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

niwrap_freesurfer/freesurfer/pointset2label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 POINTSET2LABEL_METADATA = Metadata(
-    id="8c0b512eb160ace5a62b2299a47ecd6a1783aaf7.boutiques",
+    id="f4764059902744375dae92014efd3b4f3d42b929.boutiques",
     name="pointset2label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ POINTSET2LABEL_METADATA = Metadata(
 
 
 Pointset2labelParameters = typing.TypedDict('Pointset2labelParameters', {
-    "__STYXTYPE__": typing.Literal["pointset2label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/pointset2label"]],
+    "waypoint_file": InputPathType,
+    "input_volume": InputPathType,
+    "label_value": float,
+    "output_volume": str,
+    "clear_option": bool,
+})
+Pointset2labelParametersTagged = typing.TypedDict('Pointset2labelParametersTagged', {
+    "@type": typing.Literal["freesurfer/pointset2label"],
     "waypoint_file": InputPathType,
     "input_volume": InputPathType,
     "label_value": float,
     "output_volume": str,
     "clear_option": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "pointset2label": pointset2label_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 {
-        "pointset2label": pointset2label_outputs,
-    }.get(t)
 
 
 class Pointset2labelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `pointset2label(...)`.
+    Output object returned when calling `Pointset2labelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def pointset2label_params(
     label_value: float,
     output_volume: str,
     clear_option: bool = False,
-) -> Pointset2labelParameters:
+) -> Pointset2labelParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def pointset2label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "pointset2label",
+        "@type": "freesurfer/pointset2label",
         "waypoint_file": waypoint_file,
         "input_volume": input_volume,
         "label_value": label_value,
@@ -110,11 +86,11 @@ def pointset2label_cargs(
     """
     cargs = []
     cargs.append("pointset2label")
-    cargs.append(execution.input_file(params.get("waypoint_file")))
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(str(params.get("label_value")))
-    cargs.append(params.get("output_volume"))
-    if params.get("clear_option"):
+    cargs.append(execution.input_file(params.get("waypoint_file", None)))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(str(params.get("label_value", None)))
+    cargs.append(params.get("output_volume", None))
+    if params.get("clear_option", False):
         cargs.append("-clear")
     return cargs
 
@@ -134,16 +110,18 @@ def pointset2label_outputs(
     """
     ret = Pointset2labelOutputs(
         root=execution.output_file("."),
-        output_label_volume=execution.output_file(params.get("output_volume")),
+        output_label_volume=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def pointset2label_execute(
     params: Pointset2labelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Pointset2labelOutputs:
     """
+    pointset2label
+    
     Tool for applying waypoint labels to a volume.
     
     Author: FreeSurfer Developers
@@ -152,10 +130,12 @@ def pointset2label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Pointset2labelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(POINTSET2LABEL_METADATA)
     params = execution.params(params)
     cargs = pointset2label_cargs(params, execution)
     ret = pointset2label_outputs(params, execution)
@@ -172,6 +152,8 @@ def pointset2label(
     runner: Runner | None = None,
 ) -> Pointset2labelOutputs:
     """
+    pointset2label
+    
     Tool for applying waypoint labels to a volume.
     
     Author: FreeSurfer Developers
@@ -188,8 +170,6 @@ def pointset2label(
     Returns:
         NamedTuple of outputs (described in `Pointset2labelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(POINTSET2LABEL_METADATA)
     params = pointset2label_params(
         waypoint_file=waypoint_file,
         input_volume=input_volume,
@@ -197,13 +177,13 @@ def pointset2label(
         output_volume=output_volume,
         clear_option=clear_option,
     )
-    return pointset2label_execute(params, execution)
+    return pointset2label_execute(params, runner)
 
 
 __all__ = [
     "POINTSET2LABEL_METADATA",
     "Pointset2labelOutputs",
-    "Pointset2labelParameters",
     "pointset2label",
+    "pointset2label_execute",
     "pointset2label_params",
 ]

niwrap_freesurfer/freesurfer/polyorder.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 POLYORDER_METADATA = Metadata(
-    id="e6d4be8d2371cbb8cd8b9c4ced96e4b035574b00.boutiques",
+    id="2b601fbf0ae32a926483834344de385bcab3fb0f.boutiques",
     name="polyorder",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ POLYORDER_METADATA = Metadata(
 
