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

niwrap_freesurfer/freesurfer/fiducials_correction.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIDUCIALS_CORRECTION_METADATA = Metadata(
-    id="6d397bd18ad19fd8e968a667c38712a47c10b334.boutiques",
+    id="80fca1b56b5a25bee2228827e9acaebc9dc96725.boutiques",
     name="fiducials_correction",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ FIDUCIALS_CORRECTION_METADATA = Metadata(
 
 
 FiducialsCorrectionParameters = typing.TypedDict('FiducialsCorrectionParameters', {
-    "__STYXTYPE__": typing.Literal["fiducials_correction"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fiducials_correction"]],
+    "input_file": InputPathType,
+    "output_file": str,
+})
+FiducialsCorrectionParametersTagged = typing.TypedDict('FiducialsCorrectionParametersTagged', {
+    "@type": typing.Literal["freesurfer/fiducials_correction"],
     "input_file": InputPathType,
     "output_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fiducials_correction": fiducials_correction_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 {
-        "fiducials_correction": fiducials_correction_outputs,
-    }.get(t)
 
 
 class FiducialsCorrectionOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fiducials_correction(...)`.
+    Output object returned when calling `FiducialsCorrectionParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class FiducialsCorrectionOutputs(typing.NamedTuple):
 def fiducials_correction_params(
     input_file: InputPathType,
     output_file: str,
-) -> FiducialsCorrectionParameters:
+) -> FiducialsCorrectionParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +50,7 @@ def fiducials_correction_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fiducials_correction",
+        "@type": "freesurfer/fiducials_correction",
         "input_file": input_file,
         "output_file": output_file,
     }
@@ -99,8 +72,8 @@ def fiducials_correction_cargs(
     """
     cargs = []
     cargs.append("fiducials_correction")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -119,19 +92,21 @@ def fiducials_correction_outputs(
     """
     ret = FiducialsCorrectionOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")),
+        output_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def fiducials_correction_execute(
     params: FiducialsCorrectionParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FiducialsCorrectionOutputs:
     """
-    A tool for correcting fiducial markers in imaging data. Note: This command has
-    dependency issues with the Qt platform plugin 'xcb'. Ensure dependencies are
-    properly configured.
+    fiducials_correction
+    
+    A tool for correcting fiducial markers in imaging data. Note: This command
+    has dependency issues with the Qt platform plugin 'xcb'. Ensure dependencies
+    are properly configured.
     
     Author: FreeSurfer Developers
     
@@ -139,10 +114,12 @@ def fiducials_correction_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FiducialsCorrectionOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIDUCIALS_CORRECTION_METADATA)
     params = execution.params(params)
     cargs = fiducials_correction_cargs(params, execution)
     ret = fiducials_correction_outputs(params, execution)
@@ -156,9 +133,11 @@ def fiducials_correction(
     runner: Runner | None = None,
 ) -> FiducialsCorrectionOutputs:
     """
-    A tool for correcting fiducial markers in imaging data. Note: This command has
-    dependency issues with the Qt platform plugin 'xcb'. Ensure dependencies are
-    properly configured.
+    fiducials_correction
+    
+    A tool for correcting fiducial markers in imaging data. Note: This command
+    has dependency issues with the Qt platform plugin 'xcb'. Ensure dependencies
+    are properly configured.
     
     Author: FreeSurfer Developers
     
@@ -172,19 +151,17 @@ def fiducials_correction(
     Returns:
         NamedTuple of outputs (described in `FiducialsCorrectionOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIDUCIALS_CORRECTION_METADATA)
     params = fiducials_correction_params(
         input_file=input_file,
         output_file=output_file,
     )
-    return fiducials_correction_execute(params, execution)
+    return fiducials_correction_execute(params, runner)
 
 
 __all__ = [
     "FIDUCIALS_CORRECTION_METADATA",
     "FiducialsCorrectionOutputs",
-    "FiducialsCorrectionParameters",
     "fiducials_correction",
+    "fiducials_correction_execute",
     "fiducials_correction_params",
 ]

niwrap_freesurfer/freesurfer/fix_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIX_SUBJECT_METADATA = Metadata(
-    id="61bfaf4767ebcb038e8eec8be58f3650a3ee7f43.boutiques",
+    id="861f378dbb7b637df9bb663f1304d9a47d7c1f99.boutiques",
     name="fix_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ FIX_SUBJECT_METADATA = Metadata(
 
