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

niwrap_afni/afni/v_3d_pval.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_PVAL_METADATA = Metadata(
-    id="724a7212deebf60511bbed100d1d685ab6d47da3.boutiques",
+    id="9479f35d3dad112060e6205271ed4c0ae7fe30e3.boutiques",
     name="3dPval",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_PVAL_METADATA = Metadata(
 
 
 V3dPvalParameters = typing.TypedDict('V3dPvalParameters', {
-    "__STYXTYPE__": typing.Literal["3dPval"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dPval"]],
+    "input_dataset": InputPathType,
+    "zscore": bool,
+    "log2": bool,
+    "log10": bool,
+    "qval": bool,
+    "prefix": typing.NotRequired[str | None],
+})
+V3dPvalParametersTagged = typing.TypedDict('V3dPvalParametersTagged', {
+    "@type": typing.Literal["afni/3dPval"],
     "input_dataset": InputPathType,
     "zscore": bool,
     "log2": bool,
@@ -22,43 +31,11 @@ V3dPvalParameters = typing.TypedDict('V3dPvalParameters', {
     "qval": bool,
     "prefix": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dPval": v_3d_pval_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 {
-        "3dPval": v_3d_pval_outputs,
-    }.get(t)
 
 
 class V3dPvalOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_pval(...)`.
+    Output object returned when calling `V3dPvalParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +51,7 @@ def v_3d_pval_params(
     log10: bool = False,
     qval: bool = False,
     prefix: str | None = None,
-) -> V3dPvalParameters:
+) -> V3dPvalParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +68,7 @@ def v_3d_pval_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dPval",
+        "@type": "afni/3dPval",
         "input_dataset": input_dataset,
         "zscore": zscore,
         "log2": log2,
@@ -118,19 +95,19 @@ def v_3d_pval_cargs(
     """
     cargs = []
     cargs.append("3dPval")
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    if params.get("zscore"):
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
+    if params.get("zscore", False):
         cargs.append("-zscore")
-    if params.get("log2"):
+    if params.get("log2", False):
         cargs.append("-log2")
-    if params.get("log10"):
+    if params.get("log10", False):
         cargs.append("-log10")
-    if params.get("qval"):
+    if params.get("qval", False):
         cargs.append("-qval")
-    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)
         ])
     return cargs
 
@@ -150,16 +127,18 @@ def v_3d_pval_outputs(
     """
     ret = V3dPvalOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_pval_execute(
     params: V3dPvalParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dPvalOutputs:
     """
+    3dPval
+    
     Convert a dataset's statistical sub-bricks to p-values or other statistical
     representations.
     
@@ -169,10 +148,12 @@ def v_3d_pval_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dPvalOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_PVAL_METADATA)
     params = execution.params(params)
     cargs = v_3d_pval_cargs(params, execution)
     ret = v_3d_pval_outputs(params, execution)
@@ -190,6 +171,8 @@ def v_3d_pval(
     runner: Runner | None = None,
 ) -> V3dPvalOutputs:
     """
+    3dPval
+    
     Convert a dataset's statistical sub-bricks to p-values or other statistical
     representations.
     
@@ -210,8 +193,6 @@ def v_3d_pval(
     Returns:
         NamedTuple of outputs (described in `V3dPvalOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_PVAL_METADATA)
     params = v_3d_pval_params(
         input_dataset=input_dataset,
         zscore=zscore,
@@ -220,13 +201,13 @@ def v_3d_pval(
         qval=qval,
         prefix=prefix,
     )
-    return v_3d_pval_execute(params, execution)
+    return v_3d_pval_execute(params, runner)
 
 
 __all__ = [
     "V3dPvalOutputs",
-    "V3dPvalParameters",
     "V_3D_PVAL_METADATA",
     "v_3d_pval",
+    "v_3d_pval_execute",
     "v_3d_pval_params",
 ]

niwrap_afni/afni/v_3d_pvmap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_PVMAP_METADATA = Metadata(
-    id="b74a0e29a3cca7e68ec694345e79805eec69c8a4.boutiques",
+    id="f988d7429cad2c301278f66bcd355958109df768.boutiques",
     name="3dPVmap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V_3D_PVMAP_METADATA = Metadata(
 
