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

niwrap_freesurfer/freesurfer/reregister_subject_mixed.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REREGISTER_SUBJECT_MIXED_METADATA = Metadata(
-    id="ca61724bb570a3556d0152f9f5aef400e41c3b8d.boutiques",
+    id="53bd102622c7195f920f7e8d8406505e8cf5d933.boutiques",
     name="reregister_subject_mixed",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ REREGISTER_SUBJECT_MIXED_METADATA = Metadata(
 
 
 ReregisterSubjectMixedParameters = typing.TypedDict('ReregisterSubjectMixedParameters', {
-    "__STYXTYPE__": typing.Literal["reregister_subject_mixed"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/reregister_subject_mixed"]],
+    "input_volume": InputPathType,
+    "output_directory": str,
+    "threads": typing.NotRequired[float | None],
+})
+ReregisterSubjectMixedParametersTagged = typing.TypedDict('ReregisterSubjectMixedParametersTagged', {
+    "@type": typing.Literal["freesurfer/reregister_subject_mixed"],
     "input_volume": InputPathType,
     "output_directory": str,
     "threads": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "reregister_subject_mixed": reregister_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 {
-        "reregister_subject_mixed": reregister_subject_mixed_outputs,
-    }.get(t)
 
 
 class ReregisterSubjectMixedOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `reregister_subject_mixed(...)`.
+    Output object returned when calling `ReregisterSubjectMixedParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,8 +44,8 @@ class ReregisterSubjectMixedOutputs(typing.NamedTuple):
 def reregister_subject_mixed_params(
     input_volume: InputPathType,
     output_directory: str,
-    threads: float | None = 1,
-) -> ReregisterSubjectMixedParameters:
+    threads: float | None = None,
+) -> ReregisterSubjectMixedParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +58,7 @@ def reregister_subject_mixed_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "reregister_subject_mixed",
+        "@type": "freesurfer/reregister_subject_mixed",
         "input_volume": input_volume,
         "output_directory": output_directory,
     }
@@ -108,10 +82,10 @@ def reregister_subject_mixed_cargs(
     """
     cargs = []
     cargs.append("reregister_subject_mixed")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(params.get("output_directory"))
-    if params.get("threads") is not None:
-        cargs.append(str(params.get("threads")))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(params.get("output_directory", None))
+    if params.get("threads", None) is not None:
+        cargs.append(str(params.get("threads", None)))
     return cargs
 
 
@@ -130,8 +104,8 @@ def reregister_subject_mixed_outputs(
     """
     ret = ReregisterSubjectMixedOutputs(
         root=execution.output_file("."),
-        control_points=execution.output_file(params.get("output_directory") + "/mri/fsamples"),
-        intensity_normalized=execution.output_file(params.get("output_directory") + "/mri/norm"),
+        control_points=execution.output_file(params.get("output_directory", None) + "/mri/fsamples"),
+        intensity_normalized=execution.output_file(params.get("output_directory", None) + "/mri/norm"),
         log_file=execution.output_file("talairach.log"),
     )
     return ret
@@ -139,9 +113,11 @@ def reregister_subject_mixed_outputs(
 
 def reregister_subject_mixed_execute(
     params: ReregisterSubjectMixedParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ReregisterSubjectMixedOutputs:
     """
+    reregister_subject_mixed
+    
     Tool for re-registering a subject's MRI volumes using Freesurfer.
     
     Author: FreeSurfer Developers
@@ -150,10 +126,12 @@ def reregister_subject_mixed_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ReregisterSubjectMixedOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REREGISTER_SUBJECT_MIXED_METADATA)
     params = execution.params(params)
     cargs = reregister_subject_mixed_cargs(params, execution)
     ret = reregister_subject_mixed_outputs(params, execution)
@@ -164,10 +142,12 @@ def reregister_subject_mixed_execute(
 def reregister_subject_mixed(
     input_volume: InputPathType,
     output_directory: str,
-    threads: float | None = 1,
+    threads: float | None = None,
     runner: Runner | None = None,
 ) -> ReregisterSubjectMixedOutputs:
     """
+    reregister_subject_mixed
+    
     Tool for re-registering a subject's MRI volumes using Freesurfer.
     
