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

niwrap_afni/afni/v_3dretroicor.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DRETROICOR_METADATA = Metadata(
-    id="925ba5dcd931de5a0a798d7af5a4598a7437092e.boutiques",
+    id="ac5b72f1993f14309c37ea9caf0344ab63a04ab3.boutiques",
     name="3dretroicor",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3DRETROICOR_METADATA = Metadata(
 
 
 V3dretroicorParameters = typing.TypedDict('V3dretroicorParameters', {
-    "__STYXTYPE__": typing.Literal["3dretroicor"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dretroicor"]],
+    "ignore": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "card": typing.NotRequired[InputPathType | None],
+    "cardphase": typing.NotRequired[str | None],
+    "threshold": typing.NotRequired[float | None],
+    "resp": typing.NotRequired[InputPathType | None],
+    "respphase": typing.NotRequired[str | None],
+    "order": typing.NotRequired[float | None],
+    "dataset": InputPathType,
+})
+V3dretroicorParametersTagged = typing.TypedDict('V3dretroicorParametersTagged', {
+    "@type": typing.Literal["afni/3dretroicor"],
     "ignore": typing.NotRequired[float | None],
     "prefix": typing.NotRequired[str | None],
     "card": typing.NotRequired[InputPathType | None],
@@ -25,43 +37,11 @@ V3dretroicorParameters = typing.TypedDict('V3dretroicorParameters', {
     "order": typing.NotRequired[float | None],
     "dataset": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dretroicor": v_3dretroicor_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 {
-        "3dretroicor": v_3dretroicor_outputs,
-    }.get(t)
 
 
 class V3dretroicorOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dretroicor(...)`.
+    Output object returned when calling `V3dretroicorParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +63,7 @@ def v_3dretroicor_params(
     resp: InputPathType | None = None,
     respphase: str | None = None,
     order: float | None = None,
-) -> V3dretroicorParameters:
+) -> V3dretroicorParametersTagged:
     """
     Build parameters.
     
@@ -105,7 +85,7 @@ def v_3dretroicor_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dretroicor",
+        "@type": "afni/3dretroicor",
         "dataset": dataset,
     }
     if ignore is not None:
@@ -142,47 +122,47 @@ def v_3dretroicor_cargs(
     """
     cargs = []
     cargs.append("3dretroicor")
-    if params.get("ignore") is not None:
+    if params.get("ignore", None) is not None:
         cargs.extend([
             "-ignore",
-            str(params.get("ignore"))
+            str(params.get("ignore", None))
         ])
-    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)
         ])
-    if params.get("card") is not None:
+    if params.get("card", None) is not None:
         cargs.extend([
             "-card",
-            execution.input_file(params.get("card"))
+            execution.input_file(params.get("card", None))
         ])
-    if params.get("cardphase") is not None:
+    if params.get("cardphase", None) is not None:
         cargs.extend([
             "-cardphase",
-            params.get("cardphase")
+            params.get("cardphase", None)
         ])
-    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("resp") is not None:
+    if params.get("resp", None) is not None:
         cargs.extend([
             "-resp",
-            execution.input_file(params.get("resp"))
+            execution.input_file(params.get("resp", None))
         ])
-    if params.get("respphase") is not None:
+    if params.get("respphase", None) is not None:
         cargs.extend([
             "-respphase",
-            params.get("respphase")
+            params.get("respphase", None)
         ])
-    if params.get("order") is not None:
+    if params.get("order", None) is not None:
         cargs.extend([
             "-order",
-            str(params.get("order"))
+            str(params.get("order", None))
         ])
-    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(execution.input_file(params.get("dataset", None)))
     return cargs
 
 
@@ -201,20 +181,22 @@ def v_3dretroicor_outputs(
     """
     ret = V3dretroicorOutputs(
         root=execution.output_file("."),
-        corrected_dataset=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
-        output_cardiac_phase=execution.output_file(params.get("cardphase")) if (params.get("cardphase") is not None) else None,
-        output_resp_phase=execution.output_file(params.get("respphase")) if (params.get("respphase") is not None) else None,
+        corrected_dataset=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
+        output_cardiac_phase=execution.output_file(params.get("cardphase", None)) if (params.get("cardphase") is not None) else None,
+        output_resp_phase=execution.output_file(params.get("respphase", None)) if (params.get("respphase") is not None) else None,
     )
     return ret
 
 
 def v_3dretroicor_execute(
     params: V3dretroicorParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dretroicorOutputs:
     """
-    Performs Retrospective Image Correction for physiological motion effects using a
-    modified RETROICOR algorithm.
+    3dretroicor
+    
+    Performs Retrospective Image Correction for physiological motion effects
+    using a modified RETROICOR algorithm.
     
