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

niwrap_freesurfer/freesurfer/bugr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BUGR_METADATA = Metadata(
-    id="c59ecc18f09513a64d6c410b4046dd59f641fd90.boutiques",
+    id="807792016b12ce5d8a6fee4fc70af6b9a40e4f20.boutiques",
     name="bugr",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ BUGR_METADATA = Metadata(
 
 
 BugrParameters = typing.TypedDict('BugrParameters', {
-    "__STYXTYPE__": typing.Literal["bugr"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/bugr"]],
+    "subject_name": str,
+    "command_line": str,
+    "error_message": str,
+    "log_file": typing.NotRequired[InputPathType | None],
+})
+BugrParametersTagged = typing.TypedDict('BugrParametersTagged', {
+    "@type": typing.Literal["freesurfer/bugr"],
     "subject_name": str,
     "command_line": str,
     "error_message": str,
     "log_file": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "bugr": bugr_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 BugrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `bugr(...)`.
+    Output object returned when calling `BugrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def bugr_params(
     command_line: str,
     error_message: str,
     log_file: InputPathType | None = None,
-) -> BugrParameters:
+) -> BugrParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def bugr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "bugr",
+        "@type": "freesurfer/bugr",
         "subject_name": subject_name,
         "command_line": command_line,
         "error_message": error_message,
@@ -106,20 +82,20 @@ def bugr_cargs(
     cargs.append("bugr")
     cargs.extend([
         "-subject",
-        params.get("subject_name")
+        params.get("subject_name", None)
     ])
     cargs.extend([
         "-command",
-        params.get("command_line")
+        params.get("command_line", None)
     ])
     cargs.extend([
         "-error",
-        params.get("error_message")
+        params.get("error_message", None)
     ])
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "-log",
-            execution.input_file(params.get("log_file"))
+            execution.input_file(params.get("log_file", None))
         ])
     return cargs
 
@@ -145,9 +121,11 @@ def bugr_outputs(
 
 def bugr_execute(
     params: BugrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BugrOutputs:
     """
+    bugr
+    
     Utility for generating and reporting FreeSurfer bugs.
     
     Author: FreeSurfer Developers
@@ -156,10 +134,12 @@ def bugr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BugrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BUGR_METADATA)
     params = execution.params(params)
     cargs = bugr_cargs(params, execution)
     ret = bugr_outputs(params, execution)
@@ -175,6 +155,8 @@ def bugr(
     runner: Runner | None = None,
 ) -> BugrOutputs:
     """
+    bugr
+    
     Utility for generating and reporting FreeSurfer bugs.
     
     Author: FreeSurfer Developers
@@ -190,21 +172,19 @@ def bugr(
     Returns:
         NamedTuple of outputs (described in `BugrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BUGR_METADATA)
     params = bugr_params(
         subject_name=subject_name,
         command_line=command_line,
         error_message=error_message,
         log_file=log_file,
     )
-    return bugr_execute(params, execution)
+    return bugr_execute(params, runner)
 
 
 __all__ = [
     "BUGR_METADATA",
     "BugrOutputs",
-    "BugrParameters",
     "bugr",
+    "bugr_execute",
     "bugr_params",
 ]

niwrap_freesurfer/freesurfer/build_desikan_killiany_gcs_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BUILD_DESIKAN_KILLIANY_GCS_CSH_METADATA = Metadata(
-    id="5e5a2f630a4fc0d2ffc6f6330bdbd3389407c897.boutiques",
+    id="c49d04436582b3a7e97b189ad8a57b6bfabd4d9d.boutiques",
     name="build_desikan_killiany_gcs.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ BUILD_DESIKAN_KILLIANY_GCS_CSH_METADATA = Metadata(
 
