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

niwrap_afni/afni/v_3d_winsor.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_WINSOR_METADATA = Metadata(
-    id="ae0f40a7e76cc9dd4e8f1de77208f94a02310050.boutiques",
+    id="63d591ddd595415c5679482f5edf0c3b0117e9eb.boutiques",
     name="3dWinsor",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_WINSOR_METADATA = Metadata(
 
 
 V3dWinsorParameters = typing.TypedDict('V3dWinsorParameters', {
-    "__STYXTYPE__": typing.Literal["3dWinsor"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dWinsor"]],
+    "irad": typing.NotRequired[float | None],
+    "cbot": typing.NotRequired[float | None],
+    "ctop": typing.NotRequired[float | None],
+    "nrep": typing.NotRequired[float | None],
+    "keepzero": bool,
+    "clip": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "dataset": InputPathType,
+})
+V3dWinsorParametersTagged = typing.TypedDict('V3dWinsorParametersTagged', {
+    "@type": typing.Literal["afni/3dWinsor"],
     "irad": typing.NotRequired[float | None],
     "cbot": typing.NotRequired[float | None],
     "ctop": typing.NotRequired[float | None],
@@ -25,43 +37,11 @@ V3dWinsorParameters = typing.TypedDict('V3dWinsorParameters', {
     "mask": typing.NotRequired[InputPathType | 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 {
-        "3dWinsor": v_3d_winsor_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 {
-        "3dWinsor": v_3d_winsor_outputs,
-    }.get(t)
 
 
 class V3dWinsorOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_winsor(...)`.
+    Output object returned when calling `V3dWinsorParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def v_3d_winsor_params(
     clip: float | None = None,
     prefix: str | None = None,
     mask: InputPathType | None = None,
-) -> V3dWinsorParameters:
+) -> V3dWinsorParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +83,7 @@ def v_3d_winsor_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dWinsor",
+        "@type": "afni/3dWinsor",
         "keepzero": keepzero,
         "dataset": dataset,
     }
@@ -139,44 +119,44 @@ def v_3d_winsor_cargs(
     """
     cargs = []
     cargs.append("3dWinsor")
-    if params.get("irad") is not None:
+    if params.get("irad", None) is not None:
         cargs.extend([
             "-irad",
-            str(params.get("irad"))
+            str(params.get("irad", None))
         ])
-    if params.get("cbot") is not None:
+    if params.get("cbot", None) is not None:
         cargs.extend([
             "-cbot",
-            str(params.get("cbot"))
+            str(params.get("cbot", None))
         ])
-    if params.get("ctop") is not None:
+    if params.get("ctop", None) is not None:
         cargs.extend([
             "-ctop",
-            str(params.get("ctop"))
+            str(params.get("ctop", None))
         ])
-    if params.get("nrep") is not None:
+    if params.get("nrep", None) is not None:
         cargs.extend([
             "-nrep",
-            str(params.get("nrep"))
+            str(params.get("nrep", None))
         ])
-    if params.get("keepzero"):
+    if params.get("keepzero", False):
         cargs.append("-keepzero")
-    if params.get("clip") is not None:
+    if params.get("clip", None) is not None:
         cargs.extend([
             "-clip",
-            str(params.get("clip"))
+            str(params.get("clip", 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("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))
         ])
-    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(execution.input_file(params.get("dataset", None)))
     return cargs
 
 
@@ -195,17 +175,19 @@ def v_3d_winsor_outputs(
     """
     ret = V3dWinsorOutputs(
         root=execution.output_file("."),
-        outfile_head=execution.output_file(params.get("prefix") + "+*.HEAD") if (params.get("prefix") is not None) else None,
-        outfile_brik=execution.output_file(params.get("prefix") + "+*.BRIK") if (params.get("prefix") is not None) else None,
+        outfile_head=execution.output_file(params.get("prefix", None) + ".HEAD") if (params.get("prefix") is not None) else None,
+        outfile_brik=execution.output_file(params.get("prefix", None) + ".BRIK") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_winsor_execute(
     params: V3dWinsorParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dWinsorOutputs:
     """
+    3dWinsor
+    
     Apply a 3D 'Winsorizing' filter to a short-valued dataset.
     
