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

niwrap_afni/afni/v_3d_retino_phase.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_RETINO_PHASE_METADATA = Metadata(
-    id="2d3b9af035089d0168b16f53cd54b736189187db.boutiques",
+    id="6034f5fb3167fcd5bd50da0a1b2a534f011a35b2.boutiques",
     name="3dRetinoPhase",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,26 @@ V_3D_RETINO_PHASE_METADATA = Metadata(
 
 
 V3dRetinoPhaseParameters = typing.TypedDict('V3dRetinoPhaseParameters', {
-    "__STYXTYPE__": typing.Literal["3dRetinoPhase"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dRetinoPhase"]],
+    "prefix": str,
+    "dataset": InputPathType,
+    "exp": typing.NotRequired[str | None],
+    "con": typing.NotRequired[str | None],
+    "clw": typing.NotRequired[str | None],
+    "ccw": typing.NotRequired[str | None],
+    "spectra": bool,
+    "tstim": typing.NotRequired[float | None],
+    "nrings": typing.NotRequired[float | None],
+    "nwedges": typing.NotRequired[float | None],
+    "ort_adjust": typing.NotRequired[float | None],
+    "pre_stim": typing.NotRequired[float | None],
+    "sum_adjust": typing.NotRequired[str | None],
+    "phase_estimate": typing.NotRequired[str | None],
+    "ref_ts": typing.NotRequired[InputPathType | None],
+    "multi_ref_ts": typing.NotRequired[InputPathType | None],
+})
+V3dRetinoPhaseParametersTagged = typing.TypedDict('V3dRetinoPhaseParametersTagged', {
+    "@type": typing.Literal["afni/3dRetinoPhase"],
     "prefix": str,
     "dataset": InputPathType,
     "exp": typing.NotRequired[str | None],
@@ -32,43 +51,11 @@ V3dRetinoPhaseParameters = typing.TypedDict('V3dRetinoPhaseParameters', {
     "ref_ts": typing.NotRequired[InputPathType | None],
     "multi_ref_ts": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dRetinoPhase": v_3d_retino_phase_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 {
-        "3dRetinoPhase": v_3d_retino_phase_outputs,
-    }.get(t)
 
 
 class V3dRetinoPhaseOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_retino_phase(...)`.
+    Output object returned when calling `V3dRetinoPhaseParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +86,7 @@ def v_3d_retino_phase_params(
     phase_estimate: str | None = None,
     ref_ts: InputPathType | None = None,
     multi_ref_ts: InputPathType | None = None,
-) -> V3dRetinoPhaseParameters:
+) -> V3dRetinoPhaseParametersTagged:
     """
     Build parameters.
     
