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

niwrap_afni/afni/v_3d_setup_group_in_corr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SETUP_GROUP_IN_CORR_METADATA = Metadata(
-    id="f4fdb6eb2bdc0a77fec3e1f1a2cc5b51172322c2.boutiques",
+    id="1683850374da35dcf958ddc69409cefbc1f13897.boutiques",
     name="3dSetupGroupInCorr",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_SETUP_GROUP_IN_CORR_METADATA = Metadata(
 
 
 V3dSetupGroupInCorrParameters = typing.TypedDict('V3dSetupGroupInCorrParameters', {
-    "__STYXTYPE__": typing.Literal["3dSetupGroupInCorr"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSetupGroupInCorr"]],
+    "datasets": list[InputPathType],
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "short_flag": bool,
+    "byte_flag": bool,
+    "labels_file": typing.NotRequired[InputPathType | None],
+    "delete_flag": bool,
+    "prep_method": typing.NotRequired[str | None],
+    "lr_pairs": typing.NotRequired[list[str] | None],
+})
+V3dSetupGroupInCorrParametersTagged = typing.TypedDict('V3dSetupGroupInCorrParametersTagged', {
+    "@type": typing.Literal["afni/3dSetupGroupInCorr"],
     "datasets": list[InputPathType],
     "mask_dataset": typing.NotRequired[InputPathType | None],
     "prefix": str,
@@ -25,43 +37,11 @@ V3dSetupGroupInCorrParameters = typing.TypedDict('V3dSetupGroupInCorrParameters'
     "prep_method": typing.NotRequired[str | None],
     "lr_pairs": typing.NotRequired[list[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 {
-        "3dSetupGroupInCorr": v_3d_setup_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 {
-        "3dSetupGroupInCorr": v_3d_setup_group_in_corr_outputs,
-    }.get(t)
 
 
 class V3dSetupGroupInCorrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_setup_group_in_corr(...)`.
+    Output object returned when calling `V3dSetupGroupInCorrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def v_3d_setup_group_in_corr_params(
     delete_flag: bool = False,
     prep_method: str | None = None,
     lr_pairs: list[str] | None = None,
-) -> V3dSetupGroupInCorrParameters:
+) -> V3dSetupGroupInCorrParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +81,7 @@ def v_3d_setup_group_in_corr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSetupGroupInCorr",
+        "@type": "afni/3dSetupGroupInCorr",
         "datasets": datasets,
         "prefix": prefix,
         "short_flag": short_flag,
@@ -134,36 +114,36 @@ def v_3d_setup_group_in_corr_cargs(
     """
     cargs = []
     cargs.append("3dSetupGroupInCorr")
-    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
-    if params.get("mask_dataset") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("datasets", None)])
+    if params.get("mask_dataset", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_dataset"))
+            execution.input_file(params.get("mask_dataset", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("short_flag"):
+    if params.get("short_flag", False):
         cargs.append("-short")
-    if params.get("byte_flag"):
+    if params.get("byte_flag", False):
         cargs.append("-byte")
-    if params.get("labels_file") is not None:
+    if params.get("labels_file", None) is not None:
         cargs.extend([
             "-labels",
-            execution.input_file(params.get("labels_file"))
+            execution.input_file(params.get("labels_file", None))
         ])
-    if params.get("delete_flag"):
+    if params.get("delete_flag", False):
         cargs.append("-DELETE")
-    if params.get("prep_method") is not None:
+    if params.get("prep_method", None) is not None:
         cargs.extend([
             "-prep",
-            params.get("prep_method")
+            params.get("prep_method", None)
         ])
-    if params.get("lr_pairs") is not None:
+    if params.get("lr_pairs", None) is not None:
         cargs.extend([
             "-LRpairs",
-            *params.get("lr_pairs")
+            *params.get("lr_pairs", None)
         ])
     return cargs
 
