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

niwrap_freesurfer/freesurfer/tal_compare.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TAL_COMPARE_METADATA = Metadata(
-    id="48a87dd18545a8514cefe13e747f2239a4b0468e.boutiques",
+    id="69e7450b13f782d1237ff9c2a94dbb046eb71dae.boutiques",
     name="tal_compare",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ TAL_COMPARE_METADATA = Metadata(
 
 
 TalCompareParameters = typing.TypedDict('TalCompareParameters', {
-    "__STYXTYPE__": typing.Literal["tal_compare"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/tal_compare"]],
+    "ref_file": InputPathType,
+    "moving_file": InputPathType,
+    "output_file": str,
+    "verbose": bool,
+})
+TalCompareParametersTagged = typing.TypedDict('TalCompareParametersTagged', {
+    "@type": typing.Literal["freesurfer/tal_compare"],
     "ref_file": InputPathType,
     "moving_file": InputPathType,
     "output_file": str,
     "verbose": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "tal_compare": tal_compare_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 {
-        "tal_compare": tal_compare_outputs,
-    }.get(t)
 
 
 class TalCompareOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tal_compare(...)`.
+    Output object returned when calling `TalCompareParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def tal_compare_params(
     moving_file: InputPathType,
     output_file: str,
     verbose: bool = False,
-) -> TalCompareParameters:
+) -> TalCompareParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def tal_compare_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tal_compare",
+        "@type": "freesurfer/tal_compare",
         "ref_file": ref_file,
         "moving_file": moving_file,
         "output_file": output_file,
@@ -106,10 +81,10 @@ def tal_compare_cargs(
     """
     cargs = []
     cargs.append("tal_compare")
-    cargs.append(execution.input_file(params.get("ref_file")))
-    cargs.append(execution.input_file(params.get("moving_file")))
-    cargs.append(params.get("output_file"))
-    if params.get("verbose"):
+    cargs.append(execution.input_file(params.get("ref_file", None)))
+    cargs.append(execution.input_file(params.get("moving_file", None)))
+    cargs.append(params.get("output_file", None))
+    if params.get("verbose", False):
         cargs.append("-v")
     return cargs
 
@@ -129,16 +104,18 @@ def tal_compare_outputs(
     """
     ret = TalCompareOutputs(
         root=execution.output_file("."),
-        comparison_results=execution.output_file(params.get("output_file")),
+        comparison_results=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def tal_compare_execute(
     params: TalCompareParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TalCompareOutputs:
     """
+    tal_compare
+    
     Tool for comparing TAL databases.
     
     Author: FreeSurfer Developers
@@ -147,10 +124,12 @@ def tal_compare_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TalCompareOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TAL_COMPARE_METADATA)
     params = execution.params(params)
     cargs = tal_compare_cargs(params, execution)
     ret = tal_compare_outputs(params, execution)
@@ -166,6 +145,8 @@ def tal_compare(
     runner: Runner | None = None,
 ) -> TalCompareOutputs:
     """
+    tal_compare
+    
     Tool for comparing TAL databases.
     
     Author: FreeSurfer Developers
@@ -181,21 +162,19 @@ def tal_compare(
     Returns:
         NamedTuple of outputs (described in `TalCompareOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TAL_COMPARE_METADATA)
     params = tal_compare_params(
         ref_file=ref_file,
         moving_file=moving_file,
         output_file=output_file,
         verbose=verbose,
     )
-    return tal_compare_execute(params, execution)
+    return tal_compare_execute(params, runner)
 
 
 __all__ = [
     "TAL_COMPARE_METADATA",
     "TalCompareOutputs",
-    "TalCompareParameters",
     "tal_compare",
+    "tal_compare_execute",
     "tal_compare_params",
 ]

niwrap_freesurfer/freesurfer/tal_qc_azs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TAL_QC_AZS_METADATA = Metadata(
-    id="886563f0c6afbd7ecc04616fab1fcccc741bff0c.boutiques",
+    id="ba15945e9f7433adbd377a8a840d236dd9d40a78.boutiques",
     name="tal_QC_AZS",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ TAL_QC_AZS_METADATA = Metadata(
 