 
 FixSubjectParameters = typing.TypedDict('FixSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["fix_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fix_subject"]],
+    "arguments": typing.NotRequired[str | None],
+})
+FixSubjectParametersTagged = typing.TypedDict('FixSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/fix_subject"],
     "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 {
-        "fix_subject": fix_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 {
-    }.get(t)
 
 
 class FixSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fix_subject(...)`.
+    Output object returned when calling `FixSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class FixSubjectOutputs(typing.NamedTuple):
 
 def fix_subject_params(
     arguments: str | None = None,
-) -> FixSubjectParameters:
+) -> FixSubjectParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def fix_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fix_subject",
+        "@type": "freesurfer/fix_subject",
     }
     if arguments is not None:
         params["arguments"] = arguments
@@ -93,8 +66,8 @@ def fix_subject_cargs(
     """
     cargs = []
     cargs.append("fix_subject")
-    if params.get("arguments") is not None:
-        cargs.append(params.get("arguments"))
+    if params.get("arguments", None) is not None:
+        cargs.append(params.get("arguments", None))
     return cargs
 
 
@@ -119,9 +92,11 @@ def fix_subject_outputs(
 
 def fix_subject_execute(
     params: FixSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FixSubjectOutputs:
     """
+    fix_subject
+    
     Tool to fix subjects in FreeSurfer, encountered errors due to incorrect path
     handling.
     
@@ -131,10 +106,12 @@ def fix_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FixSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIX_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = fix_subject_cargs(params, execution)
     ret = fix_subject_outputs(params, execution)
@@ -147,6 +124,8 @@ def fix_subject(
     runner: Runner | None = None,
 ) -> FixSubjectOutputs:
     """
+    fix_subject
+    
     Tool to fix subjects in FreeSurfer, encountered errors due to incorrect path
     handling.
     
@@ -161,18 +140,16 @@ def fix_subject(
     Returns:
         NamedTuple of outputs (described in `FixSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIX_SUBJECT_METADATA)
     params = fix_subject_params(
         arguments=arguments,
     )
-    return fix_subject_execute(params, execution)
+    return fix_subject_execute(params, runner)
 
 
 __all__ = [
     "FIX_SUBJECT_METADATA",
     "FixSubjectOutputs",
-    "FixSubjectParameters",
     "fix_subject",
+    "fix_subject_execute",
     "fix_subject_params",
 ]

niwrap_freesurfer/freesurfer/fix_subject_corrected.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIX_SUBJECT_CORRECTED_METADATA = Metadata(
-    id="e9683c6b2300288726f90faacf8034788b095c6c.boutiques",
+    id="37aedcb6955e632e84589ffaec6cf6b262cfcf65.boutiques",
     name="fix_subject_corrected",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ FIX_SUBJECT_CORRECTED_METADATA = Metadata(
 
 
 FixSubjectCorrectedParameters = typing.TypedDict('FixSubjectCorrectedParameters', {
-    "__STYXTYPE__": typing.Literal["fix_subject_corrected"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fix_subject_corrected"]],
+    "subject_directory": str,
+    "output_directory": str,
+})
+FixSubjectCorrectedParametersTagged = typing.TypedDict('FixSubjectCorrectedParametersTagged', {
+    "@type": typing.Literal["freesurfer/fix_subject_corrected"],
     "subject_directory": str,
     "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 {
-        "fix_subject_corrected": fix_subject_corrected_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 FixSubjectCorrectedOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fix_subject_corrected(...)`.
+    Output object returned when calling `FixSubjectCorrectedParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class FixSubjectCorrectedOutputs(typing.NamedTuple):
 def fix_subject_corrected_params(
     subject_directory: str,
     output_directory: str,
-) -> FixSubjectCorrectedParameters:
+) -> FixSubjectCorrectedParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def fix_subject_corrected_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fix_subject_corrected",
+        "@type": "freesurfer/fix_subject_corrected",
         "subject_directory": subject_directory,
         "output_directory": output_directory,
     }
@@ -95,8 +69,8 @@ def fix_subject_corrected_cargs(
     """
     cargs = []
     cargs.append("fix_subject_corrected")
-    cargs.append(params.get("subject_directory"))
-    cargs.append(params.get("output_directory"))
+    cargs.append(params.get("subject_directory", None))
+    cargs.append(params.get("output_directory", None))
     return cargs
 
 
@@ -121,9 +95,11 @@ def fix_subject_corrected_outputs(
 
 def fix_subject_corrected_execute(
     params: FixSubjectCorrectedParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FixSubjectCorrectedOutputs:
     """
+    fix_subject_corrected
+    
     Corrects subject data in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -132,10 +108,12 @@ def fix_subject_corrected_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FixSubjectCorrectedOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIX_SUBJECT_CORRECTED_METADATA)
     params = execution.params(params)
     cargs = fix_subject_corrected_cargs(params, execution)
     ret = fix_subject_corrected_outputs(params, execution)
@@ -149,6 +127,8 @@ def fix_subject_corrected(
     runner: Runner | None = None,
 ) -> FixSubjectCorrectedOutputs:
     """
+    fix_subject_corrected
+    
     Corrects subject data in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -162,19 +142,17 @@ def fix_subject_corrected(
     Returns:
         NamedTuple of outputs (described in `FixSubjectCorrectedOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIX_SUBJECT_CORRECTED_METADATA)
     params = fix_subject_corrected_params(
         subject_directory=subject_directory,
         output_directory=output_directory,
     )
-    return fix_subject_corrected_execute(params, execution)
+    return fix_subject_corrected_execute(params, runner)
 