@@ -183,18 +163,21 @@ def v_3d_setup_group_in_corr_outputs(
     """
     ret = V3dSetupGroupInCorrOutputs(
         root=execution.output_file("."),
-        niml_file=execution.output_file(params.get("prefix") + ".grpincorr.niml"),
-        data_file=execution.output_file(params.get("prefix") + ".grpincorr.data"),
+        niml_file=execution.output_file(params.get("prefix", None) + ".grpincorr.niml"),
+        data_file=execution.output_file(params.get("prefix", None) + ".grpincorr.data"),
     )
     return ret
 
 
 def v_3d_setup_group_in_corr_execute(
     params: V3dSetupGroupInCorrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSetupGroupInCorrOutputs:
     """
-    Pre-process a collection of AFNI 3D+time datasets for use with Group InstaCorr.
+    3dSetupGroupInCorr
+    
+    Pre-process a collection of AFNI 3D+time datasets for use with Group
+    InstaCorr.
     
     Author: AFNI Developers
     
@@ -202,10 +185,12 @@ def v_3d_setup_group_in_corr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSetupGroupInCorrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SETUP_GROUP_IN_CORR_METADATA)
     params = execution.params(params)
     cargs = v_3d_setup_group_in_corr_cargs(params, execution)
     ret = v_3d_setup_group_in_corr_outputs(params, execution)
@@ -226,7 +211,10 @@ def v_3d_setup_group_in_corr(
     runner: Runner | None = None,
 ) -> V3dSetupGroupInCorrOutputs:
     """
-    Pre-process a collection of AFNI 3D+time datasets for use with Group InstaCorr.
+    3dSetupGroupInCorr
+    
+    Pre-process a collection of AFNI 3D+time datasets for use with Group
+    InstaCorr.
     
     Author: AFNI Developers
     
@@ -248,8 +236,6 @@ def v_3d_setup_group_in_corr(
     Returns:
         NamedTuple of outputs (described in `V3dSetupGroupInCorrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SETUP_GROUP_IN_CORR_METADATA)
     params = v_3d_setup_group_in_corr_params(
         datasets=datasets,
         mask_dataset=mask_dataset,
@@ -261,13 +247,13 @@ def v_3d_setup_group_in_corr(
         prep_method=prep_method,
         lr_pairs=lr_pairs,
     )
-    return v_3d_setup_group_in_corr_execute(params, execution)
+    return v_3d_setup_group_in_corr_execute(params, runner)
 
 
 __all__ = [
     "V3dSetupGroupInCorrOutputs",
-    "V3dSetupGroupInCorrParameters",
     "V_3D_SETUP_GROUP_IN_CORR_METADATA",
     "v_3d_setup_group_in_corr",
+    "v_3d_setup_group_in_corr_execute",
     "v_3d_setup_group_in_corr_params",
 ]

niwrap_afni/afni/v_3d_sharpen.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SHARPEN_METADATA = Metadata(
-    id="bcc67a227d911d875ee67c8740d94a7a8b8e5f4f.boutiques",
+    id="89056aeedfed68e218f19e717bb779c41496827e.boutiques",
     name="3dSharpen",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_3D_SHARPEN_METADATA = Metadata(
 
 
 V3dSharpenParameters = typing.TypedDict('V3dSharpenParameters', {
-    "__STYXTYPE__": typing.Literal["3dSharpen"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSharpen"]],
+    "sharpening_factor": typing.NotRequired[float | None],
+    "input_dataset": InputPathType,
+    "output_prefix": str,
+})
+V3dSharpenParametersTagged = typing.TypedDict('V3dSharpenParametersTagged', {
+    "@type": typing.Literal["afni/3dSharpen"],
     "sharpening_factor": typing.NotRequired[float | None],
     "input_dataset": InputPathType,
     "output_prefix": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dSharpen": v_3d_sharpen_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 {
-        "3dSharpen": v_3d_sharpen_outputs,
-    }.get(t)
 
 
 class V3dSharpenOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_sharpen(...)`.
+    Output object returned when calling `V3dSharpenParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def v_3d_sharpen_params(
     input_dataset: InputPathType,
     output_prefix: str,
     sharpening_factor: float | None = None,
-) -> V3dSharpenParameters:
+) -> V3dSharpenParametersTagged:
     """
     Build parameters.
     