 
 TalQcAzsParameters = typing.TypedDict('TalQcAzsParameters', {
-    "__STYXTYPE__": typing.Literal["tal_QC_AZS"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/tal_QC_AZS"]],
+    "logfile": InputPathType,
+})
+TalQcAzsParametersTagged = typing.TypedDict('TalQcAzsParametersTagged', {
+    "@type": typing.Literal["freesurfer/tal_QC_AZS"],
     "logfile": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "tal_QC_AZS": tal_qc_azs_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 TalQcAzsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tal_qc_azs(...)`.
+    Output object returned when calling `TalQcAzsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class TalQcAzsOutputs(typing.NamedTuple):
 
 def tal_qc_azs_params(
     logfile: InputPathType,
-) -> TalQcAzsParameters:
+) -> TalQcAzsParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def tal_qc_azs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tal_QC_AZS",
+        "@type": "freesurfer/tal_QC_AZS",
         "logfile": logfile,
     }
     return params
@@ -91,7 +64,7 @@ def tal_qc_azs_cargs(
     """
     cargs = []
     cargs.append("tal_QC_AZS")
-    cargs.append(execution.input_file(params.get("logfile")))
+    cargs.append(execution.input_file(params.get("logfile", None)))
     return cargs
 
 
@@ -116,9 +89,11 @@ def tal_qc_azs_outputs(
 
 def tal_qc_azs_execute(
     params: TalQcAzsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TalQcAzsOutputs:
     """
+    tal_QC_AZS
+    
     A tool that processes a logfile.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def tal_qc_azs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TalQcAzsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TAL_QC_AZS_METADATA)
     params = execution.params(params)
     cargs = tal_qc_azs_cargs(params, execution)
     ret = tal_qc_azs_outputs(params, execution)
@@ -143,6 +120,8 @@ def tal_qc_azs(
     runner: Runner | None = None,
 ) -> TalQcAzsOutputs:
     """
+    tal_QC_AZS
+    
     A tool that processes a logfile.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def tal_qc_azs(
     Returns:
         NamedTuple of outputs (described in `TalQcAzsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TAL_QC_AZS_METADATA)
     params = tal_qc_azs_params(
         logfile=logfile,
     )
-    return tal_qc_azs_execute(params, execution)
+    return tal_qc_azs_execute(params, runner)
 
 
 __all__ = [
     "TAL_QC_AZS_METADATA",
     "TalQcAzsOutputs",
-    "TalQcAzsParameters",
     "tal_qc_azs",
+    "tal_qc_azs_execute",
     "tal_qc_azs_params",
 ]

niwrap_freesurfer/freesurfer/talairach.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TALAIRACH_METADATA = Metadata(
-    id="f6adc68ec57f0d05e6401ff9644b4f91929f7293.boutiques",
+    id="9eee2557d6100e1b4597a972b7852b28d1472d3c.boutiques",
     name="talairach",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ TALAIRACH_METADATA = Metadata(
 
 
 TalairachParameters = typing.TypedDict('TalairachParameters', {
-    "__STYXTYPE__": typing.Literal["talairach"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/talairach"]],
+    "input_volume": InputPathType,
+    "output_transform": str,
+    "log_flag": bool,
+    "debug_flag": bool,
+})
+TalairachParametersTagged = typing.TypedDict('TalairachParametersTagged', {
+    "@type": typing.Literal["freesurfer/talairach"],
     "input_volume": InputPathType,
     "output_transform": str,
     "log_flag": bool,
     "debug_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 {
-        "talairach": talairach_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 {
-        "talairach": talairach_outputs,
-    }.get(t)
 
 
 class TalairachOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `talairach(...)`.
+    Output object returned when calling `TalairachParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def talairach_params(
     output_transform: str,
     log_flag: bool = False,
     debug_flag: bool = False,
-) -> TalairachParameters:
+) -> TalairachParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def talairach_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "talairach",
+        "@type": "freesurfer/talairach",
         "input_volume": input_volume,
         "output_transform": output_transform,
         "log_flag": log_flag,
@@ -108,15 +83,15 @@ def talairach_cargs(
     cargs.append("talairach")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "-xfm",
-        params.get("output_transform")
+        params.get("output_transform", None)
     ])
-    if params.get("log_flag"):
+    if params.get("log_flag", False):
         cargs.append("--log")
-    if params.get("debug_flag"):
+    if params.get("debug_flag", False):
         cargs.append("--debug")
     return cargs
 
@@ -136,16 +111,18 @@ def talairach_outputs(
     """
     ret = TalairachOutputs(
         root=execution.output_file("."),
-        xfm_output=execution.output_file(params.get("output_transform")),
+        xfm_output=execution.output_file(params.get("output_transform", None)),
     )
     return ret
 
 
 def talairach_execute(
     params: TalairachParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TalairachOutputs:
     """
+    talairach
+    
     Front-end for MINC's mritotal to compute the Talairach transform mapping the
     input volume to the MNI305.
     