     Author: FreeSurfer Developers
@@ -183,20 +163,18 @@ def reregister_subject_mixed(
     Returns:
         NamedTuple of outputs (described in `ReregisterSubjectMixedOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REREGISTER_SUBJECT_MIXED_METADATA)
     params = reregister_subject_mixed_params(
         input_volume=input_volume,
         output_directory=output_directory,
         threads=threads,
     )
-    return reregister_subject_mixed_execute(params, execution)
+    return reregister_subject_mixed_execute(params, runner)
 
 
 __all__ = [
     "REREGISTER_SUBJECT_MIXED_METADATA",
     "ReregisterSubjectMixedOutputs",
-    "ReregisterSubjectMixedParameters",
     "reregister_subject_mixed",
+    "reregister_subject_mixed_execute",
     "reregister_subject_mixed_params",
 ]

niwrap_freesurfer/freesurfer/rtview.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RTVIEW_METADATA = Metadata(
-    id="830ebe4bbc214db991c14d0846c93a10414a4c26.boutiques",
+    id="2ef4bce55220bcf276d003816688864a2de209aa.boutiques",
     name="rtview",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ RTVIEW_METADATA = Metadata(
 
 
 RtviewParameters = typing.TypedDict('RtviewParameters', {
-    "__STYXTYPE__": typing.Literal["rtview"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/rtview"]],
+    "subject": typing.NotRequired[str | None],
+    "hemi": typing.NotRequired[str | None],
+    "left_hemi": bool,
+    "right_hemi": bool,
+    "eccen": bool,
+    "polar": bool,
+    "real_file": typing.NotRequired[InputPathType | None],
+    "imag_file": typing.NotRequired[InputPathType | None],
+    "fsig_file": typing.NotRequired[InputPathType | None],
+    "reg_file": typing.NotRequired[InputPathType | None],
+    "flat_display": bool,
+    "patch": typing.NotRequired[str | None],
+    "tcl_file": typing.NotRequired[InputPathType | None],
+    "no_cleanup": bool,
+})
+RtviewParametersTagged = typing.TypedDict('RtviewParametersTagged', {
+    "@type": typing.Literal["freesurfer/rtview"],
     "subject": typing.NotRequired[str | None],
     "hemi": typing.NotRequired[str | None],
     "left_hemi": bool,
@@ -30,42 +47,11 @@ RtviewParameters = typing.TypedDict('RtviewParameters', {
     "tcl_file": typing.NotRequired[InputPathType | None],
     "no_cleanup": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "rtview": rtview_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 RtviewOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rtview(...)`.
+    Output object returned when calling `RtviewParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -86,7 +72,7 @@ def rtview_params(
     patch: str | None = None,
     tcl_file: InputPathType | None = None,
     no_cleanup: bool = False,
-) -> RtviewParameters:
+) -> RtviewParametersTagged:
     """
     Build parameters.
     
