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

niwrap_afni/afni/v_3d_warp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_WARP_METADATA = Metadata(
-    id="20e7717e6fe44e3192a9a8b3cbb0fc5ec57f7b95.boutiques",
+    id="3cc4b83e99b0d4bb9865a424333eb9d9321024b5.boutiques",
     name="3dWarp",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,8 +14,32 @@ V_3D_WARP_METADATA = Metadata(
 
 
 V3dWarpParameters = typing.TypedDict('V3dWarpParameters', {
-    "__STYXTYPE__": typing.Literal["3dWarp"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dWarp"]],
+    "matvec_in2out": typing.NotRequired[InputPathType | None],
+    "matvec_out2in": typing.NotRequired[InputPathType | None],
+    "tta2mni": bool,
+    "mni2tta": bool,
+    "matparent": typing.NotRequired[str | None],
+    "card2oblique": typing.NotRequired[str | None],
+    "oblique_parent": typing.NotRequired[str | None],
+    "deoblique": bool,
+    "oblique2card": bool,
+    "disp_obl_xform_only": bool,
+    "linear": bool,
+    "cubic": bool,
+    "NN": bool,
+    "quintic": bool,
+    "wsinc5": bool,
+    "fsl_matvec": bool,
+    "newgrid": typing.NotRequired[float | None],
+    "gridset": typing.NotRequired[str | None],
+    "zpad": typing.NotRequired[float | None],
+    "verb": bool,
+    "prefix": typing.NotRequired[str | None],
     "dataset": str,
+})
+V3dWarpParametersTagged = typing.TypedDict('V3dWarpParametersTagged', {
+    "@type": typing.Literal["afni/3dWarp"],
     "matvec_in2out": typing.NotRequired[InputPathType | None],
     "matvec_out2in": typing.NotRequired[InputPathType | None],
     "tta2mni": bool,
@@ -37,43 +61,13 @@ V3dWarpParameters = typing.TypedDict('V3dWarpParameters', {
     "zpad": typing.NotRequired[float | None],
     "verb": bool,
     "prefix": typing.NotRequired[str | None],
+    "dataset": str,
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dWarp": v_3d_warp_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 {
-    }.get(t)
-
-
 class V3dWarpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_warp(...)`.
+    Output object returned when calling `V3dWarpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -102,7 +96,7 @@ def v_3d_warp_params(
     zpad: float | None = None,
     verb: bool = False,
     prefix: str | None = None,
-) -> V3dWarpParameters:
+) -> V3dWarpParametersTagged:
     """
     Build parameters.
     
