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

niwrap_afni/afni/v__simulate_motion.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SIMULATE_MOTION_METADATA = Metadata(
-    id="81ca0292d10cb27ca6eec2771f9556bf24d569dc.boutiques",
+    id="7806e5a3157aef86617e16840ac5ed147efa9cc4.boutiques",
     name="@simulate_motion",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,26 @@ V__SIMULATE_MOTION_METADATA = Metadata(
 
 
 VSimulateMotionParameters = typing.TypedDict('VSimulateMotionParameters', {
-    "__STYXTYPE__": typing.Literal["@simulate_motion"],
+    "@type": typing.NotRequired[typing.Literal["afni/@simulate_motion"]],
+    "epi": InputPathType,
+    "motion_file": InputPathType,
+    "epi_timing": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "save_workdir": bool,
+    "test": bool,
+    "verb_level": typing.NotRequired[float | None],
+    "vr_base": typing.NotRequired[float | None],
+    "warp_method": typing.NotRequired[str | None],
+    "warp_1D": typing.NotRequired[InputPathType | None],
+    "warp_master": typing.NotRequired[InputPathType | None],
+    "wsinc5": bool,
+    "help": bool,
+    "hist": bool,
+    "todo": bool,
+    "ver": bool,
+})
+VSimulateMotionParametersTagged = typing.TypedDict('VSimulateMotionParametersTagged', {
+    "@type": typing.Literal["afni/@simulate_motion"],
     "epi": InputPathType,
     "motion_file": InputPathType,
     "epi_timing": typing.NotRequired[InputPathType | None],
@@ -32,43 +51,11 @@ VSimulateMotionParameters = typing.TypedDict('VSimulateMotionParameters', {
     "todo": bool,
     "ver": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@simulate_motion": v__simulate_motion_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 {
-        "@simulate_motion": v__simulate_motion_outputs,
-    }.get(t)
 
 
 class VSimulateMotionOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__simulate_motion(...)`.
+    Output object returned when calling `VSimulateMotionParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +80,7 @@ def v__simulate_motion_params(
     hist: bool = False,
     todo: bool = False,
     ver: bool = False,
-) -> VSimulateMotionParameters:
+) -> VSimulateMotionParametersTagged:
     """
     Build parameters.
     
@@ -120,7 +107,7 @@ def v__simulate_motion_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@simulate_motion",
+        "@type": "afni/@simulate_motion",
         "epi": epi,
         "motion_file": motion_file,
         "save_workdir": save_workdir,
@@ -165,60 +152,60 @@ def v__simulate_motion_cargs(
     cargs.append("@simulate_motion")
     cargs.extend([
         "-epi",
-        execution.input_file(params.get("epi"))
+        execution.input_file(params.get("epi", None))
     ])
     cargs.extend([
         "-motion_file",
-        execution.input_file(params.get("motion_file"))
+        execution.input_file(params.get("motion_file", None))
     ])
-    if params.get("epi_timing") is not None:
+    if params.get("epi_timing", None) is not None:
         cargs.extend([
             "-epi_timing",
-            execution.input_file(params.get("epi_timing"))
+            execution.input_file(params.get("epi_timing", 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("save_workdir"):
+    if params.get("save_workdir", False):
         cargs.append("-save_workdir")
-    if params.get("test"):
+    if params.get("test", False):
         cargs.append("-test")
-    if params.get("verb_level") is not None:
+    if params.get("verb_level", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verb_level"))
+            str(params.get("verb_level", None))
         ])
-    if params.get("vr_base") is not None:
+    if params.get("vr_base", None) is not None:
         cargs.extend([
             "-vr_base",
-            str(params.get("vr_base"))
+            str(params.get("vr_base", None))
         ])
-    if params.get("warp_method") is not None:
+    if params.get("warp_method", None) is not None:
         cargs.extend([
             "-warp_method",
-            params.get("warp_method")
+            params.get("warp_method", None)
         ])
-    if params.get("warp_1D") is not None:
+    if params.get("warp_1D", None) is not None:
         cargs.extend([
             "-warp_1D",
-            execution.input_file(params.get("warp_1D"))
+            execution.input_file(params.get("warp_1D", None))
         ])
-    if params.get("warp_master") is not None:
+    if params.get("warp_master", None) is not None:
         cargs.extend([
             "-warp_master",
-            execution.input_file(params.get("warp_master"))
+            execution.input_file(params.get("warp_master", None))
         ])
-    if params.get("wsinc5"):
+    if params.get("wsinc5", False):
         cargs.append("-wsinc5")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("hist"):
+    if params.get("hist", False):
         cargs.append("-hist")
-    if params.get("todo"):
+    if params.get("todo", False):
         cargs.append("-todo")
-    if params.get("ver"):
+    if params.get("ver", False):
         cargs.append("-ver")
     return cargs
 
