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

niwrap_afni/afni/roi2dataset.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ROI2DATASET_METADATA = Metadata(
-    id="5d5ce9ca7d281ca079da489d9aa946cea52cf676.boutiques",
+    id="95919d130a43b738fd4be5b9f406f11c46290e50.boutiques",
     name="ROI2dataset",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ ROI2DATASET_METADATA = Metadata(
 
 
 Roi2datasetParameters = typing.TypedDict('Roi2datasetParameters', {
-    "__STYXTYPE__": typing.Literal["ROI2dataset"],
+    "@type": typing.NotRequired[typing.Literal["afni/ROI2dataset"]],
+    "prefix": str,
+    "input_rois": list[InputPathType],
+    "keep_separate": bool,
+    "nodelist": typing.NotRequired[str | None],
+    "nodelist_nodups": typing.NotRequired[str | None],
+    "nodelist_with_roival": bool,
+    "label_dset": typing.NotRequired[str | None],
+    "output_format": typing.NotRequired[str | None],
+    "domain_parent_id": typing.NotRequired[str | None],
+    "pad_to_node": typing.NotRequired[float | None],
+    "pad_label": typing.NotRequired[float | None],
+})
+Roi2datasetParametersTagged = typing.TypedDict('Roi2datasetParametersTagged', {
+    "@type": typing.Literal["afni/ROI2dataset"],
     "prefix": str,
     "input_rois": list[InputPathType],
     "keep_separate": bool,
@@ -27,42 +41,11 @@ Roi2datasetParameters = typing.TypedDict('Roi2datasetParameters', {
     "pad_to_node": typing.NotRequired[float | None],
     "pad_label": 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 {
-        "ROI2dataset": roi2dataset_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 Roi2datasetOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `roi2dataset(...)`.
+    Output object returned when calling `Roi2datasetParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -80,7 +63,7 @@ def roi2dataset_params(
     domain_parent_id: str | None = None,
     pad_to_node: float | None = None,
     pad_label: float | None = None,
-) -> Roi2datasetParameters:
+) -> Roi2datasetParametersTagged:
     """
     Build parameters.
     
@@ -109,7 +92,7 @@ def roi2dataset_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ROI2dataset",
+        "@type": "afni/ROI2dataset",
         "prefix": prefix,
         "input_rois": input_rois,
         "keep_separate": keep_separate,
@@ -149,47 +132,47 @@ def roi2dataset_cargs(
     cargs.append("ROI2dataset")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    cargs.extend([execution.input_file(f) for f in params.get("input_rois")])
-    if params.get("keep_separate"):
+    cargs.extend([execution.input_file(f) for f in params.get("input_rois", None)])
+    if params.get("keep_separate", False):
         cargs.append("-keep_separate")
-    if params.get("nodelist") is not None:
+    if params.get("nodelist", None) is not None:
         cargs.extend([
             "-nodelist",
-            params.get("nodelist")
+            params.get("nodelist", None)
         ])
-    if params.get("nodelist_nodups") is not None:
+    if params.get("nodelist_nodups", None) is not None:
         cargs.extend([
             "-nodelist.nodups",
-            params.get("nodelist_nodups")
+            params.get("nodelist_nodups", None)
         ])
-    if params.get("nodelist_with_roival"):
+    if params.get("nodelist_with_roival", False):
         cargs.append("-nodelist_with_ROIval")
-    if params.get("label_dset") is not None:
+    if params.get("label_dset", None) is not None:
         cargs.extend([
             "-label_dset",
-            params.get("label_dset")
+            params.get("label_dset", None)
         ])
-    if params.get("output_format") is not None:
+    if params.get("output_format", None) is not None:
         cargs.extend([
             "-of",
-            params.get("output_format")
+            params.get("output_format", None)
         ])
-    if params.get("domain_parent_id") is not None:
+    if params.get("domain_parent_id", None) is not None:
         cargs.extend([
             "-dom_par_id",
-            params.get("domain_parent_id")
+            params.get("domain_parent_id", None)
         ])
-    if params.get("pad_to_node") is not None:
+    if params.get("pad_to_node", None) is not None:
         cargs.extend([
             "-pad_to_node",
-            str(params.get("pad_to_node"))
+            str(params.get("pad_to_node", None))
         ])
-    if params.get("pad_label") is not None:
+    if params.get("pad_label", None) is not None:
         cargs.extend([
             "-pad_label",
-            str(params.get("pad_label"))
+            str(params.get("pad_label", None))
         ])
     return cargs
 
@@ -215,9 +198,11 @@ def roi2dataset_outputs(
 
 def roi2dataset_execute(
     params: Roi2datasetParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Roi2datasetOutputs:
     """
+    ROI2dataset
+    
     Transforms a series of ROI files to a node dataset.
     