@@ -127,7 +114,7 @@ def v_3d_retino_phase_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dRetinoPhase",
+        "@type": "afni/3dRetinoPhase",
         "prefix": prefix,
         "dataset": dataset,
         "spectra": spectra,
@@ -176,74 +163,74 @@ def v_3d_retino_phase_cargs(
     """
     cargs = []
     cargs.append("3dRetinoPhase")
-    cargs.append(params.get("prefix"))
-    cargs.append(execution.input_file(params.get("dataset")))
-    if params.get("exp") is not None:
+    cargs.append(params.get("prefix", None))
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    if params.get("exp", None) is not None:
         cargs.extend([
             "-exp",
-            params.get("exp")
+            params.get("exp", None)
         ])
-    if params.get("con") is not None:
+    if params.get("con", None) is not None:
         cargs.extend([
             "-con",
-            params.get("con")
+            params.get("con", None)
         ])
-    if params.get("clw") is not None:
+    if params.get("clw", None) is not None:
         cargs.extend([
             "-clw",
-            params.get("clw")
+            params.get("clw", None)
         ])
-    if params.get("ccw") is not None:
+    if params.get("ccw", None) is not None:
         cargs.extend([
             "-ccw",
-            params.get("ccw")
+            params.get("ccw", None)
         ])
-    if params.get("spectra"):
+    if params.get("spectra", False):
         cargs.append("-spectra")
-    if params.get("tstim") is not None:
+    if params.get("tstim", None) is not None:
         cargs.extend([
             "-Tstim",
-            str(params.get("tstim"))
+            str(params.get("tstim", None))
         ])
-    if params.get("nrings") is not None:
+    if params.get("nrings", None) is not None:
         cargs.extend([
             "-nrings",
-            str(params.get("nrings"))
+            str(params.get("nrings", None))
         ])
-    if params.get("nwedges") is not None:
+    if params.get("nwedges", None) is not None:
         cargs.extend([
             "-nwedges",
-            str(params.get("nwedges"))
+            str(params.get("nwedges", None))
         ])
-    if params.get("ort_adjust") is not None:
+    if params.get("ort_adjust", None) is not None:
         cargs.extend([
             "-ort_adjust",
-            str(params.get("ort_adjust"))
+            str(params.get("ort_adjust", None))
         ])
-    if params.get("pre_stim") is not None:
+    if params.get("pre_stim", None) is not None:
         cargs.extend([
             "-pre_stim",
-            str(params.get("pre_stim"))
+            str(params.get("pre_stim", None))
         ])
-    if params.get("sum_adjust") is not None:
+    if params.get("sum_adjust", None) is not None:
         cargs.extend([
             "-sum_adjust",
-            params.get("sum_adjust")
+            params.get("sum_adjust", None)
         ])
-    if params.get("phase_estimate") is not None:
+    if params.get("phase_estimate", None) is not None:
         cargs.extend([
             "-phase_estimate",
-            params.get("phase_estimate")
+            params.get("phase_estimate", None)
         ])
-    if params.get("ref_ts") is not None:
+    if params.get("ref_ts", None) is not None:
         cargs.extend([
             "-ref_ts",
-            execution.input_file(params.get("ref_ts"))
+            execution.input_file(params.get("ref_ts", None))
         ])
-    if params.get("multi_ref_ts") is not None:
+    if params.get("multi_ref_ts", None) is not None:
         cargs.extend([
             "-multi_ref_ts",
-            execution.input_file(params.get("multi_ref_ts"))
+            execution.input_file(params.get("multi_ref_ts", None))
         ])
     return cargs
 
@@ -263,21 +250,23 @@ def v_3d_retino_phase_outputs(
     """
     ret = V3dRetinoPhaseOutputs(
         root=execution.output_file("."),
-        ecc_plus=execution.output_file(params.get("prefix") + ".ecc+"),
-        ecc_minus=execution.output_file(params.get("prefix") + ".ecc-"),
-        pol_plus=execution.output_file(params.get("prefix") + ".pol+"),
-        pol_minus=execution.output_file(params.get("prefix") + ".pol-"),
+        ecc_plus=execution.output_file(params.get("prefix", None) + ".ecc+"),
+        ecc_minus=execution.output_file(params.get("prefix", None) + ".ecc-"),
+        pol_plus=execution.output_file(params.get("prefix", None) + ".pol+"),
+        pol_minus=execution.output_file(params.get("prefix", None) + ".pol-"),
     )
     return ret
 
 
 def v_3d_retino_phase_execute(
     params: V3dRetinoPhaseParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dRetinoPhaseOutputs:
     """
-    Process time series from retinotopy stimuli to create phase datasets and visual
-    field angle datasets.
+    3dRetinoPhase
+    
+    Process time series from retinotopy stimuli to create phase datasets and
+    visual field angle datasets.
     
     Author: AFNI Developers
     
@@ -285,10 +274,12 @@ def v_3d_retino_phase_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRetinoPhaseOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RETINO_PHASE_METADATA)
     params = execution.params(params)
     cargs = v_3d_retino_phase_cargs(params, execution)
     ret = v_3d_retino_phase_outputs(params, execution)
@@ -316,8 +307,10 @@ def v_3d_retino_phase(
     runner: Runner | None = None,
 ) -> V3dRetinoPhaseOutputs:
     """
-    Process time series from retinotopy stimuli to create phase datasets and visual
-    field angle datasets.
+    3dRetinoPhase
+    
+    Process time series from retinotopy stimuli to create phase datasets and
+    visual field angle datasets.
     