     Author: AFNI Developers
@@ -214,10 +196,12 @@ def v_3d_winsor_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dWinsorOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_WINSOR_METADATA)
     params = execution.params(params)
     cargs = v_3d_winsor_cargs(params, execution)
     ret = v_3d_winsor_outputs(params, execution)
@@ -238,6 +222,8 @@ def v_3d_winsor(
     runner: Runner | None = None,
 ) -> V3dWinsorOutputs:
     """
+    3dWinsor
+    
     Apply a 3D 'Winsorizing' filter to a short-valued dataset.
     
     Author: AFNI Developers
@@ -262,8 +248,6 @@ def v_3d_winsor(
     Returns:
         NamedTuple of outputs (described in `V3dWinsorOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_WINSOR_METADATA)
     params = v_3d_winsor_params(
         irad=irad,
         cbot=cbot,
@@ -275,13 +259,13 @@ def v_3d_winsor(
         mask=mask,
         dataset=dataset,
     )
-    return v_3d_winsor_execute(params, execution)
+    return v_3d_winsor_execute(params, runner)
 
 
 __all__ = [
     "V3dWinsorOutputs",
-    "V3dWinsorParameters",
     "V_3D_WINSOR_METADATA",
     "v_3d_winsor",
+    "v_3d_winsor_execute",
     "v_3d_winsor_params",
 ]

niwrap_afni/afni/v_3d_xclust_sim.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_XCLUST_SIM_METADATA = Metadata(
-    id="19280688ca72a431cebefdabca1d25ef8f5de5db.boutiques",
+    id="efbc399cad29d2ac5b2bb8a45940bf52699805cd.boutiques",
     name="3dXClustSim",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,28 @@ V_3D_XCLUST_SIM_METADATA = Metadata(
 
 
 V3dXclustSimParameters = typing.TypedDict('V3dXclustSimParameters', {
-    "__STYXTYPE__": typing.Literal["3dXClustSim"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dXClustSim"]],
+    "inset": InputPathType,
+    "insdat": typing.NotRequired[InputPathType | None],
+    "nn": typing.NotRequired[float | None],
+    "sid": typing.NotRequired[float | None],
+    "hpow": typing.NotRequired[list[float] | None],
+    "ncase": typing.NotRequired[list[str] | None],
+    "pthr": typing.NotRequired[list[float] | None],
+    "fpr": typing.NotRequired[float | None],
+    "multiFPR": bool,
+    "minclust": typing.NotRequired[float | None],
+    "local": bool,
+    "global": bool,
+    "nolocal": bool,
+    "noglobal": bool,
+    "splitfrac": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "verbose": bool,
+    "quiet": bool,
+})
+V3dXclustSimParametersTagged = typing.TypedDict('V3dXclustSimParametersTagged', {
+    "@type": typing.Literal["afni/3dXClustSim"],
     "inset": InputPathType,
     "insdat": typing.NotRequired[InputPathType | None],
     "nn": typing.NotRequired[float | None],
@@ -34,48 +55,14 @@ V3dXclustSimParameters = typing.TypedDict('V3dXclustSimParameters', {
     "verbose": 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 {
-        "3dXClustSim": v_3d_xclust_sim_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 {
-        "3dXClustSim": v_3d_xclust_sim_outputs,
-    }.get(t)
 
 
 class V3dXclustSimOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_xclust_sim(...)`.
+    Output object returned when calling `V3dXclustSimParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    out_mthresh: OutputPathType | None
-    """Output multi-threshold files for each -ncase input"""
 
 
 def v_3d_xclust_sim_params(
@@ -97,7 +84,7 @@ def v_3d_xclust_sim_params(
     prefix: str | None = None,
     verbose: bool = False,
     quiet: bool = False,
-) -> V3dXclustSimParameters:
+) -> V3dXclustSimParametersTagged:
     """
     Build parameters.
     
