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

niwrap_afni/afni/v_3d_mepfm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MEPFM_METADATA = Metadata(
-    id="d38c4d0eb3693584d4549cd2a7bc0b493dbd1836.boutiques",
+    id="47039e7d1a0984627d35edea09227fa136adbbff.boutiques",
     name="3dMEPFM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V_3D_MEPFM_METADATA = Metadata(
 
 
 V3dMepfmParameters = typing.TypedDict('V3dMepfmParameters', {
-    "__STYXTYPE__": typing.Literal["3dMEPFM"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMEPFM"]],
+    "input_files": list[str],
+    "dbgArgs": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "hrf_model": typing.NotRequired[str | None],
+    "verbosity": typing.NotRequired[int | None],
+})
+V3dMepfmParametersTagged = typing.TypedDict('V3dMepfmParametersTagged', {
+    "@type": typing.Literal["afni/3dMEPFM"],
     "input_files": list[str],
     "dbgArgs": bool,
     "mask": typing.NotRequired[InputPathType | None],
     "hrf_model": typing.NotRequired[str | None],
     "verbosity": typing.NotRequired[int | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dMEPFM": v_3d_mepfm_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 {
-        "3dMEPFM": v_3d_mepfm_outputs,
-    }.get(t)
 
 
 class V3dMepfmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_mepfm(...)`.
+    Output object returned when calling `V3dMepfmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +60,7 @@ def v_3d_mepfm_params(
     mask: InputPathType | None = None,
     hrf_model: str | None = None,
     verbosity: int | None = None,
-) -> V3dMepfmParameters:
+) -> V3dMepfmParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +77,7 @@ def v_3d_mepfm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMEPFM",
+        "@type": "afni/3dMEPFM",
         "input_files": input_files,
         "dbgArgs": dbg_args,
     }
@@ -131,24 +107,24 @@ def v_3d_mepfm_cargs(
     cargs.append("3dMEPFM")
     cargs.extend([
         "-input",
-        *params.get("input_files")
+        *params.get("input_files", None)
     ])
-    if params.get("dbgArgs"):
+    if params.get("dbgArgs", False):
         cargs.append("-dbgArgs")
-    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("hrf_model") is not None:
+    if params.get("hrf_model", None) is not None:
         cargs.extend([
             "-hrf",
-            params.get("hrf_model")
+            params.get("hrf_model", None)
         ])
-    if params.get("verbosity") is not None:
+    if params.get("verbosity", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity"))
+            str(params.get("verbosity", None))
         ])
     return cargs
 
@@ -168,24 +144,26 @@ def v_3d_mepfm_outputs(
     """
     ret = V3dMepfmOutputs(
         root=execution.output_file("."),
-        dr2_output=execution.output_file("DR2_[PREFIX]_*.nii.gz"),
-        dr2fit_output=execution.output_file("DR2fit_[PREFIX]_*.nii.gz"),
-        ds0_output=execution.output_file("DS0_[PREFIX]_*.nii.gz"),
-        lambda_output=execution.output_file("lambda_[PREFIX]_*.nii.gz"),
-        sigmas_mad_output=execution.output_file("sigmas_MAD_[PREFIX]_*.nii.gz"),
-        costs_output=execution.output_file("costs_[PREFIX]_*.nii.gz"),
+        dr2_output=execution.output_file("DR2_[PREFIX].nii.gz"),
+        dr2fit_output=execution.output_file("DR2fit_[PREFIX].nii.gz"),
+        ds0_output=execution.output_file("DS0_[PREFIX].nii.gz"),
+        lambda_output=execution.output_file("lambda_[PREFIX].nii.gz"),
+        sigmas_mad_output=execution.output_file("sigmas_MAD_[PREFIX].nii.gz"),
+        costs_output=execution.output_file("costs_[PREFIX].nii.gz"),
     )
     return ret
 
 
 def v_3d_mepfm_execute(
     params: V3dMepfmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMepfmOutputs:
     """
-    Voxelwise deconvolution of Multiecho fMRI data to yield time-varying estimates
-    of changes in transverse relaxation (DR2*) and optionally, net magnetization
-    (DS0).
+    3dMEPFM
+    
+    Voxelwise deconvolution of Multiecho fMRI data to yield time-varying
+    estimates of changes in transverse relaxation (DR2*) and optionally, net
+    magnetization (DS0).
     
     Author: AFNI Developers
     
@@ -193,10 +171,12 @@ def v_3d_mepfm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMepfmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MEPFM_METADATA)
     params = execution.params(params)
     cargs = v_3d_mepfm_cargs(params, execution)
     ret = v_3d_mepfm_outputs(params, execution)
@@ -213,9 +193,11 @@ def v_3d_mepfm(
     runner: Runner | None = None,
 ) -> V3dMepfmOutputs:
     """
-    Voxelwise deconvolution of Multiecho fMRI data to yield time-varying estimates
-    of changes in transverse relaxation (DR2*) and optionally, net magnetization
-    (DS0).
+    3dMEPFM
+    
+    Voxelwise deconvolution of Multiecho fMRI data to yield time-varying
+    estimates of changes in transverse relaxation (DR2*) and optionally, net
+    magnetization (DS0).
     
