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

niwrap_afni/afni/v_3dsvm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DSVM_METADATA = Metadata(
-    id="c9d5f8db5e44fe471c2ae707fdea9be43c26edb5.boutiques",
+    id="3ad70f45d095b310a05d2e815ab123318d7dff8f.boutiques",
     name="3dsvm",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,37 @@ V_3DSVM_METADATA = Metadata(
 
 
 V3dsvmParameters = typing.TypedDict('V3dsvmParameters', {
-    "__STYXTYPE__": typing.Literal["3dsvm"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dsvm"]],
+    "train_vol": typing.NotRequired[InputPathType | None],
+    "train_labels": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "no_model_mask": bool,
+    "model": str,
+    "alpha": typing.NotRequired[str | None],
+    "bucket": typing.NotRequired[str | None],
+    "type": typing.NotRequired[typing.Literal["classification", "regression"] | None],
+    "c_value": typing.NotRequired[float | None],
+    "epsilon": typing.NotRequired[float | None],
+    "kernel": typing.NotRequired[typing.Literal["linear", "polynomial", "rbf", "sigmoid"] | None],
+    "d_value": typing.NotRequired[float | None],
+    "gamma": typing.NotRequired[float | None],
+    "s_value": typing.NotRequired[float | None],
+    "r_value": typing.NotRequired[float | None],
+    "max_iterations": typing.NotRequired[float | None],
+    "wout": bool,
+    "test_vol": typing.NotRequired[InputPathType | None],
+    "predictions": typing.NotRequired[str | None],
+    "classout": bool,
+    "nopred_censored": bool,
+    "nodetrend": bool,
+    "nopred_scale": bool,
+    "test_labels": typing.NotRequired[InputPathType | None],
+    "multiclass": typing.NotRequired[typing.Literal["DAG", "vote"] | None],
+    "help": bool,
+    "version": bool,
+})
+V3dsvmParametersTagged = typing.TypedDict('V3dsvmParametersTagged', {
+    "@type": typing.Literal["afni/3dsvm"],
     "train_vol": typing.NotRequired[InputPathType | None],
     "train_labels": typing.NotRequired[InputPathType | None],
     "mask": typing.NotRequired[InputPathType | None],
@@ -43,43 +73,11 @@ V3dsvmParameters = typing.TypedDict('V3dsvmParameters', {
     "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 {
-        "3dsvm": v_3dsvm_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 {
-        "3dsvm": v_3dsvm_outputs,
-    }.get(t)
 
 
 class V3dsvmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dsvm(...)`.
+    Output object returned when calling `V3dsvmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -121,7 +119,7 @@ def v_3dsvm_params(
     multiclass: typing.Literal["DAG", "vote"] | None = None,
     help_: bool = False,
     version: bool = False,
-) -> V3dsvmParameters:
+) -> V3dsvmParametersTagged:
     """
     Build parameters.
     
