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

niwrap_afni/afni/v_3d_attribute.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ATTRIBUTE_METADATA = Metadata(
-    id="d1172ce42bca626c6612506d8a90643475b32da8.boutiques",
+    id="e6921eafc1dfa857e7555005a71fea332d795365.boutiques",
     name="3dAttribute",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_ATTRIBUTE_METADATA = Metadata(
 
 
 V3dAttributeParameters = typing.TypedDict('V3dAttributeParameters', {
-    "__STYXTYPE__": typing.Literal["3dAttribute"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAttribute"]],
+    "all": bool,
+    "name": bool,
+    "center": bool,
+    "ssep": typing.NotRequired[str | None],
+    "sprep": typing.NotRequired[str | None],
+    "quote": bool,
+    "aname": str,
+    "dset": InputPathType,
+})
+V3dAttributeParametersTagged = typing.TypedDict('V3dAttributeParametersTagged', {
+    "@type": typing.Literal["afni/3dAttribute"],
     "all": bool,
     "name": bool,
     "center": bool,
@@ -24,43 +35,11 @@ V3dAttributeParameters = typing.TypedDict('V3dAttributeParameters', {
     "aname": str,
     "dset": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dAttribute": v_3d_attribute_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 {
-        "3dAttribute": v_3d_attribute_outputs,
-    }.get(t)
 
 
 class V3dAttributeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_attribute(...)`.
+    Output object returned when calling `V3dAttributeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def v_3d_attribute_params(
     ssep: str | None = None,
     sprep: str | None = None,
     quote: bool = False,
-) -> V3dAttributeParameters:
+) -> V3dAttributeParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +74,7 @@ def v_3d_attribute_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAttribute",
+        "@type": "afni/3dAttribute",
         "all": all_,
         "name": name,
         "center": center,
@@ -125,26 +104,26 @@ def v_3d_attribute_cargs(
     """
     cargs = []
     cargs.append("3dAttribute")
-    if params.get("all"):
+    if params.get("all", False):
         cargs.append("-all")
-    if params.get("name"):
+    if params.get("name", False):
         cargs.append("-name")
-    if params.get("center"):
+    if params.get("center", False):
         cargs.append("-center")
-    if params.get("ssep") is not None:
+    if params.get("ssep", None) is not None:
         cargs.extend([
             "-ssep",
-            params.get("ssep")
+            params.get("ssep", None)
         ])
-    if params.get("sprep") is not None:
+    if params.get("sprep", None) is not None:
         cargs.extend([
             "-sprep",
-            params.get("sprep")
+            params.get("sprep", None)
         ])
-    if params.get("quote"):
+    if params.get("quote", False):
         cargs.append("-quote")
-    cargs.append(params.get("aname"))
-    cargs.append(execution.input_file(params.get("dset")))
+    cargs.append(params.get("aname", None))
+    cargs.append(execution.input_file(params.get("dset", None)))
     return cargs
 
 
@@ -170,10 +149,13 @@ def v_3d_attribute_outputs(
 
 def v_3d_attribute_execute(
     params: V3dAttributeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAttributeOutputs:
     """
-    Prints the value of the attribute 'aname' from the header of the dataset 'dset'.
+    3dAttribute
+    
+    Prints the value of the attribute 'aname' from the header of the dataset
+    'dset'.
     
     Author: AFNI Developers
     
@@ -181,10 +163,12 @@ def v_3d_attribute_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAttributeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ATTRIBUTE_METADATA)
     params = execution.params(params)
     cargs = v_3d_attribute_cargs(params, execution)
     ret = v_3d_attribute_outputs(params, execution)
@@ -204,7 +188,10 @@ def v_3d_attribute(
     runner: Runner | None = None,
 ) -> V3dAttributeOutputs:
     """
-    Prints the value of the attribute 'aname' from the header of the dataset 'dset'.
+    3dAttribute
+    
+    Prints the value of the attribute 'aname' from the header of the dataset
+    'dset'.
     
