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

niwrap_afni/afni/v_3d_tsgen.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TSGEN_METADATA = Metadata(
-    id="cdf7418bc42352fc7dbfd986bc66d59a6325538b.boutiques",
+    id="b0c7bd6475eba69a0c6af0e385626961ae80a12c.boutiques",
     name="3dTSgen",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ V_3D_TSGEN_METADATA = Metadata(
 
 
 V3dTsgenParameters = typing.TypedDict('V3dTsgenParameters', {
-    "__STYXTYPE__": typing.Literal["3dTSgen"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTSgen"]],
+    "input_file": InputPathType,
+    "in_tr_flag": bool,
+    "signal_label": str,
+    "noise_label": str,
+    "signal_constr": typing.NotRequired[str | None],
+    "noise_constr": typing.NotRequired[str | None],
+    "sigma_value": float,
+    "voxel_number": typing.NotRequired[float | None],
+    "output_file": str,
+    "signal_coef": typing.NotRequired[str | None],
+    "noise_coef": typing.NotRequired[str | None],
+    "bucket_config": typing.NotRequired[str | None],
+    "brick_config": typing.NotRequired[str | None],
+})
+V3dTsgenParametersTagged = typing.TypedDict('V3dTsgenParametersTagged', {
+    "@type": typing.Literal["afni/3dTSgen"],
     "input_file": InputPathType,
     "in_tr_flag": bool,
     "signal_label": str,
@@ -29,42 +45,11 @@ V3dTsgenParameters = typing.TypedDict('V3dTsgenParameters', {
     "bucket_config": typing.NotRequired[str | None],
     "brick_config": 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 {
-        "3dTSgen": v_3d_tsgen_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 V3dTsgenOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_tsgen(...)`.
+    Output object returned when calling `V3dTsgenParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +69,7 @@ def v_3d_tsgen_params(
     noise_coef: str | None = None,
     bucket_config: str | None = None,
     brick_config: str | None = None,
-) -> V3dTsgenParameters:
+) -> V3dTsgenParametersTagged:
     """
     Build parameters.
     
@@ -115,7 +100,7 @@ def v_3d_tsgen_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTSgen",
+        "@type": "afni/3dTSgen",
         "input_file": input_file,
         "in_tr_flag": in_tr_flag,
         "signal_label": signal_label,
@@ -155,59 +140,59 @@ def v_3d_tsgen_cargs(
     """
     cargs = []
     cargs.append("3dTSgen")
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("in_tr_flag"):
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    if params.get("in_tr_flag", False):
         cargs.append("-inTR")
     cargs.extend([
         "-signal",
-        params.get("signal_label")
+        params.get("signal_label", None)
     ])
     cargs.extend([
         "-noise",
-        params.get("noise_label")
+        params.get("noise_label", None)
     ])
-    if params.get("signal_constr") is not None:
+    if params.get("signal_constr", None) is not None:
         cargs.extend([
             "-sconstr",
-            params.get("signal_constr")
+            params.get("signal_constr", None)
         ])
-    if params.get("noise_constr") is not None:
+    if params.get("noise_constr", None) is not None:
         cargs.extend([
             "-nconstr",
-            params.get("noise_constr")
+            params.get("noise_constr", None)
         ])
     cargs.extend([
         "-sigma",
-        str(params.get("sigma_value"))
+        str(params.get("sigma_value", None))
     ])
-    if params.get("voxel_number") is not None:
+    if params.get("voxel_number", None) is not None:
         cargs.extend([
             "-voxel",
-            str(params.get("voxel_number"))
+            str(params.get("voxel_number", None))
         ])
     cargs.extend([
         "-output",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("signal_coef") is not None:
+    if params.get("signal_coef", None) is not None:
         cargs.extend([
             "-scoef",
-            params.get("signal_coef")
+            params.get("signal_coef", None)
         ])
-    if params.get("noise_coef") is not None:
+    if params.get("noise_coef", None) is not None:
         cargs.extend([
             "-ncoef",
-            params.get("noise_coef")
+            params.get("noise_coef", None)
         ])
-    if params.get("bucket_config") is not None:
+    if params.get("bucket_config", None) is not None:
         cargs.extend([
             "-bucket",
-            params.get("bucket_config")
+            params.get("bucket_config", None)
         ])
-    if params.get("brick_config") is not None:
+    if params.get("brick_config", None) is not None:
         cargs.extend([
             "-brick",
-            params.get("brick_config")
+            params.get("brick_config", None)
         ])
     return cargs
 
@@ -233,11 +218,13 @@ def v_3d_tsgen_outputs(
 
 def v_3d_tsgen_execute(
     params: V3dTsgenParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTsgenOutputs:
     """
-    This program generates an AFNI 3d+time data set based on user-specified signal
-    and noise models for each voxel.
+    3dTSgen
+    
+    This program generates an AFNI 3d+time data set based on user-specified
+    signal and noise models for each voxel.
     