@@ -169,7 +167,7 @@ def v_3dsvm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dsvm",
+        "@type": "afni/3dsvm",
         "no_model_mask": no_model_mask,
         "model": model,
         "wout": wout,
@@ -234,115 +232,115 @@ def v_3dsvm_cargs(
     """
     cargs = []
     cargs.append("3dsvm")
-    if params.get("train_vol") is not None:
+    if params.get("train_vol", None) is not None:
         cargs.extend([
             "-trainvol",
-            execution.input_file(params.get("train_vol"))
+            execution.input_file(params.get("train_vol", None))
         ])
-    if params.get("train_labels") is not None:
+    if params.get("train_labels", None) is not None:
         cargs.extend([
             "-trainlabels",
-            execution.input_file(params.get("train_labels"))
+            execution.input_file(params.get("train_labels", None))
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("no_model_mask"):
+    if params.get("no_model_mask", False):
         cargs.append("-nomodelmask")
     cargs.extend([
         "-model",
-        params.get("model")
+        params.get("model", None)
     ])
-    if params.get("alpha") is not None:
+    if params.get("alpha", None) is not None:
         cargs.extend([
             "-alpha",
-            params.get("alpha")
+            params.get("alpha", None)
         ])
-    if params.get("bucket") is not None:
+    if params.get("bucket", None) is not None:
         cargs.extend([
             "-bucket",
-            params.get("bucket")
+            params.get("bucket", None)
         ])
-    if params.get("type") is not None:
+    if params.get("type", None) is not None:
         cargs.extend([
             "-type",
-            params.get("type")
+            params.get("type", None)
         ])
-    if params.get("c_value") is not None:
+    if params.get("c_value", None) is not None:
         cargs.extend([
             "-c",
-            str(params.get("c_value"))
+            str(params.get("c_value", None))
         ])
-    if params.get("epsilon") is not None:
+    if params.get("epsilon", None) is not None:
         cargs.extend([
             "-e",
-            str(params.get("epsilon"))
+            str(params.get("epsilon", None))
         ])
-    if params.get("kernel") is not None:
+    if params.get("kernel", None) is not None:
         cargs.extend([
             "-kernel",
-            params.get("kernel")
+            params.get("kernel", None)
         ])
-    if params.get("d_value") is not None:
+    if params.get("d_value", None) is not None:
         cargs.extend([
             "-d",
-            str(params.get("d_value"))
+            str(params.get("d_value", None))
         ])
-    if params.get("gamma") is not None:
+    if params.get("gamma", None) is not None:
         cargs.extend([
             "-g",
-            str(params.get("gamma"))
+            str(params.get("gamma", None))
         ])
-    if params.get("s_value") is not None:
+    if params.get("s_value", None) is not None:
         cargs.extend([
             "-s",
-            str(params.get("s_value"))
+            str(params.get("s_value", None))
         ])
-    if params.get("r_value") is not None:
+    if params.get("r_value", None) is not None:
         cargs.extend([
             "-r",
-            str(params.get("r_value"))
+            str(params.get("r_value", None))
         ])
-    if params.get("max_iterations") is not None:
+    if params.get("max_iterations", None) is not None:
         cargs.extend([
             "-max_iterations",
-            str(params.get("max_iterations"))
+            str(params.get("max_iterations", None))
         ])
-    if params.get("wout"):
+    if params.get("wout", False):
         cargs.append("-wout")
-    if params.get("test_vol") is not None:
+    if params.get("test_vol", None) is not None:
         cargs.extend([
             "-testvol",
-            execution.input_file(params.get("test_vol"))
+            execution.input_file(params.get("test_vol", None))
         ])
-    if params.get("predictions") is not None:
+    if params.get("predictions", None) is not None:
         cargs.extend([
             "-predictions",
-            params.get("predictions")
+            params.get("predictions", None)
         ])
-    if params.get("classout"):
+    if params.get("classout", False):
         cargs.append("-classout")
-    if params.get("nopred_censored"):
+    if params.get("nopred_censored", False):
         cargs.append("-nopredcensored")
-    if params.get("nodetrend"):
+    if params.get("nodetrend", False):
         cargs.append("-nodetrend")
-    if params.get("nopred_scale"):
+    if params.get("nopred_scale", False):
         cargs.append("-nopredscale")
-    if params.get("test_labels") is not None:
+    if params.get("test_labels", None) is not None:
         cargs.extend([
             "-testlabels",
-            execution.input_file(params.get("test_labels"))
+            execution.input_file(params.get("test_labels", None))
         ])
-    if params.get("multiclass") is not None:
+    if params.get("multiclass", None) is not None:
         cargs.extend([
             "-multiclass",
-            params.get("multiclass")
+            params.get("multiclass", None)
         ])
-    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
 
@@ -372,9 +370,11 @@ def v_3dsvm_outputs(
 
 def v_3dsvm_execute(
     params: V3dsvmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dsvmOutputs:
     """
+    3dsvm
+    
     Support vector machine analysis of brain data using the SVM-light package.
     
     Author: AFNI Developers
@@ -383,10 +383,12 @@ def v_3dsvm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dsvmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DSVM_METADATA)
     params = execution.params(params)
     cargs = v_3dsvm_cargs(params, execution)
     ret = v_3dsvm_outputs(params, execution)
@@ -425,6 +427,8 @@ def v_3dsvm(
     runner: Runner | None = None,
 ) -> V3dsvmOutputs:
     """
+    3dsvm
+    
     Support vector machine analysis of brain data using the SVM-light package.
     
