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

niwrap_freesurfer/freesurfer/talsegprob.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TALSEGPROB_METADATA = Metadata(
-    id="142e86d75f85ace3810b1f5f3d1f754943e9619f.boutiques",
+    id="626aac96dc3c17343bf04b0cc1216d01a05c06b7.boutiques",
     name="talsegprob",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,27 @@ TALSEGPROB_METADATA = Metadata(
 
 
 TalsegprobParameters = typing.TypedDict('TalsegprobParameters', {
-    "__STYXTYPE__": typing.Literal["talsegprob"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/talsegprob"]],
+    "subjects_list": typing.NotRequired[list[str] | None],
+    "fsgd_file": typing.NotRequired[InputPathType | None],
+    "segmentation_number": typing.NotRequired[float | None],
+    "second_segmentation_number": typing.NotRequired[float | None],
+    "hippo_flag": bool,
+    "left_hippo_flag": bool,
+    "right_hippo_flag": bool,
+    "segmentation_file": typing.NotRequired[InputPathType | None],
+    "probability_output": typing.NotRequired[str | None],
+    "vote_output": typing.NotRequired[str | None],
+    "concat_output": typing.NotRequired[str | None],
+    "xform_file": typing.NotRequired[InputPathType | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "tmpdir": typing.NotRequired[str | None],
+    "nocleanup_flag": bool,
+    "version_flag": bool,
+    "echo_flag": bool,
+})
+TalsegprobParametersTagged = typing.TypedDict('TalsegprobParametersTagged', {
+    "@type": typing.Literal["freesurfer/talsegprob"],
     "subjects_list": typing.NotRequired[list[str] | None],
     "fsgd_file": typing.NotRequired[InputPathType | None],
     "segmentation_number": typing.NotRequired[float | None],
@@ -33,43 +53,11 @@ TalsegprobParameters = typing.TypedDict('TalsegprobParameters', {
     "version_flag": bool,
     "echo_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 {
-        "talsegprob": talsegprob_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 {
-        "talsegprob": talsegprob_outputs,
-    }.get(t)
 
 
 class TalsegprobOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `talsegprob(...)`.
+    Output object returned when calling `TalsegprobParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +87,7 @@ def talsegprob_params(
     nocleanup_flag: bool = False,
     version_flag: bool = False,
     echo_flag: bool = False,
-) -> TalsegprobParameters:
+) -> TalsegprobParametersTagged:
     """
     Build parameters.
     