@@ -238,16 +225,18 @@ def v__simulate_motion_outputs(
     """
     ret = VSimulateMotionOutputs(
         root=execution.output_file("."),
-        simulated_motion_output=execution.output_file(params.get("prefix") + "_simulated_motion.nii.gz") if (params.get("prefix") is not None) else None,
+        simulated_motion_output=execution.output_file(params.get("prefix", None) + "_simulated_motion.nii.gz") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v__simulate_motion_execute(
     params: VSimulateMotionParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSimulateMotionOutputs:
     """
+    @simulate_motion
+    
     Create simulated motion time series in an EPI dataset based on the provided
     motion parameters and an input volume.
     
@@ -257,10 +246,12 @@ def v__simulate_motion_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSimulateMotionOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SIMULATE_MOTION_METADATA)
     params = execution.params(params)
     cargs = v__simulate_motion_cargs(params, execution)
     ret = v__simulate_motion_outputs(params, execution)
@@ -288,6 +279,8 @@ def v__simulate_motion(
     runner: Runner | None = None,
 ) -> VSimulateMotionOutputs:
     """
+    @simulate_motion
+    
     Create simulated motion time series in an EPI dataset based on the provided
     motion parameters and an input volume.
     
@@ -318,8 +311,6 @@ def v__simulate_motion(
     Returns:
         NamedTuple of outputs (described in `VSimulateMotionOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SIMULATE_MOTION_METADATA)
     params = v__simulate_motion_params(
         epi=epi,
         motion_file=motion_file,
@@ -338,13 +329,13 @@ def v__simulate_motion(
         todo=todo,
         ver=ver,
     )
-    return v__simulate_motion_execute(params, execution)
+    return v__simulate_motion_execute(params, runner)
 
 
 __all__ = [
     "VSimulateMotionOutputs",
-    "VSimulateMotionParameters",
     "V__SIMULATE_MOTION_METADATA",
     "v__simulate_motion",
+    "v__simulate_motion_execute",
     "v__simulate_motion_params",
 ]

niwrap_afni/afni/v__skull_strip_touch_up.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SKULL_STRIP_TOUCH_UP_METADATA = Metadata(
-    id="9f2f6c87f11ad6568c143e9302cc39f55ec33279.boutiques",
+    id="6c2944dd523c28bc9850a8eb4db4c81926ee4298.boutiques",
     name="@SkullStrip_TouchUp",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V__SKULL_STRIP_TOUCH_UP_METADATA = Metadata(
 
 
 VSkullStripTouchUpParameters = typing.TypedDict('VSkullStripTouchUpParameters', {
-    "__STYXTYPE__": typing.Literal["@SkullStrip_TouchUp"],
+    "@type": typing.NotRequired[typing.Literal["afni/@SkullStrip_TouchUp"]],
+    "prefix": str,
+    "brain_dataset": InputPathType,
+    "head_dataset": InputPathType,
+    "mask_out": bool,
+    "orig_dim": bool,
+    "help": bool,
+})
+VSkullStripTouchUpParametersTagged = typing.TypedDict('VSkullStripTouchUpParametersTagged', {
+    "@type": typing.Literal["afni/@SkullStrip_TouchUp"],
     "prefix": str,
     "brain_dataset": InputPathType,
     "head_dataset": InputPathType,
@@ -22,43 +31,11 @@ VSkullStripTouchUpParameters = typing.TypedDict('VSkullStripTouchUpParameters',
     "orig_dim": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@SkullStrip_TouchUp": v__skull_strip_touch_up_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 {
-        "@SkullStrip_TouchUp": v__skull_strip_touch_up_outputs,
-    }.get(t)
 