     Author: AFNI Developers
@@ -475,8 +479,6 @@ def v_3dsvm(
     Returns:
         NamedTuple of outputs (described in `V3dsvmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DSVM_METADATA)
     params = v_3dsvm_params(
         train_vol=train_vol,
         train_labels=train_labels,
@@ -506,13 +508,13 @@ def v_3dsvm(
         help_=help_,
         version=version,
     )
-    return v_3dsvm_execute(params, execution)
+    return v_3dsvm_execute(params, runner)
 
 
 __all__ = [
     "V3dsvmOutputs",
-    "V3dsvmParameters",
     "V_3DSVM_METADATA",
     "v_3dsvm",
+    "v_3dsvm_execute",
     "v_3dsvm_params",
 ]

niwrap_afni/afni/v_3dsvm_linpredict.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DSVM_LINPREDICT_METADATA = Metadata(
-    id="75accbcc401ca78691df247e44440c27677dbbec.boutiques",
+    id="0dff3a78cf5e724eaa03100a73cf96116889b8fb.boutiques",
     name="3dsvm_linpredict",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_3DSVM_LINPREDICT_METADATA = Metadata(
 
 
 V3dsvmLinpredictParameters = typing.TypedDict('V3dsvmLinpredictParameters', {
-    "__STYXTYPE__": typing.Literal["3dsvm_linpredict"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dsvm_linpredict"]],
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "weight_vector": InputPathType,
+    "input_dataset": str,
+})
+V3dsvmLinpredictParametersTagged = typing.TypedDict('V3dsvmLinpredictParametersTagged', {
+    "@type": typing.Literal["afni/3dsvm_linpredict"],
     "mask_dataset": typing.NotRequired[InputPathType | None],
     "weight_vector": InputPathType,
     "input_dataset": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dsvm_linpredict": v_3dsvm_linpredict_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 {
-        "3dsvm_linpredict": v_3dsvm_linpredict_outputs,
-    }.get(t)
 
 
 class V3dsvmLinpredictOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dsvm_linpredict(...)`.
+    Output object returned when calling `V3dsvmLinpredictParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def v_3dsvm_linpredict_params(
     weight_vector: InputPathType,
     input_dataset: str,
     mask_dataset: InputPathType | None = None,
-) -> V3dsvmLinpredictParameters:
+) -> V3dsvmLinpredictParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +56,7 @@ def v_3dsvm_linpredict_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dsvm_linpredict",
+        "@type": "afni/3dsvm_linpredict",
         "weight_vector": weight_vector,
         "input_dataset": input_dataset,
     }
@@ -106,13 +80,13 @@ def v_3dsvm_linpredict_cargs(
     """
     cargs = []
     cargs.append("3dsvm_linpredict")
-    if params.get("mask_dataset") is not None:
+    if params.get("mask_dataset", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_dataset"))
+            execution.input_file(params.get("mask_dataset", None))
         ])
-    cargs.append(execution.input_file(params.get("weight_vector")))
-    cargs.append(params.get("input_dataset"))
+    cargs.append(execution.input_file(params.get("weight_vector", None)))
+    cargs.append(params.get("input_dataset", None))
     return cargs
 
 
@@ -138,9 +112,11 @@ def v_3dsvm_linpredict_outputs(
 
 def v_3dsvm_linpredict_execute(
     params: V3dsvmLinpredictParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dsvmLinpredictOutputs:
     """
+    3dsvm_linpredict
+    
     Linear prediction for weights from 3dsvm.
     
     Author: AFNI Developers
@@ -149,10 +125,12 @@ def v_3dsvm_linpredict_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dsvmLinpredictOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DSVM_LINPREDICT_METADATA)
     params = execution.params(params)
     cargs = v_3dsvm_linpredict_cargs(params, execution)
     ret = v_3dsvm_linpredict_outputs(params, execution)
@@ -167,6 +145,8 @@ def v_3dsvm_linpredict(
     runner: Runner | None = None,
 ) -> V3dsvmLinpredictOutputs:
     """
+    3dsvm_linpredict
+    
     Linear prediction for weights from 3dsvm.
     