 
 BuildDesikanKillianyGcsCshParameters = typing.TypedDict('BuildDesikanKillianyGcsCshParameters', {
-    "__STYXTYPE__": typing.Literal["build_desikan_killiany_gcs.csh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/build_desikan_killiany_gcs.csh"]],
+    "hemi": str,
+})
+BuildDesikanKillianyGcsCshParametersTagged = typing.TypedDict('BuildDesikanKillianyGcsCshParametersTagged', {
+    "@type": typing.Literal["freesurfer/build_desikan_killiany_gcs.csh"],
     "hemi": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "build_desikan_killiany_gcs.csh": build_desikan_killiany_gcs_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 {
-    }.get(t)
 
 
 class BuildDesikanKillianyGcsCshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `build_desikan_killiany_gcs_csh(...)`.
+    Output object returned when calling `BuildDesikanKillianyGcsCshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class BuildDesikanKillianyGcsCshOutputs(typing.NamedTuple):
 
 def build_desikan_killiany_gcs_csh_params(
     hemi: str,
-) -> BuildDesikanKillianyGcsCshParameters:
+) -> BuildDesikanKillianyGcsCshParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def build_desikan_killiany_gcs_csh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "build_desikan_killiany_gcs.csh",
+        "@type": "freesurfer/build_desikan_killiany_gcs.csh",
         "hemi": hemi,
     }
     return params
@@ -92,7 +65,7 @@ def build_desikan_killiany_gcs_csh_cargs(
     """
     cargs = []
     cargs.append("build_desikan_killiany_gcs.csh")
-    cargs.append(params.get("hemi"))
+    cargs.append(params.get("hemi", None))
     return cargs
 
 
@@ -117,9 +90,11 @@ def build_desikan_killiany_gcs_csh_outputs(
 
 def build_desikan_killiany_gcs_csh_execute(
     params: BuildDesikanKillianyGcsCshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BuildDesikanKillianyGcsCshOutputs:
     """
+    build_desikan_killiany_gcs.csh
+    
     Tool to build Desikan-Killiany cortical parcellation in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -128,10 +103,12 @@ def build_desikan_killiany_gcs_csh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BuildDesikanKillianyGcsCshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BUILD_DESIKAN_KILLIANY_GCS_CSH_METADATA)
     params = execution.params(params)
     cargs = build_desikan_killiany_gcs_csh_cargs(params, execution)
     ret = build_desikan_killiany_gcs_csh_outputs(params, execution)
@@ -144,6 +121,8 @@ def build_desikan_killiany_gcs_csh(
     runner: Runner | None = None,
 ) -> BuildDesikanKillianyGcsCshOutputs:
     """
+    build_desikan_killiany_gcs.csh
+    
     Tool to build Desikan-Killiany cortical parcellation in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -157,18 +136,16 @@ def build_desikan_killiany_gcs_csh(
     Returns:
         NamedTuple of outputs (described in `BuildDesikanKillianyGcsCshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BUILD_DESIKAN_KILLIANY_GCS_CSH_METADATA)
     params = build_desikan_killiany_gcs_csh_params(
         hemi=hemi,
     )
-    return build_desikan_killiany_gcs_csh_execute(params, execution)
+    return build_desikan_killiany_gcs_csh_execute(params, runner)
 
 
 __all__ = [
     "BUILD_DESIKAN_KILLIANY_GCS_CSH_METADATA",
     "BuildDesikanKillianyGcsCshOutputs",
-    "BuildDesikanKillianyGcsCshParameters",
     "build_desikan_killiany_gcs_csh",
+    "build_desikan_killiany_gcs_csh_execute",
     "build_desikan_killiany_gcs_csh_params",
 ]

niwrap_freesurfer/freesurfer/cblumwmgyri.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CBLUMWMGYRI_METADATA = Metadata(
-    id="564e3588afc9810c3dc5013f2e056c14a2f92213.boutiques",
+    id="cf23c8c61932b9a4c478cc41c4057f558a73f699.boutiques",
     name="cblumwmgyri",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ CBLUMWMGYRI_METADATA = Metadata(
 