     Author: AFNI Developers
     
@@ -245,10 +232,12 @@ def v_3d_tsgen_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTsgenOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TSGEN_METADATA)
     params = execution.params(params)
     cargs = v_3d_tsgen_cargs(params, execution)
     ret = v_3d_tsgen_outputs(params, execution)
@@ -273,8 +262,10 @@ def v_3d_tsgen(
     runner: Runner | None = None,
 ) -> V3dTsgenOutputs:
     """
-    This program generates an AFNI 3d+time data set based on user-specified signal
-    and noise models for each voxel.
+    3dTSgen
+    
+    This program generates an AFNI 3d+time data set based on user-specified
+    signal and noise models for each voxel.
     
     Author: AFNI Developers
     
@@ -307,8 +298,6 @@ def v_3d_tsgen(
     Returns:
         NamedTuple of outputs (described in `V3dTsgenOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TSGEN_METADATA)
     params = v_3d_tsgen_params(
         input_file=input_file,
         in_tr_flag=in_tr_flag,
@@ -324,13 +313,13 @@ def v_3d_tsgen(
         bucket_config=bucket_config,
         brick_config=brick_config,
     )
-    return v_3d_tsgen_execute(params, execution)
+    return v_3d_tsgen_execute(params, runner)
 
 
 __all__ = [
     "V3dTsgenOutputs",
-    "V3dTsgenParameters",
     "V_3D_TSGEN_METADATA",
     "v_3d_tsgen",
+    "v_3d_tsgen_execute",
     "v_3d_tsgen_params",
 ]

niwrap_afni/afni/v_3d_tshift.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_TSHIFT_METADATA = Metadata(
-    id="fd213829ad2ee5b31fc3c535852e595608b30547.boutiques",
+    id="49f64f2ab2eda625043b5f3a63bc8849ce8c369c.boutiques",
     name="3dTshift",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ V_3D_TSHIFT_METADATA = Metadata(
 
 
 V3dTshiftParameters = typing.TypedDict('V3dTshiftParameters', {
-    "__STYXTYPE__": typing.Literal["3dTshift"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dTshift"]],
+    "prefix": typing.NotRequired[str | None],
+    "ignore": typing.NotRequired[int | None],
+    "in_file": InputPathType,
+    "interp": typing.NotRequired[typing.Literal["Fourier", "linear", "cubic", "quintic", "heptic"] | None],
+    "num_threads": typing.NotRequired[int | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "rlt": bool,
+    "rltplus": bool,
+    "slice_encoding_direction": typing.NotRequired[typing.Literal["k", "k-"] | None],
+    "tpattern": typing.NotRequired[typing.Literal["alt+z", "altplus", "alt+z2", "alt-z", "altminus", "alt-z2", "seq+z", "seqplus", "seq-z", "seqminus"] | None],
+    "tr": typing.NotRequired[float | None],
+    "tslice": typing.NotRequired[int | None],
+    "tzero": typing.NotRequired[float | None],
+})
+V3dTshiftParametersTagged = typing.TypedDict('V3dTshiftParametersTagged', {
+    "@type": typing.Literal["afni/3dTshift"],
     "prefix": typing.NotRequired[str | None],
     "ignore": typing.NotRequired[int | None],
     "in_file": InputPathType,
@@ -29,43 +45,11 @@ V3dTshiftParameters = typing.TypedDict('V3dTshiftParameters', {
     "tslice": typing.NotRequired[int | None],
     "tzero": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dTshift": v_3d_tshift_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 {
-        "3dTshift": v_3d_tshift_outputs,
-    }.get(t)
 
 
 class V3dTshiftOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_tshift(...)`.
+    Output object returned when calling `V3dTshiftParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +73,7 @@ def v_3d_tshift_params(
     tr: float | None = None,
     tslice: int | None = None,
     tzero: float | None = None,
-) -> V3dTshiftParameters:
+) -> V3dTshiftParametersTagged:
     """
     Build parameters.
     