     Author: AFNI Developers
@@ -184,20 +164,18 @@ def v_3dsvm_linpredict(
     Returns:
         NamedTuple of outputs (described in `V3dsvmLinpredictOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DSVM_LINPREDICT_METADATA)
     params = v_3dsvm_linpredict_params(
         mask_dataset=mask_dataset,
         weight_vector=weight_vector,
         input_dataset=input_dataset,
     )
-    return v_3dsvm_linpredict_execute(params, execution)
+    return v_3dsvm_linpredict_execute(params, runner)
 
 
 __all__ = [
     "V3dsvmLinpredictOutputs",
-    "V3dsvmLinpredictParameters",
     "V_3DSVM_LINPREDICT_METADATA",
     "v_3dsvm_linpredict",
+    "v_3dsvm_linpredict_execute",
     "v_3dsvm_linpredict_params",
 ]

niwrap_afni/afni/v_3dto_xdataset.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DTO_XDATASET_METADATA = Metadata(
-    id="9009e607061b1ff9ecff65e2bed0504b53b16aea.boutiques",
+    id="d2eac774e19a889458cfb0fa5143f310fa015e21.boutiques",
     name="3dtoXdataset",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_3DTO_XDATASET_METADATA = Metadata(
 
 
 V3dtoXdatasetParameters = typing.TypedDict('V3dtoXdatasetParameters', {
-    "__STYXTYPE__": typing.Literal["3dtoXdataset"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dtoXdataset"]],
+    "prefix": str,
+    "mask": InputPathType,
+    "input_files": list[InputPathType],
+})
+V3dtoXdatasetParametersTagged = typing.TypedDict('V3dtoXdatasetParametersTagged', {
+    "@type": typing.Literal["afni/3dtoXdataset"],
     "prefix": str,
     "mask": InputPathType,
     "input_files": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dtoXdataset": v_3dto_xdataset_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 {
-        "3dtoXdataset": v_3dto_xdataset_outputs,
-    }.get(t)
 
 
 class V3dtoXdatasetOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dto_xdataset(...)`.
+    Output object returned when calling `V3dtoXdatasetParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def v_3dto_xdataset_params(
     prefix: str,
     mask: InputPathType,
     input_files: list[InputPathType],
-) -> V3dtoXdatasetParameters:
+) -> V3dtoXdatasetParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def v_3dto_xdataset_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dtoXdataset",
+        "@type": "afni/3dtoXdataset",
         "prefix": prefix,
         "mask": mask,
         "input_files": input_files,
@@ -104,10 +78,10 @@ def v_3dto_xdataset_cargs(
     cargs.append("3dtoXdataset")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    cargs.append(execution.input_file(params.get("mask")))
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    cargs.append(execution.input_file(params.get("mask", None)))
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
     return cargs
 
 
@@ -126,16 +100,18 @@ def v_3dto_xdataset_outputs(
     """
     ret = V3dtoXdatasetOutputs(
         root=execution.output_file("."),
-        output_sdat=execution.output_file(params.get("prefix") + ".sdat"),
+        output_sdat=execution.output_file(params.get("prefix", None) + ".sdat"),
     )
     return ret
 
 
 def v_3dto_xdataset_execute(
     params: V3dtoXdatasetParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dtoXdatasetOutputs:
     """
+    3dtoXdataset
+    
     Convert input datasets to the format needed for 3dClustSimX.
     
     Author: AFNI Developers
@@ -144,10 +120,12 @@ def v_3dto_xdataset_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dtoXdatasetOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DTO_XDATASET_METADATA)
     params = execution.params(params)
     cargs = v_3dto_xdataset_cargs(params, execution)
     ret = v_3dto_xdataset_outputs(params, execution)
@@ -162,6 +140,8 @@ def v_3dto_xdataset(
     runner: Runner | None = None,
 ) -> V3dtoXdatasetOutputs:
     """
+    3dtoXdataset
+    
     Convert input datasets to the format needed for 3dClustSimX.
     
     Author: AFNI Developers
@@ -176,20 +156,18 @@ def v_3dto_xdataset(
     Returns:
         NamedTuple of outputs (described in `V3dtoXdatasetOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DTO_XDATASET_METADATA)
     params = v_3dto_xdataset_params(
         prefix=prefix,
         mask=mask,
         input_files=input_files,
     )
-    return v_3dto_xdataset_execute(params, execution)
+    return v_3dto_xdataset_execute(params, runner)
 
 
 __all__ = [
     "V3dtoXdatasetOutputs",
-    "V3dtoXdatasetParameters",
     "V_3DTO_XDATASET_METADATA",
     "v_3dto_xdataset",
+    "v_3dto_xdataset_execute",
     "v_3dto_xdataset_params",
 ]