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

niwrap_afni/afni/v_3dttest__.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DTTEST___METADATA = Metadata(
-    id="2157f069ac2e26af804825ecbaaba893074f562c.boutiques",
+    id="b6f6e0eb079a523b8cc03b4a1cb912072699dd19.boutiques",
     name="3dttest++",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,31 @@ V_3DTTEST___METADATA = Metadata(
 
 
 V3dttestParameters = typing.TypedDict('V3dttestParameters', {
-    "__STYXTYPE__": typing.Literal["3dttest++"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dttest++"]],
+    "setA": list[str],
+    "setB": typing.NotRequired[list[str] | None],
+    "setA_long": typing.NotRequired[list[str] | None],
+    "setB_long": typing.NotRequired[list[str] | None],
+    "covariates": typing.NotRequired[InputPathType | None],
+    "labelA": typing.NotRequired[str | None],
+    "labelB": typing.NotRequired[str | None],
+    "setweightA": typing.NotRequired[InputPathType | None],
+    "setweightB": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "resid": typing.NotRequired[str | None],
+    "paired": bool,
+    "unpooled": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "exblur": typing.NotRequired[int | None],
+    "randomsign": bool,
+    "permute": bool,
+    "ETAC": bool,
+    "ETAC_blur": typing.NotRequired[list[float] | None],
+    "ETAC_opt": typing.NotRequired[list[str] | None],
+    "seed": typing.NotRequired[float | None],
+})
+V3dttestParametersTagged = typing.TypedDict('V3dttestParametersTagged', {
+    "@type": typing.Literal["afni/3dttest++"],
     "setA": list[str],
     "setB": typing.NotRequired[list[str] | None],
     "setA_long": typing.NotRequired[list[str] | None],
@@ -37,43 +61,11 @@ V3dttestParameters = typing.TypedDict('V3dttestParameters', {
     "ETAC_opt": typing.NotRequired[list[str] | None],
     "seed": 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 {
-        "3dttest++": v_3dttest___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 {
-        "3dttest++": v_3dttest___outputs,
-    }.get(t)
 
 
 class V3dttestOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dttest__(...)`.
+    Output object returned when calling `V3dttestParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -105,7 +97,7 @@ def v_3dttest___params(
     etac_blur: list[float] | None = None,
     etac_opt: list[str] | None = None,
     seed: float | None = None,
-) -> V3dttestParameters:
+) -> V3dttestParametersTagged:
     """
     Build parameters.
     
@@ -146,7 +138,7 @@ def v_3dttest___params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dttest++",
+        "@type": "afni/3dttest++",
         "setA": set_a,
         "paired": paired,
         "unpooled": unpooled,
@@ -204,92 +196,92 @@ def v_3dttest___cargs(
     cargs.append("3dttest++")
     cargs.extend([
         "-setA",
-        *params.get("setA")
+        *params.get("setA", None)
     ])
-    if params.get("setB") is not None:
+    if params.get("setB", None) is not None:
         cargs.extend([
             "-setB",
-            *params.get("setB")
+            *params.get("setB", None)
         ])
-    if params.get("setA_long") is not None:
+    if params.get("setA_long", None) is not None:
         cargs.extend([
             "-setA",
-            *params.get("setA_long")
+            *params.get("setA_long", None)
         ])
-    if params.get("setB_long") is not None:
+    if params.get("setB_long", None) is not None:
         cargs.extend([
             "-setB",
-            *params.get("setB_long")
+            *params.get("setB_long", None)
         ])
-    if params.get("covariates") is not None:
+    if params.get("covariates", None) is not None:
         cargs.extend([
             "-covariates",
-            execution.input_file(params.get("covariates"))
+            execution.input_file(params.get("covariates", None))
         ])
-    if params.get("labelA") is not None:
+    if params.get("labelA", None) is not None:
         cargs.extend([
             "-labelA",
-            params.get("labelA")
+            params.get("labelA", None)
         ])
-    if params.get("labelB") is not None:
+    if params.get("labelB", None) is not None:
         cargs.extend([
             "-labelB",
-            params.get("labelB")
+            params.get("labelB", None)
         ])
-    if params.get("setweightA") is not None:
+    if params.get("setweightA", None) is not None:
         cargs.extend([
             "-setweightA",
-            execution.input_file(params.get("setweightA"))
+            execution.input_file(params.get("setweightA", None))
         ])
-    if params.get("setweightB") is not None:
+    if params.get("setweightB", None) is not None:
         cargs.extend([
             "-setweightB",
-            execution.input_file(params.get("setweightB"))
+            execution.input_file(params.get("setweightB", 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("resid") is not None:
+    if params.get("resid", None) is not None:
         cargs.extend([
             "-resid",
-            params.get("resid")
+            params.get("resid", None)
         ])
-    if params.get("paired"):
+    if params.get("paired", False):
         cargs.append("-paired")
-    if params.get("unpooled"):
+    if params.get("unpooled", False):
         cargs.append("-unpooled")
-    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("exblur") is not None:
+    if params.get("exblur", None) is not None:
         cargs.extend([
             "-exblur",
-            str(params.get("exblur"))
+            str(params.get("exblur", None))
         ])
-    if params.get("randomsign"):
+    if params.get("randomsign", False):
         cargs.append("-randomsign")
-    if params.get("permute"):
+    if params.get("permute", False):
         cargs.append("-permute")
-    if params.get("ETAC"):
+    if params.get("ETAC", False):
         cargs.append("-ETAC")
-    if params.get("ETAC_blur") is not None:
+    if params.get("ETAC_blur", None) is not None:
         cargs.extend([
             "-ETAC_blur",
-            *map(str, params.get("ETAC_blur"))
+            *map(str, params.get("ETAC_blur", None))
         ])
-    if params.get("ETAC_opt") is not None:
+    if params.get("ETAC_opt", None) is not None:
         cargs.extend([
             "-ETAC_opt",
-            *params.get("ETAC_opt")
+            *params.get("ETAC_opt", None)
         ])
-    if params.get("seed") is not None:
+    if params.get("seed", None) is not None:
         cargs.extend([
             "-seed",
-            str(params.get("seed"))
+            str(params.get("seed", None))
         ])
     return cargs
 