@@ -126,7 +113,7 @@ def v_3d_xclust_sim_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dXClustSim",
+        "@type": "afni/3dXClustSim",
         "inset": inset,
         "multiFPR": multi_fpr,
         "local": local,
@@ -174,67 +161,67 @@ def v_3d_xclust_sim_cargs(
     """
     cargs = []
     cargs.append("3dXClustSim")
-    cargs.append(execution.input_file(params.get("inset")))
-    if params.get("insdat") is not None:
-        cargs.append(execution.input_file(params.get("insdat")))
-    if params.get("nn") is not None:
+    cargs.append(execution.input_file(params.get("inset", None)))
+    if params.get("insdat", None) is not None:
+        cargs.append(execution.input_file(params.get("insdat", None)))
+    if params.get("nn", None) is not None:
         cargs.extend([
             "-NN",
-            str(params.get("nn"))
+            str(params.get("nn", None))
         ])
-    if params.get("sid") is not None:
+    if params.get("sid", None) is not None:
         cargs.extend([
             "-sid",
-            str(params.get("sid"))
+            str(params.get("sid", None))
         ])
-    if params.get("hpow") is not None:
+    if params.get("hpow", None) is not None:
         cargs.extend([
             "-hpow",
-            *map(str, params.get("hpow"))
+            *map(str, params.get("hpow", None))
         ])
-    if params.get("ncase") is not None:
+    if params.get("ncase", None) is not None:
         cargs.extend([
             "-ncase",
-            *params.get("ncase")
+            *params.get("ncase", None)
         ])
-    if params.get("pthr") is not None:
+    if params.get("pthr", None) is not None:
         cargs.extend([
             "-pthr",
-            *map(str, params.get("pthr"))
+            *map(str, params.get("pthr", None))
         ])
-    if params.get("fpr") is not None:
+    if params.get("fpr", None) is not None:
         cargs.extend([
             "-FPR",
-            str(params.get("fpr"))
+            str(params.get("fpr", None))
         ])
-    if params.get("multiFPR"):
+    if params.get("multiFPR", False):
         cargs.append("-multiFPR")
-    if params.get("minclust") is not None:
+    if params.get("minclust", None) is not None:
         cargs.extend([
             "-minclust",
-            str(params.get("minclust"))
+            str(params.get("minclust", None))
         ])
-    if params.get("local"):
+    if params.get("local", False):
         cargs.append("-local")
-    if params.get("global"):
+    if params.get("global", False):
         cargs.append("-global")
-    if params.get("nolocal"):
+    if params.get("nolocal", False):
         cargs.append("-nolocal")
-    if params.get("noglobal"):
+    if params.get("noglobal", False):
         cargs.append("-noglobal")
-    if params.get("splitfrac") is not None:
+    if params.get("splitfrac", None) is not None:
         cargs.extend([
             "-splitfrac",
-            str(params.get("splitfrac"))
+            str(params.get("splitfrac", 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("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
     return cargs
 
@@ -254,16 +241,17 @@ def v_3d_xclust_sim_outputs(
     """
     ret = V3dXclustSimOutputs(
         root=execution.output_file("."),
-        out_mthresh=execution.output_file(params.get("prefix") + ".mthresh.*.nii") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_xclust_sim_execute(
     params: V3dXclustSimParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dXclustSimOutputs:
     """
+    3dXClustSim
+    
     ETAC processing tool to find cluster figure of merit (FOM) thresholds.
     
     Author: AFNI Developers
@@ -272,10 +260,12 @@ def v_3d_xclust_sim_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dXclustSimOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_XCLUST_SIM_METADATA)
     params = execution.params(params)
     cargs = v_3d_xclust_sim_cargs(params, execution)
     ret = v_3d_xclust_sim_outputs(params, execution)
@@ -305,6 +295,8 @@ def v_3d_xclust_sim(
     runner: Runner | None = None,
 ) -> V3dXclustSimOutputs:
     """
+    3dXClustSim
+    
     ETAC processing tool to find cluster figure of merit (FOM) thresholds.
     