     Author: AFNI Developers
     
@@ -347,8 +340,6 @@ def v_3d_retino_phase(
     Returns:
         NamedTuple of outputs (described in `V3dRetinoPhaseOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_RETINO_PHASE_METADATA)
     params = v_3d_retino_phase_params(
         prefix=prefix,
         dataset=dataset,
@@ -367,13 +358,13 @@ def v_3d_retino_phase(
         ref_ts=ref_ts,
         multi_ref_ts=multi_ref_ts,
     )
-    return v_3d_retino_phase_execute(params, execution)
+    return v_3d_retino_phase_execute(params, runner)
 
 
 __all__ = [
     "V3dRetinoPhaseOutputs",
-    "V3dRetinoPhaseParameters",
     "V_3D_RETINO_PHASE_METADATA",
     "v_3d_retino_phase",
+    "v_3d_retino_phase_execute",
     "v_3d_retino_phase_params",
 ]

niwrap_afni/afni/{v_3_droimaker.py → v_3d_roimaker.py}

@@ -5,16 +5,39 @@ import typing
 import pathlib
 from styxdefs import *
 
-V_3_DROIMAKER_METADATA = Metadata(
-    id="5b3355492db520e49a5f6a884aa39664389df7ac.boutiques",
-    name="3DROIMaker",
+V_3D_ROIMAKER_METADATA = Metadata(
+    id="69620c1a87f0694cec0d446d98ee3d79ce4d24a9.boutiques",
+    name="3dROIMaker",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-V3DroimakerParameters = typing.TypedDict('V3DroimakerParameters', {
-    "__STYXTYPE__": typing.Literal["3DROIMaker"],
+V3dRoimakerParameters = typing.TypedDict('V3dRoimakerParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/3dROIMaker"]],
+    "inset": InputPathType,
+    "thresh": float,
+    "prefix": str,
+    "refset": typing.NotRequired[InputPathType | None],
+    "volthr": typing.NotRequired[float | None],
+    "only_some_top": typing.NotRequired[float | None],
+    "only_conn_top": typing.NotRequired[float | None],
+    "inflate": typing.NotRequired[float | None],
+    "trim_off_wm": bool,
+    "wm_skel": typing.NotRequired[InputPathType | None],
+    "skel_thr": typing.NotRequired[float | None],
+    "skel_stop": bool,
+    "skel_stop_strict": bool,
+    "csf_skel": typing.NotRequired[InputPathType | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "neigh_upto_vert": bool,
+    "nifti": bool,
+    "preinfl_inset": typing.NotRequired[InputPathType | None],
+    "preinfl_inflate": typing.NotRequired[float | None],
+    "dump_no_labtab": bool,
+})
+V3dRoimakerParametersTagged = typing.TypedDict('V3dRoimakerParametersTagged', {
+    "@type": typing.Literal["afni/3dROIMaker"],
     "inset": InputPathType,
     "thresh": float,
     "prefix": str,
@@ -38,41 +61,9 @@ V3DroimakerParameters = typing.TypedDict('V3DroimakerParameters', {
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3DROIMaker": v_3_droimaker_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 {
-        "3DROIMaker": v_3_droimaker_outputs,
-    }.get(t)
-
-
-class V3DroimakerOutputs(typing.NamedTuple):
+class V3dRoimakerOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3_droimaker(...)`.
+    Output object returned when calling `V3dRoimakerParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +75,7 @@ class V3DroimakerOutputs(typing.NamedTuple):
     user-design or WM skeleton."""
 
 
-def v_3_droimaker_params(
+def v_3d_roimaker_params(
     inset: InputPathType,
     thresh: float,
     prefix: str,
@@ -105,7 +96,7 @@ def v_3_droimaker_params(
     preinfl_inset: InputPathType | None = None,
     preinfl_inflate: float | None = None,
     dump_no_labtab: bool = False,
-) -> V3DroimakerParameters:
+) -> V3dRoimakerParametersTagged:
     """
     Build parameters.
     
