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

niwrap_afni/afni/v_3d_blur_in_mask.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_BLUR_IN_MASK_METADATA = Metadata(
-    id="78220f12aa00c67903fa95e35580c1c0e4f335bd.boutiques",
+    id="7d11a949fcd62857812c515832cdb994a44ec7c6.boutiques",
     name="3dBlurInMask",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ V_3D_BLUR_IN_MASK_METADATA = Metadata(
 
 
 V3dBlurInMaskParameters = typing.TypedDict('V3dBlurInMaskParameters', {
-    "__STYXTYPE__": typing.Literal["3dBlurInMask"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dBlurInMask"]],
+    "input_file": InputPathType,
+    "output_prefix": str,
+    "fwhm": float,
+    "fwhm_dataset": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "multi_mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "preserve": bool,
+    "quiet": bool,
+    "float": bool,
+    "fwhm_xyz": typing.NotRequired[list[float] | None],
+})
+V3dBlurInMaskParametersTagged = typing.TypedDict('V3dBlurInMaskParametersTagged', {
+    "@type": typing.Literal["afni/3dBlurInMask"],
     "input_file": InputPathType,
     "output_prefix": str,
     "fwhm": float,
@@ -27,43 +41,11 @@ V3dBlurInMaskParameters = typing.TypedDict('V3dBlurInMaskParameters', {
     "float": bool,
     "fwhm_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 {
-        "3dBlurInMask": v_3d_blur_in_mask_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 {
-        "3dBlurInMask": v_3d_blur_in_mask_outputs,
-    }.get(t)
 
 
 class V3dBlurInMaskOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_blur_in_mask(...)`.
+    Output object returned when calling `V3dBlurInMaskParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +65,7 @@ def v_3d_blur_in_mask_params(
     quiet: bool = False,
     float_: bool = False,
     fwhm_xyz: list[float] | None = None,
-) -> V3dBlurInMaskParameters:
+) -> V3dBlurInMaskParametersTagged:
     """
     Build parameters.
     
@@ -107,7 +89,7 @@ def v_3d_blur_in_mask_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dBlurInMask",
+        "@type": "afni/3dBlurInMask",
         "input_file": input_file,
         "output_prefix": output_prefix,
         "fwhm": fwhm,
@@ -142,39 +124,39 @@ def v_3d_blur_in_mask_cargs(
     """
     cargs = []
     cargs.append("3dBlurInMask")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_prefix"))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_prefix", None))
     cargs.extend([
         "-FWHM",
-        str(params.get("fwhm"))
+        str(params.get("fwhm", None))
     ])
-    if params.get("fwhm_dataset") is not None:
+    if params.get("fwhm_dataset", None) is not None:
         cargs.extend([
             "-FWHMdset",
-            execution.input_file(params.get("fwhm_dataset"))
+            execution.input_file(params.get("fwhm_dataset", 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("multi_mask") is not None:
+    if params.get("multi_mask", None) is not None:
         cargs.extend([
             "-Mmask",
-            execution.input_file(params.get("multi_mask"))
+            execution.input_file(params.get("multi_mask", None))
         ])
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("preserve"):
+    if params.get("preserve", False):
         cargs.append("-preserve")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("float"):
+    if params.get("float", False):
         cargs.append("-float")
-    if params.get("fwhm_xyz") is not None:
+    if params.get("fwhm_xyz", None) is not None:
         cargs.extend([
             "-FWHMxyz",
-            *map(str, params.get("fwhm_xyz"))
+            *map(str, params.get("fwhm_xyz", None))
         ])
     return cargs
 
@@ -194,16 +176,18 @@ def v_3d_blur_in_mask_outputs(
     """
     ret = V3dBlurInMaskOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_prefix")),
+        output_file=execution.output_file(params.get("output_prefix", None)),
     )
     return ret
 
 
 def v_3d_blur_in_mask_execute(
     params: V3dBlurInMaskParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dBlurInMaskOutputs:
     """
+    3dBlurInMask
+    
     Blurs a dataset spatially inside a mask.
     
