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

niwrap_afni/afni/v_3d_skull_strip.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SKULL_STRIP_METADATA = Metadata(
-    id="ab34e8a40a7c57dd3421d932dc0cf51d69472c21.boutiques",
+    id="fbceed0eb269040c8046f3ad034c5816057f27c3.boutiques",
     name="3dSkullStrip",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_3D_SKULL_STRIP_METADATA = Metadata(
 
 
 V3dSkullStripParameters = typing.TypedDict('V3dSkullStripParameters', {
-    "__STYXTYPE__": typing.Literal["3dSkullStrip"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSkullStrip"]],
+    "in_file": InputPathType,
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+})
+V3dSkullStripParametersTagged = typing.TypedDict('V3dSkullStripParametersTagged', {
+    "@type": typing.Literal["afni/3dSkullStrip"],
     "in_file": InputPathType,
     "num_threads": typing.NotRequired[int | None],
     "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dSkullStrip": v_3d_skull_strip_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 {
-        "3dSkullStrip": v_3d_skull_strip_outputs,
-    }.get(t)
 
 
 class V3dSkullStripOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_skull_strip(...)`.
+    Output object returned when calling `V3dSkullStripParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +43,7 @@ def v_3d_skull_strip_params(
     in_file: InputPathType,
     num_threads: int | None = None,
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
-) -> V3dSkullStripParameters:
+) -> V3dSkullStripParametersTagged:
     """
     Build parameters.
     
@@ -81,7 +55,7 @@ def v_3d_skull_strip_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSkullStrip",
+        "@type": "afni/3dSkullStrip",
         "in_file": in_file,
     }
     if num_threads is not None:
@@ -108,12 +82,12 @@ def v_3d_skull_strip_cargs(
     cargs.append("3dSkullStrip")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("in_file"))
+        execution.input_file(params.get("in_file", None))
     ])
-    if params.get("num_threads") is not None:
-        cargs.append(str(params.get("num_threads")))
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
+    if params.get("num_threads", None) is not None:
+        cargs.append(str(params.get("num_threads", None)))
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
     return cargs
 
 
@@ -132,7 +106,7 @@ def v_3d_skull_strip_outputs(
     """
     ret = V3dSkullStripOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(pathlib.Path(params.get("in_file")).name + "_skullstrip"),
+        out_file=execution.output_file(pathlib.Path(params.get("in_file", None)).name + "_skullstrip"),
         out_file_=execution.output_file("out_file"),
     )
     return ret
@@ -140,9 +114,11 @@ def v_3d_skull_strip_outputs(
 
 def v_3d_skull_strip_execute(
     params: V3dSkullStripParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSkullStripOutputs:
     """
+    3dSkullStrip
+    
     A program to extract the brain from surrounding tissue from MRI T1-weighted
     images.
     
@@ -152,10 +128,12 @@ def v_3d_skull_strip_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSkullStripOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SKULL_STRIP_METADATA)
     params = execution.params(params)
     cargs = v_3d_skull_strip_cargs(params, execution)
     ret = v_3d_skull_strip_outputs(params, execution)
@@ -170,6 +148,8 @@ def v_3d_skull_strip(
     runner: Runner | None = None,
 ) -> V3dSkullStripOutputs:
     """
+    3dSkullStrip
+    
     A program to extract the brain from surrounding tissue from MRI T1-weighted
     images.
     
