.get("log", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
     return cargs
 
@@ -140,18 +115,20 @@ def segment_subject_sc_outputs(
     """
     ret = SegmentSubjectScOutputs(
         root=execution.output_file("."),
-        output_xfm_file=execution.output_file(pathlib.Path(params.get("outxfm")).name),
+        output_xfm_file=execution.output_file(pathlib.Path(params.get("outxfm", None)).name),
     )
     return ret
 
 
 def segment_subject_sc_execute(
     params: SegmentSubjectScParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentSubjectScOutputs:
     """
-    Front-end for MINC's mritotal. Computes the Talairach transform for mapping the
-    input volume to the MNI305 space.
+    segment_subject_sc
+    
+    Front-end for MINC's mritotal. Computes the Talairach transform for mapping
+    the input volume to the MNI305 space.
     
     Author: FreeSurfer Developers
     
@@ -159,10 +136,12 @@ def segment_subject_sc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectScOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_SUBJECT_SC_METADATA)
     params = execution.params(params)
     cargs = segment_subject_sc_cargs(params, execution)
     ret = segment_subject_sc_outputs(params, execution)
@@ -173,13 +152,15 @@ def segment_subject_sc_execute(
 def segment_subject_sc(
     invol: InputPathType,
     outxfm: InputPathType,
-    log: str | None = "outdir/talarach.log",
+    log: str | None = None,
     debug: bool = False,
     runner: Runner | None = None,
 ) -> SegmentSubjectScOutputs:
     """
-    Front-end for MINC's mritotal. Computes the Talairach transform for mapping the
-    input volume to the MNI305 space.
+    segment_subject_sc
+    
+    Front-end for MINC's mritotal. Computes the Talairach transform for mapping
+    the input volume to the MNI305 space.
     
     Author: FreeSurfer Developers
     
@@ -194,21 +175,19 @@ def segment_subject_sc(
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectScOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_SUBJECT_SC_METADATA)
     params = segment_subject_sc_params(
         invol=invol,
         outxfm=outxfm,
         log=log,
         debug=debug,
     )
-    return segment_subject_sc_execute(params, execution)
+    return segment_subject_sc_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_SUBJECT_SC_METADATA",
     "SegmentSubjectScOutputs",
-    "SegmentSubjectScParameters",
     "segment_subject_sc",
+    "segment_subject_sc_execute",
     "segment_subject_sc_params",
 ]

niwrap_freesurfer/freesurfer/segment_subject_t1_auto_estimate_alveus_ml.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SEGMENT_SUBJECT_T1_AUTO_ESTIMATE_ALVEUS_ML_METADATA = Metadata(
-    id="d368e081e4e2e487dc1349e034b665a2cdf1f6d5.boutiques",
+    id="789d1c27dc21ca8762405d55ea7fbad93c1f0204.boutiques",
     name="segmentSubjectT1_autoEstimateAlveusML",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ SEGMENT_SUBJECT_T1_AUTO_ESTIMATE_ALVEUS_ML_METADATA = Metadata(
 
 
 SegmentSubjectT1AutoEstimateAlveusMlParameters = typing.TypedDict('SegmentSubjectT1AutoEstimateAlveusMlParameters', {
-    "__STYXTYPE__": typing.Literal["segmentSubjectT1_autoEstimateAlveusML"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/segmentSubjectT1_autoEstimateAlveusML"]],
+    "t1_file": InputPathType,
+    "output_folder": str,
+})
+SegmentSubjectT1AutoEstimateAlveusMlParametersTagged = typing.TypedDict('SegmentSubjectT1AutoEstimateAlveusMlParametersTagged', {
+    "@type": typing.Literal["freesurfer/segmentSubjectT1_autoEstimateAlveusML"],
     "t1_file": InputPathType,
     "output_folder": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "segmentSubjectT1_autoEstimateAlveusML": segment_subject_t1_auto_estimate_alveus_ml_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 {
-        "segmentSubjectT1_autoEstimateAlveusML": segment_subject_t1_auto_estimate_alveus_ml_outputs,
-    }.get(t)
 