@@ -309,17 +301,19 @@ def v_3dttest___outputs(
     """
     ret = V3dttestOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
-        residuals=execution.output_file(params.get("resid") + ".nii.gz") if (params.get("resid") is not None) else None,
+        out_file=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
+        residuals=execution.output_file(params.get("resid", None) + ".nii.gz") if (params.get("resid") is not None) else None,
     )
     return ret
 
 
 def v_3dttest___execute(
     params: V3dttestParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dttestOutputs:
     """
+    3dttest++
+    
     Gosset (Student) t-test of sets of 3D datasets in AFNI.
     
     Author: AFNI Developers
@@ -328,10 +322,12 @@ def v_3dttest___execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dttestOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DTTEST___METADATA)
     params = execution.params(params)
     cargs = v_3dttest___cargs(params, execution)
     ret = v_3dttest___outputs(params, execution)
@@ -364,6 +360,8 @@ def v_3dttest__(
     runner: Runner | None = None,
 ) -> V3dttestOutputs:
     """
+    3dttest++
+    
     Gosset (Student) t-test of sets of 3D datasets in AFNI.
     
     Author: AFNI Developers
@@ -407,8 +405,6 @@ def v_3dttest__(
     Returns:
         NamedTuple of outputs (described in `V3dttestOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DTTEST___METADATA)
     params = v_3dttest___params(
         set_a=set_a,
         set_b=set_b,
@@ -432,13 +428,13 @@ def v_3dttest__(
         etac_opt=etac_opt,
         seed=seed,
     )
-    return v_3dttest___execute(params, execution)
+    return v_3dttest___execute(params, runner)
 
 
 __all__ = [
     "V3dttestOutputs",
-    "V3dttestParameters",
     "V_3DTTEST___METADATA",
     "v_3dttest__",
+    "v_3dttest___execute",
     "v_3dttest___params",
 ]

niwrap_afni/afni/v_3dvolreg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3DVOLREG_METADATA = Metadata(
-    id="568c36c7af9d384ea17acfcd37efb9dd6f74758e.boutiques",
+    id="6a91f264e1e34e3d73c66cff9c688faa39d2b0de.boutiques",
     name="3dvolreg",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ V_3DVOLREG_METADATA = Metadata(
 
 
 V3dvolregParameters = typing.TypedDict('V3dvolregParameters', {
-    "__STYXTYPE__": typing.Literal["3dvolreg"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dvolreg"]],
+    "copyorigin": bool,
+    "twopass": bool,
+    "Fourier": bool,
+    "in_weight_volume": typing.NotRequired[list[str] | None],
+    "in_weight_volume_2": typing.NotRequired[InputPathType | None],
+    "interp": typing.NotRequired[typing.Literal["fourier", "cubic", "heptic", "quintic", "linear"] | None],
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "timeshift": bool,
+    "verbose": bool,
+    "basefile": typing.NotRequired[InputPathType | None],
+    "zpad": typing.NotRequired[int | None],
+    "prefix": str,
+    "Maxdisp1d": typing.NotRequired[str | None],
+    "in_file": InputPathType,
+})
+V3dvolregParametersTagged = typing.TypedDict('V3dvolregParametersTagged', {
+    "@type": typing.Literal["afni/3dvolreg"],
     "copyorigin": bool,
     "twopass": bool,
     "Fourier": bool,
@@ -31,43 +49,11 @@ V3dvolregParameters = typing.TypedDict('V3dvolregParameters', {
     "Maxdisp1d": typing.NotRequired[str | None],
     "in_file": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dvolreg": v_3dvolreg_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 {
-        "3dvolreg": v_3dvolreg_outputs,
-    }.get(t)
 
 
 class V3dvolregOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3dvolreg(...)`.
+    Output object returned when calling `V3dvolregParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +89,7 @@ def v_3dvolreg_params(
     basefile: InputPathType | None = None,
     zpad: int | None = None,
     maxdisp1d: str | None = None,
-) -> V3dvolregParameters:
+) -> V3dvolregParametersTagged:
     """
     Build parameters.
     