@@ -155,10 +132,12 @@ def talairach_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TalairachOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TALAIRACH_METADATA)
     params = execution.params(params)
     cargs = talairach_cargs(params, execution)
     ret = talairach_outputs(params, execution)
@@ -174,6 +153,8 @@ def talairach(
     runner: Runner | None = None,
 ) -> TalairachOutputs:
     """
+    talairach
+    
     Front-end for MINC's mritotal to compute the Talairach transform mapping the
     input volume to the MNI305.
     
@@ -190,21 +171,19 @@ def talairach(
     Returns:
         NamedTuple of outputs (described in `TalairachOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TALAIRACH_METADATA)
     params = talairach_params(
         input_volume=input_volume,
         output_transform=output_transform,
         log_flag=log_flag,
         debug_flag=debug_flag,
     )
-    return talairach_execute(params, execution)
+    return talairach_execute(params, runner)
 
 
 __all__ = [
     "TALAIRACH_METADATA",
     "TalairachOutputs",
-    "TalairachParameters",
     "talairach",
+    "talairach_execute",
     "talairach_params",
 ]

niwrap_freesurfer/freesurfer/talairach2.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TALAIRACH2_METADATA = Metadata(
-    id="200a3bdd395b88d5b03ecdc9cf8d79338e29d2f2.boutiques",
+    id="961c2dcdf92fb148ac4017a4846e6e14777807c9.boutiques",
     name="talairach2",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ TALAIRACH2_METADATA = Metadata(
 
 
 Talairach2Parameters = typing.TypedDict('Talairach2Parameters', {
-    "__STYXTYPE__": typing.Literal["talairach2"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/talairach2"]],
+    "subject_id": str,
+    "mgz_flag": typing.NotRequired[str | None],
+})
+Talairach2ParametersTagged = typing.TypedDict('Talairach2ParametersTagged', {
+    "@type": typing.Literal["freesurfer/talairach2"],
     "subject_id": str,
     "mgz_flag": 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 {
-        "talairach2": talairach2_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 Talairach2Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `talairach2(...)`.
+    Output object returned when calling `Talairach2Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class Talairach2Outputs(typing.NamedTuple):
 def talairach2_params(
     subject_id: str,
     mgz_flag: str | None = None,
-) -> Talairach2Parameters:
+) -> Talairach2ParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def talairach2_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "talairach2",
+        "@type": "freesurfer/talairach2",
         "subject_id": subject_id,
     }
     if mgz_flag is not None:
@@ -96,9 +70,9 @@ def talairach2_cargs(
     """
     cargs = []
     cargs.append("talairach2")
-    cargs.append(params.get("subject_id"))
-    if params.get("mgz_flag") is not None:
-        cargs.append(params.get("mgz_flag"))
+    cargs.append(params.get("subject_id", None))
+    if params.get("mgz_flag", None) is not None:
+        cargs.append(params.get("mgz_flag", None))
     return cargs
 
 
@@ -123,9 +97,11 @@ def talairach2_outputs(
 
 def talairach2_execute(
     params: Talairach2Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Talairach2Outputs:
     """
+    talairach2
+    
     Tool for processing and converting talairach transformation files.
     
     Author: FreeSurfer Developers
@@ -134,10 +110,12 @@ def talairach2_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Talairach2Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TALAIRACH2_METADATA)
     params = execution.params(params)
     cargs = talairach2_cargs(params, execution)
     ret = talairach2_outputs(params, execution)
@@ -151,6 +129,8 @@ def talairach2(
     runner: Runner | None = None,
 ) -> Talairach2Outputs:
     """
+    talairach2
+    
     Tool for processing and converting talairach transformation files.
     
     Author: FreeSurfer Developers
@@ -164,19 +144,17 @@ def talairach2(
     Returns:
         NamedTuple of outputs (described in `Talairach2Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TALAIRACH2_METADATA)
     params = talairach2_params(
         subject_id=subject_id,
         mgz_flag=mgz_flag,
     )
-    return talairach2_execute(params, execution)
+    return talairach2_execute(params, runner)
 
 
 __all__ = [
     "TALAIRACH2_METADATA",
     "Talairach2Outputs",
-    "Talairach2Parameters",
     "talairach2",
+    "talairach2_execute",
     "talairach2_params",
 ]