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

niwrap_freesurfer/freesurfer/mris_ca_label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_CA_LABEL_METADATA = Metadata(
-    id="c1ae5127f6f6b5ab0ae06b72523899f5770f008a.boutiques",
+    id="4e3030103a9aec1b341435a33d42bf9625db48d8.boutiques",
     name="mris_ca_label",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,29 @@ MRIS_CA_LABEL_METADATA = Metadata(
 
 
 MrisCaLabelParameters = typing.TypedDict('MrisCaLabelParameters', {
-    "__STYXTYPE__": typing.Literal["mris_ca_label"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_ca_label"]],
+    "subject": str,
+    "hemi": str,
+    "canonsurf": InputPathType,
+    "classifier": InputPathType,
+    "outputfile": str,
+    "seed": typing.NotRequired[float | None],
+    "sdir": typing.NotRequired[str | None],
+    "orig": typing.NotRequired[str | None],
+    "long_flag": bool,
+    "r": typing.NotRequired[InputPathType | None],
+    "novar_flag": bool,
+    "nbrs": typing.NotRequired[float | None],
+    "f": typing.NotRequired[float | None],
+    "t": typing.NotRequired[InputPathType | None],
+    "p": typing.NotRequired[str | None],
+    "v": typing.NotRequired[float | None],
+    "w": typing.NotRequired[str | None],
+    "help_flag": bool,
+    "version_flag": bool,
+})
+MrisCaLabelParametersTagged = typing.TypedDict('MrisCaLabelParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_ca_label"],
     "subject": str,
     "hemi": str,
     "canonsurf": InputPathType,
@@ -35,43 +57,11 @@ MrisCaLabelParameters = typing.TypedDict('MrisCaLabelParameters', {
     "help_flag": bool,
     "version_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 {
-        "mris_ca_label": mris_ca_label_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 {
-        "mris_ca_label": mris_ca_label_outputs,
-    }.get(t)
 
 
 class MrisCaLabelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_ca_label(...)`.
+    Output object returned when calling `MrisCaLabelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +89,7 @@ def mris_ca_label_params(
     w: str | None = None,
     help_flag: bool = False,
     version_flag: bool = False,
-) -> MrisCaLabelParameters:
+) -> MrisCaLabelParametersTagged:
     """
     Build parameters.
     
@@ -133,7 +123,7 @@ def mris_ca_label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_ca_label",
+        "@type": "freesurfer/mris_ca_label",
         "subject": subject,
         "hemi": hemi,
         "canonsurf": canonsurf,
@@ -182,68 +172,68 @@ def mris_ca_label_cargs(
     """
     cargs = []
     cargs.append("mris_ca_label")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("canonsurf")))
-    cargs.append(execution.input_file(params.get("classifier")))
-    cargs.append(params.get("outputfile"))
-    if params.get("seed") is not None:
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("canonsurf", None)))
+    cargs.append(execution.input_file(params.get("classifier", None)))
+    cargs.append(params.get("outputfile", None))
+    if params.get("seed", None) is not None:
         cargs.extend([
             "-seed",
-            str(params.get("seed"))
+            str(params.get("seed", None))
         ])
-    if params.get("sdir") is not None:
+    if params.get("sdir", None) is not None:
         cargs.extend([
             "-sdir",
-            params.get("sdir")
+            params.get("sdir", None)
         ])
-    if params.get("orig") is not None:
+    if params.get("orig", None) is not None:
         cargs.extend([
             "-orig",
-            params.get("orig")
+            params.get("orig", None)
         ])
-    if params.get("long_flag"):
+    if params.get("long_flag", False):
         cargs.append("-long")
-    if params.get("r") is not None:
+    if params.get("r", None) is not None:
         cargs.extend([
             "-r",
-            execution.input_file(params.get("r"))
+            execution.input_file(params.get("r", None))
         ])
-    if params.get("novar_flag"):
+    if params.get("novar_flag", False):
         cargs.append("-novar")
-    if params.get("nbrs") is not None:
+    if params.get("nbrs", None) is not None:
         cargs.extend([
             "-nbrs",
-            str(params.get("nbrs"))
+            str(params.get("nbrs", None))
         ])
-    if params.get("f") is not None:
+    if params.get("f", None) is not None:
         cargs.extend([
             "-f",
-            str(params.get("f"))
+            str(params.get("f", None))
         ])
-    if params.get("t") is not None:
+    if params.get("t", None) is not None:
         cargs.extend([
             "-t",
-            execution.input_file(params.get("t"))
+            execution.input_file(params.get("t", None))
         ])
-    if params.get("p") is not None:
+    if params.get("p", None) is not None:
         cargs.extend([
             "-p",
-            params.get("p")
+            params.get("p", None)
         ])
-    if params.get("v") is not None:
+    if params.get("v", None) is not None:
         cargs.extend([
             "-v",
-            str(params.get("v"))
+            str(params.get("v", None))
         ])
-    if params.get("w") is not None:
+    if params.get("w", None) is not None:
         cargs.extend([
             "-w",
-            params.get("w")
+            params.get("w", None)
         ])
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("--help")
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("--version")
     return cargs
 