 
 class VSkullStripTouchUpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__skull_strip_touch_up(...)`.
+    Output object returned when calling `VSkullStripTouchUpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def v__skull_strip_touch_up_params(
     mask_out: bool = False,
     orig_dim: bool = False,
     help_: bool = False,
-) -> VSkullStripTouchUpParameters:
+) -> VSkullStripTouchUpParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def v__skull_strip_touch_up_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@SkullStrip_TouchUp",
+        "@type": "afni/@SkullStrip_TouchUp",
         "prefix": prefix,
         "brain_dataset": brain_dataset,
         "head_dataset": head_dataset,
@@ -118,21 +95,21 @@ def v__skull_strip_touch_up_cargs(
     cargs.append("@SkullStrip_TouchUp")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "-brain",
-        execution.input_file(params.get("brain_dataset"))
+        execution.input_file(params.get("brain_dataset", None))
     ])
     cargs.extend([
         "-head",
-        execution.input_file(params.get("head_dataset"))
+        execution.input_file(params.get("head_dataset", None))
     ])
-    if params.get("mask_out"):
+    if params.get("mask_out", False):
         cargs.append("-mask_out")
-    if params.get("orig_dim"):
+    if params.get("orig_dim", False):
         cargs.append("-orig_dim")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -152,19 +129,21 @@ def v__skull_strip_touch_up_outputs(
     """
     ret = VSkullStripTouchUpOutputs(
         root=execution.output_file("."),
-        output_folder=execution.output_file(params.get("prefix") + "_SS_touch_up"),
-        output_mask=execution.output_file(params.get("prefix") + "_mask.nii.gz"),
+        output_folder=execution.output_file(params.get("prefix", None) + "_SS_touch_up"),
+        output_mask=execution.output_file(params.get("prefix", None) + "_mask.nii.gz"),
     )
     return ret
 
 
 def v__skull_strip_touch_up_execute(
     params: VSkullStripTouchUpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSkullStripTouchUpOutputs:
     """
-    Helper program to touch up failed skull stripping by resampling data, allowing
-    manual edits, and outputting corrected data.
+    @SkullStrip_TouchUp
+    
+    Helper program to touch up failed skull stripping by resampling data,
+    allowing manual edits, and outputting corrected data.
     
     Author: AFNI Developers
     
@@ -172,10 +151,12 @@ def v__skull_strip_touch_up_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSkullStripTouchUpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SKULL_STRIP_TOUCH_UP_METADATA)
     params = execution.params(params)
     cargs = v__skull_strip_touch_up_cargs(params, execution)
     ret = v__skull_strip_touch_up_outputs(params, execution)
@@ -193,8 +174,10 @@ def v__skull_strip_touch_up(
     runner: Runner | None = None,
 ) -> VSkullStripTouchUpOutputs:
     """
-    Helper program to touch up failed skull stripping by resampling data, allowing
-    manual edits, and outputting corrected data.
+    @SkullStrip_TouchUp
+    
+    Helper program to touch up failed skull stripping by resampling data,
+    allowing manual edits, and outputting corrected data.
     
     Author: AFNI Developers
     
@@ -211,8 +194,6 @@ def v__skull_strip_touch_up(
     Returns:
         NamedTuple of outputs (described in `VSkullStripTouchUpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SKULL_STRIP_TOUCH_UP_METADATA)
     params = v__skull_strip_touch_up_params(
         prefix=prefix,
         brain_dataset=brain_dataset,
@@ -221,13 +202,13 @@ def v__skull_strip_touch_up(
         orig_dim=orig_dim,
         help_=help_,
     )
-    return v__skull_strip_touch_up_execute(params, execution)
+    return v__skull_strip_touch_up_execute(params, runner)
 
 
 __all__ = [
     "VSkullStripTouchUpOutputs",
-    "VSkullStripTouchUpParameters",
     "V__SKULL_STRIP_TOUCH_UP_METADATA",
     "v__skull_strip_touch_up",
+    "v__skull_strip_touch_up_execute",
     "v__skull_strip_touch_up_params",
 ]

niwrap_afni/afni/v__snapshot_volreg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SNAPSHOT_VOLREG_METADATA = Metadata(
-    id="0ab483377c7792acf3771a7e98a2455e1c16e3fd.boutiques",
+    id="ea426c0369e8313557cfb4056ece5365e472d055.boutiques",
     name="@snapshot_volreg",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ V__SNAPSHOT_VOLREG_METADATA = Metadata(
 