@@ -122,7 +106,7 @@ def v_3d_tshift_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dTshift",
+        "@type": "afni/3dTshift",
         "in_file": in_file,
         "rlt": rlt,
         "rltplus": rltplus,
@@ -165,51 +149,51 @@ def v_3d_tshift_cargs(
     """
     cargs = []
     cargs.append("3dTshift")
-    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("ignore") is not None:
+    if params.get("ignore", None) is not None:
         cargs.extend([
             "-ignore",
-            str(params.get("ignore"))
+            str(params.get("ignore", None))
         ])
-    cargs.append(execution.input_file(params.get("in_file")))
-    if params.get("interp") is not None:
+    cargs.append(execution.input_file(params.get("in_file", None)))
+    if params.get("interp", None) is not None:
         cargs.extend([
             "-",
-            params.get("interp")
+            params.get("interp", None)
         ])
-    if params.get("num_threads") is not None:
-        cargs.append(str(params.get("num_threads")))
-    if params.get("outputtype") is not None:
-        cargs.append(params.get("outputtype"))
-    if params.get("rlt"):
+    if params.get("num_threads", None) is not None:
+        cargs.append(str(params.get("num_threads", None)))
+    if params.get("outputtype", None) is not None:
+        cargs.append(params.get("outputtype", None))
+    if params.get("rlt", False):
         cargs.append("-rlt")
-    if params.get("rltplus"):
+    if params.get("rltplus", False):
         cargs.append("-rlt+")
-    if params.get("slice_encoding_direction") is not None:
-        cargs.append(params.get("slice_encoding_direction"))
-    if params.get("tpattern") is not None:
+    if params.get("slice_encoding_direction", None) is not None:
+        cargs.append(params.get("slice_encoding_direction", None))
+    if params.get("tpattern", None) is not None:
         cargs.extend([
             "-tpattern",
-            params.get("tpattern")
+            params.get("tpattern", None)
         ])
-    if params.get("tr") is not None:
+    if params.get("tr", None) is not None:
         cargs.extend([
             "-TR",
-            str(params.get("tr"))
+            str(params.get("tr", None))
         ])
-    if params.get("tslice") is not None:
+    if params.get("tslice", None) is not None:
         cargs.extend([
             "-slice",
-            str(params.get("tslice"))
+            str(params.get("tslice", None))
         ])
-    if params.get("tzero") is not None:
+    if params.get("tzero", None) is not None:
         cargs.extend([
             "-tzero",
-            str(params.get("tzero"))
+            str(params.get("tzero", None))
         ])
     return cargs
 
@@ -229,7 +213,7 @@ def v_3d_tshift_outputs(
     """
     ret = V3dTshiftOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        out_file=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
         timing_file=execution.output_file("timing_file"),
     )
     return ret
@@ -237,11 +221,13 @@ def v_3d_tshift_outputs(
 
 def v_3d_tshift_execute(
     params: V3dTshiftParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dTshiftOutputs:
     """
-    Shifts voxel time series from input so that separate slices are aligned to the
-    same temporal origin.
+    3dTshift
+    
+    Shifts voxel time series from input so that separate slices are aligned to
+    the same temporal origin.
     
     Author: AFNI Developers
     
@@ -249,10 +235,12 @@ def v_3d_tshift_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dTshiftOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TSHIFT_METADATA)
     params = execution.params(params)
     cargs = v_3d_tshift_cargs(params, execution)
     ret = v_3d_tshift_outputs(params, execution)
@@ -277,8 +265,10 @@ def v_3d_tshift(
     runner: Runner | None = None,
 ) -> V3dTshiftOutputs:
     """
-    Shifts voxel time series from input so that separate slices are aligned to the
-    same temporal origin.
+    3dTshift
+    
+    Shifts voxel time series from input so that separate slices are aligned to
+    the same temporal origin.
     
     Author: AFNI Developers
     
@@ -313,8 +303,6 @@ def v_3d_tshift(
     Returns:
         NamedTuple of outputs (described in `V3dTshiftOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_TSHIFT_METADATA)
     params = v_3d_tshift_params(
         prefix=prefix,
         ignore=ignore,
@@ -330,13 +318,13 @@ def v_3d_tshift(
         tslice=tslice,
         tzero=tzero,
     )
-    return v_3d_tshift_execute(params, execution)
+    return v_3d_tshift_execute(params, runner)
 
 
 __all__ = [
     "V3dTshiftOutputs",
-    "V3dTshiftParameters",
     "V_3D_TSHIFT_METADATA",
     "v_3d_tshift",
+    "v_3d_tshift_execute",
     "v_3d_tshift_params",
 ]