@@ -263,18 +253,20 @@ def mris_ca_label_outputs(
     """
     ret = MrisCaLabelOutputs(
         root=execution.output_file("."),
-        labeled_surface=execution.output_file(params.get("outputfile")),
+        labeled_surface=execution.output_file(params.get("outputfile", None)),
     )
     return ret
 
 
 def mris_ca_label_execute(
     params: MrisCaLabelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisCaLabelOutputs:
     """
-    Produces an annotation file in which each cortical surface vertex is assigned a
-    neuroanatomical label using a previously-prepared atlas file.
+    mris_ca_label
+    
+    Produces an annotation file in which each cortical surface vertex is
+    assigned a neuroanatomical label using a previously-prepared atlas file.
     
     Author: FreeSurfer Developers
     
@@ -282,10 +274,12 @@ def mris_ca_label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisCaLabelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_CA_LABEL_METADATA)
     params = execution.params(params)
     cargs = mris_ca_label_cargs(params, execution)
     ret = mris_ca_label_outputs(params, execution)
@@ -316,8 +310,10 @@ def mris_ca_label(
     runner: Runner | None = None,
 ) -> MrisCaLabelOutputs:
     """
-    Produces an annotation file in which each cortical surface vertex is assigned a
-    neuroanatomical label using a previously-prepared atlas file.
+    mris_ca_label
+    
+    Produces an annotation file in which each cortical surface vertex is
+    assigned a neuroanatomical label using a previously-prepared atlas file.
     
     Author: FreeSurfer Developers
     
@@ -353,8 +349,6 @@ def mris_ca_label(
     Returns:
         NamedTuple of outputs (described in `MrisCaLabelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_CA_LABEL_METADATA)
     params = mris_ca_label_params(
         subject=subject,
         hemi=hemi,
@@ -376,13 +370,13 @@ def mris_ca_label(
         help_flag=help_flag,
         version_flag=version_flag,
     )
-    return mris_ca_label_execute(params, execution)
+    return mris_ca_label_execute(params, runner)
 
 
 __all__ = [
     "MRIS_CA_LABEL_METADATA",
     "MrisCaLabelOutputs",
-    "MrisCaLabelParameters",
     "mris_ca_label",
+    "mris_ca_label_execute",
     "mris_ca_label_params",
 ]

niwrap_freesurfer/freesurfer/mris_ca_train.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_CA_TRAIN_METADATA = Metadata(
-    id="59032030ae6b27b6bf93c0bcf469d00b88f21d33.boutiques",
+    id="cd97052518777c2c7d614dd41b63597ccc99fc63.boutiques",
     name="mris_ca_train",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,36 @@ MRIS_CA_TRAIN_METADATA = Metadata(
 