 
 VSnapshotVolregParameters = typing.TypedDict('VSnapshotVolregParameters', {
-    "__STYXTYPE__": typing.Literal["@snapshot_volreg"],
+    "@type": typing.NotRequired[typing.Literal["afni/@snapshot_volreg"]],
+    "anatdataset": InputPathType,
+    "epidataset": InputPathType,
+    "jname": typing.NotRequired[str | None],
+    "xdisplay": typing.NotRequired[str | None],
+})
+VSnapshotVolregParametersTagged = typing.TypedDict('VSnapshotVolregParametersTagged', {
+    "@type": typing.Literal["afni/@snapshot_volreg"],
     "anatdataset": InputPathType,
     "epidataset": InputPathType,
     "jname": typing.NotRequired[str | None],
     "xdisplay": 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 {
-        "@snapshot_volreg": v__snapshot_volreg_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 {
-        "@snapshot_volreg": v__snapshot_volreg_outputs,
-    }.get(t)
 
 
 class VSnapshotVolregOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__snapshot_volreg(...)`.
+    Output object returned when calling `VSnapshotVolregParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +45,7 @@ def v__snapshot_volreg_params(
     epidataset: InputPathType,
     jname: str | None = None,
     xdisplay: str | None = None,
-) -> VSnapshotVolregParameters:
+) -> VSnapshotVolregParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def v__snapshot_volreg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@snapshot_volreg",
+        "@type": "afni/@snapshot_volreg",
         "anatdataset": anatdataset,
         "epidataset": epidataset,
     }
@@ -109,12 +84,12 @@ def v__snapshot_volreg_cargs(
     """
     cargs = []
     cargs.append("@snapshot_volreg")
-    cargs.append(execution.input_file(params.get("anatdataset")))
-    cargs.append(execution.input_file(params.get("epidataset")))
-    if params.get("jname") is not None:
-        cargs.append(params.get("jname"))
-    if params.get("xdisplay") is not None:
-        cargs.append(params.get("xdisplay"))
+    cargs.append(execution.input_file(params.get("anatdataset", None)))
+    cargs.append(execution.input_file(params.get("epidataset", None)))
+    if params.get("jname", None) is not None:
+        cargs.append(params.get("jname", None))
+    if params.get("xdisplay", None) is not None:
+        cargs.append(params.get("xdisplay", None))
     return cargs
 
 
@@ -133,16 +108,18 @@ def v__snapshot_volreg_outputs(
     """
     ret = VSnapshotVolregOutputs(
         root=execution.output_file("."),
-        output_jpeg=execution.output_file(params.get("jname") + ".jpg") if (params.get("jname") is not None) else None,
+        output_jpeg=execution.output_file(params.get("jname", None) + ".jpg") if (params.get("jname") is not None) else None,
     )
     return ret
 
 
 def v__snapshot_volreg_execute(
     params: VSnapshotVolregParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSnapshotVolregOutputs:
     """
+    @snapshot_volreg
+    
     Create a JPEG image showing the edges of an EPI dataset overlayed on an
     anatomical dataset to judge 3D registration quality.
     
@@ -152,10 +129,12 @@ def v__snapshot_volreg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSnapshotVolregOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SNAPSHOT_VOLREG_METADATA)
     params = execution.params(params)
     cargs = v__snapshot_volreg_cargs(params, execution)
     ret = v__snapshot_volreg_outputs(params, execution)
@@ -171,6 +150,8 @@ def v__snapshot_volreg(
     runner: Runner | None = None,
 ) -> VSnapshotVolregOutputs:
     """
+    @snapshot_volreg
+    
     Create a JPEG image showing the edges of an EPI dataset overlayed on an
     anatomical dataset to judge 3D registration quality.
     
@@ -187,21 +168,19 @@ def v__snapshot_volreg(
     Returns:
         NamedTuple of outputs (described in `VSnapshotVolregOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SNAPSHOT_VOLREG_METADATA)
     params = v__snapshot_volreg_params(
         anatdataset=anatdataset,
         epidataset=epidataset,
         jname=jname,
         xdisplay=xdisplay,
     )
-    return v__snapshot_volreg_execute(params, execution)
+    return v__snapshot_volreg_execute(params, runner)
 
 
 __all__ = [
     "VSnapshotVolregOutputs",
-    "VSnapshotVolregParameters",
     "V__SNAPSHOT_VOLREG_METADATA",
     "v__snapshot_volreg",
+    "v__snapshot_volreg_execute",
     "v__snapshot_volreg_params",
 ]