 
 PolyorderParameters = typing.TypedDict('PolyorderParameters', {
-    "__STYXTYPE__": typing.Literal["polyorder"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/polyorder"]],
+    "ntp": float,
+    "tr": float,
+    "cutoff": float,
+})
+PolyorderParametersTagged = typing.TypedDict('PolyorderParametersTagged', {
+    "@type": typing.Literal["freesurfer/polyorder"],
     "ntp": float,
     "tr": float,
     "cutoff": float,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "polyorder": polyorder_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 PolyorderOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `polyorder(...)`.
+    Output object returned when calling `PolyorderParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def polyorder_params(
     ntp: float,
     tr: float,
     cutoff: float,
-) -> PolyorderParameters:
+) -> PolyorderParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def polyorder_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "polyorder",
+        "@type": "freesurfer/polyorder",
         "ntp": ntp,
         "tr": tr,
         "cutoff": cutoff,
@@ -101,15 +76,15 @@ def polyorder_cargs(
     cargs.append("polyorder")
     cargs.extend([
         "--ntp",
-        str(params.get("ntp"))
+        str(params.get("ntp", None))
     ])
     cargs.extend([
         "--TR",
-        str(params.get("tr"))
+        str(params.get("tr", None))
     ])
     cargs.extend([
         "--cutoff",
-        str(params.get("cutoff"))
+        str(params.get("cutoff", None))
     ])
     return cargs
 
@@ -135,11 +110,13 @@ def polyorder_outputs(
 
 def polyorder_execute(
     params: PolyorderParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> PolyorderOutputs:
     """
-    Computes the order of polynomial regressors needed to achieve a highpass filter
-    with the given cutoff frequency.
+    polyorder
+    
+    Computes the order of polynomial regressors needed to achieve a highpass
+    filter with the given cutoff frequency.
     
     Author: FreeSurfer Developers
     
@@ -147,10 +124,12 @@ def polyorder_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `PolyorderOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(POLYORDER_METADATA)
     params = execution.params(params)
     cargs = polyorder_cargs(params, execution)
     ret = polyorder_outputs(params, execution)
@@ -165,8 +144,10 @@ def polyorder(
     runner: Runner | None = None,
 ) -> PolyorderOutputs:
     """
-    Computes the order of polynomial regressors needed to achieve a highpass filter
-    with the given cutoff frequency.
+    polyorder
+    
+    Computes the order of polynomial regressors needed to achieve a highpass
+    filter with the given cutoff frequency.
     
     Author: FreeSurfer Developers
     
@@ -180,20 +161,18 @@ def polyorder(
     Returns:
         NamedTuple of outputs (described in `PolyorderOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(POLYORDER_METADATA)
     params = polyorder_params(
         ntp=ntp,
         tr=tr,
         cutoff=cutoff,
     )
-    return polyorder_execute(params, execution)
+    return polyorder_execute(params, runner)
 
 
 __all__ = [
     "POLYORDER_METADATA",
     "PolyorderOutputs",
-    "PolyorderParameters",
     "polyorder",
+    "polyorder_execute",
     "polyorder_params",
 ]

niwrap_freesurfer/freesurfer/post_recon_all.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 POST_RECON_ALL_METADATA = Metadata(
-    id="443d2c2f1f0c66f957a9df0b715dcdbe0c5294e5.boutiques",
+    id="c54b224b59c4b007fe53766975991354248ee76a.boutiques",
     name="post-recon-all",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,30 @@ POST_RECON_ALL_METADATA = Metadata(
 
 
 PostReconAllParameters = typing.TypedDict('PostReconAllParameters', {
-    "__STYXTYPE__": typing.Literal["post-recon-all"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/post-recon-all"]],
+    "subject": str,
+    "subfields": bool,
+    "no_subfields": bool,
+    "subregions": bool,
+    "no_subregions": bool,
+    "cvs": bool,
+    "no_cvs": bool,
+    "qcache": bool,
+    "no_qcache": bool,
+    "no_sclimbic": bool,
+    "no_hthsu": bool,
+    "no_synthstrip": bool,
+    "no_synthseg": bool,
+    "no_qastats": bool,
+    "no_samseg": bool,
+    "no_xhemi": bool,
+    "no_cos7": bool,
+    "threads": typing.NotRequired[float | None],
+    "force": bool,
+    "exit_on_error": bool,
+})
+PostReconAllParametersTagged = typing.TypedDict('PostReconAllParametersTagged', {
+    "@type": typing.Literal["freesurfer/post-recon-all"],
     "subject": str,
     "subfields": bool,
     "no_subfields": bool,
@@ -36,42 +59,11 @@ PostReconAllParameters = typing.TypedDict('PostReconAllParameters', {
     "force": bool,
     "exit_on_error": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "post-recon-all": post_recon_all_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 PostReconAllOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `post_recon_all(...)`.
+    Output object returned when calling `PostReconAllParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -98,7 +90,7 @@ def post_recon_all_params(
     threads: float | None = None,
     force: bool = False,
     exit_on_error: bool = False,
-) -> PostReconAllParameters:
+) -> PostReconAllParametersTagged:
     """
     Build parameters.
     