@@ -138,8 +132,7 @@ def v_3d_warp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dWarp",
-        "dataset": dataset,
+        "@type": "afni/3dWarp",
         "tta2mni": tta2mni,
         "mni2tta": mni2tta,
         "deoblique": deoblique,
@@ -152,6 +145,7 @@ def v_3d_warp_params(
         "wsinc5": wsinc5,
         "fsl_matvec": fsl_matvec,
         "verb": verb,
+        "dataset": dataset,
     }
     if matvec_in2out is not None:
         params["matvec_in2out"] = matvec_in2out
@@ -189,76 +183,76 @@ def v_3d_warp_cargs(
     """
     cargs = []
     cargs.append("3dWarp")
-    cargs.append(params.get("dataset"))
-    if params.get("matvec_in2out") is not None:
+    if params.get("matvec_in2out", None) is not None:
         cargs.extend([
             "-matvec_in2out",
-            execution.input_file(params.get("matvec_in2out"))
+            execution.input_file(params.get("matvec_in2out", None))
         ])
-    if params.get("matvec_out2in") is not None:
+    if params.get("matvec_out2in", None) is not None:
         cargs.extend([
             "-matvec_out2in",
-            execution.input_file(params.get("matvec_out2in"))
+            execution.input_file(params.get("matvec_out2in", None))
         ])
-    if params.get("tta2mni"):
+    if params.get("tta2mni", False):
         cargs.append("-tta2mni")
-    if params.get("mni2tta"):
+    if params.get("mni2tta", False):
         cargs.append("-mni2tta")
-    if params.get("matparent") is not None:
+    if params.get("matparent", None) is not None:
         cargs.extend([
             "-matparent",
-            params.get("matparent")
+            params.get("matparent", None)
         ])
-    if params.get("card2oblique") is not None:
+    if params.get("card2oblique", None) is not None:
         cargs.extend([
             "-card2oblique",
-            params.get("card2oblique")
+            params.get("card2oblique", None)
         ])
-    if params.get("oblique_parent") is not None:
+    if params.get("oblique_parent", None) is not None:
         cargs.extend([
             "-oblique_parent",
-            params.get("oblique_parent")
+            params.get("oblique_parent", None)
         ])
-    if params.get("deoblique"):
+    if params.get("deoblique", False):
         cargs.append("-deoblique")
-    if params.get("oblique2card"):
+    if params.get("oblique2card", False):
         cargs.append("-oblique2card")
-    if params.get("disp_obl_xform_only"):
+    if params.get("disp_obl_xform_only", False):
         cargs.append("-disp_obl_xform_only")
-    if params.get("linear"):
+    if params.get("linear", False):
         cargs.append("-linear")
-    if params.get("cubic"):
+    if params.get("cubic", False):
         cargs.append("-cubic")
-    if params.get("NN"):
+    if params.get("NN", False):
         cargs.append("-NN")
-    if params.get("quintic"):
+    if params.get("quintic", False):
         cargs.append("-quintic")
-    if params.get("wsinc5"):
+    if params.get("wsinc5", False):
         cargs.append("-wsinc5")
-    if params.get("fsl_matvec"):
+    if params.get("fsl_matvec", False):
         cargs.append("-fsl_matvec")
-    if params.get("newgrid") is not None:
+    if params.get("newgrid", None) is not None:
         cargs.extend([
             "-newgrid",
-            str(params.get("newgrid"))
+            str(params.get("newgrid", None))
         ])
-    if params.get("gridset") is not None:
+    if params.get("gridset", None) is not None:
         cargs.extend([
             "-gridset",
-            params.get("gridset")
+            params.get("gridset", None)
         ])
-    if params.get("zpad") is not None:
+    if params.get("zpad", None) is not None:
         cargs.extend([
             "-zpad",
-            str(params.get("zpad"))
+            str(params.get("zpad", None))
         ])
-    if params.get("verb"):
+    if params.get("verb", False):
         cargs.append("-verb")
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
+    cargs.append(params.get("dataset", None))
     return cargs
 
 
@@ -283,9 +277,11 @@ def v_3d_warp_outputs(
 
 def v_3d_warp_execute(
     params: V3dWarpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dWarpOutputs:
     """
+    3dWarp
+    
     Warp (spatially transform) one 3D dataset.
     
     Author: AFNI Developers
@@ -294,10 +290,12 @@ def v_3d_warp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dWarpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_WARP_METADATA)
     params = execution.params(params)
     cargs = v_3d_warp_cargs(params, execution)
     ret = v_3d_warp_outputs(params, execution)
@@ -331,6 +329,8 @@ def v_3d_warp(
     runner: Runner | None = None,
 ) -> V3dWarpOutputs:
     """
+    3dWarp
+    
     Warp (spatially transform) one 3D dataset.
     