@@ -110,7 +96,7 @@ def rtview_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rtview",
+        "@type": "freesurfer/rtview",
         "left_hemi": left_hemi,
         "right_hemi": right_hemi,
         "eccen": eccen,
@@ -152,57 +138,57 @@ def rtview_cargs(
     """
     cargs = []
     cargs.append("rtview")
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "--s",
-            params.get("subject")
+            params.get("subject", None)
         ])
-    if params.get("hemi") is not None:
+    if params.get("hemi", None) is not None:
         cargs.extend([
             "--hemi",
-            params.get("hemi")
+            params.get("hemi", None)
         ])
-    if params.get("left_hemi"):
+    if params.get("left_hemi", False):
         cargs.append("--lh")
-    if params.get("right_hemi"):
+    if params.get("right_hemi", False):
         cargs.append("--rh")
-    if params.get("eccen"):
+    if params.get("eccen", False):
         cargs.append("--eccen")
-    if params.get("polar"):
+    if params.get("polar", False):
         cargs.append("--polar")
-    if params.get("real_file") is not None:
+    if params.get("real_file", None) is not None:
         cargs.extend([
             "--real",
-            execution.input_file(params.get("real_file"))
+            execution.input_file(params.get("real_file", None))
         ])
-    if params.get("imag_file") is not None:
+    if params.get("imag_file", None) is not None:
         cargs.extend([
             "--imag",
-            execution.input_file(params.get("imag_file"))
+            execution.input_file(params.get("imag_file", None))
         ])
-    if params.get("fsig_file") is not None:
+    if params.get("fsig_file", None) is not None:
         cargs.extend([
             "--fsig",
-            execution.input_file(params.get("fsig_file"))
+            execution.input_file(params.get("fsig_file", None))
         ])
-    if params.get("reg_file") is not None:
+    if params.get("reg_file", None) is not None:
         cargs.extend([
             "--reg",
-            execution.input_file(params.get("reg_file"))
+            execution.input_file(params.get("reg_file", None))
         ])
-    if params.get("flat_display"):
+    if params.get("flat_display", False):
         cargs.append("--flat")
-    if params.get("patch") is not None:
+    if params.get("patch", None) is not None:
         cargs.extend([
             "--patch",
-            params.get("patch")
+            params.get("patch", None)
         ])
-    if params.get("tcl_file") is not None:
+    if params.get("tcl_file", None) is not None:
         cargs.extend([
             "--tcl",
-            execution.input_file(params.get("tcl_file"))
+            execution.input_file(params.get("tcl_file", None))
         ])
-    if params.get("no_cleanup"):
+    if params.get("no_cleanup", False):
         cargs.append("--no-cleanup")
     return cargs
 
@@ -228,11 +214,14 @@ def rtview_outputs(
 
 def rtview_execute(
     params: RtviewParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RtviewOutputs:
     """
-    View FSFAST version 5 retinotopy data using the color wheel. This is a front-end
-    for tksurfer, setting up the environment for using the color wheel.
+    rtview
+    
+    View FSFAST version 5 retinotopy data using the color wheel. This is a
+    front-end for tksurfer, setting up the environment for using the color
+    wheel.
     
     Author: FreeSurfer Developers
     
@@ -240,10 +229,12 @@ def rtview_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RtviewOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RTVIEW_METADATA)
     params = execution.params(params)
     cargs = rtview_cargs(params, execution)
     ret = rtview_outputs(params, execution)
@@ -269,8 +260,11 @@ def rtview(
     runner: Runner | None = None,
 ) -> RtviewOutputs:
     """
-    View FSFAST version 5 retinotopy data using the color wheel. This is a front-end
-    for tksurfer, setting up the environment for using the color wheel.
+    rtview
+    
+    View FSFAST version 5 retinotopy data using the color wheel. This is a
+    front-end for tksurfer, setting up the environment for using the color
+    wheel.
     
     Author: FreeSurfer Developers
     
@@ -296,8 +290,6 @@ def rtview(
     Returns:
         NamedTuple of outputs (described in `RtviewOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RTVIEW_METADATA)
     params = rtview_params(
         subject=subject,
         hemi=hemi,
@@ -314,13 +306,13 @@ def rtview(
         tcl_file=tcl_file,
         no_cleanup=no_cleanup,
     )
-    return rtview_execute(params, execution)
+    return rtview_execute(params, runner)
 