     Author: AFNI Developers
@@ -226,10 +211,12 @@ def roi2dataset_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Roi2datasetOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ROI2DATASET_METADATA)
     params = execution.params(params)
     cargs = roi2dataset_cargs(params, execution)
     ret = roi2dataset_outputs(params, execution)
@@ -252,6 +239,8 @@ def roi2dataset(
     runner: Runner | None = None,
 ) -> Roi2datasetOutputs:
     """
+    ROI2dataset
+    
     Transforms a series of ROI files to a node dataset.
     
     Author: AFNI Developers
@@ -283,8 +272,6 @@ def roi2dataset(
     Returns:
         NamedTuple of outputs (described in `Roi2datasetOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ROI2DATASET_METADATA)
     params = roi2dataset_params(
         prefix=prefix,
         input_rois=input_rois,
@@ -298,13 +285,13 @@ def roi2dataset(
         pad_to_node=pad_to_node,
         pad_label=pad_label,
     )
-    return roi2dataset_execute(params, execution)
+    return roi2dataset_execute(params, runner)
 
 
 __all__ = [
     "ROI2DATASET_METADATA",
     "Roi2datasetOutputs",
-    "Roi2datasetParameters",
     "roi2dataset",
+    "roi2dataset_execute",
     "roi2dataset_params",
 ]

niwrap_afni/afni/roigrow.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ROIGROW_METADATA = Metadata(
-    id="f4aa7a593eb763743bac7b66d6cbfc7d7a8e1e49.boutiques",
+    id="893b3e6beea2d4e9cedff33cfd4e0a638591b4f8.boutiques",
     name="ROIgrow",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ ROIGROW_METADATA = Metadata(
 
 
 RoigrowParameters = typing.TypedDict('RoigrowParameters', {
-    "__STYXTYPE__": typing.Literal["ROIgrow"],
+    "@type": typing.NotRequired[typing.Literal["afni/ROIgrow"]],
+    "input_surface": str,
+    "roi_labels": str,
+    "lim_distance": float,
+    "output_prefix": typing.NotRequired[str | None],
+    "full_list": bool,
+    "grow_from_edge": bool,
+    "insphere_diameter": typing.NotRequired[float | None],
+    "inbox_edges": typing.NotRequired[list[float] | None],
+})
+RoigrowParametersTagged = typing.TypedDict('RoigrowParametersTagged', {
+    "@type": typing.Literal["afni/ROIgrow"],
     "input_surface": str,
     "roi_labels": str,
     "lim_distance": float,
@@ -24,43 +35,11 @@ RoigrowParameters = typing.TypedDict('RoigrowParameters', {
     "insphere_diameter": typing.NotRequired[float | None],
     "inbox_edges": typing.NotRequired[list[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 {
-        "ROIgrow": roigrow_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 {
-        "ROIgrow": roigrow_outputs,
-    }.get(t)
 
 
 class RoigrowOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `roigrow(...)`.
+    Output object returned when calling `RoigrowParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def roigrow_params(
     grow_from_edge: bool = False,
     insphere_diameter: float | None = None,
     inbox_edges: list[float] | None = None,
-) -> RoigrowParameters:
+) -> RoigrowParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +82,7 @@ def roigrow_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ROIgrow",
+        "@type": "afni/ROIgrow",
         "input_surface": input_surface,
         "roi_labels": roi_labels,
         "lim_distance": lim_distance,
@@ -136,34 +115,34 @@ def roigrow_cargs(
     cargs.append("ROIgrow")
     cargs.extend([
         "-i_TYPE",
-        params.get("input_surface")
+        params.get("input_surface", None)
     ])
     cargs.extend([
         "-roi_labels",
-        params.get("roi_labels")
+        params.get("roi_labels", None)
     ])
     cargs.extend([
         "-lim",
-        str(params.get("lim_distance"))
+        str(params.get("lim_distance", None))
     ])
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("full_list"):
+    if params.get("full_list", False):
         cargs.append("-full_list")
-    if params.get("grow_from_edge"):
+    if params.get("grow_from_edge", False):
         cargs.append("-grow_from_edge")
-    if params.get("insphere_diameter") is not None:
+    if params.get("insphere_diameter", None) is not None:
         cargs.extend([
             "-insphere",
-            str(params.get("insphere_diameter"))
+            str(params.get("insphere_diameter", None))
         ])
-    if params.get("inbox_edges") is not None:
+    if params.get("inbox_edges", None) is not None:
         cargs.extend([
             "-inbox",
-            *map(str, params.get("inbox_edges"))
+            *map(str, params.get("inbox_edges", None))
         ])
     return cargs
 
@@ -183,16 +162,18 @@ def roigrow_outputs(
     """
     ret = RoigrowOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_prefix") + ".1D") if (params.get("output_prefix") is not None) else None,
+        output_file=execution.output_file(params.get("output_prefix", None) + ".1D") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def roigrow_execute(
     params: RoigrowParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RoigrowOutputs:
     """
+    ROIgrow
+    
     A program to expand an ROI on the surface.
     
