niwrap-afni 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v_3dmaxdisp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DMAXDISP_METADATA = Metadata(
-    id="a6aa9cced188a32fdfff9cb9b8e0dd6ed83c244c.boutiques",
+    id="df5cebff8f2b1777c51dee0444455c1379652c77.boutiques",
     name="3dmaxdisp",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V_3DMAXDISP_METADATA = Metadata(
 
 
 V3dmaxdispParameters = typing.TypedDict('V3dmaxdispParameters', {
-    "__STYXTYPE__": typing.Literal["3dmaxdisp"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dmaxdisp"]],
+    "inset": InputPathType,
+    "matrix": InputPathType,
+    "verbose": bool,
+})
+V3dmaxdispParametersTagged = typing.TypedDict('V3dmaxdispParametersTagged', {
+    "@type": typing.Literal["afni/3dmaxdisp"],
     "inset": InputPathType,
     "matrix": InputPathType,
     "verbose": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dmaxdisp": v_3dmaxdisp_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 {
-        "3dmaxdisp": v_3dmaxdisp_outputs,
-    }.get(t)
 
 
 class V3dmaxdispOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dmaxdisp(...)`.
+    Output object returned when calling `V3dmaxdispParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def v_3dmaxdisp_params(
     inset: InputPathType,
     matrix: InputPathType,
     verbose: bool = False,
-) -> V3dmaxdispParameters:
+) -> V3dmaxdispParametersTagged:
     """
     Build parameters.
     
@@ -81,7 +55,7 @@ def v_3dmaxdisp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dmaxdisp",
+        "@type": "afni/3dmaxdisp",
         "inset": inset,
         "matrix": matrix,
         "verbose": verbose,
@@ -106,13 +80,13 @@ def v_3dmaxdisp_cargs(
     cargs.append("3dmaxdisp")
     cargs.extend([
         "-inset",
-        execution.input_file(params.get("inset"))
+        execution.input_file(params.get("inset", None))
     ])
     cargs.extend([
         "-matrix",
-        execution.input_file(params.get("matrix"))
+        execution.input_file(params.get("matrix", None))
     ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
     return cargs
 
@@ -139,11 +113,14 @@ def v_3dmaxdisp_outputs(
 
 def v_3dmaxdisp_execute(
     params: V3dmaxdispParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dmaxdispOutputs:
     """
-    Reads in a 3D dataset and a DICOM-based affine matrix to output the average and
-    maximum displacement applied to the edge voxels of the 3D dataset's automask.
+    3dmaxdisp
+    
+    Reads in a 3D dataset and a DICOM-based affine matrix to output the average
+    and maximum displacement applied to the edge voxels of the 3D dataset's
+    automask.
     
     Author: AFNI Developers
     
@@ -151,10 +128,12 @@ def v_3dmaxdisp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dmaxdispOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMAXDISP_METADATA)
     params = execution.params(params)
     cargs = v_3dmaxdisp_cargs(params, execution)
     ret = v_3dmaxdisp_outputs(params, execution)
@@ -169,8 +148,11 @@ def v_3dmaxdisp(
     runner: Runner | None = None,
 ) -> V3dmaxdispOutputs:
     """
-    Reads in a 3D dataset and a DICOM-based affine matrix to output the average and
-    maximum displacement applied to the edge voxels of the 3D dataset's automask.
+    3dmaxdisp
+    
+    Reads in a 3D dataset and a DICOM-based affine matrix to output the average
+    and maximum displacement applied to the edge voxels of the 3D dataset's
+    automask.
     
     Author: AFNI Developers
     
@@ -186,20 +168,18 @@ def v_3dmaxdisp(
     Returns:
         NamedTuple of outputs (described in `V3dmaxdispOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DMAXDISP_METADATA)
     params = v_3dmaxdisp_params(
         inset=inset,
         matrix=matrix,
         verbose=verbose,
     )
-    return v_3dmaxdisp_execute(params, execution)
+    return v_3dmaxdisp_execute(params, runner)
 