@@ -185,20 +165,18 @@ def v_3d_skull_strip(
     Returns:
         NamedTuple of outputs (described in `V3dSkullStripOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SKULL_STRIP_METADATA)
     params = v_3d_skull_strip_params(
         in_file=in_file,
         num_threads=num_threads,
         outputtype=outputtype,
     )
-    return v_3d_skull_strip_execute(params, execution)
+    return v_3d_skull_strip_execute(params, runner)
 
 
 __all__ = [
     "V3dSkullStripOutputs",
-    "V3dSkullStripParameters",
     "V_3D_SKULL_STRIP_METADATA",
     "v_3d_skull_strip",
+    "v_3d_skull_strip_execute",
     "v_3d_skull_strip_params",
 ]

niwrap_afni/afni/v_3d_slice_ndice.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SLICE_NDICE_METADATA = Metadata(
-    id="998a2cd5417c4b5430994f6eaffe16312f3012f7.boutiques",
+    id="47faa2b7fa568539489509b1d3737397345c1187.boutiques",
     name="3dSliceNDice",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V_3D_SLICE_NDICE_METADATA = Metadata(
 
 
 V3dSliceNdiceParameters = typing.TypedDict('V3dSliceNdiceParameters', {
-    "__STYXTYPE__": typing.Literal["3dSliceNDice"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSliceNDice"]],
+    "infile_a": InputPathType,
+    "infile_b": InputPathType,
+    "output_prefix": str,
+    "out_domain": typing.NotRequired[typing.Literal["all", "AorB", "AandB", "Amask", "Bmask"] | None],
+    "no_cmd_echo": bool,
+})
+V3dSliceNdiceParametersTagged = typing.TypedDict('V3dSliceNdiceParametersTagged', {
+    "@type": typing.Literal["afni/3dSliceNDice"],
     "infile_a": InputPathType,
     "infile_b": InputPathType,
     "output_prefix": str,
     "out_domain": typing.NotRequired[typing.Literal["all", "AorB", "AandB", "Amask", "Bmask"] | None],
     "no_cmd_echo": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dSliceNDice": v_3d_slice_ndice_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 {
-        "3dSliceNDice": v_3d_slice_ndice_outputs,
-    }.get(t)
 
 
 class V3dSliceNdiceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_slice_ndice(...)`.
+    Output object returned when calling `V3dSliceNdiceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +53,7 @@ def v_3d_slice_ndice_params(
     output_prefix: str,
     out_domain: typing.Literal["all", "AorB", "AandB", "Amask", "Bmask"] | None = None,
     no_cmd_echo: bool = False,
-) -> V3dSliceNdiceParameters:
+) -> V3dSliceNdiceParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +69,7 @@ def v_3d_slice_ndice_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSliceNDice",
+        "@type": "afni/3dSliceNDice",
         "infile_a": infile_a,
         "infile_b": infile_b,
         "output_prefix": output_prefix,
@@ -121,22 +97,22 @@ def v_3d_slice_ndice_cargs(
     cargs.append("3dSliceNDice")
     cargs.extend([
         "-insetA",
-        execution.input_file(params.get("infile_a"))
+        execution.input_file(params.get("infile_a", None))
     ])
     cargs.extend([
         "-insetB",
-        execution.input_file(params.get("infile_b"))
+        execution.input_file(params.get("infile_b", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
-    if params.get("out_domain") is not None:
+    if params.get("out_domain", None) is not None:
         cargs.extend([
             "-out_domain",
-            params.get("out_domain")
+            params.get("out_domain", None)
         ])
-    if params.get("no_cmd_echo"):
+    if params.get("no_cmd_echo", False):
         cargs.append("-no_cmd_echo")
     return cargs
 
@@ -156,19 +132,22 @@ def v_3d_slice_ndice_outputs(
     """
     ret = V3dSliceNdiceOutputs(
         root=execution.output_file("."),
-        output_rl=execution.output_file(params.get("output_prefix") + "_0_RL.1D"),
-        output_ap=execution.output_file(params.get("output_prefix") + "_1_AP.1D"),
-        output_is=execution.output_file(params.get("output_prefix") + "_2_IS.1D"),
+        output_rl=execution.output_file(params.get("output_prefix", None) + "_0_RL.1D"),
+        output_ap=execution.output_file(params.get("output_prefix", None) + "_1_AP.1D"),
+        output_is=execution.output_file(params.get("output_prefix", None) + "_2_IS.1D"),
     )
     return ret
 
 
 def v_3d_slice_ndice_execute(
     params: V3dSliceNdiceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSliceNdiceOutputs:
     """
-    Calculates the Dice coefficient between two volumes on a slice-by-slice basis.
+    3dSliceNDice
+    
+    Calculates the Dice coefficient between two volumes on a slice-by-slice
+    basis.
     