@@ -150,7 +141,7 @@ def v_3_droimaker_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3DROIMaker",
+        "@type": "afni/3dROIMaker",
         "inset": inset,
         "thresh": thresh,
         "prefix": prefix,
@@ -186,8 +177,8 @@ def v_3_droimaker_params(
     return params
 
 
-def v_3_droimaker_cargs(
-    params: V3DroimakerParameters,
+def v_3d_roimaker_cargs(
+    params: V3dRoimakerParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -201,89 +192,89 @@ def v_3_droimaker_cargs(
     """
     cargs = []
     cargs.append("3dROIMaker")
-    cargs.append(execution.input_file(params.get("inset")))
+    cargs.append(execution.input_file(params.get("inset", None)))
     cargs.extend([
         "-thresh",
-        str(params.get("thresh"))
+        str(params.get("thresh", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("refset") is not None:
+    if params.get("refset", None) is not None:
         cargs.extend([
             "-refset",
-            execution.input_file(params.get("refset"))
+            execution.input_file(params.get("refset", None))
         ])
-    if params.get("volthr") is not None:
+    if params.get("volthr", None) is not None:
         cargs.extend([
             "-volthr",
-            str(params.get("volthr"))
+            str(params.get("volthr", None))
         ])
-    if params.get("only_some_top") is not None:
+    if params.get("only_some_top", None) is not None:
         cargs.extend([
             "-only_some_top",
-            str(params.get("only_some_top"))
+            str(params.get("only_some_top", None))
         ])
-    if params.get("only_conn_top") is not None:
+    if params.get("only_conn_top", None) is not None:
         cargs.extend([
             "-only_conn_top",
-            str(params.get("only_conn_top"))
+            str(params.get("only_conn_top", None))
         ])
-    if params.get("inflate") is not None:
+    if params.get("inflate", None) is not None:
         cargs.extend([
             "-inflate",
-            str(params.get("inflate"))
+            str(params.get("inflate", None))
         ])
-    if params.get("trim_off_wm"):
+    if params.get("trim_off_wm", False):
         cargs.append("-trim_off_wm")
-    if params.get("wm_skel") is not None:
+    if params.get("wm_skel", None) is not None:
         cargs.extend([
             "-wm_skel",
-            execution.input_file(params.get("wm_skel"))
+            execution.input_file(params.get("wm_skel", None))
         ])
-    if params.get("skel_thr") is not None:
+    if params.get("skel_thr", None) is not None:
         cargs.extend([
             "-skel_thr",
-            str(params.get("skel_thr"))
+            str(params.get("skel_thr", None))
         ])
-    if params.get("skel_stop"):
+    if params.get("skel_stop", False):
         cargs.append("-skel_stop")
-    if params.get("skel_stop_strict"):
+    if params.get("skel_stop_strict", False):
         cargs.append("-skel_stop_strict")
-    if params.get("csf_skel") is not None:
+    if params.get("csf_skel", None) is not None:
         cargs.extend([
             "-csf_skel",
-            execution.input_file(params.get("csf_skel"))
+            execution.input_file(params.get("csf_skel", 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("neigh_upto_vert"):
+    if params.get("neigh_upto_vert", False):
         cargs.append("-neigh_upto_vert")
-    if params.get("nifti"):
+    if params.get("nifti", False):
         cargs.append("-nifti")
-    if params.get("preinfl_inset") is not None:
+    if params.get("preinfl_inset", None) is not None:
         cargs.extend([
             "-preinfl_inset",
-            execution.input_file(params.get("preinfl_inset"))
+            execution.input_file(params.get("preinfl_inset", None))
         ])
-    if params.get("preinfl_inflate") is not None:
+    if params.get("preinfl_inflate", None) is not None:
         cargs.extend([
             "-preinfl_inflate",
-            str(params.get("preinfl_inflate"))
+            str(params.get("preinfl_inflate", None))
         ])
-    if params.get("dump_no_labtab"):
+    if params.get("dump_no_labtab", False):
         cargs.append("-dump_no_labtab")
     return cargs
 