     Author: AFNI Developers
@@ -369,10 +369,7 @@ def v_3d_warp(
     Returns:
         NamedTuple of outputs (described in `V3dWarpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_WARP_METADATA)
     params = v_3d_warp_params(
-        dataset=dataset,
         matvec_in2out=matvec_in2out,
         matvec_out2in=matvec_out2in,
         tta2mni=tta2mni,
@@ -394,14 +391,15 @@ def v_3d_warp(
         zpad=zpad,
         verb=verb,
         prefix=prefix,
+        dataset=dataset,
     )
-    return v_3d_warp_execute(params, execution)
+    return v_3d_warp_execute(params, runner)
 
 
 __all__ = [
     "V3dWarpOutputs",
-    "V3dWarpParameters",
     "V_3D_WARP_METADATA",
     "v_3d_warp",
+    "v_3d_warp_execute",
     "v_3d_warp_params",
 ]

niwrap_afni/afni/v_3d_warp_drive.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_WARP_DRIVE_METADATA = Metadata(
-    id="33208eefe90260d6cab1186f27531c4689ab5559.boutiques",
+    id="d358dceea8739c4cfdb249a910db1747ee75090e.boutiques",
     name="3dWarpDrive",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,46 @@ V_3D_WARP_DRIVE_METADATA = Metadata(
 
 
 V3dWarpDriveParameters = typing.TypedDict('V3dWarpDriveParameters', {
-    "__STYXTYPE__": typing.Literal["3dWarpDrive"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dWarpDrive"]],
+    "dataset": InputPathType,
+    "base_dataset": InputPathType,
+    "prefix": str,
+    "shift_only": bool,
+    "shift_rotate": bool,
+    "shift_rotate_scale": bool,
+    "affine_general": bool,
+    "bilinear_general": bool,
+    "linear": bool,
+    "cubic": bool,
+    "NN": bool,
+    "quintic": bool,
+    "input_dataset": typing.NotRequired[InputPathType | None],
+    "verbosity_flag": bool,
+    "summary_file": typing.NotRequired[str | None],
+    "max_iterations": typing.NotRequired[int | None],
+    "delta": typing.NotRequired[float | None],
+    "weight": typing.NotRequired[str | None],
+    "convergence_thresh": typing.NotRequired[float | None],
+    "twopass": bool,
+    "final_mode": typing.NotRequired[str | None],
+    "parfix": typing.NotRequired[list[str] | None],
+    "oned_file": typing.NotRequired[InputPathType | None],
+    "float_format": bool,
+    "coarserot_init": bool,
+    "oned_matrix_save": typing.NotRequired[InputPathType | None],
+    "sdu_order": bool,
+    "sud_order": bool,
+    "dsu_order": bool,
+    "dus_order": bool,
+    "usd_order": bool,
+    "uds_order": bool,
+    "supper_s_matrix": bool,
+    "slower_s_matrix": bool,
+    "ashift": bool,
+    "bshift": bool,
+})
+V3dWarpDriveParametersTagged = typing.TypedDict('V3dWarpDriveParametersTagged', {
+    "@type": typing.Literal["afni/3dWarpDrive"],
     "dataset": InputPathType,
     "base_dataset": InputPathType,
     "prefix": str,
@@ -52,43 +91,11 @@ V3dWarpDriveParameters = typing.TypedDict('V3dWarpDriveParameters', {
     "ashift": bool,
     "bshift": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dWarpDrive": v_3d_warp_drive_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 {
-        "3dWarpDrive": v_3d_warp_drive_outputs,
-    }.get(t)
 
 
 class V3dWarpDriveOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_warp_drive(...)`.
+    Output object returned when calling `V3dWarpDriveParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -139,7 +146,7 @@ def v_3d_warp_drive_params(
     slower_s_matrix: bool = False,
     ashift: bool = False,
     bshift: bool = False,
-) -> V3dWarpDriveParameters:
+) -> V3dWarpDriveParametersTagged:
     """
     Build parameters.
     