 
 __all__ = [
     "RTVIEW_METADATA",
     "RtviewOutputs",
-    "RtviewParameters",
     "rtview",
+    "rtview_execute",
     "rtview_params",
 ]

niwrap_freesurfer/freesurfer/run_mris_preproc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RUN_MRIS_PREPROC_METADATA = Metadata(
-    id="3629333e45a8eb1987148cec6b9546163e9cda0d.boutiques",
+    id="62685a598a1cb5e769fc7cc5827353bbdd0e1d41.boutiques",
     name="run_mris_preproc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ RUN_MRIS_PREPROC_METADATA = Metadata(
 
 
 RunMrisPreprocParameters = typing.TypedDict('RunMrisPreprocParameters', {
-    "__STYXTYPE__": typing.Literal["run_mris_preproc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/run_mris_preproc"]],
+    "qdec_table": InputPathType,
+    "target_average": typing.NotRequired[str | None],
+})
+RunMrisPreprocParametersTagged = typing.TypedDict('RunMrisPreprocParametersTagged', {
+    "@type": typing.Literal["freesurfer/run_mris_preproc"],
     "qdec_table": InputPathType,
     "target_average": 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 {
-        "run_mris_preproc": run_mris_preproc_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 RunMrisPreprocOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `run_mris_preproc(...)`.
+    Output object returned when calling `RunMrisPreprocParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class RunMrisPreprocOutputs(typing.NamedTuple):
 def run_mris_preproc_params(
     qdec_table: InputPathType,
     target_average: str | None = None,
-) -> RunMrisPreprocParameters:
+) -> RunMrisPreprocParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def run_mris_preproc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "run_mris_preproc",
+        "@type": "freesurfer/run_mris_preproc",
         "qdec_table": qdec_table,
     }
     if target_average is not None:
@@ -96,9 +70,9 @@ def run_mris_preproc_cargs(
     """
     cargs = []
     cargs.append("run_mris_preproc")
-    cargs.append(execution.input_file(params.get("qdec_table")))
-    if params.get("target_average") is not None:
-        cargs.append(params.get("target_average"))
+    cargs.append(execution.input_file(params.get("qdec_table", None)))
+    if params.get("target_average", None) is not None:
+        cargs.append(params.get("target_average", None))
     return cargs
 
 
@@ -123,11 +97,13 @@ def run_mris_preproc_outputs(
 
 def run_mris_preproc_execute(
     params: RunMrisPreprocParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RunMrisPreprocOutputs:
     """
-    Utility to create pre-smoothed surface data on a target average subject for Qdec
-    application.
+    run_mris_preproc
+    
+    Utility to create pre-smoothed surface data on a target average subject for
+    Qdec application.
     
     Author: FreeSurfer Developers
     
@@ -135,10 +111,12 @@ def run_mris_preproc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RunMrisPreprocOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RUN_MRIS_PREPROC_METADATA)
     params = execution.params(params)
     cargs = run_mris_preproc_cargs(params, execution)
     ret = run_mris_preproc_outputs(params, execution)
@@ -152,8 +130,10 @@ def run_mris_preproc(
     runner: Runner | None = None,
 ) -> RunMrisPreprocOutputs:
     """
-    Utility to create pre-smoothed surface data on a target average subject for Qdec
-    application.
+    run_mris_preproc
+    
+    Utility to create pre-smoothed surface data on a target average subject for
+    Qdec application.
     
     Author: FreeSurfer Developers
     
@@ -166,19 +146,17 @@ def run_mris_preproc(
     Returns:
         NamedTuple of outputs (described in `RunMrisPreprocOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RUN_MRIS_PREPROC_METADATA)
     params = run_mris_preproc_params(
         qdec_table=qdec_table,
         target_average=target_average,
     )
-    return run_mris_preproc_execute(params, execution)
+    return run_mris_preproc_execute(params, runner)
 
 
 __all__ = [
     "RUN_MRIS_PREPROC_METADATA",
     "RunMrisPreprocOutputs",
-    "RunMrisPreprocParameters",
     "run_mris_preproc",
+    "run_mris_preproc_execute",
     "run_mris_preproc_params",
 ]