 
 __all__ = [
     "V3dmaxdispOutputs",
-    "V3dmaxdispParameters",
     "V_3DMAXDISP_METADATA",
     "v_3dmaxdisp",
+    "v_3dmaxdisp_execute",
     "v_3dmaxdisp_params",
 ]

niwrap_afni/afni/v_3dmaxima.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DMAXIMA_METADATA = Metadata(
-    id="0315ff99294041a685b14686e0066820acd7ec57.boutiques",
+    id="942fd5d4e896fb166b717953b82c141e702ff733.boutiques",
     name="3dmaxima",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,30 @@ V_3DMAXIMA_METADATA = Metadata(
 
 
 V3dmaximaParameters = typing.TypedDict('V3dmaximaParameters', {
-    "__STYXTYPE__": typing.Literal["3dmaxima"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dmaxima"]],
+    "input_dataset": InputPathType,
+    "output_prefix": typing.NotRequired[str | None],
+    "threshold": typing.NotRequired[float | None],
+    "min_dist": typing.NotRequired[float | None],
+    "out_rad": typing.NotRequired[float | None],
+    "input_flag": bool,
+    "spheres_1_flag": bool,
+    "spheres_1toN_flag": bool,
+    "spheres_Nto1_flag": bool,
+    "neg_ext_flag": bool,
+    "true_max_flag": bool,
+    "dset_coords_flag": bool,
+    "no_text_flag": bool,
+    "coords_only_flag": bool,
+    "n_style_sort_flag": bool,
+    "n_style_weight_ave_flag": bool,
+    "debug_level": typing.NotRequired[float | None],
+    "help_flag": bool,
+    "hist_flag": bool,
+    "ver_flag": bool,
+})
+V3dmaximaParametersTagged = typing.TypedDict('V3dmaximaParametersTagged', {
+    "@type": typing.Literal["afni/3dmaxima"],
     "input_dataset": InputPathType,
     "output_prefix": typing.NotRequired[str | None],
     "threshold": typing.NotRequired[float | None],
@@ -36,47 +59,17 @@ V3dmaximaParameters = typing.TypedDict('V3dmaximaParameters', {
     "hist_flag": bool,
     "ver_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dmaxima": v_3dmaxima_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 {
-        "3dmaxima": v_3dmaxima_outputs,
-    }.get(t)
 
 
 class V3dmaximaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dmaxima(...)`.
+    Output object returned when calling `V3dmaximaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_mask: OutputPathType | None
+    output_mask_head: OutputPathType | None
+    """Output mask dataset with extrema locations"""
+    output_mask_brik: OutputPathType | None
     """Output mask dataset with extrema locations"""
 
 
@@ -101,7 +94,7 @@ def v_3dmaxima_params(
     help_flag: bool = False,
     hist_flag: bool = False,
     ver_flag: bool = False,
-) -> V3dmaximaParameters:
+) -> V3dmaximaParametersTagged:
     """
     Build parameters.
     
@@ -133,7 +126,7 @@ def v_3dmaxima_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dmaxima",
+        "@type": "afni/3dmaxima",
         "input_dataset": input_dataset,
         "input_flag": input_flag,
         "spheres_1_flag": spheres_1_flag,
@@ -178,59 +171,59 @@ def v_3dmaxima_cargs(
     """
     cargs = []
     cargs.append("3dmaxima")
-    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("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-thresh",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("min_dist") is not None:
+    if params.get("min_dist", None) is not None:
         cargs.extend([
             "-min_dist",
-            str(params.get("min_dist"))
+            str(params.get("min_dist", None))
         ])
-    if params.get("out_rad") is not None:
+    if params.get("out_rad", None) is not None:
         cargs.extend([
             "-out_rad",
-            str(params.get("out_rad"))
+            str(params.get("out_rad", None))
         ])
-    if params.get("input_flag"):
+    if params.get("input_flag", False):
         cargs.append("-input")
-    if params.get("spheres_1_flag"):
+    if params.get("spheres_1_flag", False):
         cargs.append("-spheres_1")
-    if params.get("spheres_1toN_flag"):
+    if params.get("spheres_1toN_flag", False):
         cargs.append("-spheres_1toN")
-    if params.get("spheres_Nto1_flag"):
+    if params.get("spheres_Nto1_flag", False):
         cargs.append("-spheres_Nto1")
-    if params.get("neg_ext_flag"):
+    if params.get("neg_ext_flag", False):
         cargs.append("-neg_ext")
-    if params.get("true_max_flag"):
+    if params.get("true_max_flag", False):
         cargs.append("-true_max")
-    if params.get("dset_coords_flag"):
+    if params.get("dset_coords_flag", False):
         cargs.append("-dset_coords")
-    if params.get("no_text_flag"):
+    if params.get("no_text_flag", False):
         cargs.append("-no_text")
-    if params.get("coords_only_flag"):
+    if params.get("coords_only_flag", False):
         cargs.append("-coords_only")
-    if params.get("n_style_sort_flag"):
+    if params.get("n_style_sort_flag", False):
         cargs.append("-n_style_sort")
-    if params.get("n_style_weight_ave_flag"):
+    if params.get("n_style_weight_ave_flag", False):
         cargs.append("-n_style_weight_ave")
-    if params.get("debug_level") is not None:
+    if params.get("debug_level", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug_level"))
+            str(params.get("debug_level", None))
         ])
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-help")
-    if params.get("hist_flag"):
+    if params.get("hist_flag", False):
         cargs.append("-hist")
-    if params.get("ver_flag"):
+    if params.get("ver_flag", False):
         cargs.append("-ver")
     return cargs
 