 
 V3dPvmapParameters = typing.TypedDict('V3dPvmapParameters', {
-    "__STYXTYPE__": typing.Literal["3dPVmap"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dPVmap"]],
+    "prefix": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "inputdataset": InputPathType,
+})
+V3dPvmapParametersTagged = typing.TypedDict('V3dPvmapParametersTagged', {
+    "@type": typing.Literal["afni/3dPVmap"],
     "prefix": typing.NotRequired[str | None],
     "mask": typing.NotRequired[InputPathType | None],
     "automask": bool,
     "inputdataset": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dPVmap": v_3d_pvmap_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 {
-        "3dPVmap": v_3d_pvmap_outputs,
-    }.get(t)
 
 
 class V3dPvmapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_pvmap(...)`.
+    Output object returned when calling `V3dPvmapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +48,7 @@ def v_3d_pvmap_params(
     prefix: str | None = None,
     mask: InputPathType | None = None,
     automask: bool = False,
-) -> V3dPvmapParameters:
+) -> V3dPvmapParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +61,7 @@ def v_3d_pvmap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dPVmap",
+        "@type": "afni/3dPVmap",
         "automask": automask,
         "inputdataset": inputdataset,
     }
@@ -112,19 +87,19 @@ def v_3d_pvmap_cargs(
     """
     cargs = []
     cargs.append("3dPVmap")
-    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))
         ])
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    cargs.append(execution.input_file(params.get("inputdataset")))
+    cargs.append(execution.input_file(params.get("inputdataset", None)))
     return cargs
 
 
@@ -143,18 +118,20 @@ def v_3d_pvmap_outputs(
     """
     ret = V3dPvmapOutputs(
         root=execution.output_file("."),
-        outbrik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
-        outhead=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
-        pc_vectors=execution.output_file(params.get("prefix") + ".1D") if (params.get("prefix") is not None) else None,
+        outbrik=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        outhead=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        pc_vectors=execution.output_file(params.get("prefix", None) + ".1D") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_pvmap_execute(
     params: V3dPvmapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dPvmapOutputs:
     """
+    3dPVmap
+    
     Computes the first two principal component vectors of a time series dataset,
     then outputs the R-squared coefficient of each voxel time series with these
     first two components.
@@ -165,10 +142,12 @@ def v_3d_pvmap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dPvmapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_PVMAP_METADATA)
     params = execution.params(params)
     cargs = v_3d_pvmap_cargs(params, execution)
     ret = v_3d_pvmap_outputs(params, execution)
@@ -184,6 +163,8 @@ def v_3d_pvmap(
     runner: Runner | None = None,
 ) -> V3dPvmapOutputs:
     """
+    3dPVmap
+    
     Computes the first two principal component vectors of a time series dataset,
     then outputs the R-squared coefficient of each voxel time series with these
     first two components.
@@ -201,21 +182,19 @@ def v_3d_pvmap(
     Returns:
         NamedTuple of outputs (described in `V3dPvmapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_PVMAP_METADATA)
     params = v_3d_pvmap_params(
         prefix=prefix,
         mask=mask,
         automask=automask,
         inputdataset=inputdataset,
     )
-    return v_3d_pvmap_execute(params, execution)
+    return v_3d_pvmap_execute(params, runner)
 
 
 __all__ = [
     "V3dPvmapOutputs",
-    "V3dPvmapParameters",
     "V_3D_PVMAP_METADATA",
     "v_3d_pvmap",
+    "v_3d_pvmap_execute",
     "v_3d_pvmap_params",
 ]

niwrap_afni/afni/v_3d_qwarp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_QWARP_METADATA = Metadata(
-    id="cc213324798c478d3e72e48a943b6932f8735e9d.boutiques",
+    id="6de643b301465958f6dc83399eef2305f9613e56.boutiques",
     name="3dQwarp",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,30 @@ V_3D_QWARP_METADATA = Metadata(
 
 
 V3dQwarpParameters = typing.TypedDict('V3dQwarpParameters', {
-    "__STYXTYPE__": typing.Literal["3dQwarp"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dQwarp"]],
+    "base_dataset": InputPathType,
+    "source_dataset": InputPathType,
+    "prefix": str,
+    "no_warp": bool,
+    "inverse_warp": bool,
+    "no_dataset": bool,
+    "a_warp": bool,
+    "pcl": bool,
+    "pear": bool,
+    "hel": bool,
+    "mi": bool,
+    "nmi": bool,
+    "lpc": bool,
+    "lpa": bool,
+    "noneg": bool,
+    "nopenalty": bool,
+    "minpatch": typing.NotRequired[float | None],
+    "maxlev": typing.NotRequired[float | None],
+    "verbose": bool,
+    "quiet": bool,
+})
+V3dQwarpParametersTagged = typing.TypedDict('V3dQwarpParametersTagged', {
+    "@type": typing.Literal["afni/3dQwarp"],
     "base_dataset": InputPathType,
     "source_dataset": InputPathType,
     "prefix": str,
@@ -36,43 +59,11 @@ V3dQwarpParameters = typing.TypedDict('V3dQwarpParameters', {
     "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 {
-        "3dQwarp": v_3d_qwarp_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 {
-        "3dQwarp": v_3d_qwarp_outputs,
-    }.get(t)
 
 
 class V3dQwarpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_qwarp(...)`.
+    Output object returned when calling `V3dQwarpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -105,7 +96,7 @@ def v_3d_qwarp_params(
     maxlev: float | None = None,
     verbose: bool = False,
     quiet: bool = False,
-) -> V3dQwarpParameters:
+) -> V3dQwarpParametersTagged:
     """
     Build parameters.
     