     Author: AFNI Developers
     
@@ -234,8 +216,6 @@ def v_3d_mepfm(
     Returns:
         NamedTuple of outputs (described in `V3dMepfmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_MEPFM_METADATA)
     params = v_3d_mepfm_params(
         input_files=input_files,
         dbg_args=dbg_args,
@@ -243,13 +223,13 @@ def v_3d_mepfm(
         hrf_model=hrf_model,
         verbosity=verbosity,
     )
-    return v_3d_mepfm_execute(params, execution)
+    return v_3d_mepfm_execute(params, runner)
 
 
 __all__ = [
     "V3dMepfmOutputs",
-    "V3dMepfmParameters",
     "V_3D_MEPFM_METADATA",
     "v_3d_mepfm",
+    "v_3d_mepfm_execute",
     "v_3d_mepfm_params",
 ]

niwrap_afni/afni/v_3d_mse.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MSE_METADATA = Metadata(
-    id="f6ca026af1cb73e73646daceebece681cda8d8dc.boutiques",
+    id="e37acc9dc60aae7b5c9f472849f90ad2dcc4f64a.boutiques",
     name="3dMSE",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_MSE_METADATA = Metadata(
 
 
 V3dMseParameters = typing.TypedDict('V3dMseParameters', {
-    "__STYXTYPE__": typing.Literal["3dMSE"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMSE"]],
+    "polynomial_order": typing.NotRequired[int | None],
+    "autoclip": bool,
+    "automask": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "scales": typing.NotRequired[float | None],
+    "entwin": typing.NotRequired[float | None],
+    "rthresh": typing.NotRequired[float | None],
+    "dset": InputPathType,
+})
+V3dMseParametersTagged = typing.TypedDict('V3dMseParametersTagged', {
+    "@type": typing.Literal["afni/3dMSE"],
     "polynomial_order": typing.NotRequired[int | None],
     "autoclip": bool,
     "automask": bool,
@@ -25,43 +37,11 @@ V3dMseParameters = typing.TypedDict('V3dMseParameters', {
     "rthresh": typing.NotRequired[float | None],
     "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 {
-        "3dMSE": v_3d_mse_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 {
-        "3dMSE": v_3d_mse_outputs,
-    }.get(t)
 
 
 class V3dMseOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_mse(...)`.
+    Output object returned when calling `V3dMseParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def v_3d_mse_params(
     scales: float | None = None,
     entwin: float | None = None,
     rthresh: float | None = None,
-) -> V3dMseParameters:
+) -> V3dMseParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +83,7 @@ def v_3d_mse_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMSE",
+        "@type": "afni/3dMSE",
         "autoclip": autoclip,
         "automask": automask,
         "dset": dset,
@@ -138,41 +118,41 @@ def v_3d_mse_cargs(
     """
     cargs = []
     cargs.append("3dMSE")
-    if params.get("polynomial_order") is not None:
+    if params.get("polynomial_order", None) is not None:
         cargs.extend([
             "-polort",
-            str(params.get("polynomial_order"))
+            str(params.get("polynomial_order", 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("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("scales") is not None:
+    if params.get("scales", None) is not None:
         cargs.extend([
             "-scales",
-            str(params.get("scales"))
+            str(params.get("scales", None))
         ])
-    if params.get("entwin") is not None:
+    if params.get("entwin", None) is not None:
         cargs.extend([
             "-entwin",
-            str(params.get("entwin"))
+            str(params.get("entwin", None))
         ])
-    if params.get("rthresh") is not None:
+    if params.get("rthresh", None) is not None:
         cargs.extend([
             "-rthresh",
-            str(params.get("rthresh"))
+            str(params.get("rthresh", None))
         ])
-    cargs.append(execution.input_file(params.get("dset")))
+    cargs.append(execution.input_file(params.get("dset", None)))
     return cargs
 
 
@@ -191,17 +171,19 @@ def v_3d_mse_outputs(
     """
     ret = V3dMseOutputs(
         root=execution.output_file("."),
-        out_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
-        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        out_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        out_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_mse_execute(
     params: V3dMseParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMseOutputs:
     """
+    3dMSE
+    
     Computes voxelwise multi-scale entropy.
     
     Author: AFNI Developers
@@ -210,10 +192,12 @@ def v_3d_mse_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMseOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MSE_METADATA)
     params = execution.params(params)
     cargs = v_3d_mse_cargs(params, execution)
     ret = v_3d_mse_outputs(params, execution)
@@ -234,6 +218,8 @@ def v_3d_mse(
     runner: Runner | None = None,
 ) -> V3dMseOutputs:
     """
+    3dMSE
+    
     Computes voxelwise multi-scale entropy.
     
     Author: AFNI Developers
@@ -258,8 +244,6 @@ def v_3d_mse(
     Returns:
         NamedTuple of outputs (described in `V3dMseOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_MSE_METADATA)
     params = v_3d_mse_params(
         polynomial_order=polynomial_order,
         autoclip=autoclip,
@@ -271,13 +255,13 @@ def v_3d_mse(
         rthresh=rthresh,
         dset=dset,
     )
-    return v_3d_mse_execute(params, execution)
+    return v_3d_mse_execute(params, runner)
 
 
 __all__ = [
     "V3dMseOutputs",
-    "V3dMseParameters",
     "V_3D_MSE_METADATA",
     "v_3d_mse",
+    "v_3d_mse_execute",
     "v_3d_mse_params",
 ]