 
 MrisCaTrainParameters = typing.TypedDict('MrisCaTrainParameters', {
-    "__STYXTYPE__": typing.Literal["mris_ca_train"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_ca_train"]],
+    "hemi": str,
+    "canonsurf": InputPathType,
+    "annot_file": InputPathType,
+    "subjects": list[str],
+    "output_file": str,
+    "sdir": typing.NotRequired[str | None],
+    "nbrs": typing.NotRequired[float | None],
+    "orig": typing.NotRequired[InputPathType | None],
+    "norm1": bool,
+    "norm2": bool,
+    "norm3": bool,
+    "ic": typing.NotRequired[str | None],
+    "sulc": bool,
+    "sulconly": bool,
+    "a": typing.NotRequired[float | None],
+    "parcellation_table": typing.NotRequired[InputPathType | None],
+    "n": typing.NotRequired[float | None],
+    "verbose": typing.NotRequired[float | None],
+    "debug_vertex": typing.NotRequired[float | None],
+    "gcs_means": typing.NotRequired[str | None],
+    "gcs_priors": typing.NotRequired[str | None],
+    "gcs_diff": typing.NotRequired[str | None],
+    "nfill": typing.NotRequired[float | None],
+    "no_fill": bool,
+    "help": bool,
+    "version": bool,
+})
+MrisCaTrainParametersTagged = typing.TypedDict('MrisCaTrainParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_ca_train"],
     "hemi": str,
     "canonsurf": InputPathType,
     "annot_file": InputPathType,
@@ -42,43 +71,11 @@ MrisCaTrainParameters = typing.TypedDict('MrisCaTrainParameters', {
     "help": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_ca_train": mris_ca_train_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 {
-        "mris_ca_train": mris_ca_train_outputs,
-    }.get(t)
 
 
 class MrisCaTrainOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_ca_train(...)`.
+    Output object returned when calling `MrisCaTrainParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -113,7 +110,7 @@ def mris_ca_train_params(
     no_fill: bool = False,
     help_: bool = False,
     version: bool = False,
-) -> MrisCaTrainParameters:
+) -> MrisCaTrainParametersTagged:
     """
     Build parameters.
     
