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

niwrap_freesurfer/freesurfer/label_elderly_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LABEL_ELDERLY_SUBJECT_METADATA = Metadata(
-    id="49fd247159ed8fb4cfcd93e1479cc302731742ef.boutiques",
+    id="88f5056d9cc874dcca1d06d2abc3d8a98af0f7d4.boutiques",
     name="label_elderly_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ LABEL_ELDERLY_SUBJECT_METADATA = Metadata(
 
 
 LabelElderlySubjectParameters = typing.TypedDict('LabelElderlySubjectParameters', {
-    "__STYXTYPE__": typing.Literal["label_elderly_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/label_elderly_subject"]],
+    "norm_volume": InputPathType,
+    "transform_lta": InputPathType,
+    "classifier_array": typing.NotRequired[InputPathType | None],
+    "aseg_volume": InputPathType,
+})
+LabelElderlySubjectParametersTagged = typing.TypedDict('LabelElderlySubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/label_elderly_subject"],
     "norm_volume": InputPathType,
     "transform_lta": InputPathType,
     "classifier_array": typing.NotRequired[InputPathType | None],
     "aseg_volume": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "label_elderly_subject": label_elderly_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 {
-        "label_elderly_subject": label_elderly_subject_outputs,
-    }.get(t)
 
 
 class LabelElderlySubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `label_elderly_subject(...)`.
+    Output object returned when calling `LabelElderlySubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def label_elderly_subject_params(
     transform_lta: InputPathType,
     aseg_volume: InputPathType,
     classifier_array: InputPathType | None = None,
-) -> LabelElderlySubjectParameters:
+) -> LabelElderlySubjectParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def label_elderly_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "label_elderly_subject",
+        "@type": "freesurfer/label_elderly_subject",
         "norm_volume": norm_volume,
         "transform_lta": transform_lta,
         "aseg_volume": aseg_volume,
@@ -107,11 +82,11 @@ def label_elderly_subject_cargs(
     """
     cargs = []
     cargs.append("label_elderly_subject")
-    cargs.append(execution.input_file(params.get("norm_volume")))
-    cargs.append(execution.input_file(params.get("transform_lta")))
-    if params.get("classifier_array") is not None:
-        cargs.append(execution.input_file(params.get("classifier_array")))
-    cargs.append(execution.input_file(params.get("aseg_volume")))
+    cargs.append(execution.input_file(params.get("norm_volume", None)))
+    cargs.append(execution.input_file(params.get("transform_lta", None)))
+    if params.get("classifier_array", None) is not None:
+        cargs.append(execution.input_file(params.get("classifier_array", None)))
+    cargs.append(execution.input_file(params.get("aseg_volume", None)))
     return cargs
 
 
@@ -130,16 +105,18 @@ def label_elderly_subject_outputs(
     """
     ret = LabelElderlySubjectOutputs(
         root=execution.output_file("."),
-        labeled_volume=execution.output_file(pathlib.Path(params.get("aseg_volume")).name + "_labeled.mgz"),
+        labeled_volume=execution.output_file(pathlib.Path(params.get("aseg_volume", None)).name + "_labeled.mgz"),
     )
     return ret
 
 
 def label_elderly_subject_execute(
     params: LabelElderlySubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LabelElderlySubjectOutputs:
     """
+    label_elderly_subject
+    
     Tool for labeling brain structures in MRI images of elderly subjects using
     Freesurfer.
     
@@ -149,10 +126,12 @@ def label_elderly_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LabelElderlySubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LABEL_ELDERLY_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = label_elderly_subject_cargs(params, execution)
     ret = label_elderly_subject_outputs(params, execution)
@@ -168,6 +147,8 @@ def label_elderly_subject(
     runner: Runner | None = None,
 ) -> LabelElderlySubjectOutputs:
     """
+    label_elderly_subject
+    
     Tool for labeling brain structures in MRI images of elderly subjects using
     Freesurfer.
     