@@ -250,16 +243,19 @@ def v_3dmaxima_outputs(
     """
     ret = V3dmaximaOutputs(
         root=execution.output_file("."),
-        output_mask=execution.output_file(params.get("output_prefix") + "_mask+orig.[HEAD | BRIK]") if (params.get("output_prefix") is not None) else None,
+        output_mask_head=execution.output_file(params.get("output_prefix", None) + "_mask+orig.HEAD") if (params.get("output_prefix") is not None) else None,
+        output_mask_brik=execution.output_file(params.get("output_prefix", None) + "_mask+orig.BRIK") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def v_3dmaxima_execute(
     params: V3dmaximaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dmaximaOutputs:
     """
+    3dmaxima
+    
     Locate extrema in a functional dataset.
     
     Author: AFNI Developers
@@ -268,10 +264,12 @@ def v_3dmaxima_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dmaximaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMAXIMA_METADATA)
     params = execution.params(params)
     cargs = v_3dmaxima_cargs(params, execution)
     ret = v_3dmaxima_outputs(params, execution)
@@ -303,6 +301,8 @@ def v_3dmaxima(
     runner: Runner | None = None,
 ) -> V3dmaximaOutputs:
     """
+    3dmaxima
+    
     Locate extrema in a functional dataset.
     
     Author: AFNI Developers
@@ -337,8 +337,6 @@ def v_3dmaxima(
     Returns:
         NamedTuple of outputs (described in `V3dmaximaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DMAXIMA_METADATA)
     params = v_3dmaxima_params(
         input_dataset=input_dataset,
         output_prefix=output_prefix,
@@ -361,13 +359,13 @@ def v_3dmaxima(
         hist_flag=hist_flag,
         ver_flag=ver_flag,
     )
-    return v_3dmaxima_execute(params, execution)
+    return v_3dmaxima_execute(params, runner)
 
 
 __all__ = [
     "V3dmaximaOutputs",
-    "V3dmaximaParameters",
     "V_3DMAXIMA_METADATA",
     "v_3dmaxima",
+    "v_3dmaxima_execute",
     "v_3dmaxima_params",
 ]

niwrap_afni/afni/v_3dmerge.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DMERGE_METADATA = Metadata(
-    id="b4bc137cd47dc951a1ce4996b1bce347a13b1474.boutiques",
+    id="adf15b50bd188615828c5d85748b7e28454ee6b6.boutiques",
     name="3dmerge",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ V_3DMERGE_METADATA = Metadata(
 
 
 V3dmergeParameters = typing.TypedDict('V3dmergeParameters', {
-    "__STYXTYPE__": typing.Literal["3dmerge"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dmerge"]],
+    "input_files": list[InputPathType],
+    "output_file": str,
+    "blur_fwhm": typing.NotRequired[float | None],
+    "threshold": typing.NotRequired[float | None],
+    "clust": typing.NotRequired[list[float] | None],
+    "dindex": typing.NotRequired[float | None],
+    "tindex": typing.NotRequired[float | None],
+    "absolute": bool,
+    "dxyz": bool,
+    "gmean": bool,
+    "gmax": bool,
+    "quiet": bool,
+})
+V3dmergeParametersTagged = typing.TypedDict('V3dmergeParametersTagged', {
+    "@type": typing.Literal["afni/3dmerge"],
     "input_files": list[InputPathType],
     "output_file": str,
     "blur_fwhm": typing.NotRequired[float | None],
@@ -28,43 +43,11 @@ V3dmergeParameters = typing.TypedDict('V3dmergeParameters', {
     "gmax": bool,
     "quiet": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dmerge": v_3dmerge_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 {
-        "3dmerge": v_3dmerge_outputs,
-    }.get(t)
 