 
 CblumwmgyriParameters = typing.TypedDict('CblumwmgyriParameters', {
-    "__STYXTYPE__": typing.Literal["cblumwmgyri"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/cblumwmgyri"]],
+    "subject": str,
+    "source_seg": typing.NotRequired[InputPathType | None],
+    "n_erodes_dilates": typing.NotRequired[float | None],
+    "out_seg": typing.NotRequired[str | None],
+    "no_segstats": bool,
+    "subjects_dir": typing.NotRequired[str | None],
+})
+CblumwmgyriParametersTagged = typing.TypedDict('CblumwmgyriParametersTagged', {
+    "@type": typing.Literal["freesurfer/cblumwmgyri"],
     "subject": str,
     "source_seg": typing.NotRequired[InputPathType | None],
     "n_erodes_dilates": typing.NotRequired[float | None],
@@ -22,43 +31,11 @@ CblumwmgyriParameters = typing.TypedDict('CblumwmgyriParameters', {
     "no_segstats": bool,
     "subjects_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 {
-        "cblumwmgyri": cblumwmgyri_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 {
-        "cblumwmgyri": cblumwmgyri_outputs,
-    }.get(t)
 
 
 class CblumwmgyriOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `cblumwmgyri(...)`.
+    Output object returned when calling `CblumwmgyriParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,11 +46,11 @@ class CblumwmgyriOutputs(typing.NamedTuple):
 def cblumwmgyri_params(
     subject: str,
     source_seg: InputPathType | None = None,
-    n_erodes_dilates: float | None = 2,
-    out_seg: str | None = "sourceseg+cblumwmgyri.mgz",
+    n_erodes_dilates: float | None = None,
+    out_seg: str | None = None,
     no_segstats: bool = False,
     subjects_dir: str | None = None,
-) -> CblumwmgyriParameters:
+) -> CblumwmgyriParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def cblumwmgyri_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "cblumwmgyri",
+        "@type": "freesurfer/cblumwmgyri",
         "subject": subject,
         "no_segstats": no_segstats,
     }
@@ -120,29 +97,29 @@ def cblumwmgyri_cargs(
     cargs.append("cblumwmgyri")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("source_seg") is not None:
+    if params.get("source_seg", None) is not None:
         cargs.extend([
             "--seg",
-            execution.input_file(params.get("source_seg"))
+            execution.input_file(params.get("source_seg", None))
         ])
-    if params.get("n_erodes_dilates") is not None:
+    if params.get("n_erodes_dilates", None) is not None:
         cargs.extend([
             "--n",
-            str(params.get("n_erodes_dilates"))
+            str(params.get("n_erodes_dilates", None))
         ])
-    if params.get("out_seg") is not None:
+    if params.get("out_seg", None) is not None:
         cargs.extend([
             "--o",
-            params.get("out_seg")
+            params.get("out_seg", None)
         ])
-    if params.get("no_segstats"):
+    if params.get("no_segstats", False):
         cargs.append("--no-segstats")
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
     return cargs
 
@@ -162,16 +139,18 @@ def cblumwmgyri_outputs(
     """
     ret = CblumwmgyriOutputs(
         root=execution.output_file("."),
-        output_seg_file=execution.output_file(params.get("out_seg")) if (params.get("out_seg") is not None) else None,
+        output_seg_file=execution.output_file(params.get("out_seg", None)) if (params.get("out_seg") is not None) else None,
     )
     return ret
 
 
 def cblumwmgyri_execute(
     params: CblumwmgyriParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> CblumwmgyriOutputs:
     """
+    cblumwmgyri
+    
     Segments cerebellar white matter into gyral and core components using
     geometrical constraints.
     
@@ -181,10 +160,12 @@ def cblumwmgyri_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `CblumwmgyriOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CBLUMWMGYRI_METADATA)
     params = execution.params(params)
     cargs = cblumwmgyri_cargs(params, execution)
     ret = cblumwmgyri_outputs(params, execution)
@@ -195,13 +176,15 @@ def cblumwmgyri_execute(
 def cblumwmgyri(
     subject: str,
     source_seg: InputPathType | None = None,
-    n_erodes_dilates: float | None = 2,
-    out_seg: str | None = "sourceseg+cblumwmgyri.mgz",
+    n_erodes_dilates: float | None = None,
+    out_seg: str | None = None,
     no_segstats: bool = False,
     subjects_dir: str | None = None,
     runner: Runner | None = None,
 ) -> CblumwmgyriOutputs:
     """
+    cblumwmgyri
+    
     Segments cerebellar white matter into gyral and core components using
     geometrical constraints.
     
