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

niwrap_afni/afni/v_3dnewid.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DNEWID_METADATA = Metadata(
-    id="b25222575203795168350c6d683d99ee6f9c65d5.boutiques",
+    id="d9631a81a6ce88bab00129e99a4fffcedf738735.boutiques",
     name="3dnewid",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3DNEWID_METADATA = Metadata(
 
 
 V3dnewidParameters = typing.TypedDict('V3dnewidParameters', {
-    "__STYXTYPE__": typing.Literal["3dnewid"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dnewid"]],
+    "datasets": list[InputPathType],
+    "fun": typing.NotRequired[float | None],
+    "fun11": bool,
+    "int": bool,
+    "hash": typing.NotRequired[str | None],
+    "MD5": typing.NotRequired[str | None],
+})
+V3dnewidParametersTagged = typing.TypedDict('V3dnewidParametersTagged', {
+    "@type": typing.Literal["afni/3dnewid"],
     "datasets": list[InputPathType],
     "fun": typing.NotRequired[float | None],
     "fun11": bool,
@@ -22,42 +31,11 @@ V3dnewidParameters = typing.TypedDict('V3dnewidParameters', {
     "hash": typing.NotRequired[str | None],
     "MD5": 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 {
-        "3dnewid": v_3dnewid_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 V3dnewidOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dnewid(...)`.
+    Output object returned when calling `V3dnewidParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def v_3dnewid_params(
     int_: bool = False,
     hash_: str | None = None,
     md5: str | None = None,
-) -> V3dnewidParameters:
+) -> V3dnewidParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +68,7 @@ def v_3dnewid_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dnewid",
+        "@type": "afni/3dnewid",
         "datasets": datasets,
         "fun11": fun11,
         "int": int_,
@@ -119,25 +97,25 @@ def v_3dnewid_cargs(
     """
     cargs = []
     cargs.append("3dnewid")
-    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
-    if params.get("fun") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("datasets", None)])
+    if params.get("fun", None) is not None:
         cargs.extend([
             "-fun",
-            str(params.get("fun"))
+            str(params.get("fun", None))
         ])
-    if params.get("fun11"):
+    if params.get("fun11", False):
         cargs.append("-fun11")
-    if params.get("int"):
+    if params.get("int", False):
         cargs.append("-int")
-    if params.get("hash") is not None:
+    if params.get("hash", None) is not None:
         cargs.extend([
             "-hash",
-            params.get("hash")
+            params.get("hash", None)
         ])
-    if params.get("MD5") is not None:
+    if params.get("MD5", None) is not None:
         cargs.extend([
             "-MD5",
-            params.get("MD5")
+            params.get("MD5", None)
         ])
     return cargs
 
@@ -163,10 +141,13 @@ def v_3dnewid_outputs(
 
 def v_3dnewid_execute(
     params: V3dnewidParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dnewidOutputs:
     """
-    Assigns a new ID code to a dataset, ensuring internal ID codes remain unique.
+    3dnewid
+    
+    Assigns a new ID code to a dataset, ensuring internal ID codes remain
+    unique.
     
     Author: AFNI Developers
     
@@ -174,10 +155,12 @@ def v_3dnewid_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dnewidOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DNEWID_METADATA)
     params = execution.params(params)
     cargs = v_3dnewid_cargs(params, execution)
     ret = v_3dnewid_outputs(params, execution)
@@ -195,7 +178,10 @@ def v_3dnewid(
     runner: Runner | None = None,
 ) -> V3dnewidOutputs:
     """
-    Assigns a new ID code to a dataset, ensuring internal ID codes remain unique.
+    3dnewid
+    
+    Assigns a new ID code to a dataset, ensuring internal ID codes remain
+    unique.
     
     Author: AFNI Developers
     
@@ -217,8 +203,6 @@ def v_3dnewid(
     Returns:
         NamedTuple of outputs (described in `V3dnewidOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DNEWID_METADATA)
     params = v_3dnewid_params(
         datasets=datasets,
         fun=fun,
@@ -227,13 +211,13 @@ def v_3dnewid(
         hash_=hash_,
         md5=md5,
     )
-    return v_3dnewid_execute(params, execution)
+    return v_3dnewid_execute(params, runner)
 
 
 __all__ = [
     "V3dnewidOutputs",
-    "V3dnewidParameters",
     "V_3DNEWID_METADATA",
     "v_3dnewid",
+    "v_3dnewid_execute",
     "v_3dnewid_params",
 ]

niwrap_afni/afni/v_3dnvals.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DNVALS_METADATA = Metadata(
-    id="66222ac3c17c8520079e76cf7dbfad8d6035e687.boutiques",
+    id="d32979be81ea2707669bbfdc54a5b8ae7ef58f3d.boutiques",
     name="3dnvals",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,22 @@ V_3DNVALS_METADATA = Metadata(
 
