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

niwrap_afni/afni/v_3d_exchange.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_EXCHANGE_METADATA = Metadata(
-    id="8ebdac99ebedc55c0168065b2a71ca0f78056aac.boutiques",
+    id="718b78c0aa7d2f4eb3cb6a05bf3fe4b27fbec0cd.boutiques",
     name="3dExchange",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V_3D_EXCHANGE_METADATA = Metadata(
 
 
 V3dExchangeParameters = typing.TypedDict('V3dExchangeParameters', {
-    "__STYXTYPE__": typing.Literal["3dExchange"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dExchange"]],
+    "prefix": str,
+    "infile": InputPathType,
+    "mapfile": InputPathType,
+    "version": bool,
+    "help": bool,
+})
+V3dExchangeParametersTagged = typing.TypedDict('V3dExchangeParametersTagged', {
+    "@type": typing.Literal["afni/3dExchange"],
     "prefix": str,
     "infile": InputPathType,
     "mapfile": InputPathType,
     "version": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dExchange": v_3d_exchange_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 {
-        "3dExchange": v_3d_exchange_outputs,
-    }.get(t)
 
 
 class V3dExchangeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_exchange(...)`.
+    Output object returned when calling `V3dExchangeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +49,7 @@ def v_3d_exchange_params(
     mapfile: InputPathType,
     version: bool = False,
     help_: bool = False,
-) -> V3dExchangeParameters:
+) -> V3dExchangeParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +65,7 @@ def v_3d_exchange_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dExchange",
+        "@type": "afni/3dExchange",
         "prefix": prefix,
         "infile": infile,
         "mapfile": mapfile,
@@ -116,19 +92,19 @@ def v_3d_exchange_cargs(
     cargs.append("3dExchange")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("infile"))
+        execution.input_file(params.get("infile", None))
     ])
     cargs.extend([
         "-map",
-        execution.input_file(params.get("mapfile"))
+        execution.input_file(params.get("mapfile", None))
     ])
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-ver")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -148,17 +124,19 @@ def v_3d_exchange_outputs(
     """
     ret = V3dExchangeOutputs(
         root=execution.output_file("."),
-        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
-        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+        output_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD"),
+        output_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK"),
     )
     return ret
 
 
 def v_3d_exchange_execute(
     params: V3dExchangeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dExchangeOutputs:
     """
+    3dExchange
+    
     Replaces voxel values using a mapping file with specified columns.
     
     Author: AFNI Developers
@@ -167,10 +145,12 @@ def v_3d_exchange_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dExchangeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EXCHANGE_METADATA)
     params = execution.params(params)
     cargs = v_3d_exchange_cargs(params, execution)
     ret = v_3d_exchange_outputs(params, execution)
@@ -187,6 +167,8 @@ def v_3d_exchange(
     runner: Runner | None = None,
 ) -> V3dExchangeOutputs:
     """
+    3dExchange
+    
     Replaces voxel values using a mapping file with specified columns.
     
     Author: AFNI Developers
@@ -205,8 +187,6 @@ def v_3d_exchange(
     Returns:
         NamedTuple of outputs (described in `V3dExchangeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_EXCHANGE_METADATA)
     params = v_3d_exchange_params(
         prefix=prefix,
         infile=infile,
@@ -214,13 +194,13 @@ def v_3d_exchange(
         version=version,
         help_=help_,
     )
-    return v_3d_exchange_execute(params, execution)
+    return v_3d_exchange_execute(params, runner)
 
 
 __all__ = [
     "V3dExchangeOutputs",
-    "V3dExchangeParameters",
     "V_3D_EXCHANGE_METADATA",
     "v_3d_exchange",
+    "v_3d_exchange_execute",
     "v_3d_exchange_params",
 ]

niwrap_afni/afni/v_3d_extract_group_in_corr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_EXTRACT_GROUP_IN_CORR_METADATA = Metadata(
-    id="db8b581acc747baf59f28e6dc59ae40bd84d02f5.boutiques",
+    id="bf4ab9978725a057e015773eda00c5d63ac89f4d.boutiques",
     name="3dExtractGroupInCorr",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,20 @@ V_3D_EXTRACT_GROUP_IN_CORR_METADATA = Metadata(
 