     Author: AFNI Developers
@@ -212,10 +196,12 @@ def v_3d_blur_in_mask_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dBlurInMaskOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BLUR_IN_MASK_METADATA)
     params = execution.params(params)
     cargs = v_3d_blur_in_mask_cargs(params, execution)
     ret = v_3d_blur_in_mask_outputs(params, execution)
@@ -238,6 +224,8 @@ def v_3d_blur_in_mask(
     runner: Runner | None = None,
 ) -> V3dBlurInMaskOutputs:
     """
+    3dBlurInMask
+    
     Blurs a dataset spatially inside a mask.
     
     Author: AFNI Developers
@@ -264,8 +252,6 @@ def v_3d_blur_in_mask(
     Returns:
         NamedTuple of outputs (described in `V3dBlurInMaskOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_BLUR_IN_MASK_METADATA)
     params = v_3d_blur_in_mask_params(
         input_file=input_file,
         output_prefix=output_prefix,
@@ -279,13 +265,13 @@ def v_3d_blur_in_mask(
         float_=float_,
         fwhm_xyz=fwhm_xyz,
     )
-    return v_3d_blur_in_mask_execute(params, execution)
+    return v_3d_blur_in_mask_execute(params, runner)
 
 
 __all__ = [
     "V3dBlurInMaskOutputs",
-    "V3dBlurInMaskParameters",
     "V_3D_BLUR_IN_MASK_METADATA",
     "v_3d_blur_in_mask",
+    "v_3d_blur_in_mask_execute",
     "v_3d_blur_in_mask_params",
 ]

niwrap_afni/afni/v_3d_blur_to_fwhm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_BLUR_TO_FWHM_METADATA = Metadata(
-    id="e3c0c223285ad52e0076e3b433c4e9372a9374b3.boutiques",
+    id="12e7d81671107d9ada75a687d37b1447e3899716.boutiques",
     name="3dBlurToFWHM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_BLUR_TO_FWHM_METADATA = Metadata(
 
 
 V3dBlurToFwhmParameters = typing.TypedDict('V3dBlurToFwhmParameters', {
-    "__STYXTYPE__": typing.Literal["3dBlurToFWHM"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dBlurToFWHM"]],
+    "automask": bool,
+    "blurmaster": typing.NotRequired[InputPathType | None],
+    "fwhm": typing.NotRequired[float | None],
+    "fwhmxy": typing.NotRequired[float | None],
+    "in_file": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "prefix": typing.NotRequired[str | None],
+})
+V3dBlurToFwhmParametersTagged = typing.TypedDict('V3dBlurToFwhmParametersTagged', {
+    "@type": typing.Literal["afni/3dBlurToFWHM"],
     "automask": bool,
     "blurmaster": typing.NotRequired[InputPathType | None],
     "fwhm": typing.NotRequired[float | None],
@@ -24,43 +35,11 @@ V3dBlurToFwhmParameters = typing.TypedDict('V3dBlurToFwhmParameters', {
     "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
     "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 {
-        "3dBlurToFWHM": v_3d_blur_to_fwhm_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 {
-        "3dBlurToFWHM": v_3d_blur_to_fwhm_outputs,
-    }.get(t)
 
 
 class V3dBlurToFwhmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_blur_to_fwhm(...)`.
+    Output object returned when calling `V3dBlurToFwhmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def v_3d_blur_to_fwhm_params(
     mask: InputPathType | None = None,
     outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
     prefix: str | None = None,
-) -> V3dBlurToFwhmParameters:
+) -> V3dBlurToFwhmParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +74,7 @@ def v_3d_blur_to_fwhm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dBlurToFWHM",
+        "@type": "afni/3dBlurToFWHM",
         "automask": automask,
         "in_file": in_file,
     }
@@ -129,38 +108,38 @@ def v_3d_blur_to_fwhm_cargs(
     """
     cargs = []
     cargs.append("3dBlurToFWHM")
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    if params.get("blurmaster") is not None:
+    if params.get("blurmaster", None) is not None:
         cargs.extend([
             "-blurmaster",
-            execution.input_file(params.get("blurmaster"))
+            execution.input_file(params.get("blurmaster", None))
         ])
-    if params.get("fwhm") is not None:
+    if params.get("fwhm", None) is not None:
         cargs.extend([
             "-FWHM",
-            str(params.get("fwhm"))
+            str(params.get("fwhm", None))
         ])
-    if params.get("fwhmxy") is not None:
+    if params.get("fwhmxy", None) is not None:
         cargs.extend([
             "-FWHMxy",
-            str(params.get("fwhmxy"))
+            str(params.get("fwhmxy", None))
         ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("in_file"))
+        execution.input_file(params.get("in_file", 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("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    if params.get("prefix") is not None:
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
     return cargs
 