@@ -134,7 +125,7 @@ def v_3d_qwarp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dQwarp",
+        "@type": "afni/3dQwarp",
         "base_dataset": base_dataset,
         "source_dataset": source_dataset,
         "prefix": prefix,
@@ -176,48 +167,48 @@ def v_3d_qwarp_cargs(
     """
     cargs = []
     cargs.append("3dQwarp")
-    cargs.append(execution.input_file(params.get("base_dataset")))
-    cargs.append(execution.input_file(params.get("source_dataset")))
-    cargs.append(params.get("prefix"))
-    if params.get("no_warp"):
+    cargs.append(execution.input_file(params.get("base_dataset", None)))
+    cargs.append(execution.input_file(params.get("source_dataset", None)))
+    cargs.append(params.get("prefix", None))
+    if params.get("no_warp", False):
         cargs.append("-nowarp")
-    if params.get("inverse_warp"):
+    if params.get("inverse_warp", False):
         cargs.append("-iwarp")
-    if params.get("no_dataset"):
+    if params.get("no_dataset", False):
         cargs.append("-nodset")
-    if params.get("a_warp"):
+    if params.get("a_warp", False):
         cargs.append("-awarp")
-    if params.get("pcl"):
+    if params.get("pcl", False):
         cargs.append("-pcl")
-    if params.get("pear"):
+    if params.get("pear", False):
         cargs.append("-pear")
-    if params.get("hel"):
+    if params.get("hel", False):
         cargs.append("-hel")
-    if params.get("mi"):
+    if params.get("mi", False):
         cargs.append("-mi")
-    if params.get("nmi"):
+    if params.get("nmi", False):
         cargs.append("-nmi")
-    if params.get("lpc"):
+    if params.get("lpc", False):
         cargs.append("-lpc")
-    if params.get("lpa"):
+    if params.get("lpa", False):
         cargs.append("-lpa")
-    if params.get("noneg"):
+    if params.get("noneg", False):
         cargs.append("-noneg")
-    if params.get("nopenalty"):
+    if params.get("nopenalty", False):
         cargs.append("-nopenalty")
-    if params.get("minpatch") is not None:
+    if params.get("minpatch", None) is not None:
         cargs.extend([
             "-minpatch",
-            str(params.get("minpatch"))
+            str(params.get("minpatch", None))
         ])
-    if params.get("maxlev") is not None:
+    if params.get("maxlev", None) is not None:
         cargs.extend([
             "-maxlev",
-            str(params.get("maxlev"))
+            str(params.get("maxlev", 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
 
@@ -246,10 +237,13 @@ def v_3d_qwarp_outputs(
 
 def v_3d_qwarp_execute(
     params: V3dQwarpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dQwarpOutputs:
     """
-    Computes a nonlinearly warped version of source_dataset to match base_dataset.
+    3dQwarp
+    
+    Computes a nonlinearly warped version of source_dataset to match
+    base_dataset.
     
     Author: AFNI Developers
     
@@ -257,10 +251,12 @@ def v_3d_qwarp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dQwarpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_QWARP_METADATA)
     params = execution.params(params)
     cargs = v_3d_qwarp_cargs(params, execution)
     ret = v_3d_qwarp_outputs(params, execution)
@@ -292,7 +288,10 @@ def v_3d_qwarp(
     runner: Runner | None = None,
 ) -> V3dQwarpOutputs:
     """
-    Computes a nonlinearly warped version of source_dataset to match base_dataset.
+    3dQwarp
+    
+    Computes a nonlinearly warped version of source_dataset to match
+    base_dataset.
     
     Author: AFNI Developers
     
@@ -323,8 +322,6 @@ def v_3d_qwarp(
     Returns:
         NamedTuple of outputs (described in `V3dQwarpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_QWARP_METADATA)
     params = v_3d_qwarp_params(
         base_dataset=base_dataset,
         source_dataset=source_dataset,
@@ -347,13 +344,13 @@ def v_3d_qwarp(
         verbose=verbose,
         quiet=quiet,
     )
-    return v_3d_qwarp_execute(params, execution)
+    return v_3d_qwarp_execute(params, runner)
 
 
 __all__ = [
     "V3dQwarpOutputs",
-    "V3dQwarpParameters",
     "V_3D_QWARP_METADATA",
     "v_3d_qwarp",
+    "v_3d_qwarp_execute",
     "v_3d_qwarp_params",
 ]