 
 V3dnvalsParameters = typing.TypedDict('V3dnvalsParameters', {
-    "__STYXTYPE__": typing.Literal["3dnvals"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dnvals"]],
+    "datasets": list[InputPathType],
+    "all_flag": bool,
+    "verbose_flag": bool,
+})
+V3dnvalsParametersTagged = typing.TypedDict('V3dnvalsParametersTagged', {
+    "@type": typing.Literal["afni/3dnvals"],
     "datasets": list[InputPathType],
     "all_flag": bool,
     "verbose_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 {
-        "3dnvals": v_3dnvals_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 V3dnvalsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dnvals(...)`.
+    Output object returned when calling `V3dnvalsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def v_3dnvals_params(
     datasets: list[InputPathType],
     all_flag: bool = False,
     verbose_flag: bool = False,
-) -> V3dnvalsParameters:
+) -> V3dnvalsParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def v_3dnvals_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dnvals",
+        "@type": "afni/3dnvals",
         "datasets": datasets,
         "all_flag": all_flag,
         "verbose_flag": verbose_flag,
@@ -99,10 +74,10 @@ def v_3dnvals_cargs(
     """
     cargs = []
     cargs.append("3dnvals")
-    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
-    if params.get("all_flag"):
+    cargs.extend([execution.input_file(f) for f in params.get("datasets", None)])
+    if params.get("all_flag", False):
         cargs.append("-all")
-    if params.get("verbose_flag"):
+    if params.get("verbose_flag", False):
         cargs.append("-verbose")
     return cargs
 
@@ -128,9 +103,11 @@ def v_3dnvals_outputs(
 
 def v_3dnvals_execute(
     params: V3dnvalsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dnvalsOutputs:
     """
+    3dnvals
+    
     Tool to print the number of sub-bricks in a 3D dataset.
     
     Author: AFNI Developers
@@ -139,10 +116,12 @@ def v_3dnvals_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dnvalsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DNVALS_METADATA)
     params = execution.params(params)
     cargs = v_3dnvals_cargs(params, execution)
     ret = v_3dnvals_outputs(params, execution)
@@ -157,6 +136,8 @@ def v_3dnvals(
     runner: Runner | None = None,
 ) -> V3dnvalsOutputs:
     """
+    3dnvals
+    
     Tool to print the number of sub-bricks in a 3D dataset.
     
     Author: AFNI Developers
@@ -171,20 +152,18 @@ def v_3dnvals(
     Returns:
         NamedTuple of outputs (described in `V3dnvalsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DNVALS_METADATA)
     params = v_3dnvals_params(
         datasets=datasets,
         all_flag=all_flag,
         verbose_flag=verbose_flag,
     )
-    return v_3dnvals_execute(params, execution)
+    return v_3dnvals_execute(params, runner)
 
 
 __all__ = [
     "V3dnvalsOutputs",
-    "V3dnvalsParameters",
     "V_3DNVALS_METADATA",
     "v_3dnvals",
+    "v_3dnvals_execute",
     "v_3dnvals_params",
 ]

niwrap_afni/afni/v_3dpc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DPC_METADATA = Metadata(
-    id="aa84aba2b62d9b7a4e468237b32c0eb69d2496f8.boutiques",
+    id="cb83a78d80ca40f71ab808cf9db4c7db704ac5bb.boutiques",
     name="3dpc",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ V_3DPC_METADATA = Metadata(
 
 
 V3dpcParameters = typing.TypedDict('V3dpcParameters', {
-    "__STYXTYPE__": typing.Literal["3dpc"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dpc"]],
+    "datasets": list[InputPathType],
+    "dmean": bool,
+    "vmean": bool,
+    "vnorm": bool,
+    "normalize": bool,
+    "nscale": bool,
+    "pcsave": typing.NotRequired[str | None],
+    "reduce": typing.NotRequired[list[str] | None],
+    "prefix": typing.NotRequired[str | None],
+    "dummy_lines": typing.NotRequired[int | None],
+    "verbose": bool,
+    "quiet": bool,
+    "eigonly": bool,
+    "float": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+})
+V3dpcParametersTagged = typing.TypedDict('V3dpcParametersTagged', {
+    "@type": typing.Literal["afni/3dpc"],
     "datasets": list[InputPathType],
     "dmean": bool,
     "vmean": bool,
@@ -31,43 +49,11 @@ V3dpcParameters = typing.TypedDict('V3dpcParameters', {
     "float": bool,
     "mask": 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 {
-        "3dpc": v_3dpc_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 {
-        "3dpc": v_3dpc_outputs,
-    }.get(t)
 
 
 class V3dpcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dpc(...)`.
+    Output object returned when calling `V3dpcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +85,7 @@ def v_3dpc_params(
     eigonly: bool = False,
     float_: bool = False,
     mask: InputPathType | None = None,
-) -> V3dpcParameters:
+) -> V3dpcParametersTagged:
     """
     Build parameters.
     