     Author: AFNI Developers
     
@@ -222,10 +204,12 @@ def v_3dretroicor_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dretroicorOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DRETROICOR_METADATA)
     params = execution.params(params)
     cargs = v_3dretroicor_cargs(params, execution)
     ret = v_3dretroicor_outputs(params, execution)
@@ -246,8 +230,10 @@ def v_3dretroicor(
     runner: Runner | None = None,
 ) -> V3dretroicorOutputs:
     """
-    Performs Retrospective Image Correction for physiological motion effects using a
-    modified RETROICOR algorithm.
+    3dretroicor
+    
+    Performs Retrospective Image Correction for physiological motion effects
+    using a modified RETROICOR algorithm.
     
     Author: AFNI Developers
     
@@ -271,8 +257,6 @@ def v_3dretroicor(
     Returns:
         NamedTuple of outputs (described in `V3dretroicorOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DRETROICOR_METADATA)
     params = v_3dretroicor_params(
         ignore=ignore,
         prefix=prefix,
@@ -284,13 +268,13 @@ def v_3dretroicor(
         order=order,
         dataset=dataset,
     )
-    return v_3dretroicor_execute(params, execution)
+    return v_3dretroicor_execute(params, runner)
 
 
 __all__ = [
     "V3dretroicorOutputs",
-    "V3dretroicorParameters",
     "V_3DRETROICOR_METADATA",
     "v_3dretroicor",
+    "v_3dretroicor_execute",
     "v_3dretroicor_params",
 ]

niwrap_afni/afni/v_3drotate.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DROTATE_METADATA = Metadata(
-    id="bedf388c506ade76e3d20b0cde9521d511961b2e.boutiques",
+    id="faff662007ce788fdeb0edbcc281fab85f7a83d9.boutiques",
     name="3drotate",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,35 @@ V_3DROTATE_METADATA = Metadata(
 
 
 V3drotateParameters = typing.TypedDict('V3drotateParameters', {
-    "__STYXTYPE__": typing.Literal["3drotate"],
+    "@type": typing.NotRequired[typing.Literal["afni/3drotate"]],
+    "dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "verbose": bool,
+    "ashift": typing.NotRequired[list[float] | None],
+    "bshift": typing.NotRequired[list[float] | None],
+    "rotate": typing.NotRequired[list[str] | None],
+    "rotparent": typing.NotRequired[InputPathType | None],
+    "gridparent": typing.NotRequired[InputPathType | None],
+    "matvec_dicom": typing.NotRequired[InputPathType | None],
+    "matvec_order": typing.NotRequired[InputPathType | None],
+    "matvec_dset": typing.NotRequired[InputPathType | None],
+    "dfile": typing.NotRequired[InputPathType | None],
+    "1Dfile": typing.NotRequired[InputPathType | None],
+    "points": bool,
+    "origin": typing.NotRequired[list[float] | None],
+    "Fourier": bool,
+    "NN": bool,
+    "linear": bool,
+    "cubic": bool,
+    "quintic": bool,
+    "heptic": bool,
+    "Fourier_nopad": bool,
+    "clipit": bool,
+    "noclip": bool,
+    "zpad": typing.NotRequired[float | None],
+})
+V3drotateParametersTagged = typing.TypedDict('V3drotateParametersTagged', {
+    "@type": typing.Literal["afni/3drotate"],
     "dataset": InputPathType,
     "prefix": typing.NotRequired[str | None],
     "verbose": bool,
@@ -41,43 +69,11 @@ V3drotateParameters = typing.TypedDict('V3drotateParameters', {
     "noclip": bool,
     "zpad": 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 {
-        "3drotate": v_3drotate_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 {
-        "3drotate": v_3drotate_outputs,
-    }.get(t)
 
 
 class V3drotateOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3drotate(...)`.
+    Output object returned when calling `V3drotateParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -113,7 +109,7 @@ def v_3drotate_params(
     clipit: bool = False,
     noclip: bool = False,
     zpad: float | None = None,
-) -> V3drotateParameters:
+) -> V3drotateParametersTagged:
     """
     Build parameters.
     