@@ -127,7 +119,7 @@ def post_recon_all_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "post-recon-all",
+        "@type": "freesurfer/post-recon-all",
         "subject": subject,
         "subfields": subfields,
         "no_subfields": no_subfields,
@@ -170,48 +162,48 @@ def post_recon_all_cargs(
     cargs.append("post-recon-all")
     cargs.extend([
         "-all",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("subfields"):
+    if params.get("subfields", False):
         cargs.append("--subfields")
-    if params.get("no_subfields"):
+    if params.get("no_subfields", False):
         cargs.append("--no-subfields")
-    if params.get("subregions"):
+    if params.get("subregions", False):
         cargs.append("--subregions")
-    if params.get("no_subregions"):
+    if params.get("no_subregions", False):
         cargs.append("--no-subregions")
-    if params.get("cvs"):
+    if params.get("cvs", False):
         cargs.append("--cvs")
-    if params.get("no_cvs"):
+    if params.get("no_cvs", False):
         cargs.append("--no-cvs")
-    if params.get("qcache"):
+    if params.get("qcache", False):
         cargs.append("--qcache")
-    if params.get("no_qcache"):
+    if params.get("no_qcache", False):
         cargs.append("--no-qcache")
-    if params.get("no_sclimbic"):
+    if params.get("no_sclimbic", False):
         cargs.append("--no-sclimbic")
-    if params.get("no_hthsu"):
+    if params.get("no_hthsu", False):
         cargs.append("--no-hthsu")
-    if params.get("no_synthstrip"):
+    if params.get("no_synthstrip", False):
         cargs.append("--no-synthstrip")
-    if params.get("no_synthseg"):
+    if params.get("no_synthseg", False):
         cargs.append("--no-synthseg")
-    if params.get("no_qastats"):
+    if params.get("no_qastats", False):
         cargs.append("--no-qastats")
-    if params.get("no_samseg"):
+    if params.get("no_samseg", False):
         cargs.append("--no-samseg")
-    if params.get("no_xhemi"):
+    if params.get("no_xhemi", False):
         cargs.append("--no-xhemi")
-    if params.get("no_cos7"):
+    if params.get("no_cos7", False):
         cargs.append("--no-cos7")
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
-    if params.get("force"):
+    if params.get("force", False):
         cargs.append("--force")
-    if params.get("exit_on_error"):
+    if params.get("exit_on_error", False):
         cargs.append("--exit-on-error")
     return cargs
 
@@ -237,9 +229,11 @@ def post_recon_all_outputs(
 
 def post_recon_all_execute(
     params: PostReconAllParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> PostReconAllOutputs:
     """
+    post-recon-all
+    
     Post-processing script typically run after recon-all in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -248,10 +242,12 @@ def post_recon_all_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `PostReconAllOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(POST_RECON_ALL_METADATA)
     params = execution.params(params)
     cargs = post_recon_all_cargs(params, execution)
     ret = post_recon_all_outputs(params, execution)
@@ -283,6 +279,8 @@ def post_recon_all(
     runner: Runner | None = None,
 ) -> PostReconAllOutputs:
     """
+    post-recon-all
+    
     Post-processing script typically run after recon-all in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -314,8 +312,6 @@ def post_recon_all(
     Returns:
         NamedTuple of outputs (described in `PostReconAllOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(POST_RECON_ALL_METADATA)
     params = post_recon_all_params(
         subject=subject,
         subfields=subfields,
@@ -338,13 +334,13 @@ def post_recon_all(
         force=force,
         exit_on_error=exit_on_error,
     )
-    return post_recon_all_execute(params, execution)
+    return post_recon_all_execute(params, runner)
 
 
 __all__ = [
     "POST_RECON_ALL_METADATA",
     "PostReconAllOutputs",
-    "PostReconAllParameters",
     "post_recon_all",
+    "post_recon_all_execute",
     "post_recon_all_params",
 ]