@@ -180,16 +159,18 @@ def v_3d_blur_to_fwhm_outputs(
     """
     ret = V3dBlurToFwhmOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        out_file=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_blur_to_fwhm_execute(
     params: V3dBlurToFwhmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dBlurToFwhmOutputs:
     """
+    3dBlurToFWHM
+    
     Blurs a 'master' dataset until it reaches a specified FWHM smoothness
     (approximately).
     
@@ -199,10 +180,12 @@ def v_3d_blur_to_fwhm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dBlurToFwhmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BLUR_TO_FWHM_METADATA)
     params = execution.params(params)
     cargs = v_3d_blur_to_fwhm_cargs(params, execution)
     ret = v_3d_blur_to_fwhm_outputs(params, execution)
@@ -222,6 +205,8 @@ def v_3d_blur_to_fwhm(
     runner: Runner | None = None,
 ) -> V3dBlurToFwhmOutputs:
     """
+    3dBlurToFWHM
+    
     Blurs a 'master' dataset until it reaches a specified FWHM smoothness
     (approximately).
     
@@ -243,8 +228,6 @@ def v_3d_blur_to_fwhm(
     Returns:
         NamedTuple of outputs (described in `V3dBlurToFwhmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_BLUR_TO_FWHM_METADATA)
     params = v_3d_blur_to_fwhm_params(
         automask=automask,
         blurmaster=blurmaster,
@@ -255,13 +238,13 @@ def v_3d_blur_to_fwhm(
         outputtype=outputtype,
         prefix=prefix,
     )
-    return v_3d_blur_to_fwhm_execute(params, execution)
+    return v_3d_blur_to_fwhm_execute(params, runner)
 
 
 __all__ = [
     "V3dBlurToFwhmOutputs",
-    "V3dBlurToFwhmParameters",
     "V_3D_BLUR_TO_FWHM_METADATA",
     "v_3d_blur_to_fwhm",
+    "v_3d_blur_to_fwhm_execute",
     "v_3d_blur_to_fwhm_params",
 ]

niwrap_afni/afni/v_3d_brain_sync.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_BRAIN_SYNC_METADATA = Metadata(
-    id="508af7da56bddf5a954492ce4305cdd0edc2a285.boutiques",
+    id="36cb746b4c748e8e57c312e3792ccd7d013e7b17.boutiques",
     name="3dBrainSync",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V_3D_BRAIN_SYNC_METADATA = Metadata(
 
 
 V3dBrainSyncParameters = typing.TypedDict('V3dBrainSyncParameters', {
-    "__STYXTYPE__": typing.Literal["3dBrainSync"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dBrainSync"]],
+    "inset1": InputPathType,
+    "inset2": InputPathType,
+    "qprefix": typing.NotRequired[str | None],
+    "pprefix": typing.NotRequired[str | None],
+    "normalize": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "verb": bool,
+})
+V3dBrainSyncParametersTagged = typing.TypedDict('V3dBrainSyncParametersTagged', {
+    "@type": typing.Literal["afni/3dBrainSync"],
     "inset1": InputPathType,
     "inset2": InputPathType,
     "qprefix": typing.NotRequired[str | None],
@@ -23,43 +33,11 @@ V3dBrainSyncParameters = typing.TypedDict('V3dBrainSyncParameters', {
     "mask": typing.NotRequired[InputPathType | None],
     "verb": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dBrainSync": v_3d_brain_sync_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 {
-        "3dBrainSync": v_3d_brain_sync_outputs,
-    }.get(t)
 