@@ -126,7 +114,7 @@ def talsegprob_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "talsegprob",
+        "@type": "freesurfer/talsegprob",
         "hippo_flag": hippo_flag,
         "left_hippo_flag": left_hippo_flag,
         "right_hippo_flag": right_hippo_flag,
@@ -174,72 +162,72 @@ def talsegprob_cargs(
     """
     cargs = []
     cargs.append("talsegprob")
-    if params.get("subjects_list") is not None:
+    if params.get("subjects_list", None) is not None:
         cargs.extend([
             "--subjects",
-            *params.get("subjects_list")
+            *params.get("subjects_list", None)
         ])
-    if params.get("fsgd_file") is not None:
+    if params.get("fsgd_file", None) is not None:
         cargs.extend([
             "--fsgd",
-            execution.input_file(params.get("fsgd_file"))
+            execution.input_file(params.get("fsgd_file", None))
         ])
-    if params.get("segmentation_number") is not None:
+    if params.get("segmentation_number", None) is not None:
         cargs.extend([
             "--seg",
-            str(params.get("segmentation_number"))
+            str(params.get("segmentation_number", None))
         ])
-    if params.get("second_segmentation_number") is not None:
+    if params.get("second_segmentation_number", None) is not None:
         cargs.extend([
             "<--seg",
-            str(params.get("second_segmentation_number"))
+            str(params.get("second_segmentation_number", None))
         ])
-    if params.get("hippo_flag"):
+    if params.get("hippo_flag", False):
         cargs.append("--hippo")
-    if params.get("left_hippo_flag"):
+    if params.get("left_hippo_flag", False):
         cargs.append("--left-hippo")
-    if params.get("right_hippo_flag"):
+    if params.get("right_hippo_flag", False):
         cargs.append("--right-hippo")
-    if params.get("segmentation_file") is not None:
+    if params.get("segmentation_file", None) is not None:
         cargs.extend([
             "--segmentation",
-            execution.input_file(params.get("segmentation_file"))
+            execution.input_file(params.get("segmentation_file", None))
         ])
-    if params.get("probability_output") is not None:
+    if params.get("probability_output", None) is not None:
         cargs.extend([
             "--p",
-            params.get("probability_output")
+            params.get("probability_output", None)
         ])
-    if params.get("vote_output") is not None:
+    if params.get("vote_output", None) is not None:
         cargs.extend([
             "--vote",
-            params.get("vote_output")
+            params.get("vote_output", None)
         ])
-    if params.get("concat_output") is not None:
+    if params.get("concat_output", None) is not None:
         cargs.extend([
             "--c",
-            params.get("concat_output")
+            params.get("concat_output", None)
         ])
-    if params.get("xform_file") is not None:
+    if params.get("xform_file", None) is not None:
         cargs.extend([
             "--xform",
-            execution.input_file(params.get("xform_file"))
+            execution.input_file(params.get("xform_file", None))
         ])
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "--sdir",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("tmpdir") is not None:
+    if params.get("tmpdir", None) is not None:
         cargs.extend([
             "--tmpdir",
-            params.get("tmpdir")
+            params.get("tmpdir", None)
         ])
-    if params.get("nocleanup_flag"):
+    if params.get("nocleanup_flag", False):
         cargs.append("--nocleanup")
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("--version")
-    if params.get("echo_flag"):
+    if params.get("echo_flag", False):
         cargs.append("--echo")
     return cargs
 
@@ -259,20 +247,22 @@ def talsegprob_outputs(
     """
     ret = TalsegprobOutputs(
         root=execution.output_file("."),
-        probability_output_file=execution.output_file(params.get("probability_output")) if (params.get("probability_output") is not None) else None,
-        vote_output_file=execution.output_file(params.get("vote_output")) if (params.get("vote_output") is not None) else None,
-        concat_output_file=execution.output_file(params.get("concat_output")) if (params.get("concat_output") is not None) else None,
+        probability_output_file=execution.output_file(params.get("probability_output", None)) if (params.get("probability_output") is not None) else None,
+        vote_output_file=execution.output_file(params.get("vote_output", None)) if (params.get("vote_output") is not None) else None,
+        concat_output_file=execution.output_file(params.get("concat_output", None)) if (params.get("concat_output") is not None) else None,
     )
     return ret
 
 
 def talsegprob_execute(
     params: TalsegprobParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TalsegprobOutputs:
     """
-    Tool to create a binary probability volume from aseg.mgz based on segmentation
-    numbers, resliced to talirach/MNI305/fsaverage space.
+    talsegprob
+    
+    Tool to create a binary probability volume from aseg.mgz based on
+    segmentation numbers, resliced to talirach/MNI305/fsaverage space.
     
     Author: FreeSurfer Developers
     
@@ -280,10 +270,12 @@ def talsegprob_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TalsegprobOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TALSEGPROB_METADATA)
     params = execution.params(params)
     cargs = talsegprob_cargs(params, execution)
     ret = talsegprob_outputs(params, execution)
@@ -312,8 +304,10 @@ def talsegprob(
     runner: Runner | None = None,
 ) -> TalsegprobOutputs:
     """
-    Tool to create a binary probability volume from aseg.mgz based on segmentation
-    numbers, resliced to talirach/MNI305/fsaverage space.
+    talsegprob
+    
+    Tool to create a binary probability volume from aseg.mgz based on
+    segmentation numbers, resliced to talirach/MNI305/fsaverage space.
     