 
-def v_3_droimaker_outputs(
-    params: V3DroimakerParameters,
+def v_3d_roimaker_outputs(
+    params: V3dRoimakerParameters,
     execution: Execution,
-) -> V3DroimakerOutputs:
+) -> V3dRoimakerOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -293,21 +284,23 @@ def v_3_droimaker_outputs(
     Returns:
         Outputs object.
     """
-    ret = V3DroimakerOutputs(
+    ret = V3dRoimakerOutputs(
         root=execution.output_file("."),
-        gm_map=execution.output_file(params.get("prefix") + "_GM+orig.*.HEAD"),
-        gmi_map=execution.output_file(params.get("prefix") + "_GMI+orig.*.HEAD"),
+        gm_map=execution.output_file(params.get("prefix", None) + "_GM+orig.HEAD"),
+        gmi_map=execution.output_file(params.get("prefix", None) + "_GMI+orig.HEAD"),
     )
     return ret
 
 
-def v_3_droimaker_execute(
-    params: V3DroimakerParameters,
-    execution: Execution,
-) -> V3DroimakerOutputs:
+def v_3d_roimaker_execute(
+    params: V3dRoimakerParameters,
+    runner: Runner | None = None,
+) -> V3dRoimakerOutputs:
     """
-    Create a labelled set of ROIs from input data, useful in combining functional
-    and tractographic/structural data.
+    3dROIMaker
+    
+    Create a labelled set of ROIs from input data, useful in combining
+    functional and tractographic/structural data.
     
     Author: AFNI Developers
     
@@ -315,18 +308,20 @@ def v_3_droimaker_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `V3DroimakerOutputs`).
+        NamedTuple of outputs (described in `V3dRoimakerOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ROIMAKER_METADATA)
     params = execution.params(params)
-    cargs = v_3_droimaker_cargs(params, execution)
-    ret = v_3_droimaker_outputs(params, execution)
+    cargs = v_3d_roimaker_cargs(params, execution)
+    ret = v_3d_roimaker_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def v_3_droimaker(
+def v_3d_roimaker(
     inset: InputPathType,
     thresh: float,
     prefix: str,
@@ -348,10 +343,12 @@ def v_3_droimaker(
     preinfl_inflate: float | None = None,
     dump_no_labtab: bool = False,
     runner: Runner | None = None,
-) -> V3DroimakerOutputs:
+) -> V3dRoimakerOutputs:
     """
-    Create a labelled set of ROIs from input data, useful in combining functional
-    and tractographic/structural data.
+    3dROIMaker
+    
+    Create a labelled set of ROIs from input data, useful in combining
+    functional and tractographic/structural data.
     
     Author: AFNI Developers
     
@@ -396,11 +393,9 @@ def v_3_droimaker(
             output GM and GMI files.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `V3DroimakerOutputs`).
+        NamedTuple of outputs (described in `V3dRoimakerOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3_DROIMAKER_METADATA)
-    params = v_3_droimaker_params(
+    params = v_3d_roimaker_params(
         inset=inset,
         thresh=thresh,
         prefix=prefix,
@@ -422,13 +417,13 @@ def v_3_droimaker(
         preinfl_inflate=preinfl_inflate,
         dump_no_labtab=dump_no_labtab,
     )
-    return v_3_droimaker_execute(params, execution)
+    return v_3d_roimaker_execute(params, runner)
 
 
 __all__ = [
-    "V3DroimakerOutputs",
-    "V3DroimakerParameters",
-    "V_3_DROIMAKER_METADATA",
-    "v_3_droimaker",
-    "v_3_droimaker_params",
+    "V3dRoimakerOutputs",
+    "V_3D_ROIMAKER_METADATA",
+    "v_3d_roimaker",
+    "v_3d_roimaker_execute",
+    "v_3d_roimaker_params",
 ]