@@ -210,7 +217,7 @@ def v_3d_warp_drive_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dWarpDrive",
+        "@type": "afni/3dWarpDrive",
         "dataset": dataset,
         "base_dataset": base_dataset,
         "prefix": prefix,
@@ -276,110 +283,110 @@ def v_3d_warp_drive_cargs(
     """
     cargs = []
     cargs.append("3dWarpDrive")
-    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(execution.input_file(params.get("dataset", None)))
     cargs.extend([
         "-base",
-        execution.input_file(params.get("base_dataset"))
+        execution.input_file(params.get("base_dataset", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("shift_only"):
+    if params.get("shift_only", False):
         cargs.append("-shift_only")
-    if params.get("shift_rotate"):
+    if params.get("shift_rotate", False):
         cargs.append("-shift_rotate")
-    if params.get("shift_rotate_scale"):
+    if params.get("shift_rotate_scale", False):
         cargs.append("-shift_rotate_scale")
-    if params.get("affine_general"):
+    if params.get("affine_general", False):
         cargs.append("-affine_general")
-    if params.get("bilinear_general"):
+    if params.get("bilinear_general", False):
         cargs.append("-bilinear_general")
-    if params.get("linear"):
+    if params.get("linear", False):
         cargs.append("-linear")
-    if params.get("cubic"):
+    if params.get("cubic", False):
         cargs.append("-cubic")
-    if params.get("NN"):
+    if params.get("NN", False):
         cargs.append("-NN")
-    if params.get("quintic"):
+    if params.get("quintic", False):
         cargs.append("-quintic")
-    if params.get("input_dataset") is not None:
+    if params.get("input_dataset", None) is not None:
         cargs.extend([
             "-input",
-            execution.input_file(params.get("input_dataset"))
+            execution.input_file(params.get("input_dataset", None))
         ])
-    if params.get("verbosity_flag"):
+    if params.get("verbosity_flag", False):
         cargs.append("-verb")
-    if params.get("summary_file") is not None:
+    if params.get("summary_file", None) is not None:
         cargs.extend([
             "-summ",
-            params.get("summary_file")
+            params.get("summary_file", None)
         ])
-    if params.get("max_iterations") is not None:
+    if params.get("max_iterations", None) is not None:
         cargs.extend([
             "-maxite",
-            str(params.get("max_iterations"))
+            str(params.get("max_iterations", None))
         ])
-    if params.get("delta") is not None:
+    if params.get("delta", None) is not None:
         cargs.extend([
             "-delta",
-            str(params.get("delta"))
+            str(params.get("delta", None))
         ])
-    if params.get("weight") is not None:
+    if params.get("weight", None) is not None:
         cargs.extend([
             "-weight",
-            params.get("weight")
+            params.get("weight", None)
         ])
-    if params.get("convergence_thresh") is not None:
+    if params.get("convergence_thresh", None) is not None:
         cargs.extend([
             "-thresh",
-            str(params.get("convergence_thresh"))
+            str(params.get("convergence_thresh", None))
         ])
-    if params.get("twopass"):
+    if params.get("twopass", False):
         cargs.append("-twopass")
-    if params.get("final_mode") is not None:
+    if params.get("final_mode", None) is not None:
         cargs.extend([
             "-final",
-            params.get("final_mode")
+            params.get("final_mode", None)
         ])
-    if params.get("parfix") is not None:
+    if params.get("parfix", None) is not None:
         cargs.extend([
             "-parfix",
-            *params.get("parfix")
+            *params.get("parfix", None)
         ])
-    if params.get("oned_file") is not None:
+    if params.get("oned_file", None) is not None:
         cargs.extend([
             "-1Dfile",
-            execution.input_file(params.get("oned_file"))
+            execution.input_file(params.get("oned_file", None))
         ])
-    if params.get("float_format"):
+    if params.get("float_format", False):
         cargs.append("-float")
-    if params.get("coarserot_init"):
+    if params.get("coarserot_init", False):
         cargs.append("-coarserot")
-    if params.get("oned_matrix_save") is not None:
+    if params.get("oned_matrix_save", None) is not None:
         cargs.extend([
             "-1Dmatrix_save",
-            execution.input_file(params.get("oned_matrix_save"))
+            execution.input_file(params.get("oned_matrix_save", None))
         ])
-    if params.get("sdu_order"):
+    if params.get("sdu_order", False):
         cargs.append("-SDU")
-    if params.get("sud_order"):
+    if params.get("sud_order", False):
         cargs.append("-SUD")
-    if params.get("dsu_order"):
+    if params.get("dsu_order", False):
         cargs.append("-DSU")
-    if params.get("dus_order"):
+    if params.get("dus_order", False):
         cargs.append("-DUS")
-    if params.get("usd_order"):
+    if params.get("usd_order", False):
         cargs.append("-USD")
-    if params.get("uds_order"):
+    if params.get("uds_order", False):
         cargs.append("-UDS")
-    if params.get("supper_s_matrix"):
+    if params.get("supper_s_matrix", False):
         cargs.append("-Supper")
-    if params.get("slower_s_matrix"):
+    if params.get("slower_s_matrix", False):
         cargs.append("-Slower")
-    if params.get("ashift"):
+    if params.get("ashift", False):
         cargs.append("-ashift")
-    if params.get("bshift"):
+    if params.get("bshift", False):
         cargs.append("-bshift")
     return cargs
 