     Author: FreeSurfer Developers
     
@@ -342,8 +336,6 @@ def talsegprob(
     Returns:
         NamedTuple of outputs (described in `TalsegprobOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TALSEGPROB_METADATA)
     params = talsegprob_params(
         subjects_list=subjects_list,
         fsgd_file=fsgd_file,
@@ -363,13 +355,13 @@ def talsegprob(
         version_flag=version_flag,
         echo_flag=echo_flag,
     )
-    return talsegprob_execute(params, execution)
+    return talsegprob_execute(params, runner)
 
 
 __all__ = [
     "TALSEGPROB_METADATA",
     "TalsegprobOutputs",
-    "TalsegprobParameters",
     "talsegprob",
+    "talsegprob_execute",
     "talsegprob_params",
 ]

niwrap_freesurfer/freesurfer/test_orientation_planes_from_parcellation.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TEST_ORIENTATION_PLANES_FROM_PARCELLATION_METADATA = Metadata(
-    id="d9e4252a13d21003be19f2759c3c32111b98c9e2.boutiques",
+    id="a0e7c2d4d564fe47df1edd4a3975b65bd96d8227.boutiques",
     name="testOrientationPlanesFromParcellation",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ TEST_ORIENTATION_PLANES_FROM_PARCELLATION_METADATA = Metadata(
 
 
 TestOrientationPlanesFromParcellationParameters = typing.TypedDict('TestOrientationPlanesFromParcellationParameters', {
-    "__STYXTYPE__": typing.Literal["testOrientationPlanesFromParcellation"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/testOrientationPlanesFromParcellation"]],
+    "input_file": InputPathType,
+    "output_file": str,
+    "bb_flag": bool,
+})
+TestOrientationPlanesFromParcellationParametersTagged = typing.TypedDict('TestOrientationPlanesFromParcellationParametersTagged', {
+    "@type": typing.Literal["freesurfer/testOrientationPlanesFromParcellation"],
     "input_file": InputPathType,
     "output_file": str,
     "bb_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 {
-        "testOrientationPlanesFromParcellation": test_orientation_planes_from_parcellation_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 TestOrientationPlanesFromParcellationOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `test_orientation_planes_from_parcellation(...)`.
+    Output object returned when calling `TestOrientationPlanesFromParcellationParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def test_orientation_planes_from_parcellation_params(
     input_file: InputPathType,
     output_file: str,
     bb_flag: bool = False,
-) -> TestOrientationPlanesFromParcellationParameters:
+) -> TestOrientationPlanesFromParcellationParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def test_orientation_planes_from_parcellation_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "testOrientationPlanesFromParcellation",
+        "@type": "freesurfer/testOrientationPlanesFromParcellation",
         "input_file": input_file,
         "output_file": output_file,
         "bb_flag": bb_flag,
@@ -101,13 +76,13 @@ def test_orientation_planes_from_parcellation_cargs(
     cargs.append("testOrientationPlanesFromParcellation")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("bb_flag"):
+    if params.get("bb_flag", False):
         cargs.append("-bb")
     return cargs
 
@@ -133,9 +108,11 @@ def test_orientation_planes_from_parcellation_outputs(
 
 def test_orientation_planes_from_parcellation_execute(
     params: TestOrientationPlanesFromParcellationParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TestOrientationPlanesFromParcellationOutputs:
     """
+    testOrientationPlanesFromParcellation
+    
     Tests orientation planes from a given parcellation using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -144,10 +121,12 @@ def test_orientation_planes_from_parcellation_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TestOrientationPlanesFromParcellationOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TEST_ORIENTATION_PLANES_FROM_PARCELLATION_METADATA)
     params = execution.params(params)
     cargs = test_orientation_planes_from_parcellation_cargs(params, execution)
     ret = test_orientation_planes_from_parcellation_outputs(params, execution)
@@ -162,6 +141,8 @@ def test_orientation_planes_from_parcellation(
     runner: Runner | None = None,
 ) -> TestOrientationPlanesFromParcellationOutputs:
     """
+    testOrientationPlanesFromParcellation
+    
     Tests orientation planes from a given parcellation using FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -176,20 +157,18 @@ def test_orientation_planes_from_parcellation(
     Returns:
         NamedTuple of outputs (described in `TestOrientationPlanesFromParcellationOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TEST_ORIENTATION_PLANES_FROM_PARCELLATION_METADATA)
     params = test_orientation_planes_from_parcellation_params(
         input_file=input_file,
         output_file=output_file,
         bb_flag=bb_flag,
     )
-    return test_orientation_planes_from_parcellation_execute(params, execution)
+    return test_orientation_planes_from_parcellation_execute(params, runner)
 