     Author: AFNI Developers
     
@@ -224,8 +211,6 @@ def v_3d_attribute(
     Returns:
         NamedTuple of outputs (described in `V3dAttributeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ATTRIBUTE_METADATA)
     params = v_3d_attribute_params(
         all_=all_,
         name=name,
@@ -236,13 +221,13 @@ def v_3d_attribute(
         aname=aname,
         dset=dset,
     )
-    return v_3d_attribute_execute(params, execution)
+    return v_3d_attribute_execute(params, runner)
 
 
 __all__ = [
     "V3dAttributeOutputs",
-    "V3dAttributeParameters",
     "V_3D_ATTRIBUTE_METADATA",
     "v_3d_attribute",
+    "v_3d_attribute_execute",
     "v_3d_attribute_params",
 ]

niwrap_afni/afni/v_3d_auto_tcorrelate.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_AUTO_TCORRELATE_METADATA = Metadata(
-    id="f8dd31b3bdbd84c61b724bec91c847beb95fd339.boutiques",
+    id="c58c29aebe6d8ed9b1f12f5985d7470add3f97dc.boutiques",
     name="3dAutoTcorrelate",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ V_3D_AUTO_TCORRELATE_METADATA = Metadata(
 
 
 V3dAutoTcorrelateParameters = typing.TypedDict('V3dAutoTcorrelateParameters', {
-    "__STYXTYPE__": typing.Literal["3dAutoTcorrelate"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAutoTcorrelate"]],
+    "input_dataset": InputPathType,
+    "pearson": bool,
+    "eta2": bool,
+    "polort": typing.NotRequired[int | None],
+    "autoclip": bool,
+    "automask": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "mask_only_targets": bool,
+    "mask_source": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "out1d": typing.NotRequired[str | None],
+    "time": bool,
+    "mmap": bool,
+})
+V3dAutoTcorrelateParametersTagged = typing.TypedDict('V3dAutoTcorrelateParametersTagged', {
+    "@type": typing.Literal["afni/3dAutoTcorrelate"],
     "input_dataset": InputPathType,
     "pearson": bool,
     "eta2": bool,
@@ -29,43 +45,11 @@ V3dAutoTcorrelateParameters = typing.TypedDict('V3dAutoTcorrelateParameters', {
     "time": bool,
     "mmap": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dAutoTcorrelate": v_3d_auto_tcorrelate_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 {
-        "3dAutoTcorrelate": v_3d_auto_tcorrelate_outputs,
-    }.get(t)
 
 
 class V3dAutoTcorrelateOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_auto_tcorrelate(...)`.
+    Output object returned when calling `V3dAutoTcorrelateParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +75,7 @@ def v_3d_auto_tcorrelate_params(
     out1d: str | None = None,
     time_: bool = False,
     mmap_: bool = False,
-) -> V3dAutoTcorrelateParameters:
+) -> V3dAutoTcorrelateParametersTagged:
     """
     Build parameters.
     
@@ -114,7 +98,7 @@ def v_3d_auto_tcorrelate_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAutoTcorrelate",
+        "@type": "afni/3dAutoTcorrelate",
         "input_dataset": input_dataset,
         "pearson": pearson,
         "eta2": eta2,
@@ -152,45 +136,45 @@ def v_3d_auto_tcorrelate_cargs(
     """
     cargs = []
     cargs.append("3dAutoTcorrelate")
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    if params.get("pearson"):
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
+    if params.get("pearson", False):
         cargs.append("-pearson")
-    if params.get("eta2"):
+    if params.get("eta2", False):
         cargs.append("-eta2")
-    if params.get("polort") is not None:
+    if params.get("polort", None) is not None:
         cargs.extend([
             "-polort",
-            str(params.get("polort"))
+            str(params.get("polort", None))
         ])
-    if params.get("autoclip"):
+    if params.get("autoclip", False):
         cargs.append("-autoclip")
-    if params.get("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    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("mask_only_targets"):
+    if params.get("mask_only_targets", False):
         cargs.append("-mask_only_targets")
-    if params.get("mask_source") is not None:
+    if params.get("mask_source", None) is not None:
         cargs.extend([
             "-mask_source",
-            execution.input_file(params.get("mask_source"))
+            execution.input_file(params.get("mask_source", 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("out1d") is not None:
+    if params.get("out1d", None) is not None:
         cargs.extend([
             "-out1D",
-            params.get("out1d")
+            params.get("out1d", None)
         ])
-    if params.get("time"):
+    if params.get("time", False):
         cargs.append("-time")
-    if params.get("mmap"):
+    if params.get("mmap", False):
         cargs.append("-mmap")
     return cargs
 