 
 V3dExtractGroupInCorrParameters = typing.TypedDict('V3dExtractGroupInCorrParameters', {
-    "__STYXTYPE__": typing.Literal["3dExtractGroupInCorr"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dExtractGroupInCorr"]],
+    "group_in_corr_file": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+})
+V3dExtractGroupInCorrParametersTagged = typing.TypedDict('V3dExtractGroupInCorrParametersTagged', {
+    "@type": typing.Literal["afni/3dExtractGroupInCorr"],
     "group_in_corr_file": InputPathType,
     "prefix": 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 {
-        "3dExtractGroupInCorr": v_3d_extract_group_in_corr_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 {
-        "3dExtractGroupInCorr": v_3d_extract_group_in_corr_outputs,
-    }.get(t)
 
 
 class V3dExtractGroupInCorrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_extract_group_in_corr(...)`.
+    Output object returned when calling `V3dExtractGroupInCorrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class V3dExtractGroupInCorrOutputs(typing.NamedTuple):
 def v_3d_extract_group_in_corr_params(
     group_in_corr_file: InputPathType,
     prefix: str | None = None,
-) -> V3dExtractGroupInCorrParameters:
+) -> V3dExtractGroupInCorrParametersTagged:
     """
     Build parameters.
     
@@ -78,7 +51,7 @@ def v_3d_extract_group_in_corr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dExtractGroupInCorr",
+        "@type": "afni/3dExtractGroupInCorr",
         "group_in_corr_file": group_in_corr_file,
     }
     if prefix is not None:
@@ -101,11 +74,11 @@ def v_3d_extract_group_in_corr_cargs(
     """
     cargs = []
     cargs.append("3dExtractGroupInCorr")
-    cargs.append(execution.input_file(params.get("group_in_corr_file")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("group_in_corr_file", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
     return cargs
 
@@ -125,18 +98,20 @@ def v_3d_extract_group_in_corr_outputs(
     """
     ret = V3dExtractGroupInCorrOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("prefix") + "_[DATASET_LABEL].nii") if (params.get("prefix") is not None) else None,
+        output_dataset=execution.output_file(params.get("prefix", None) + "_[DATASET_LABEL].nii") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_extract_group_in_corr_execute(
     params: V3dExtractGroupInCorrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dExtractGroupInCorrOutputs:
     """
-    This program breaks the collection of images from a GroupInCorr file back into
-    individual AFNI 3D+time datasets.
+    3dExtractGroupInCorr
+    
+    This program breaks the collection of images from a GroupInCorr file back
+    into individual AFNI 3D+time datasets.
     
     Author: AFNI Developers
     
@@ -144,10 +119,12 @@ def v_3d_extract_group_in_corr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dExtractGroupInCorrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EXTRACT_GROUP_IN_CORR_METADATA)
     params = execution.params(params)
     cargs = v_3d_extract_group_in_corr_cargs(params, execution)
     ret = v_3d_extract_group_in_corr_outputs(params, execution)
@@ -161,8 +138,10 @@ def v_3d_extract_group_in_corr(
     runner: Runner | None = None,
 ) -> V3dExtractGroupInCorrOutputs:
     """
-    This program breaks the collection of images from a GroupInCorr file back into
-    individual AFNI 3D+time datasets.
+    3dExtractGroupInCorr
+    
+    This program breaks the collection of images from a GroupInCorr file back
+    into individual AFNI 3D+time datasets.
     