 
 __all__ = [
     "TEST_ORIENTATION_PLANES_FROM_PARCELLATION_METADATA",
     "TestOrientationPlanesFromParcellationOutputs",
-    "TestOrientationPlanesFromParcellationParameters",
     "test_orientation_planes_from_parcellation",
+    "test_orientation_planes_from_parcellation_execute",
     "test_orientation_planes_from_parcellation_params",
 ]

niwrap_freesurfer/freesurfer/test_recon_all_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TEST_RECON_ALL_CSH_METADATA = Metadata(
-    id="ad546a46131f123c3acbd5d9a9ec493899bfd06e.boutiques",
+    id="8a506cfdb2909e12c556c93e0ac799ee0dea072c.boutiques",
     name="test_recon-all.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ TEST_RECON_ALL_CSH_METADATA = Metadata(
 
 
 TestReconAllCshParameters = typing.TypedDict('TestReconAllCshParameters', {
-    "__STYXTYPE__": typing.Literal["test_recon-all.csh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/test_recon-all.csh"]],
+    "reference_subj_source_dir": typing.NotRequired[str | None],
+    "reference_subjid": typing.NotRequired[str | None],
+    "test_subject_dest_dir": typing.NotRequired[str | None],
+    "test_subjid": typing.NotRequired[str | None],
+    "freesurfer_home": typing.NotRequired[str | None],
+    "norecon": bool,
+})
+TestReconAllCshParametersTagged = typing.TypedDict('TestReconAllCshParametersTagged', {
+    "@type": typing.Literal["freesurfer/test_recon-all.csh"],
     "reference_subj_source_dir": typing.NotRequired[str | None],
     "reference_subjid": typing.NotRequired[str | None],
     "test_subject_dest_dir": typing.NotRequired[str | None],
@@ -22,43 +31,11 @@ TestReconAllCshParameters = typing.TypedDict('TestReconAllCshParameters', {
     "freesurfer_home": typing.NotRequired[str | None],
     "norecon": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "test_recon-all.csh": test_recon_all_csh_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 {
-        "test_recon-all.csh": test_recon_all_csh_outputs,
-    }.get(t)
 
 
 class TestReconAllCshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `test_recon_all_csh(...)`.
+    Output object returned when calling `TestReconAllCshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,13 +60,13 @@ class TestReconAllCshOutputs(typing.NamedTuple):
 
 
 def test_recon_all_csh_params(
-    reference_subj_source_dir: str | None = "/space/freesurfer/subjects/test/weekly_test/subjects/x86_64",
-    reference_subjid: str | None = "bert",
-    test_subject_dest_dir: str | None = "/tmp",
-    test_subjid: str | None = "bert",
-    freesurfer_home: str | None = "/usr/local/freesurfer/stable",
+    reference_subj_source_dir: str | None = None,
+    reference_subjid: str | None = None,
+    test_subject_dest_dir: str | None = None,
+    test_subjid: str | None = None,
+    freesurfer_home: str | None = None,
     norecon: bool = False,
-) -> TestReconAllCshParameters:
+) -> TestReconAllCshParametersTagged:
     """
     Build parameters.
     