     Author: AFNI Developers
     
@@ -176,10 +155,12 @@ def v_3d_slice_ndice_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSliceNdiceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SLICE_NDICE_METADATA)
     params = execution.params(params)
     cargs = v_3d_slice_ndice_cargs(params, execution)
     ret = v_3d_slice_ndice_outputs(params, execution)
@@ -196,7 +177,10 @@ def v_3d_slice_ndice(
     runner: Runner | None = None,
 ) -> V3dSliceNdiceOutputs:
     """
-    Calculates the Dice coefficient between two volumes on a slice-by-slice basis.
+    3dSliceNDice
+    
+    Calculates the Dice coefficient between two volumes on a slice-by-slice
+    basis.
     
     Author: AFNI Developers
     
@@ -214,8 +198,6 @@ def v_3d_slice_ndice(
     Returns:
         NamedTuple of outputs (described in `V3dSliceNdiceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SLICE_NDICE_METADATA)
     params = v_3d_slice_ndice_params(
         infile_a=infile_a,
         infile_b=infile_b,
@@ -223,13 +205,13 @@ def v_3d_slice_ndice(
         out_domain=out_domain,
         no_cmd_echo=no_cmd_echo,
     )
-    return v_3d_slice_ndice_execute(params, execution)
+    return v_3d_slice_ndice_execute(params, runner)
 
 
 __all__ = [
     "V3dSliceNdiceOutputs",
-    "V3dSliceNdiceParameters",
     "V_3D_SLICE_NDICE_METADATA",
     "v_3d_slice_ndice",
+    "v_3d_slice_ndice_execute",
     "v_3d_slice_ndice_params",
 ]

niwrap_afni/afni/v_3d_space_time_corr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SPACE_TIME_CORR_METADATA = Metadata(
-    id="02283e56a615340b7f56f781bc42f0718ddae8af.boutiques",
+    id="6c145ad16f230ce2c8671d5d52e1f53f0abd0f68.boutiques",
     name="3dSpaceTimeCorr",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V_3D_SPACE_TIME_CORR_METADATA = Metadata(
 
 
 V3dSpaceTimeCorrParameters = typing.TypedDict('V3dSpaceTimeCorrParameters', {
-    "__STYXTYPE__": typing.Literal["3dSpaceTimeCorr"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSpaceTimeCorr"]],
+    "insetA": InputPathType,
+    "insetB": InputPathType,
+    "prefix": str,
+    "mask": typing.NotRequired[InputPathType | None],
+    "out_Zcorr": bool,
+    "freeze_insetA_ijk": typing.NotRequired[list[float] | None],
+    "freeze_insetA_xyz": typing.NotRequired[list[float] | None],
+})
+V3dSpaceTimeCorrParametersTagged = typing.TypedDict('V3dSpaceTimeCorrParametersTagged', {
+    "@type": typing.Literal["afni/3dSpaceTimeCorr"],
     "insetA": InputPathType,
     "insetB": InputPathType,
     "prefix": str,
@@ -23,43 +33,11 @@ V3dSpaceTimeCorrParameters = typing.TypedDict('V3dSpaceTimeCorrParameters', {
     "freeze_insetA_ijk": typing.NotRequired[list[float] | None],
     "freeze_insetA_xyz": 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 {
-        "3dSpaceTimeCorr": v_3d_space_time_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 {
-        "3dSpaceTimeCorr": v_3d_space_time_corr_outputs,
-    }.get(t)
 