@@ -81,7 +55,7 @@ def v_3d_sharpen_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSharpen",
+        "@type": "afni/3dSharpen",
         "input_dataset": input_dataset,
         "output_prefix": output_prefix,
     }
@@ -105,15 +79,15 @@ def v_3d_sharpen_cargs(
     """
     cargs = []
     cargs.append("3dSharpen")
-    if params.get("sharpening_factor") is not None:
+    if params.get("sharpening_factor", None) is not None:
         cargs.extend([
             "-phi",
-            str(params.get("sharpening_factor"))
+            str(params.get("sharpening_factor", None))
         ])
-    cargs.append(execution.input_file(params.get("input_dataset")))
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
     return cargs
 
@@ -133,18 +107,20 @@ def v_3d_sharpen_outputs(
     """
     ret = V3dSharpenOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("output_prefix") + ".nii.gz"),
+        output_dataset=execution.output_file(params.get("output_prefix", None) + ".nii.gz"),
     )
     return ret
 
 
 def v_3d_sharpen_execute(
     params: V3dSharpenParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSharpenOutputs:
     """
-    Applies a simple 3D sharpening filter to the positive values in the #0 volume of
-    the input dataset, and writes out a new dataset.
+    3dSharpen
+    
+    Applies a simple 3D sharpening filter to the positive values in the #0
+    volume of the input dataset, and writes out a new dataset.
     
     Author: AFNI Developers
     
@@ -152,10 +128,12 @@ def v_3d_sharpen_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSharpenOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SHARPEN_METADATA)
     params = execution.params(params)
     cargs = v_3d_sharpen_cargs(params, execution)
     ret = v_3d_sharpen_outputs(params, execution)
@@ -170,8 +148,10 @@ def v_3d_sharpen(
     runner: Runner | None = None,
 ) -> V3dSharpenOutputs:
     """
-    Applies a simple 3D sharpening filter to the positive values in the #0 volume of
-    the input dataset, and writes out a new dataset.
+    3dSharpen
+    
+    Applies a simple 3D sharpening filter to the positive values in the #0
+    volume of the input dataset, and writes out a new dataset.
     
     Author: AFNI Developers
     
@@ -187,20 +167,18 @@ def v_3d_sharpen(
     Returns:
         NamedTuple of outputs (described in `V3dSharpenOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SHARPEN_METADATA)
     params = v_3d_sharpen_params(
         sharpening_factor=sharpening_factor,
         input_dataset=input_dataset,
         output_prefix=output_prefix,
     )
-    return v_3d_sharpen_execute(params, execution)
+    return v_3d_sharpen_execute(params, runner)
 
 
 __all__ = [
     "V3dSharpenOutputs",
-    "V3dSharpenParameters",
     "V_3D_SHARPEN_METADATA",
     "v_3d_sharpen",
+    "v_3d_sharpen_execute",
     "v_3d_sharpen_params",
 ]

niwrap_afni/afni/v_3d_signatures.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SIGNATURES_METADATA = Metadata(
-    id="e20b04fdf19b18d2e6f8de7dfa09276b1b35f130.boutiques",
+    id="62c42f9307b68462703f2e02d462d769ea17d659.boutiques",
     name="3dSignatures",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_SIGNATURES_METADATA = Metadata(
 