@@ -104,7 +81,7 @@ def test_recon_all_csh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "test_recon-all.csh",
+        "@type": "freesurfer/test_recon-all.csh",
         "norecon": norecon,
     }
     if reference_subj_source_dir is not None:
@@ -135,32 +112,32 @@ def test_recon_all_csh_cargs(
     """
     cargs = []
     cargs.append("test_recon-all.csh")
-    if params.get("reference_subj_source_dir") is not None:
+    if params.get("reference_subj_source_dir", None) is not None:
         cargs.extend([
             "-rsd",
-            params.get("reference_subj_source_dir")
+            params.get("reference_subj_source_dir", None)
         ])
-    if params.get("reference_subjid") is not None:
+    if params.get("reference_subjid", None) is not None:
         cargs.extend([
             "-rs",
-            params.get("reference_subjid")
+            params.get("reference_subjid", None)
         ])
-    if params.get("test_subject_dest_dir") is not None:
+    if params.get("test_subject_dest_dir", None) is not None:
         cargs.extend([
             "-tsd",
-            params.get("test_subject_dest_dir")
+            params.get("test_subject_dest_dir", None)
         ])
-    if params.get("test_subjid") is not None:
+    if params.get("test_subjid", None) is not None:
         cargs.extend([
             "-ts",
-            params.get("test_subjid")
+            params.get("test_subjid", None)
         ])
-    if params.get("freesurfer_home") is not None:
+    if params.get("freesurfer_home", None) is not None:
         cargs.extend([
             "-fshome",
-            params.get("freesurfer_home")
+            params.get("freesurfer_home", None)
         ])
-    if params.get("norecon"):
+    if params.get("norecon", False):
         cargs.append("-norecon")
     return cargs
 
@@ -195,9 +172,11 @@ def test_recon_all_csh_outputs(
 
 def test_recon_all_csh_execute(
     params: TestReconAllCshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TestReconAllCshOutputs:
     """
+    test_recon-all.csh
+    
     Script for testing recon-all and other utilities with FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -206,10 +185,12 @@ def test_recon_all_csh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TestReconAllCshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TEST_RECON_ALL_CSH_METADATA)
     params = execution.params(params)
     cargs = test_recon_all_csh_cargs(params, execution)
     ret = test_recon_all_csh_outputs(params, execution)
@@ -218,15 +199,17 @@ def test_recon_all_csh_execute(
 
 
 def test_recon_all_csh(
-    reference_subj_source_dir: str | None = "/space/freesurfer/subjects/test/weekly_test/subjects/x86_64",
-    reference_subjid: str | None = "bert",
-    test_subject_dest_dir: str | None = "/tmp",
-    test_subjid: str | None = "bert",
-    freesurfer_home: str | None = "/usr/local/freesurfer/stable",
+    reference_subj_source_dir: str | None = None,
+    reference_subjid: str | None = None,
+    test_subject_dest_dir: str | None = None,
+    test_subjid: str | None = None,
+    freesurfer_home: str | None = None,
     norecon: bool = False,
     runner: Runner | None = None,
 ) -> TestReconAllCshOutputs:
     """
+    test_recon-all.csh
+    
     Script for testing recon-all and other utilities with FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -244,8 +227,6 @@ def test_recon_all_csh(
     Returns:
         NamedTuple of outputs (described in `TestReconAllCshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TEST_RECON_ALL_CSH_METADATA)
     params = test_recon_all_csh_params(
         reference_subj_source_dir=reference_subj_source_dir,
         reference_subjid=reference_subjid,
@@ -254,13 +235,13 @@ def test_recon_all_csh(
         freesurfer_home=freesurfer_home,
         norecon=norecon,
     )
-    return test_recon_all_csh_execute(params, execution)
+    return test_recon_all_csh_execute(params, runner)
 
 
 __all__ = [
     "TEST_RECON_ALL_CSH_METADATA",
     "TestReconAllCshOutputs",
-    "TestReconAllCshParameters",
     "test_recon_all_csh",
+    "test_recon_all_csh_execute",
     "test_recon_all_csh_params",
 ]