 
 class SegmentSubjectT1AutoEstimateAlveusMlOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `segment_subject_t1_auto_estimate_alveus_ml(...)`.
+    Output object returned when calling `SegmentSubjectT1AutoEstimateAlveusMlParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class SegmentSubjectT1AutoEstimateAlveusMlOutputs(typing.NamedTuple):
 def segment_subject_t1_auto_estimate_alveus_ml_params(
     t1_file: InputPathType,
     output_folder: str,
-) -> SegmentSubjectT1AutoEstimateAlveusMlParameters:
+) -> SegmentSubjectT1AutoEstimateAlveusMlParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def segment_subject_t1_auto_estimate_alveus_ml_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "segmentSubjectT1_autoEstimateAlveusML",
+        "@type": "freesurfer/segmentSubjectT1_autoEstimateAlveusML",
         "t1_file": t1_file,
         "output_folder": output_folder,
     }
@@ -98,8 +71,8 @@ def segment_subject_t1_auto_estimate_alveus_ml_cargs(
     """
     cargs = []
     cargs.append("segmentSubjectT1_autoEstimateAlveusML")
-    cargs.append(execution.input_file(params.get("t1_file")))
-    cargs.append(params.get("output_folder"))
+    cargs.append(execution.input_file(params.get("t1_file", None)))
+    cargs.append(params.get("output_folder", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def segment_subject_t1_auto_estimate_alveus_ml_outputs(
     """
     ret = SegmentSubjectT1AutoEstimateAlveusMlOutputs(
         root=execution.output_file("."),
-        segmentation_output=execution.output_file(params.get("output_folder") + "/segmented_output.nii.gz"),
+        segmentation_output=execution.output_file(params.get("output_folder", None) + "/segmented_output.nii.gz"),
     )
     return ret
 
 
 def segment_subject_t1_auto_estimate_alveus_ml_execute(
     params: SegmentSubjectT1AutoEstimateAlveusMlParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SegmentSubjectT1AutoEstimateAlveusMlOutputs:
     """
+    segmentSubjectT1_autoEstimateAlveusML
+    
     A tool that segments T1-weighted MRI data and automatically estimates the
     Alveus.
     
@@ -137,10 +112,12 @@ def segment_subject_t1_auto_estimate_alveus_ml_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectT1AutoEstimateAlveusMlOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SEGMENT_SUBJECT_T1_AUTO_ESTIMATE_ALVEUS_ML_METADATA)
     params = execution.params(params)
     cargs = segment_subject_t1_auto_estimate_alveus_ml_cargs(params, execution)
     ret = segment_subject_t1_auto_estimate_alveus_ml_outputs(params, execution)
@@ -154,6 +131,8 @@ def segment_subject_t1_auto_estimate_alveus_ml(
     runner: Runner | None = None,
 ) -> SegmentSubjectT1AutoEstimateAlveusMlOutputs:
     """
+    segmentSubjectT1_autoEstimateAlveusML
+    
     A tool that segments T1-weighted MRI data and automatically estimates the
     Alveus.
     
@@ -168,19 +147,17 @@ def segment_subject_t1_auto_estimate_alveus_ml(
     Returns:
         NamedTuple of outputs (described in `SegmentSubjectT1AutoEstimateAlveusMlOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SEGMENT_SUBJECT_T1_AUTO_ESTIMATE_ALVEUS_ML_METADATA)
     params = segment_subject_t1_auto_estimate_alveus_ml_params(
         t1_file=t1_file,
         output_folder=output_folder,
     )
-    return segment_subject_t1_auto_estimate_alveus_ml_execute(params, execution)
+    return segment_subject_t1_auto_estimate_alveus_ml_execute(params, runner)
 
 
 __all__ = [
     "SEGMENT_SUBJECT_T1_AUTO_ESTIMATE_ALVEUS_ML_METADATA",
     "SegmentSubjectT1AutoEstimateAlveusMlOutputs",
-    "SegmentSubjectT1AutoEstimateAlveusMlParameters",
     "segment_subject_t1_auto_estimate_alveus_ml",
+    "segment_subject_t1_auto_estimate_alveus_ml_execute",
     "segment_subject_t1_auto_estimate_alveus_ml_params",
 ]