     Author: AFNI Developers
     
@@ -177,19 +156,17 @@ def v_3d_extract_group_in_corr(
     Returns:
         NamedTuple of outputs (described in `V3dExtractGroupInCorrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_EXTRACT_GROUP_IN_CORR_METADATA)
     params = v_3d_extract_group_in_corr_params(
         group_in_corr_file=group_in_corr_file,
         prefix=prefix,
     )
-    return v_3d_extract_group_in_corr_execute(params, execution)
+    return v_3d_extract_group_in_corr_execute(params, runner)
 
 
 __all__ = [
     "V3dExtractGroupInCorrOutputs",
-    "V3dExtractGroupInCorrParameters",
     "V_3D_EXTRACT_GROUP_IN_CORR_METADATA",
     "v_3d_extract_group_in_corr",
+    "v_3d_extract_group_in_corr_execute",
     "v_3d_extract_group_in_corr_params",
 ]

niwrap_afni/afni/v_3d_extrema.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_EXTREMA_METADATA = Metadata(
-    id="a99e42a29322557d96803717af2d04aa40a35929.boutiques",
+    id="1b4e88acaad15e743886a4b6ef801e6fd7558f48.boutiques",
     name="3dExtrema",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,30 @@ V_3D_EXTREMA_METADATA = Metadata(
 
 
 V3dExtremaParameters = typing.TypedDict('V3dExtremaParameters', {
-    "__STYXTYPE__": typing.Literal["3dExtrema"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dExtrema"]],
+    "input_dataset": InputPathType,
+    "output_prefix": typing.NotRequired[str | None],
+    "output_session": typing.NotRequired[str | None],
+    "quiet": bool,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "mask_threshold": typing.NotRequired[float | None],
+    "data_threshold": typing.NotRequired[float | None],
+    "n_best": typing.NotRequired[float | None],
+    "separation_distance": typing.NotRequired[float | None],
+    "minima": bool,
+    "maxima": bool,
+    "strict": bool,
+    "partial": bool,
+    "interior": bool,
+    "closure": bool,
+    "slice": bool,
+    "volume": bool,
+    "remove": bool,
+    "average": bool,
+    "weight": bool,
+})
+V3dExtremaParametersTagged = typing.TypedDict('V3dExtremaParametersTagged', {
+    "@type": typing.Literal["afni/3dExtrema"],
     "input_dataset": InputPathType,
     "output_prefix": typing.NotRequired[str | None],
     "output_session": typing.NotRequired[str | None],
@@ -36,43 +59,11 @@ V3dExtremaParameters = typing.TypedDict('V3dExtremaParameters', {
     "average": bool,
     "weight": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dExtrema": v_3d_extrema_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 {
-        "3dExtrema": v_3d_extrema_outputs,
-    }.get(t)
 
 
 class V3dExtremaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_extrema(...)`.
+    Output object returned when calling `V3dExtremaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +94,7 @@ def v_3d_extrema_params(
     remove: bool = False,
     average: bool = False,
     weight: bool = False,
-) -> V3dExtremaParameters:
+) -> V3dExtremaParametersTagged:
     """
     Build parameters.
     