@@ -220,8 +203,6 @@ def cblumwmgyri(
     Returns:
         NamedTuple of outputs (described in `CblumwmgyriOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CBLUMWMGYRI_METADATA)
     params = cblumwmgyri_params(
         subject=subject,
         source_seg=source_seg,
@@ -230,13 +211,13 @@ def cblumwmgyri(
         no_segstats=no_segstats,
         subjects_dir=subjects_dir,
     )
-    return cblumwmgyri_execute(params, execution)
+    return cblumwmgyri_execute(params, runner)
 
 
 __all__ = [
     "CBLUMWMGYRI_METADATA",
     "CblumwmgyriOutputs",
-    "CblumwmgyriParameters",
     "cblumwmgyri",
+    "cblumwmgyri_execute",
     "cblumwmgyri_params",
 ]

niwrap_freesurfer/freesurfer/check_mcr_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CHECK_MCR_SH_METADATA = Metadata(
-    id="3cf223c7fdc62b166c1577a94bc2b4f19d6881da.boutiques",
+    id="26a2d886f94b630d8a88df334863e396bb69e62a.boutiques",
     name="checkMCR.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ CHECK_MCR_SH_METADATA = Metadata(
 
 
 CheckMcrShParameters = typing.TypedDict('CheckMcrShParameters', {
-    "__STYXTYPE__": typing.Literal["checkMCR.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/checkMCR.sh"]],
+    "help": bool,
+})
+CheckMcrShParametersTagged = typing.TypedDict('CheckMcrShParametersTagged', {
+    "@type": typing.Literal["freesurfer/checkMCR.sh"],
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "checkMCR.sh": check_mcr_sh_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 CheckMcrShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `check_mcr_sh(...)`.
+    Output object returned when calling `CheckMcrShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class CheckMcrShOutputs(typing.NamedTuple):
 
 def check_mcr_sh_params(
     help_: bool = False,
-) -> CheckMcrShParameters:
+) -> CheckMcrShParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def check_mcr_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "checkMCR.sh",
+        "@type": "freesurfer/checkMCR.sh",
         "help": help_,
     }
     return params
@@ -91,7 +64,7 @@ def check_mcr_sh_cargs(
     """
     cargs = []
     cargs.append("checkMCR.sh")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -117,9 +90,11 @@ def check_mcr_sh_outputs(
 
 def check_mcr_sh_execute(
     params: CheckMcrShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> CheckMcrShOutputs:
     """
+    checkMCR.sh
+    
     Script to check for the presence of Matlab Compiler Runtime (MCR) for Matlab
     2019b, used for the hippocampal/amygdala and brainstem modules.
     
@@ -129,10 +104,12 @@ def check_mcr_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `CheckMcrShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CHECK_MCR_SH_METADATA)
     params = execution.params(params)
     cargs = check_mcr_sh_cargs(params, execution)
     ret = check_mcr_sh_outputs(params, execution)
@@ -145,6 +122,8 @@ def check_mcr_sh(
     runner: Runner | None = None,
 ) -> CheckMcrShOutputs:
     """
+    checkMCR.sh
+    
     Script to check for the presence of Matlab Compiler Runtime (MCR) for Matlab
     2019b, used for the hippocampal/amygdala and brainstem modules.
     
@@ -158,18 +137,16 @@ def check_mcr_sh(
     Returns:
         NamedTuple of outputs (described in `CheckMcrShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CHECK_MCR_SH_METADATA)
     params = check_mcr_sh_params(
         help_=help_,
     )
-    return check_mcr_sh_execute(params, execution)
+    return check_mcr_sh_execute(params, runner)
 
 
 __all__ = [
     "CHECK_MCR_SH_METADATA",
     "CheckMcrShOutputs",
-    "CheckMcrShParameters",
     "check_mcr_sh",
+    "check_mcr_sh_execute",
     "check_mcr_sh_params",
 ]