@@ -184,21 +165,19 @@ def label_elderly_subject(
     Returns:
         NamedTuple of outputs (described in `LabelElderlySubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LABEL_ELDERLY_SUBJECT_METADATA)
     params = label_elderly_subject_params(
         norm_volume=norm_volume,
         transform_lta=transform_lta,
         classifier_array=classifier_array,
         aseg_volume=aseg_volume,
     )
-    return label_elderly_subject_execute(params, execution)
+    return label_elderly_subject_execute(params, runner)
 
 
 __all__ = [
     "LABEL_ELDERLY_SUBJECT_METADATA",
     "LabelElderlySubjectOutputs",
-    "LabelElderlySubjectParameters",
     "label_elderly_subject",
+    "label_elderly_subject_execute",
     "label_elderly_subject_params",
 ]

niwrap_freesurfer/freesurfer/label_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LABEL_SUBJECT_METADATA = Metadata(
-    id="2eaea9f29422b9c705dee85559c5b10d1adba05b.boutiques",
+    id="23a6609816c870b65c8a608fab4f8be9a5aa712b.boutiques",
     name="label_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ LABEL_SUBJECT_METADATA = Metadata(
 
 
 LabelSubjectParameters = typing.TypedDict('LabelSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["label_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/label_subject"]],
+    "nu_file": typing.NotRequired[InputPathType | None],
+    "orig_dir": typing.NotRequired[str | None],
+})
+LabelSubjectParametersTagged = typing.TypedDict('LabelSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/label_subject"],
     "nu_file": typing.NotRequired[InputPathType | None],
     "orig_dir": 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 {
-        "label_subject": label_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 {
-        "label_subject": label_subject_outputs,
-    }.get(t)
 
 
 class LabelSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `label_subject(...)`.
+    Output object returned when calling `LabelSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,8 +37,8 @@ class LabelSubjectOutputs(typing.NamedTuple):
 
 def label_subject_params(
     nu_file: InputPathType | None = None,
-    orig_dir: str | None = "/usr/local/freesurfer/subjects",
-) -> LabelSubjectParameters:
+    orig_dir: str | None = None,
+) -> LabelSubjectParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +50,7 @@ def label_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "label_subject",
+        "@type": "freesurfer/label_subject",
     }
     if nu_file is not None:
         params["nu_file"] = nu_file
@@ -101,10 +74,10 @@ def label_subject_cargs(
     """
     cargs = []
     cargs.append("label_subject")
-    if params.get("nu_file") is not None:
-        cargs.append(execution.input_file(params.get("nu_file")))
-    if params.get("orig_dir") is not None:
-        cargs.append(params.get("orig_dir"))
+    if params.get("nu_file", None) is not None:
+        cargs.append(execution.input_file(params.get("nu_file", None)))
+    if params.get("orig_dir", None) is not None:
+        cargs.append(params.get("orig_dir", None))
     return cargs
 
 
@@ -123,16 +96,18 @@ def label_subject_outputs(
     """
     ret = LabelSubjectOutputs(
         root=execution.output_file("."),
-        converted_mnc=execution.output_file("/tmp/nu*.mnc"),
+        converted_mnc=execution.output_file("/tmp/nu.mnc"),
     )
     return ret
 
 
 def label_subject_execute(
     params: LabelSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LabelSubjectOutputs:
     """
+    label_subject
+    
     A tool for labeling subject MRI data in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -141,10 +116,12 @@ def label_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LabelSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LABEL_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = label_subject_cargs(params, execution)
     ret = label_subject_outputs(params, execution)
@@ -154,10 +131,12 @@ def label_subject_execute(
 
 def label_subject(
     nu_file: InputPathType | None = None,
-    orig_dir: str | None = "/usr/local/freesurfer/subjects",
+    orig_dir: str | None = None,
     runner: Runner | None = None,
 ) -> LabelSubjectOutputs:
     """
+    label_subject
+    
     A tool for labeling subject MRI data in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -172,19 +151,17 @@ def label_subject(
     Returns:
         NamedTuple of outputs (described in `LabelSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LABEL_SUBJECT_METADATA)
     params = label_subject_params(
         nu_file=nu_file,
         orig_dir=orig_dir,
     )
-    return label_subject_execute(params, execution)
+    return label_subject_execute(params, runner)
 
 
 __all__ = [
     "LABEL_SUBJECT_METADATA",
     "LabelSubjectOutputs",
-    "LabelSubjectParameters",
     "label_subject",
+    "label_subject_execute",
     "label_subject_params",
 ]

niwrap_freesurfer/freesurfer/label_subject_flash.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LABEL_SUBJECT_FLASH_METADATA = Metadata(
-    id="bcad38440b77e9ce5c271bd713bdd98a72db7cf7.boutiques",
+    id="ad38c6055870e91a0f1d93ac4641df4546d2e1db.boutiques",
     name="label_subject_flash",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ LABEL_SUBJECT_FLASH_METADATA = Metadata(
 