@@ -210,18 +194,20 @@ def v_3d_auto_tcorrelate_outputs(
     """
     ret = V3dAutoTcorrelateOutputs(
         root=execution.output_file("."),
-        output_brick=execution.output_file(params.get("prefix") + ".BRIK") if (params.get("prefix") is not None) else None,
-        output_head=execution.output_file(params.get("prefix") + ".HEAD") if (params.get("prefix") is not None) else None,
-        out1d_file=execution.output_file(params.get("out1d")) if (params.get("out1d") is not None) else None,
+        output_brick=execution.output_file(params.get("prefix", None) + ".BRIK") if (params.get("prefix") is not None) else None,
+        output_head=execution.output_file(params.get("prefix", None) + ".HEAD") if (params.get("prefix") is not None) else None,
+        out1d_file=execution.output_file(params.get("out1d", None)) if (params.get("out1d") is not None) else None,
     )
     return ret
 
 
 def v_3d_auto_tcorrelate_execute(
     params: V3dAutoTcorrelateParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAutoTcorrelateOutputs:
     """
+    3dAutoTcorrelate
+    
     Computes the correlation coefficient between the time series of each pair of
     voxels in the input dataset.
     
@@ -231,10 +217,12 @@ def v_3d_auto_tcorrelate_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAutoTcorrelateOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AUTO_TCORRELATE_METADATA)
     params = execution.params(params)
     cargs = v_3d_auto_tcorrelate_cargs(params, execution)
     ret = v_3d_auto_tcorrelate_outputs(params, execution)
@@ -259,6 +247,8 @@ def v_3d_auto_tcorrelate(
     runner: Runner | None = None,
 ) -> V3dAutoTcorrelateOutputs:
     """
+    3dAutoTcorrelate
+    
     Computes the correlation coefficient between the time series of each pair of
     voxels in the input dataset.
     
@@ -285,8 +275,6 @@ def v_3d_auto_tcorrelate(
     Returns:
         NamedTuple of outputs (described in `V3dAutoTcorrelateOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_AUTO_TCORRELATE_METADATA)
     params = v_3d_auto_tcorrelate_params(
         input_dataset=input_dataset,
         pearson=pearson,
@@ -302,13 +290,13 @@ def v_3d_auto_tcorrelate(
         time_=time_,
         mmap_=mmap_,
     )
-    return v_3d_auto_tcorrelate_execute(params, execution)
+    return v_3d_auto_tcorrelate_execute(params, runner)
 
 
 __all__ = [
     "V3dAutoTcorrelateOutputs",
-    "V3dAutoTcorrelateParameters",
     "V_3D_AUTO_TCORRELATE_METADATA",
     "v_3d_auto_tcorrelate",
+    "v_3d_auto_tcorrelate_execute",
     "v_3d_auto_tcorrelate_params",
 ]

niwrap_afni/afni/v_3d_autobox.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_AUTOBOX_METADATA = Metadata(
-    id="c48b09409ec96591cf8ab9ce93ca409e6795208a.boutiques",
+    id="6e3e31b343afcbd477fc5796286883657b4ffffb.boutiques",
     name="3dAutobox",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_AUTOBOX_METADATA = Metadata(
 
 
 V3dAutoboxParameters = typing.TypedDict('V3dAutoboxParameters', {
-    "__STYXTYPE__": typing.Literal["3dAutobox"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dAutobox"]],
+    "input": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "alt_input": typing.NotRequired[InputPathType | None],
+    "noclust": bool,
+    "extent": bool,
+    "extent_ijk": bool,
+    "extent_ijk_to_file": typing.NotRequired[str | None],
+    "extent_ijk_midslice": bool,
+    "extent_ijkord": bool,
+    "extent_ijkord_to_file": typing.NotRequired[str | None],
+    "extent_xyz_to_file": typing.NotRequired[str | None],
+    "extent_xyz_midslice": bool,
+    "npad": typing.NotRequired[float | None],
+    "npad_safety_on": bool,
+})
+V3dAutoboxParametersTagged = typing.TypedDict('V3dAutoboxParametersTagged', {
+    "@type": typing.Literal["afni/3dAutobox"],
     "input": InputPathType,
     "prefix": typing.NotRequired[str | None],
     "alt_input": typing.NotRequired[InputPathType | None],
@@ -30,42 +47,11 @@ V3dAutoboxParameters = typing.TypedDict('V3dAutoboxParameters', {
     "npad": typing.NotRequired[float | None],
     "npad_safety_on": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dAutobox": v_3d_autobox_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 V3dAutoboxOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_autobox(...)`.
+    Output object returned when calling `V3dAutoboxParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -86,7 +72,7 @@ def v_3d_autobox_params(
     extent_xyz_midslice: bool = False,
     npad: float | None = None,
     npad_safety_on: bool = False,
-) -> V3dAutoboxParameters:
+) -> V3dAutoboxParametersTagged:
     """
     Build parameters.
     