@@ -149,7 +146,7 @@ def mris_ca_train_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_ca_train",
+        "@type": "freesurfer/mris_ca_train",
         "hemi": hemi,
         "canonsurf": canonsurf,
         "annot_file": annot_file,
@@ -208,91 +205,91 @@ def mris_ca_train_cargs(
     """
     cargs = []
     cargs.append("mris_ca_train")
-    cargs.append(params.get("hemi"))
-    cargs.append(execution.input_file(params.get("canonsurf")))
-    cargs.append(execution.input_file(params.get("annot_file")))
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_file"))
-    if params.get("sdir") is not None:
+    cargs.append(params.get("hemi", None))
+    cargs.append(execution.input_file(params.get("canonsurf", None)))
+    cargs.append(execution.input_file(params.get("annot_file", None)))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_file", None))
+    if params.get("sdir", None) is not None:
         cargs.extend([
             "-sdir",
-            params.get("sdir")
+            params.get("sdir", None)
         ])
-    if params.get("nbrs") is not None:
+    if params.get("nbrs", None) is not None:
         cargs.extend([
             "-nbrs",
-            str(params.get("nbrs"))
+            str(params.get("nbrs", None))
         ])
-    if params.get("orig") is not None:
+    if params.get("orig", None) is not None:
         cargs.extend([
             "-orig",
-            execution.input_file(params.get("orig"))
+            execution.input_file(params.get("orig", None))
         ])
-    if params.get("norm1"):
+    if params.get("norm1", False):
         cargs.append("-norm1")
-    if params.get("norm2"):
+    if params.get("norm2", False):
         cargs.append("-norm2")
-    if params.get("norm3"):
+    if params.get("norm3", False):
         cargs.append("-norm3")
-    if params.get("ic") is not None:
+    if params.get("ic", None) is not None:
         cargs.extend([
             "-ic",
-            params.get("ic")
+            params.get("ic", None)
         ])
-    if params.get("sulc"):
+    if params.get("sulc", False):
         cargs.append("-sulc")
-    if params.get("sulconly"):
+    if params.get("sulconly", False):
         cargs.append("-sulconly")
-    if params.get("a") is not None:
+    if params.get("a", None) is not None:
         cargs.extend([
             "-a",
-            str(params.get("a"))
+            str(params.get("a", None))
         ])
-    if params.get("parcellation_table") is not None:
+    if params.get("parcellation_table", None) is not None:
         cargs.extend([
             "-t",
-            execution.input_file(params.get("parcellation_table"))
+            execution.input_file(params.get("parcellation_table", None))
         ])
-    if params.get("n") is not None:
+    if params.get("n", None) is not None:
         cargs.extend([
             "-n",
-            str(params.get("n"))
+            str(params.get("n", None))
         ])
-    if params.get("verbose") is not None:
+    if params.get("verbose", None) is not None:
         cargs.extend([
             "-v",
-            str(params.get("verbose"))
+            str(params.get("verbose", None))
         ])
-    if params.get("debug_vertex") is not None:
+    if params.get("debug_vertex", None) is not None:
         cargs.extend([
             "-debug-vertex",
-            str(params.get("debug_vertex"))
+            str(params.get("debug_vertex", None))
         ])
-    if params.get("gcs_means") is not None:
+    if params.get("gcs_means", None) is not None:
         cargs.extend([
             "-gcs-means",
-            params.get("gcs_means")
+            params.get("gcs_means", None)
         ])
-    if params.get("gcs_priors") is not None:
+    if params.get("gcs_priors", None) is not None:
         cargs.extend([
             "-gcs-priors",
-            params.get("gcs_priors")
+            params.get("gcs_priors", None)
         ])
-    if params.get("gcs_diff") is not None:
+    if params.get("gcs_diff", None) is not None:
         cargs.extend([
             "-gcs-diff",
-            params.get("gcs_diff")
+            params.get("gcs_diff", None)
         ])
-    if params.get("nfill") is not None:
+    if params.get("nfill", None) is not None:
         cargs.extend([
             "-nfill",
-            str(params.get("nfill"))
+            str(params.get("nfill", None))
         ])
-    if params.get("no_fill"):
+    if params.get("no_fill", False):
         cargs.append("-no-fill")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -312,16 +309,18 @@ def mris_ca_train_outputs(
     """
     ret = MrisCaTrainOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_file")),
+        output_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mris_ca_train_execute(
     params: MrisCaTrainParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisCaTrainOutputs:
     """
+    mris_ca_train
+    
     Creates a cortical parcellation atlas file based on one or more annotated
     subjects using probabilistic information.
     
@@ -331,10 +330,12 @@ def mris_ca_train_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisCaTrainOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_CA_TRAIN_METADATA)
     params = execution.params(params)
     cargs = mris_ca_train_cargs(params, execution)
     ret = mris_ca_train_outputs(params, execution)
@@ -372,6 +373,8 @@ def mris_ca_train(
     runner: Runner | None = None,
 ) -> MrisCaTrainOutputs:
     """
+    mris_ca_train
+    
     Creates a cortical parcellation atlas file based on one or more annotated
     subjects using probabilistic information.
     
@@ -411,8 +414,6 @@ def mris_ca_train(
     Returns:
         NamedTuple of outputs (described in `MrisCaTrainOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_CA_TRAIN_METADATA)
     params = mris_ca_train_params(
         hemi=hemi,
         canonsurf=canonsurf,
@@ -441,13 +442,13 @@ def mris_ca_train(
         help_=help_,
         version=version,
     )
-    return mris_ca_train_execute(params, execution)
+    return mris_ca_train_execute(params, runner)
 
 
 __all__ = [
     "MRIS_CA_TRAIN_METADATA",
     "MrisCaTrainOutputs",
-    "MrisCaTrainParameters",
     "mris_ca_train",
+    "mris_ca_train_execute",
     "mris_ca_train_params",
 ]