 
 __all__ = [
     "FIX_SUBJECT_CORRECTED_METADATA",
     "FixSubjectCorrectedOutputs",
-    "FixSubjectCorrectedParameters",
     "fix_subject_corrected",
+    "fix_subject_corrected_execute",
     "fix_subject_corrected_params",
 ]

niwrap_freesurfer/freesurfer/fix_subject_corrected_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FIX_SUBJECT_CORRECTED_RH_METADATA = Metadata(
-    id="ad2ac6b571a8deba7b744b35b4b5690a15f4c644.boutiques",
+    id="f1bbdaf75a1a8e747d2ce52e84a6d82308c56081.boutiques",
     name="fix_subject_corrected-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ FIX_SUBJECT_CORRECTED_RH_METADATA = Metadata(
 
 
 FixSubjectCorrectedRhParameters = typing.TypedDict('FixSubjectCorrectedRhParameters', {
-    "__STYXTYPE__": typing.Literal["fix_subject_corrected-rh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fix_subject_corrected-rh"]],
+    "subject_dir": str,
+})
+FixSubjectCorrectedRhParametersTagged = typing.TypedDict('FixSubjectCorrectedRhParametersTagged', {
+    "@type": typing.Literal["freesurfer/fix_subject_corrected-rh"],
     "subject_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 {
-        "fix_subject_corrected-rh": fix_subject_corrected_rh_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 {
-        "fix_subject_corrected-rh": fix_subject_corrected_rh_outputs,
-    }.get(t)
 
 
 class FixSubjectCorrectedRhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fix_subject_corrected_rh(...)`.
+    Output object returned when calling `FixSubjectCorrectedRhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class FixSubjectCorrectedRhOutputs(typing.NamedTuple):
 
 def fix_subject_corrected_rh_params(
     subject_dir: str,
-) -> FixSubjectCorrectedRhParameters:
+) -> FixSubjectCorrectedRhParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def fix_subject_corrected_rh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fix_subject_corrected-rh",
+        "@type": "freesurfer/fix_subject_corrected-rh",
         "subject_dir": subject_dir,
     }
     return params
@@ -96,7 +68,7 @@ def fix_subject_corrected_rh_cargs(
     cargs.append("fix_subject_corrected-rh")
     cargs.extend([
         "-rh",
-        params.get("subject_dir")
+        params.get("subject_dir", None)
     ])
     return cargs
 
@@ -116,16 +88,18 @@ def fix_subject_corrected_rh_outputs(
     """
     ret = FixSubjectCorrectedRhOutputs(
         root=execution.output_file("."),
-        log_file=execution.output_file(params.get("subject_dir") + "/scripts_output.log"),
+        log_file=execution.output_file(params.get("subject_dir", None) + "/scripts_output.log"),
     )
     return ret
 
 
 def fix_subject_corrected_rh_execute(
     params: FixSubjectCorrectedRhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FixSubjectCorrectedRhOutputs:
     """
+    fix_subject_corrected-rh
+    
     A tool related to FreeSurfer subject correction.
     
     Author: FreeSurfer Developers
@@ -134,10 +108,12 @@ def fix_subject_corrected_rh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FixSubjectCorrectedRhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIX_SUBJECT_CORRECTED_RH_METADATA)
     params = execution.params(params)
     cargs = fix_subject_corrected_rh_cargs(params, execution)
     ret = fix_subject_corrected_rh_outputs(params, execution)
@@ -150,6 +126,8 @@ def fix_subject_corrected_rh(
     runner: Runner | None = None,
 ) -> FixSubjectCorrectedRhOutputs:
     """
+    fix_subject_corrected-rh
+    
     A tool related to FreeSurfer subject correction.
     
     Author: FreeSurfer Developers
@@ -162,18 +140,16 @@ def fix_subject_corrected_rh(
     Returns:
         NamedTuple of outputs (described in `FixSubjectCorrectedRhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FIX_SUBJECT_CORRECTED_RH_METADATA)
     params = fix_subject_corrected_rh_params(
         subject_dir=subject_dir,
     )
-    return fix_subject_corrected_rh_execute(params, execution)
+    return fix_subject_corrected_rh_execute(params, runner)
 
 
 __all__ = [
     "FIX_SUBJECT_CORRECTED_RH_METADATA",
     "FixSubjectCorrectedRhOutputs",
-    "FixSubjectCorrectedRhParameters",
     "fix_subject_corrected_rh",
+    "fix_subject_corrected_rh_execute",
     "fix_subject_corrected_rh_params",
 ]