 
 class V3dmergeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dmerge(...)`.
+    Output object returned when calling `V3dmergeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +68,7 @@ def v_3dmerge_params(
     gmean: bool = False,
     gmax: bool = False,
     quiet: bool = False,
-) -> V3dmergeParameters:
+) -> V3dmergeParametersTagged:
     """
     Build parameters.
     
@@ -109,7 +92,7 @@ def v_3dmerge_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dmerge",
+        "@type": "afni/3dmerge",
         "input_files": input_files,
         "output_file": output_file,
         "absolute": absolute,
@@ -146,45 +129,45 @@ def v_3dmerge_cargs(
     """
     cargs = []
     cargs.append("3dmerge")
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
     cargs.extend([
         "-prefix",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("blur_fwhm") is not None:
+    if params.get("blur_fwhm", None) is not None:
         cargs.extend([
             "-1blur_fwhm",
-            str(params.get("blur_fwhm"))
+            str(params.get("blur_fwhm", None))
         ])
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-1thresh",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("clust") is not None:
+    if params.get("clust", None) is not None:
         cargs.extend([
             "-1clust",
-            *map(str, params.get("clust"))
+            *map(str, params.get("clust", None))
         ])
-    if params.get("dindex") is not None:
+    if params.get("dindex", None) is not None:
         cargs.extend([
             "-1dindex",
-            str(params.get("dindex"))
+            str(params.get("dindex", None))
         ])
-    if params.get("tindex") is not None:
+    if params.get("tindex", None) is not None:
         cargs.extend([
             "-1tindex",
-            str(params.get("tindex"))
+            str(params.get("tindex", None))
         ])
-    if params.get("absolute"):
+    if params.get("absolute", False):
         cargs.append("-1abs")
-    if params.get("dxyz"):
+    if params.get("dxyz", False):
         cargs.append("-dxyz=1")
-    if params.get("gmean"):
+    if params.get("gmean", False):
         cargs.append("-gmean")
-    if params.get("gmax"):
+    if params.get("gmax", False):
         cargs.append("-gmax")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
     return cargs
 
@@ -204,16 +187,18 @@ def v_3dmerge_outputs(
     """
     ret = V3dmergeOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("output_file")),
+        output_dataset=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def v_3dmerge_execute(
     params: V3dmergeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dmergeOutputs:
     """
+    3dmerge
+    
     3dmerge edits and merges 3D datasets by applying various operations like
     thresholding, blurring, clustering, and more.
     
@@ -223,10 +208,12 @@ def v_3dmerge_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dmergeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DMERGE_METADATA)
     params = execution.params(params)
     cargs = v_3dmerge_cargs(params, execution)
     ret = v_3dmerge_outputs(params, execution)
@@ -250,6 +237,8 @@ def v_3dmerge(
     runner: Runner | None = None,
 ) -> V3dmergeOutputs:
     """
+    3dmerge
+    
     3dmerge edits and merges 3D datasets by applying various operations like
     thresholding, blurring, clustering, and more.
     
@@ -277,8 +266,6 @@ def v_3dmerge(
     Returns:
         NamedTuple of outputs (described in `V3dmergeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DMERGE_METADATA)
     params = v_3dmerge_params(
         input_files=input_files,
         output_file=output_file,
@@ -293,13 +280,13 @@ def v_3dmerge(
         gmax=gmax,
         quiet=quiet,
     )
-    return v_3dmerge_execute(params, execution)
+    return v_3dmerge_execute(params, runner)
 
 
 __all__ = [
     "V3dmergeOutputs",
-    "V3dmergeParameters",
     "V_3DMERGE_METADATA",
     "v_3dmerge",
+    "v_3dmerge_execute",
     "v_3dmerge_params",
 ]