 
 V3dSignaturesParameters = typing.TypedDict('V3dSignaturesParameters', {
-    "__STYXTYPE__": typing.Literal["3dSignatures"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSignatures"]],
+    "infile": InputPathType,
+    "outfile": str,
+    "segmentation": bool,
+    "filter": bool,
+    "threshold": typing.NotRequired[float | None],
+    "smoothing": typing.NotRequired[float | None],
+})
+V3dSignaturesParametersTagged = typing.TypedDict('V3dSignaturesParametersTagged', {
+    "@type": typing.Literal["afni/3dSignatures"],
     "infile": InputPathType,
     "outfile": str,
     "segmentation": bool,
@@ -22,43 +31,11 @@ V3dSignaturesParameters = typing.TypedDict('V3dSignaturesParameters', {
     "threshold": typing.NotRequired[float | None],
     "smoothing": 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 {
-        "3dSignatures": v_3d_signatures_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 {
-        "3dSignatures": v_3d_signatures_outputs,
-    }.get(t)
 
 
 class V3dSignaturesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_signatures(...)`.
+    Output object returned when calling `V3dSignaturesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def v_3d_signatures_params(
     filter_: bool = False,
     threshold: float | None = None,
     smoothing: float | None = None,
-) -> V3dSignaturesParameters:
+) -> V3dSignaturesParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +66,7 @@ def v_3d_signatures_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSignatures",
+        "@type": "afni/3dSignatures",
         "infile": infile,
         "outfile": outfile,
         "segmentation": segmentation,
@@ -117,21 +94,21 @@ def v_3d_signatures_cargs(
     """
     cargs = []
     cargs.append("3dSignatures")
-    cargs.append(execution.input_file(params.get("infile")))
-    cargs.append(params.get("outfile"))
-    if params.get("segmentation"):
+    cargs.append(execution.input_file(params.get("infile", None)))
+    cargs.append(params.get("outfile", None))
+    if params.get("segmentation", False):
         cargs.append("--segmentation")
-    if params.get("filter"):
+    if params.get("filter", False):
         cargs.append("--filter")
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "--threshold",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("smoothing") is not None:
+    if params.get("smoothing", None) is not None:
         cargs.extend([
             "--smoothing",
-            str(params.get("smoothing"))
+            str(params.get("smoothing", None))
         ])
     return cargs
 
@@ -151,16 +128,18 @@ def v_3d_signatures_outputs(
     """
     ret = V3dSignaturesOutputs(
         root=execution.output_file("."),
-        results_file=execution.output_file(params.get("outfile") + ".txt"),
+        results_file=execution.output_file(params.get("outfile", None) + ".txt"),
     )
     return ret
 
 
 def v_3d_signatures_execute(
     params: V3dSignaturesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSignaturesOutputs:
     """
+    3dSignatures
+    
     3dSignatures analysis tool for 3D genome organization.
     
     Author: AFNI Developers
@@ -169,10 +148,12 @@ def v_3d_signatures_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSignaturesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SIGNATURES_METADATA)
     params = execution.params(params)
     cargs = v_3d_signatures_cargs(params, execution)
     ret = v_3d_signatures_outputs(params, execution)
@@ -190,6 +171,8 @@ def v_3d_signatures(
     runner: Runner | None = None,
 ) -> V3dSignaturesOutputs:
     """
+    3dSignatures
+    
     3dSignatures analysis tool for 3D genome organization.
     
     Author: AFNI Developers
@@ -208,8 +191,6 @@ def v_3d_signatures(
     Returns:
         NamedTuple of outputs (described in `V3dSignaturesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SIGNATURES_METADATA)
     params = v_3d_signatures_params(
         infile=infile,
         outfile=outfile,
@@ -218,13 +199,13 @@ def v_3d_signatures(
         threshold=threshold,
         smoothing=smoothing,
     )
-    return v_3d_signatures_execute(params, execution)
+    return v_3d_signatures_execute(params, runner)
 
 
 __all__ = [
     "V3dSignaturesOutputs",
-    "V3dSignaturesParameters",
     "V_3D_SIGNATURES_METADATA",
     "v_3d_signatures",
+    "v_3d_signatures_execute",
     "v_3d_signatures_params",
 ]