 
 LabelSubjectFlashParameters = typing.TypedDict('LabelSubjectFlashParameters', {
-    "__STYXTYPE__": typing.Literal["label_subject_flash"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/label_subject_flash"]],
+    "tissue_params": InputPathType,
+    "norm_volume": InputPathType,
+    "transform_file": InputPathType,
+    "classifier_array": InputPathType,
+    "aseg_output": str,
+})
+LabelSubjectFlashParametersTagged = typing.TypedDict('LabelSubjectFlashParametersTagged', {
+    "@type": typing.Literal["freesurfer/label_subject_flash"],
     "tissue_params": InputPathType,
     "norm_volume": InputPathType,
     "transform_file": InputPathType,
     "classifier_array": InputPathType,
     "aseg_output": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "label_subject_flash": label_subject_flash_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 {
-        "label_subject_flash": label_subject_flash_outputs,
-    }.get(t)
 
 
 class LabelSubjectFlashOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `label_subject_flash(...)`.
+    Output object returned when calling `LabelSubjectFlashParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def label_subject_flash_params(
     transform_file: InputPathType,
     classifier_array: InputPathType,
     aseg_output: str,
-) -> LabelSubjectFlashParameters:
+) -> LabelSubjectFlashParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def label_subject_flash_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "label_subject_flash",
+        "@type": "freesurfer/label_subject_flash",
         "tissue_params": tissue_params,
         "norm_volume": norm_volume,
         "transform_file": transform_file,
@@ -112,12 +88,12 @@ def label_subject_flash_cargs(
     cargs.append("label_subject_flash")
     cargs.extend([
         "-flash",
-        execution.input_file(params.get("tissue_params"))
+        execution.input_file(params.get("tissue_params", None))
     ])
-    cargs.append(execution.input_file(params.get("norm_volume")))
-    cargs.append(execution.input_file(params.get("transform_file")))
-    cargs.append(execution.input_file(params.get("classifier_array")))
-    cargs.append(params.get("aseg_output"))
+    cargs.append(execution.input_file(params.get("norm_volume", None)))
+    cargs.append(execution.input_file(params.get("transform_file", None)))
+    cargs.append(execution.input_file(params.get("classifier_array", None)))
+    cargs.append(params.get("aseg_output", None))
     return cargs
 
 
@@ -136,18 +112,20 @@ def label_subject_flash_outputs(
     """
     ret = LabelSubjectFlashOutputs(
         root=execution.output_file("."),
-        aseg_outfile=execution.output_file(params.get("aseg_output")),
+        aseg_outfile=execution.output_file(params.get("aseg_output", None)),
     )
     return ret
 
 
 def label_subject_flash_execute(
     params: LabelSubjectFlashParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LabelSubjectFlashOutputs:
     """
-    A tool for labeling brain structures in an MRI dataset using FLASH sequences and
-    the FreeSurfer software.
+    label_subject_flash
+    
+    A tool for labeling brain structures in an MRI dataset using FLASH sequences
+    and the FreeSurfer software.
     
     Author: FreeSurfer Developers
     
@@ -155,10 +133,12 @@ def label_subject_flash_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LabelSubjectFlashOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LABEL_SUBJECT_FLASH_METADATA)
     params = execution.params(params)
     cargs = label_subject_flash_cargs(params, execution)
     ret = label_subject_flash_outputs(params, execution)
@@ -175,8 +155,10 @@ def label_subject_flash(
     runner: Runner | None = None,
 ) -> LabelSubjectFlashOutputs:
     """
-    A tool for labeling brain structures in an MRI dataset using FLASH sequences and
-    the FreeSurfer software.
+    label_subject_flash
+    
+    A tool for labeling brain structures in an MRI dataset using FLASH sequences
+    and the FreeSurfer software.
     
     Author: FreeSurfer Developers
     
@@ -192,8 +174,6 @@ def label_subject_flash(
     Returns:
         NamedTuple of outputs (described in `LabelSubjectFlashOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LABEL_SUBJECT_FLASH_METADATA)
     params = label_subject_flash_params(
         tissue_params=tissue_params,
         norm_volume=norm_volume,
@@ -201,13 +181,13 @@ def label_subject_flash(
         classifier_array=classifier_array,
         aseg_output=aseg_output,
     )
-    return label_subject_flash_execute(params, execution)
+    return label_subject_flash_execute(params, runner)
 
 
 __all__ = [
     "LABEL_SUBJECT_FLASH_METADATA",
     "LabelSubjectFlashOutputs",
-    "LabelSubjectFlashParameters",
     "label_subject_flash",
+    "label_subject_flash_execute",
     "label_subject_flash_params",
 ]

niwrap_freesurfer/freesurfer/label_subject_mixed.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LABEL_SUBJECT_MIXED_METADATA = Metadata(
-    id="3c981548ab479f97d30e80a5cf34b82cfb07797d.boutiques",
+    id="bde43c4e2e9739b290ceba8165f45cc1f30557e8.boutiques",
     name="label_subject_mixed",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ LABEL_SUBJECT_MIXED_METADATA = Metadata(
 