@@ -126,7 +112,7 @@ def v_3dpc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dpc",
+        "@type": "afni/3dpc",
         "datasets": datasets,
         "dmean": dmean,
         "vmean": vmean,
@@ -166,49 +152,49 @@ def v_3dpc_cargs(
     """
     cargs = []
     cargs.append("3dpc")
-    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
-    if params.get("dmean"):
+    cargs.extend([execution.input_file(f) for f in params.get("datasets", None)])
+    if params.get("dmean", False):
         cargs.append("-dmean")
-    if params.get("vmean"):
+    if params.get("vmean", False):
         cargs.append("-vmean")
-    if params.get("vnorm"):
+    if params.get("vnorm", False):
         cargs.append("-vnorm")
-    if params.get("normalize"):
+    if params.get("normalize", False):
         cargs.append("-normalize")
-    if params.get("nscale"):
+    if params.get("nscale", False):
         cargs.append("-nscale")
-    if params.get("pcsave") is not None:
+    if params.get("pcsave", None) is not None:
         cargs.extend([
             "-pcsave",
-            params.get("pcsave")
+            params.get("pcsave", None)
         ])
-    if params.get("reduce") is not None:
+    if params.get("reduce", None) is not None:
         cargs.extend([
             "-reduce",
-            *params.get("reduce")
+            *params.get("reduce", None)
         ])
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("dummy_lines") is not None:
+    if params.get("dummy_lines", None) is not None:
         cargs.extend([
             "-1ddum",
-            str(params.get("dummy_lines"))
+            str(params.get("dummy_lines", None))
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verbose")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("eigonly"):
+    if params.get("eigonly", False):
         cargs.append("-eigonly")
-    if params.get("float"):
+    if params.get("float", False):
         cargs.append("-float")
-    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))
         ])
     return cargs
 
@@ -228,20 +214,22 @@ def v_3dpc_outputs(
     """
     ret = V3dpcOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
-        output_header=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
-        output_eig=execution.output_file(params.get("prefix") + "_eig.1D") if (params.get("prefix") is not None) else None,
-        output_vec=execution.output_file(params.get("prefix") + "_vec.1D") if (params.get("prefix") is not None) else None,
-        output_individual_vec=execution.output_file(params.get("prefix") + "[NN].1D") if (params.get("prefix") is not None) else None,
+        output_dataset=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_header=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        output_eig=execution.output_file(params.get("prefix", None) + "_eig.1D") if (params.get("prefix") is not None) else None,
+        output_vec=execution.output_file(params.get("prefix", None) + "_vec.1D") if (params.get("prefix") is not None) else None,
+        output_individual_vec=execution.output_file(params.get("prefix", None) + "[NN].1D") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3dpc_execute(
     params: V3dpcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dpcOutputs:
     """
+    3dpc
+    
     Principal Component Analysis of 3D Datasets.
     
     Author: AFNI Developers
@@ -250,10 +238,12 @@ def v_3dpc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dpcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DPC_METADATA)
     params = execution.params(params)
     cargs = v_3dpc_cargs(params, execution)
     ret = v_3dpc_outputs(params, execution)
@@ -280,6 +270,8 @@ def v_3dpc(
     runner: Runner | None = None,
 ) -> V3dpcOutputs:
     """
+    3dpc
+    
     Principal Component Analysis of 3D Datasets.
     
     Author: AFNI Developers
@@ -309,8 +301,6 @@ def v_3dpc(
     Returns:
         NamedTuple of outputs (described in `V3dpcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DPC_METADATA)
     params = v_3dpc_params(
         datasets=datasets,
         dmean=dmean,
@@ -328,13 +318,13 @@ def v_3dpc(
         float_=float_,
         mask=mask,
     )
-    return v_3dpc_execute(params, execution)
+    return v_3dpc_execute(params, runner)
 
 
 __all__ = [
     "V3dpcOutputs",
-    "V3dpcParameters",
     "V_3DPC_METADATA",
     "v_3dpc",
+    "v_3dpc_execute",
     "v_3dpc_params",
 ]