 
 class V3dBrainSyncOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_brain_sync(...)`.
+    Output object returned when calling `V3dBrainSyncParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +61,7 @@ def v_3d_brain_sync_params(
     normalize: bool = False,
     mask: InputPathType | None = None,
     verb: bool = False,
-) -> V3dBrainSyncParameters:
+) -> V3dBrainSyncParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +80,7 @@ def v_3d_brain_sync_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dBrainSync",
+        "@type": "afni/3dBrainSync",
         "inset1": inset1,
         "inset2": inset2,
         "normalize": normalize,
@@ -134,30 +112,30 @@ def v_3d_brain_sync_cargs(
     cargs.append("3dBrainSync")
     cargs.extend([
         "-inset1",
-        execution.input_file(params.get("inset1"))
+        execution.input_file(params.get("inset1", None))
     ])
     cargs.extend([
         "-inset2",
-        execution.input_file(params.get("inset2"))
+        execution.input_file(params.get("inset2", None))
     ])
-    if params.get("qprefix") is not None:
+    if params.get("qprefix", None) is not None:
         cargs.extend([
             "-Qprefix",
-            params.get("qprefix")
+            params.get("qprefix", None)
         ])
-    if params.get("pprefix") is not None:
+    if params.get("pprefix", None) is not None:
         cargs.extend([
             "-Pprefix",
-            params.get("pprefix")
+            params.get("pprefix", None)
         ])
-    if params.get("normalize"):
+    if params.get("normalize", False):
         cargs.append("-normalize")
-    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("verb"):
+    if params.get("verb", False):
         cargs.append("-verb")
     return cargs
 
@@ -177,20 +155,22 @@ def v_3d_brain_sync_outputs(
     """
     ret = V3dBrainSyncOutputs(
         root=execution.output_file("."),
-        qprefix_output=execution.output_file(params.get("qprefix") + ".nii") if (params.get("qprefix") is not None) else None,
-        pprefix_output=execution.output_file(params.get("pprefix") + ".nii") if (params.get("pprefix") is not None) else None,
-        qprefix_sval=execution.output_file(params.get("qprefix") + ".sval.1D") if (params.get("qprefix") is not None) else None,
-        qprefix_qmat=execution.output_file(params.get("qprefix") + ".qmat.1D") if (params.get("qprefix") is not None) else None,
-        pprefix_perm=execution.output_file(params.get("pprefix") + ".perm.1D") if (params.get("pprefix") is not None) else None,
+        qprefix_output=execution.output_file(params.get("qprefix", None) + ".nii") if (params.get("qprefix") is not None) else None,
+        pprefix_output=execution.output_file(params.get("pprefix", None) + ".nii") if (params.get("pprefix") is not None) else None,
+        qprefix_sval=execution.output_file(params.get("qprefix", None) + ".sval.1D") if (params.get("qprefix") is not None) else None,
+        qprefix_qmat=execution.output_file(params.get("qprefix", None) + ".qmat.1D") if (params.get("qprefix") is not None) else None,
+        pprefix_perm=execution.output_file(params.get("pprefix", None) + ".perm.1D") if (params.get("pprefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_brain_sync_execute(
     params: V3dBrainSyncParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dBrainSyncOutputs:
     """
+    3dBrainSync
+    
     'Synchronizes' the -inset2 dataset to match the -inset1 dataset, using
     orthogonal or permutation transformation.
     
@@ -200,10 +180,12 @@ def v_3d_brain_sync_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dBrainSyncOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BRAIN_SYNC_METADATA)
     params = execution.params(params)
     cargs = v_3d_brain_sync_cargs(params, execution)
     ret = v_3d_brain_sync_outputs(params, execution)
@@ -222,6 +204,8 @@ def v_3d_brain_sync(
     runner: Runner | None = None,
 ) -> V3dBrainSyncOutputs:
     """
+    3dBrainSync
+    
     'Synchronizes' the -inset2 dataset to match the -inset1 dataset, using
     orthogonal or permutation transformation.
     
@@ -244,8 +228,6 @@ def v_3d_brain_sync(
     Returns:
         NamedTuple of outputs (described in `V3dBrainSyncOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_BRAIN_SYNC_METADATA)
     params = v_3d_brain_sync_params(
         inset1=inset1,
         inset2=inset2,
@@ -255,13 +237,13 @@ def v_3d_brain_sync(
         mask=mask,
         verb=verb,
     )
-    return v_3d_brain_sync_execute(params, execution)
+    return v_3d_brain_sync_execute(params, runner)
 
 
 __all__ = [
     "V3dBrainSyncOutputs",
-    "V3dBrainSyncParameters",
     "V_3D_BRAIN_SYNC_METADATA",
     "v_3d_brain_sync",
+    "v_3d_brain_sync_execute",
     "v_3d_brain_sync_params",
 ]