@@ -135,7 +126,7 @@ def v_3d_extrema_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dExtrema",
+        "@type": "afni/3dExtrema",
         "input_dataset": input_dataset,
         "quiet": quiet,
         "minima": minima,
@@ -182,65 +173,65 @@ def v_3d_extrema_cargs(
     """
     cargs = []
     cargs.append("3dExtrema")
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    if params.get("output_prefix") is not None:
+    cargs.append(execution.input_file(params.get("input_dataset", 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("output_session") is not None:
+    if params.get("output_session", None) is not None:
         cargs.extend([
             "-session",
-            params.get("output_session")
+            params.get("output_session", None)
         ])
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("mask_file") is not None:
+    if params.get("mask_file", None) is not None:
         cargs.extend([
             "-mask_file",
-            execution.input_file(params.get("mask_file"))
+            execution.input_file(params.get("mask_file", None))
         ])
-    if params.get("mask_threshold") is not None:
+    if params.get("mask_threshold", None) is not None:
         cargs.extend([
             "-mask_thr",
-            str(params.get("mask_threshold"))
+            str(params.get("mask_threshold", None))
         ])
-    if params.get("data_threshold") is not None:
+    if params.get("data_threshold", None) is not None:
         cargs.extend([
             "-data_thr",
-            str(params.get("data_threshold"))
+            str(params.get("data_threshold", None))
         ])
-    if params.get("n_best") is not None:
+    if params.get("n_best", None) is not None:
         cargs.extend([
             "-nbest",
-            str(params.get("n_best"))
+            str(params.get("n_best", None))
         ])
-    if params.get("separation_distance") is not None:
+    if params.get("separation_distance", None) is not None:
         cargs.extend([
             "-sep_dist",
-            str(params.get("separation_distance"))
+            str(params.get("separation_distance", None))
         ])
-    if params.get("minima"):
+    if params.get("minima", False):
         cargs.append("-minima")
-    if params.get("maxima"):
+    if params.get("maxima", False):
         cargs.append("-maxima")
-    if params.get("strict"):
+    if params.get("strict", False):
         cargs.append("-strict")
-    if params.get("partial"):
+    if params.get("partial", False):
         cargs.append("-partial")
-    if params.get("interior"):
+    if params.get("interior", False):
         cargs.append("-interior")
-    if params.get("closure"):
+    if params.get("closure", False):
         cargs.append("-closure")
-    if params.get("slice"):
+    if params.get("slice", False):
         cargs.append("-slice")
-    if params.get("volume"):
+    if params.get("volume", False):
         cargs.append("-volume")
-    if params.get("remove"):
+    if params.get("remove", False):
         cargs.append("-remove")
-    if params.get("average"):
+    if params.get("average", False):
         cargs.append("-average")
-    if params.get("weight"):
+    if params.get("weight", False):
         cargs.append("-weight")
     return cargs
 
@@ -260,17 +251,19 @@ def v_3d_extrema_outputs(
     """
     ret = V3dExtremaOutputs(
         root=execution.output_file("."),
-        output_head_file=execution.output_file(params.get("output_prefix") + ".HEAD") if (params.get("output_prefix") is not None) else None,
-        output_brik_file=execution.output_file(params.get("output_prefix") + ".BRIK") if (params.get("output_prefix") is not None) else None,
+        output_head_file=execution.output_file(params.get("output_prefix", None) + ".HEAD") if (params.get("output_prefix") is not None) else None,
+        output_brik_file=execution.output_file(params.get("output_prefix", None) + ".BRIK") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_extrema_execute(
     params: V3dExtremaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dExtremaOutputs:
     """
+    3dExtrema
+    
     Find local extrema (minima or maxima) in 3D datasets.
     
     Author: AFNI Developers
@@ -279,10 +272,12 @@ def v_3d_extrema_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dExtremaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_EXTREMA_METADATA)
     params = execution.params(params)
     cargs = v_3d_extrema_cargs(params, execution)
     ret = v_3d_extrema_outputs(params, execution)
@@ -314,6 +309,8 @@ def v_3d_extrema(
     runner: Runner | None = None,
 ) -> V3dExtremaOutputs:
     """
+    3dExtrema
+    
     Find local extrema (minima or maxima) in 3D datasets.
     
     Author: AFNI Developers
@@ -348,8 +345,6 @@ def v_3d_extrema(
     Returns:
         NamedTuple of outputs (described in `V3dExtremaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_EXTREMA_METADATA)
     params = v_3d_extrema_params(
         input_dataset=input_dataset,
         output_prefix=output_prefix,
@@ -372,13 +367,13 @@ def v_3d_extrema(
         average=average,
         weight=weight,
     )
-    return v_3d_extrema_execute(params, execution)
+    return v_3d_extrema_execute(params, runner)
 
 
 __all__ = [
     "V3dExtremaOutputs",
-    "V3dExtremaParameters",
     "V_3D_EXTREMA_METADATA",
     "v_3d_extrema",
+    "v_3d_extrema_execute",
     "v_3d_extrema_params",
 ]