 
 class V3dSpaceTimeCorrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_space_time_corr(...)`.
+    Output object returned when calling `V3dSpaceTimeCorrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def v_3d_space_time_corr_params(
     out_zcorr: bool = False,
     freeze_inset_a_ijk: list[float] | None = None,
     freeze_inset_a_xyz: list[float] | None = None,
-) -> V3dSpaceTimeCorrParameters:
+) -> V3dSpaceTimeCorrParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +76,7 @@ def v_3d_space_time_corr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSpaceTimeCorr",
+        "@type": "afni/3dSpaceTimeCorr",
         "insetA": inset_a,
         "insetB": inset_b,
         "prefix": prefix,
@@ -130,32 +108,32 @@ def v_3d_space_time_corr_cargs(
     cargs.append("3dSpaceTimeCorr")
     cargs.extend([
         "-insetA",
-        execution.input_file(params.get("insetA"))
+        execution.input_file(params.get("insetA", None))
     ])
     cargs.extend([
         "-insetB",
-        execution.input_file(params.get("insetB"))
+        execution.input_file(params.get("insetB", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", 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("out_Zcorr"):
+    if params.get("out_Zcorr", False):
         cargs.append("-out_Zcorr")
-    if params.get("freeze_insetA_ijk") is not None:
+    if params.get("freeze_insetA_ijk", None) is not None:
         cargs.extend([
             "-freeze_insetA_ijk",
-            *map(str, params.get("freeze_insetA_ijk"))
+            *map(str, params.get("freeze_insetA_ijk", None))
         ])
-    if params.get("freeze_insetA_xyz") is not None:
+    if params.get("freeze_insetA_xyz", None) is not None:
         cargs.extend([
             "-freeze_insetA_xyz",
-            *map(str, params.get("freeze_insetA_xyz"))
+            *map(str, params.get("freeze_insetA_xyz", None))
         ])
     return cargs
 
@@ -175,16 +153,18 @@ def v_3d_space_time_corr_outputs(
     """
     ret = V3dSpaceTimeCorrOutputs(
         root=execution.output_file("."),
-        output=execution.output_file(params.get("prefix") + ".nii.gz"),
+        output=execution.output_file(params.get("prefix", None) + ".nii.gz"),
     )
     return ret
 
 
 def v_3d_space_time_corr_execute(
     params: V3dSpaceTimeCorrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSpaceTimeCorrOutputs:
     """
+    3dSpaceTimeCorr
+    
     Calculates correlation coefficients between two 4D datasets using space+time
     patterns.
     
@@ -194,10 +174,12 @@ def v_3d_space_time_corr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSpaceTimeCorrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SPACE_TIME_CORR_METADATA)
     params = execution.params(params)
     cargs = v_3d_space_time_corr_cargs(params, execution)
     ret = v_3d_space_time_corr_outputs(params, execution)
@@ -216,6 +198,8 @@ def v_3d_space_time_corr(
     runner: Runner | None = None,
 ) -> V3dSpaceTimeCorrOutputs:
     """
+    3dSpaceTimeCorr
+    
     Calculates correlation coefficients between two 4D datasets using space+time
     patterns.
     
@@ -242,8 +226,6 @@ def v_3d_space_time_corr(
     Returns:
         NamedTuple of outputs (described in `V3dSpaceTimeCorrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SPACE_TIME_CORR_METADATA)
     params = v_3d_space_time_corr_params(
         inset_a=inset_a,
         inset_b=inset_b,
@@ -253,13 +235,13 @@ def v_3d_space_time_corr(
         freeze_inset_a_ijk=freeze_inset_a_ijk,
         freeze_inset_a_xyz=freeze_inset_a_xyz,
     )
-    return v_3d_space_time_corr_execute(params, execution)
+    return v_3d_space_time_corr_execute(params, runner)
 
 
 __all__ = [
     "V3dSpaceTimeCorrOutputs",
-    "V3dSpaceTimeCorrParameters",
     "V_3D_SPACE_TIME_CORR_METADATA",
     "v_3d_space_time_corr",
+    "v_3d_space_time_corr_execute",
     "v_3d_space_time_corr_params",
 ]