@@ -162,7 +158,7 @@ def v_3drotate_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3drotate",
+        "@type": "afni/3drotate",
         "dataset": dataset,
         "verbose": verbose,
         "points": points,
@@ -220,93 +216,93 @@ def v_3drotate_cargs(
     """
     cargs = []
     cargs.append("3drotate")
-    cargs.append(execution.input_file(params.get("dataset")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verbose")
-    if params.get("ashift") is not None:
+    if params.get("ashift", None) is not None:
         cargs.extend([
             "-ashift",
-            *map(str, params.get("ashift"))
+            *map(str, params.get("ashift", None))
         ])
-    if params.get("bshift") is not None:
+    if params.get("bshift", None) is not None:
         cargs.extend([
             "-bshift",
-            *map(str, params.get("bshift"))
+            *map(str, params.get("bshift", None))
         ])
-    if params.get("rotate") is not None:
+    if params.get("rotate", None) is not None:
         cargs.extend([
             "-rotate",
-            *params.get("rotate")
+            *params.get("rotate", None)
         ])
-    if params.get("rotparent") is not None:
+    if params.get("rotparent", None) is not None:
         cargs.extend([
             "-rotparent",
-            execution.input_file(params.get("rotparent"))
+            execution.input_file(params.get("rotparent", None))
         ])
-    if params.get("gridparent") is not None:
+    if params.get("gridparent", None) is not None:
         cargs.extend([
             "-gridparent",
-            execution.input_file(params.get("gridparent"))
+            execution.input_file(params.get("gridparent", None))
         ])
-    if params.get("matvec_dicom") is not None:
+    if params.get("matvec_dicom", None) is not None:
         cargs.extend([
             "-matvec_dicom",
-            execution.input_file(params.get("matvec_dicom"))
+            execution.input_file(params.get("matvec_dicom", None))
         ])
-    if params.get("matvec_order") is not None:
+    if params.get("matvec_order", None) is not None:
         cargs.extend([
             "-matvec_order",
-            execution.input_file(params.get("matvec_order"))
+            execution.input_file(params.get("matvec_order", None))
         ])
-    if params.get("matvec_dset") is not None:
+    if params.get("matvec_dset", None) is not None:
         cargs.extend([
             "-matvec_dset",
-            execution.input_file(params.get("matvec_dset"))
+            execution.input_file(params.get("matvec_dset", None))
         ])
-    if params.get("dfile") is not None:
+    if params.get("dfile", None) is not None:
         cargs.extend([
             "-dfile",
-            execution.input_file(params.get("dfile"))
+            execution.input_file(params.get("dfile", None))
         ])
-    if params.get("1Dfile") is not None:
+    if params.get("1Dfile", None) is not None:
         cargs.extend([
             "-1Dfile",
-            execution.input_file(params.get("1Dfile"))
+            execution.input_file(params.get("1Dfile", None))
         ])
-    if params.get("points"):
+    if params.get("points", False):
         cargs.append("-points")
-    if params.get("origin") is not None:
+    if params.get("origin", None) is not None:
         cargs.extend([
             "-origin",
-            *map(str, params.get("origin"))
+            *map(str, params.get("origin", None))
         ])
-    if params.get("Fourier"):
+    if params.get("Fourier", False):
         cargs.append("-Fourier")
-    if params.get("NN"):
+    if params.get("NN", False):
         cargs.append("-NN")
-    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("quintic"):
+    if params.get("quintic", False):
         cargs.append("-quintic")
-    if params.get("heptic"):
+    if params.get("heptic", False):
         cargs.append("-heptic")
-    if params.get("Fourier_nopad"):
+    if params.get("Fourier_nopad", False):
         cargs.append("-Fourier_nopad")
-    if params.get("clipit"):
+    if params.get("clipit", False):
         cargs.append("-clipit")
-    if params.get("noclip"):
+    if params.get("noclip", False):
         cargs.append("-noclip")
-    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))
         ])
     return cargs
 
@@ -326,17 +322,19 @@ def v_3drotate_outputs(
     """
     ret = V3drotateOutputs(
         root=execution.output_file("."),
-        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
-        out_brick=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        out_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        out_brick=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3drotate_execute(
     params: V3drotateParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3drotateOutputs:
     """
+    3drotate
+    
     Rotates and/or translates all bricks from an AFNI dataset.
     
     Author: AFNI Developers
@@ -345,10 +343,12 @@ def v_3drotate_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3drotateOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DROTATE_METADATA)
     params = execution.params(params)
     cargs = v_3drotate_cargs(params, execution)
     ret = v_3drotate_outputs(params, execution)
@@ -385,6 +385,8 @@ def v_3drotate(
     runner: Runner | None = None,
 ) -> V3drotateOutputs:
     """
+    3drotate
+    
     Rotates and/or translates all bricks from an AFNI dataset.
     
     Author: AFNI Developers
@@ -436,8 +438,6 @@ def v_3drotate(
     Returns:
         NamedTuple of outputs (described in `V3drotateOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DROTATE_METADATA)
     params = v_3drotate_params(
         dataset=dataset,
         prefix=prefix,
@@ -465,13 +465,13 @@ def v_3drotate(
         noclip=noclip,
         zpad=zpad,
     )
-    return v_3drotate_execute(params, execution)
+    return v_3drotate_execute(params, runner)
 
 
 __all__ = [
     "V3drotateOutputs",
-    "V3drotateParameters",
     "V_3DROTATE_METADATA",
     "v_3drotate",
+    "v_3drotate_execute",
     "v_3drotate_params",
 ]