 
 LabelSubjectMixedParameters = typing.TypedDict('LabelSubjectMixedParameters', {
-    "__STYXTYPE__": typing.Literal["label_subject_mixed"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/label_subject_mixed"]],
+    "brain_mask": InputPathType,
+    "norm_volume": InputPathType,
+    "transform": InputPathType,
+    "gca_file": InputPathType,
+    "aseg_output": str,
+})
+LabelSubjectMixedParametersTagged = typing.TypedDict('LabelSubjectMixedParametersTagged', {
+    "@type": typing.Literal["freesurfer/label_subject_mixed"],
     "brain_mask": InputPathType,
     "norm_volume": InputPathType,
     "transform": InputPathType,
     "gca_file": InputPathType,
     "aseg_output": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "label_subject_mixed": label_subject_mixed_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 {
-        "label_subject_mixed": label_subject_mixed_outputs,
-    }.get(t)
 
 
 class LabelSubjectMixedOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `label_subject_mixed(...)`.
+    Output object returned when calling `LabelSubjectMixedParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def label_subject_mixed_params(
     transform: InputPathType,
     gca_file: InputPathType,
     aseg_output: str,
-) -> LabelSubjectMixedParameters:
+) -> LabelSubjectMixedParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def label_subject_mixed_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "label_subject_mixed",
+        "@type": "freesurfer/label_subject_mixed",
         "brain_mask": brain_mask,
         "norm_volume": norm_volume,
         "transform": transform,
@@ -112,12 +88,12 @@ def label_subject_mixed_cargs(
     cargs.append("label_subject_mixed")
     cargs.extend([
         "-mask",
-        execution.input_file(params.get("brain_mask"))
+        execution.input_file(params.get("brain_mask", None))
     ])
-    cargs.append(execution.input_file(params.get("norm_volume")))
-    cargs.append(execution.input_file(params.get("transform")))
-    cargs.append(execution.input_file(params.get("gca_file")))
-    cargs.append(params.get("aseg_output"))
+    cargs.append(execution.input_file(params.get("norm_volume", None)))
+    cargs.append(execution.input_file(params.get("transform", None)))
+    cargs.append(execution.input_file(params.get("gca_file", None)))
+    cargs.append(params.get("aseg_output", None))
     return cargs
 
 
@@ -136,16 +112,18 @@ def label_subject_mixed_outputs(
     """
     ret = LabelSubjectMixedOutputs(
         root=execution.output_file("."),
-        output_aseg=execution.output_file(params.get("aseg_output")),
+        output_aseg=execution.output_file(params.get("aseg_output", None)),
     )
     return ret
 
 
 def label_subject_mixed_execute(
     params: LabelSubjectMixedParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> LabelSubjectMixedOutputs:
     """
+    label_subject_mixed
+    
     Automatic labeling of brain regions using a Gaussian classifier array.
     
     Author: FreeSurfer Developers
@@ -154,10 +132,12 @@ def label_subject_mixed_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `LabelSubjectMixedOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LABEL_SUBJECT_MIXED_METADATA)
     params = execution.params(params)
     cargs = label_subject_mixed_cargs(params, execution)
     ret = label_subject_mixed_outputs(params, execution)
@@ -174,6 +154,8 @@ def label_subject_mixed(
     runner: Runner | None = None,
 ) -> LabelSubjectMixedOutputs:
     """
+    label_subject_mixed
+    
     Automatic labeling of brain regions using a Gaussian classifier array.
     
     Author: FreeSurfer Developers
@@ -190,8 +172,6 @@ def label_subject_mixed(
     Returns:
         NamedTuple of outputs (described in `LabelSubjectMixedOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LABEL_SUBJECT_MIXED_METADATA)
     params = label_subject_mixed_params(
         brain_mask=brain_mask,
         norm_volume=norm_volume,
@@ -199,13 +179,13 @@ def label_subject_mixed(
         gca_file=gca_file,
         aseg_output=aseg_output,
     )
-    return label_subject_mixed_execute(params, execution)
+    return label_subject_mixed_execute(params, runner)
 
 
 __all__ = [
     "LABEL_SUBJECT_MIXED_METADATA",
     "LabelSubjectMixedOutputs",
-    "LabelSubjectMixedParameters",
     "label_subject_mixed",
+    "label_subject_mixed_execute",
     "label_subject_mixed_params",
 ]