@@ -133,7 +119,7 @@ def v_3dvolreg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dvolreg",
+        "@type": "afni/3dvolreg",
         "copyorigin": copyorigin,
         "twopass": twopass,
         "Fourier": fourier,
@@ -176,55 +162,55 @@ def v_3dvolreg_cargs(
     """
     cargs = []
     cargs.append("3dvolreg")
-    if params.get("copyorigin"):
+    if params.get("copyorigin", False):
         cargs.append("-twodup")
-    if params.get("twopass"):
+    if params.get("twopass", False):
         cargs.append("-twopass")
-    if params.get("Fourier"):
+    if params.get("Fourier", False):
         cargs.append("-Fourier")
-    if params.get("in_weight_volume") is not None:
+    if params.get("in_weight_volume", None) is not None:
         cargs.extend([
             "-weight '",
-            *params.get("in_weight_volume")
+            *params.get("in_weight_volume", None)
         ])
-    if params.get("in_weight_volume_2") is not None:
+    if params.get("in_weight_volume_2", None) is not None:
         cargs.extend([
             "-weight '",
-            execution.input_file(params.get("in_weight_volume_2"))
+            execution.input_file(params.get("in_weight_volume_2", None))
         ])
-    if params.get("interp") is not None:
+    if params.get("interp", None) is not None:
         cargs.extend([
             "-",
-            params.get("interp")
+            params.get("interp", None)
         ])
-    if params.get("num_threads") is not None:
-        cargs.append(str(params.get("num_threads")))
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    if params.get("timeshift"):
+    if params.get("num_threads", None) is not None:
+        cargs.append(str(params.get("num_threads", None)))
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
+    if params.get("timeshift", False):
         cargs.append("-tshift 0")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verbose")
-    if params.get("basefile") is not None:
+    if params.get("basefile", None) is not None:
         cargs.extend([
             "-base",
-            execution.input_file(params.get("basefile"))
+            execution.input_file(params.get("basefile", 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))
         ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("Maxdisp1d") is not None:
+    if params.get("Maxdisp1d", None) is not None:
         cargs.extend([
             "-maxdisp1d",
-            params.get("Maxdisp1d")
+            params.get("Maxdisp1d", None)
         ])
-    cargs.append(execution.input_file(params.get("in_file")))
+    cargs.append(execution.input_file(params.get("in_file", None)))
     return cargs
 
 
@@ -243,22 +229,24 @@ def v_3dvolreg_outputs(
     """
     ret = V3dvolregOutputs(
         root=execution.output_file("."),
-        md1d_file=execution.output_file(params.get("prefix") + "_md.1D"),
-        oned_file=execution.output_file(params.get("prefix") + ".1D"),
-        oned_matrix_save=execution.output_file(params.get("prefix") + ".aff12.1D"),
+        md1d_file=execution.output_file(params.get("prefix", None) + "_md.1D"),
+        oned_file=execution.output_file(params.get("prefix", None) + ".1D"),
+        oned_matrix_save=execution.output_file(params.get("prefix", None) + ".aff12.1D"),
         md1d_file_=execution.output_file("md1d_file"),
         oned_file_=execution.output_file("oned_file"),
         oned_matrix_save_=execution.output_file("oned_matrix_save"),
-        out_file=execution.output_file(params.get("prefix")),
+        out_file=execution.output_file(params.get("prefix", None)),
     )
     return ret
 
 
 def v_3dvolreg_execute(
     params: V3dvolregParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dvolregOutputs:
     """
+    3dvolreg
+    
     Register input volumes to a base volume using AFNI 3dvolreg command.
     
     Author: AFNI Developers
@@ -267,10 +255,12 @@ def v_3dvolreg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dvolregOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DVOLREG_METADATA)
     params = execution.params(params)
     cargs = v_3dvolreg_cargs(params, execution)
     ret = v_3dvolreg_outputs(params, execution)
@@ -297,6 +287,8 @@ def v_3dvolreg(
     runner: Runner | None = None,
 ) -> V3dvolregOutputs:
     """
+    3dvolreg
+    
     Register input volumes to a base volume using AFNI 3dvolreg command.
     
     Author: AFNI Developers
@@ -329,8 +321,6 @@ def v_3dvolreg(
     Returns:
         NamedTuple of outputs (described in `V3dvolregOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3DVOLREG_METADATA)
     params = v_3dvolreg_params(
         copyorigin=copyorigin,
         twopass=twopass,
@@ -348,13 +338,13 @@ def v_3dvolreg(
         maxdisp1d=maxdisp1d,
         in_file=in_file,
     )
-    return v_3dvolreg_execute(params, execution)
+    return v_3dvolreg_execute(params, runner)
 
 
 __all__ = [
     "V3dvolregOutputs",
-    "V3dvolregParameters",
     "V_3DVOLREG_METADATA",
     "v_3dvolreg",
+    "v_3dvolreg_execute",
     "v_3dvolreg_params",
 ]