@@ -399,20 +406,23 @@ def v_3d_warp_drive_outputs(
     """
     ret = V3dWarpDriveOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("prefix") + "+orig"),
-        output_summary=execution.output_file(params.get("summary_file")) if (params.get("summary_file") is not None) else None,
-        oned_output_file=execution.output_file(pathlib.Path(params.get("oned_file")).name) if (params.get("oned_file") is not None) else None,
-        matrix_output_file=execution.output_file(pathlib.Path(params.get("oned_matrix_save")).name) if (params.get("oned_matrix_save") is not None) else None,
+        output_dataset=execution.output_file(params.get("prefix", None) + "+orig"),
+        output_summary=execution.output_file(params.get("summary_file", None)) if (params.get("summary_file") is not None) else None,
+        oned_output_file=execution.output_file(pathlib.Path(params.get("oned_file", None)).name) if (params.get("oned_file") is not None) else None,
+        matrix_output_file=execution.output_file(pathlib.Path(params.get("oned_matrix_save", None)).name) if (params.get("oned_matrix_save") is not None) else None,
     )
     return ret
 
 
 def v_3d_warp_drive_execute(
     params: V3dWarpDriveParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dWarpDriveOutputs:
     """
-    Warp a dataset to match another one (the base) using an affine transformation.
+    3dWarpDrive
+    
+    Warp a dataset to match another one (the base) using an affine
+    transformation.
     
     Author: AFNI Developers
     
@@ -420,10 +430,12 @@ def v_3d_warp_drive_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dWarpDriveOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_WARP_DRIVE_METADATA)
     params = execution.params(params)
     cargs = v_3d_warp_drive_cargs(params, execution)
     ret = v_3d_warp_drive_outputs(params, execution)
@@ -471,7 +483,10 @@ def v_3d_warp_drive(
     runner: Runner | None = None,
 ) -> V3dWarpDriveOutputs:
     """
-    Warp a dataset to match another one (the base) using an affine transformation.
+    3dWarpDrive
+    
+    Warp a dataset to match another one (the base) using an affine
+    transformation.
     
     Author: AFNI Developers
     
@@ -544,8 +559,6 @@ def v_3d_warp_drive(
     Returns:
         NamedTuple of outputs (described in `V3dWarpDriveOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_WARP_DRIVE_METADATA)
     params = v_3d_warp_drive_params(
         dataset=dataset,
         base_dataset=base_dataset,
@@ -584,13 +597,13 @@ def v_3d_warp_drive(
         ashift=ashift,
         bshift=bshift,
     )
-    return v_3d_warp_drive_execute(params, execution)
+    return v_3d_warp_drive_execute(params, runner)
 
 
 __all__ = [
     "V3dWarpDriveOutputs",
-    "V3dWarpDriveParameters",
     "V_3D_WARP_DRIVE_METADATA",
     "v_3d_warp_drive",
+    "v_3d_warp_drive_execute",
     "v_3d_warp_drive_params",
 ]