     Author: AFNI Developers
@@ -201,10 +182,12 @@ def roigrow_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RoigrowOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ROIGROW_METADATA)
     params = execution.params(params)
     cargs = roigrow_cargs(params, execution)
     ret = roigrow_outputs(params, execution)
@@ -224,6 +207,8 @@ def roigrow(
     runner: Runner | None = None,
 ) -> RoigrowOutputs:
     """
+    ROIgrow
+    
     A program to expand an ROI on the surface.
     
     Author: AFNI Developers
@@ -252,8 +237,6 @@ def roigrow(
     Returns:
         NamedTuple of outputs (described in `RoigrowOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ROIGROW_METADATA)
     params = roigrow_params(
         input_surface=input_surface,
         roi_labels=roi_labels,
@@ -264,13 +247,13 @@ def roigrow(
         insphere_diameter=insphere_diameter,
         inbox_edges=inbox_edges,
     )
-    return roigrow_execute(params, execution)
+    return roigrow_execute(params, runner)
 
 
 __all__ = [
     "ROIGROW_METADATA",
     "RoigrowOutputs",
-    "RoigrowParameters",
     "roigrow",
+    "roigrow_execute",
     "roigrow_params",
 ]

niwrap_afni/afni/rotcom.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ROTCOM_METADATA = Metadata(
-    id="fd59ff87f6727df1beafdf436f19aba6a53a3cea.boutiques",
+    id="cedbefcf10a28280103e75a171cb3de8c47463b6.boutiques",
     name="rotcom",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,20 @@ ROTCOM_METADATA = Metadata(
 
 
 RotcomParameters = typing.TypedDict('RotcomParameters', {
-    "__STYXTYPE__": typing.Literal["rotcom"],
+    "@type": typing.NotRequired[typing.Literal["afni/rotcom"]],
+    "rotate_ashift": str,
+    "dataset": typing.NotRequired[InputPathType | None],
+})
+RotcomParametersTagged = typing.TypedDict('RotcomParametersTagged', {
+    "@type": typing.Literal["afni/rotcom"],
     "rotate_ashift": str,
     "dataset": 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 {
-        "rotcom": rotcom_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 {
-        "rotcom": rotcom_outputs,
-    }.get(t)
 
 
 class RotcomOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rotcom(...)`.
+    Output object returned when calling `RotcomParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class RotcomOutputs(typing.NamedTuple):
 def rotcom_params(
     rotate_ashift: str,
     dataset: InputPathType | None = None,
-) -> RotcomParameters:
+) -> RotcomParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +50,7 @@ def rotcom_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rotcom",
+        "@type": "afni/rotcom",
         "rotate_ashift": rotate_ashift,
     }
     if dataset is not None:
@@ -100,9 +73,9 @@ def rotcom_cargs(
     """
     cargs = []
     cargs.append("rotcom")
-    cargs.append(params.get("rotate_ashift"))
-    if params.get("dataset") is not None:
-        cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(params.get("rotate_ashift", None))
+    if params.get("dataset", None) is not None:
+        cargs.append(execution.input_file(params.get("dataset", None)))
     return cargs
 
 
@@ -128,11 +101,13 @@ def rotcom_outputs(
 
 def rotcom_execute(
     params: RotcomParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RotcomOutputs:
     """
-    Prints to stdout the 4x3 transformation matrix+vector that would be applied by
-    3drotate to the given dataset.
+    rotcom
+    
+    Prints to stdout the 4x3 transformation matrix+vector that would be applied
+    by 3drotate to the given dataset.
     
     Author: AFNI Developers
     
@@ -140,10 +115,12 @@ def rotcom_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RotcomOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ROTCOM_METADATA)
     params = execution.params(params)
     cargs = rotcom_cargs(params, execution)
     ret = rotcom_outputs(params, execution)
@@ -157,8 +134,10 @@ def rotcom(
     runner: Runner | None = None,
 ) -> RotcomOutputs:
     """
-    Prints to stdout the 4x3 transformation matrix+vector that would be applied by
-    3drotate to the given dataset.
+    rotcom
+    
+    Prints to stdout the 4x3 transformation matrix+vector that would be applied
+    by 3drotate to the given dataset.
     
     Author: AFNI Developers
     
@@ -172,19 +151,17 @@ def rotcom(
     Returns:
         NamedTuple of outputs (described in `RotcomOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ROTCOM_METADATA)
     params = rotcom_params(
         rotate_ashift=rotate_ashift,
         dataset=dataset,
     )
-    return rotcom_execute(params, execution)
+    return rotcom_execute(params, runner)
 
 
 __all__ = [
     "ROTCOM_METADATA",
     "RotcomOutputs",
-    "RotcomParameters",
     "rotcom",
+    "rotcom_execute",
     "rotcom_params",
 ]