     Author: AFNI Developers
@@ -336,8 +328,6 @@ def v_3d_xclust_sim(
     Returns:
         NamedTuple of outputs (described in `V3dXclustSimOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_XCLUST_SIM_METADATA)
     params = v_3d_xclust_sim_params(
         inset=inset,
         insdat=insdat,
@@ -358,13 +348,13 @@ def v_3d_xclust_sim(
         verbose=verbose,
         quiet=quiet,
     )
-    return v_3d_xclust_sim_execute(params, execution)
+    return v_3d_xclust_sim_execute(params, runner)
 
 
 __all__ = [
     "V3dXclustSimOutputs",
-    "V3dXclustSimParameters",
     "V_3D_XCLUST_SIM_METADATA",
     "v_3d_xclust_sim",
+    "v_3d_xclust_sim_execute",
     "v_3d_xclust_sim_params",
 ]

niwrap_afni/afni/v_3d_xyzcat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_XYZCAT_METADATA = Metadata(
-    id="6187e73a39e2b8fe582b14ee9e2a4f3ca6740b27.boutiques",
+    id="c496e923b51b6f502635d41461cd749df480851d.boutiques",
     name="3dXYZcat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3D_XYZCAT_METADATA = Metadata(
 
 
 V3dXyzcatParameters = typing.TypedDict('V3dXyzcatParameters', {
-    "__STYXTYPE__": typing.Literal["3dXYZcat"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dXYZcat"]],
+    "direction": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "verbose": bool,
+    "datasets": list[InputPathType],
+})
+V3dXyzcatParametersTagged = typing.TypedDict('V3dXyzcatParametersTagged', {
+    "@type": typing.Literal["afni/3dXYZcat"],
     "direction": typing.NotRequired[str | None],
     "prefix": typing.NotRequired[str | None],
     "verbose": bool,
     "datasets": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dXYZcat": v_3d_xyzcat_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 {
-        "3dXYZcat": v_3d_xyzcat_outputs,
-    }.get(t)
 
 
 class V3dXyzcatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_xyzcat(...)`.
+    Output object returned when calling `V3dXyzcatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +46,7 @@ def v_3d_xyzcat_params(
     direction: str | None = None,
     prefix: str | None = None,
     verbose: bool = False,
-) -> V3dXyzcatParameters:
+) -> V3dXyzcatParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +60,7 @@ def v_3d_xyzcat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dXYZcat",
+        "@type": "afni/3dXYZcat",
         "verbose": verbose,
         "datasets": datasets,
     }
@@ -111,19 +86,19 @@ def v_3d_xyzcat_cargs(
     """
     cargs = []
     cargs.append("3dXYZcat")
-    if params.get("direction") is not None:
+    if params.get("direction", None) is not None:
         cargs.extend([
             "-dir",
-            params.get("direction")
+            params.get("direction", 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("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
+    cargs.extend([execution.input_file(f) for f in params.get("datasets", None)])
     return cargs
 
 
@@ -142,17 +117,19 @@ def v_3d_xyzcat_outputs(
     """
     ret = V3dXyzcatOutputs(
         root=execution.output_file("."),
-        output_brainfile=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
-        output_headerfile=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        output_brainfile=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_headerfile=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_xyzcat_execute(
     params: V3dXyzcatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dXyzcatOutputs:
     """
+    3dXYZcat
+    
     Catenates datasets spatially.
     
     Author: AFNI Developers
@@ -161,10 +138,12 @@ def v_3d_xyzcat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dXyzcatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_XYZCAT_METADATA)
     params = execution.params(params)
     cargs = v_3d_xyzcat_cargs(params, execution)
     ret = v_3d_xyzcat_outputs(params, execution)
@@ -180,6 +159,8 @@ def v_3d_xyzcat(
     runner: Runner | None = None,
 ) -> V3dXyzcatOutputs:
     """
+    3dXYZcat
+    
     Catenates datasets spatially.
     
     Author: AFNI Developers
@@ -196,21 +177,19 @@ def v_3d_xyzcat(
     Returns:
         NamedTuple of outputs (described in `V3dXyzcatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_XYZCAT_METADATA)
     params = v_3d_xyzcat_params(
         direction=direction,
         prefix=prefix,
         verbose=verbose,
         datasets=datasets,
     )
-    return v_3d_xyzcat_execute(params, execution)
+    return v_3d_xyzcat_execute(params, runner)
 
 
 __all__ = [
     "V3dXyzcatOutputs",
-    "V3dXyzcatParameters",
     "V_3D_XYZCAT_METADATA",
     "v_3d_xyzcat",
+    "v_3d_xyzcat_execute",
     "v_3d_xyzcat_params",
 ]