@@ -119,7 +105,7 @@ def v_3d_autobox_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dAutobox",
+        "@type": "afni/3dAutobox",
         "input": input_,
         "noclust": noclust,
         "extent": extent,
@@ -159,50 +145,50 @@ def v_3d_autobox_cargs(
     """
     cargs = []
     cargs.append("3dAutobox")
-    cargs.append(execution.input_file(params.get("input")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("input", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("alt_input") is not None:
+    if params.get("alt_input", None) is not None:
         cargs.extend([
             "-input",
-            execution.input_file(params.get("alt_input"))
+            execution.input_file(params.get("alt_input", None))
         ])
-    if params.get("noclust"):
+    if params.get("noclust", False):
         cargs.append("-noclust")
-    if params.get("extent"):
+    if params.get("extent", False):
         cargs.append("-extent")
-    if params.get("extent_ijk"):
+    if params.get("extent_ijk", False):
         cargs.append("-extent_ijk")
-    if params.get("extent_ijk_to_file") is not None:
+    if params.get("extent_ijk_to_file", None) is not None:
         cargs.extend([
             "-extent_ijk_to_file",
-            params.get("extent_ijk_to_file")
+            params.get("extent_ijk_to_file", None)
         ])
-    if params.get("extent_ijk_midslice"):
+    if params.get("extent_ijk_midslice", False):
         cargs.append("-extent_ijk_midslice")
-    if params.get("extent_ijkord"):
+    if params.get("extent_ijkord", False):
         cargs.append("-extent_ijkord")
-    if params.get("extent_ijkord_to_file") is not None:
+    if params.get("extent_ijkord_to_file", None) is not None:
         cargs.extend([
             "-extent_ijkord_to_file",
-            params.get("extent_ijkord_to_file")
+            params.get("extent_ijkord_to_file", None)
         ])
-    if params.get("extent_xyz_to_file") is not None:
+    if params.get("extent_xyz_to_file", None) is not None:
         cargs.extend([
             "-extent_xyz_to_file",
-            params.get("extent_xyz_to_file")
+            params.get("extent_xyz_to_file", None)
         ])
-    if params.get("extent_xyz_midslice"):
+    if params.get("extent_xyz_midslice", False):
         cargs.append("-extent_xyz_midslice")
-    if params.get("npad") is not None:
+    if params.get("npad", None) is not None:
         cargs.extend([
             "-npad",
-            str(params.get("npad"))
+            str(params.get("npad", None))
         ])
-    if params.get("npad_safety_on"):
+    if params.get("npad_safety_on", False):
         cargs.append("-npad_safety_on")
     return cargs
 
@@ -228,11 +214,13 @@ def v_3d_autobox_outputs(
 
 def v_3d_autobox_execute(
     params: V3dAutoboxParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dAutoboxOutputs:
     """
-    Computes size of a box that fits around the volume. Can also be used to crop the
-    volume to that box.
+    3dAutobox
+    
+    Computes size of a box that fits around the volume. Can also be used to crop
+    the volume to that box.
     
     Author: AFNI Developers
     
@@ -240,10 +228,12 @@ def v_3d_autobox_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dAutoboxOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_AUTOBOX_METADATA)
     params = execution.params(params)
     cargs = v_3d_autobox_cargs(params, execution)
     ret = v_3d_autobox_outputs(params, execution)
@@ -269,8 +259,10 @@ def v_3d_autobox(
     runner: Runner | None = None,
 ) -> V3dAutoboxOutputs:
     """
-    Computes size of a box that fits around the volume. Can also be used to crop the
-    volume to that box.
+    3dAutobox
+    
+    Computes size of a box that fits around the volume. Can also be used to crop
+    the volume to that box.
     
     Author: AFNI Developers
     
@@ -305,8 +297,6 @@ def v_3d_autobox(
     Returns:
         NamedTuple of outputs (described in `V3dAutoboxOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_AUTOBOX_METADATA)
     params = v_3d_autobox_params(
         input_=input_,
         prefix=prefix,
@@ -323,13 +313,13 @@ def v_3d_autobox(
         npad=npad,
         npad_safety_on=npad_safety_on,
     )
-    return v_3d_autobox_execute(params, execution)
+    return v_3d_autobox_execute(params, runner)
 
 
 __all__ = [
     "V3dAutoboxOutputs",
-    "V3dAutoboxParameters",
     "V_3D_AUTOBOX_METADATA",
     "v_3d_autobox",
+    "v_3d_autobox_execute",
     "v_3d_autobox_params",
 ]