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

niwrap_afni/afni/v_3d_dwito_dt.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DWITO_DT_METADATA = Metadata(
-    id="9a917bfe0fc87dc6e13908baec1679a6c7340c54.boutiques",
+    id="51a7f77a7416de75f60a0bd1b73f425b06e42563.boutiques",
     name="3dDWItoDT",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,36 @@ V_3D_DWITO_DT_METADATA = Metadata(
 
 
 V3dDwitoDtParameters = typing.TypedDict('V3dDwitoDtParameters', {
-    "__STYXTYPE__": typing.Literal["3dDWItoDT"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDWItoDT"]],
+    "gradient_file": InputPathType,
+    "dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "automask": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "bmatrix_NZ": typing.NotRequired[InputPathType | None],
+    "bmatrix_Z": typing.NotRequired[InputPathType | None],
+    "bmatrix_FULL": typing.NotRequired[InputPathType | None],
+    "scale_out_1000": bool,
+    "bmax_ref": typing.NotRequired[float | None],
+    "nonlinear": bool,
+    "linear": bool,
+    "reweight": bool,
+    "max_iter": typing.NotRequired[int | None],
+    "max_iter_rw": typing.NotRequired[int | None],
+    "eigs": bool,
+    "debug_briks": bool,
+    "cumulative_wts": bool,
+    "verbose": typing.NotRequired[int | None],
+    "drive_afni": typing.NotRequired[int | None],
+    "sep_dsets": bool,
+    "csf_val": typing.NotRequired[float | None],
+    "min_bad_md": typing.NotRequired[int | None],
+    "csf_fa": typing.NotRequired[float | None],
+    "opt": typing.NotRequired[str | None],
+    "mean_b0": bool,
+})
+V3dDwitoDtParametersTagged = typing.TypedDict('V3dDwitoDtParametersTagged', {
+    "@type": typing.Literal["afni/3dDWItoDT"],
     "gradient_file": InputPathType,
     "dataset": InputPathType,
     "prefix": typing.NotRequired[str | None],
@@ -42,48 +71,14 @@ V3dDwitoDtParameters = typing.TypedDict('V3dDwitoDtParameters', {
     "opt": typing.NotRequired[str | None],
     "mean_b0": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dDWItoDT": v_3d_dwito_dt_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 {
-        "3dDWItoDT": v_3d_dwito_dt_outputs,
-    }.get(t)
 
 
 class V3dDwitoDtOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_dwito_dt(...)`.
+    Output object returned when calling `V3dDwitoDtParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_dataset: OutputPathType
-    """Output dataset"""
 
 
 def v_3d_dwito_dt_params(
@@ -113,7 +108,7 @@ def v_3d_dwito_dt_params(
     csf_fa: float | None = None,
     opt: str | None = None,
     mean_b0: bool = False,
-) -> V3dDwitoDtParameters:
+) -> V3dDwitoDtParametersTagged:
     """
     Build parameters.
     
@@ -163,7 +158,7 @@ def v_3d_dwito_dt_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDWItoDT",
+        "@type": "afni/3dDWItoDT",
         "gradient_file": gradient_file,
         "dataset": dataset,
         "automask": automask,
@@ -223,97 +218,97 @@ def v_3d_dwito_dt_cargs(
     """
     cargs = []
     cargs.append("3dDWItoDT")
-    cargs.append(execution.input_file(params.get("gradient_file")))
-    cargs.append(execution.input_file(params.get("dataset")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("gradient_file", None)))
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    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("bmatrix_NZ") is not None:
+    if params.get("bmatrix_NZ", None) is not None:
         cargs.extend([
             "-bmatrix_NZ",
-            execution.input_file(params.get("bmatrix_NZ"))
+            execution.input_file(params.get("bmatrix_NZ", None))
         ])
-    if params.get("bmatrix_Z") is not None:
+    if params.get("bmatrix_Z", None) is not None:
         cargs.extend([
             "-bmatrix_Z",
-            execution.input_file(params.get("bmatrix_Z"))
+            execution.input_file(params.get("bmatrix_Z", None))
         ])
-    if params.get("bmatrix_FULL") is not None:
+    if params.get("bmatrix_FULL", None) is not None:
         cargs.extend([
             "-bmatrix_FULL",
-            execution.input_file(params.get("bmatrix_FULL"))
+            execution.input_file(params.get("bmatrix_FULL", None))
         ])
-    if params.get("scale_out_1000"):
+    if params.get("scale_out_1000", False):
         cargs.append("-scale_out_1000")
-    if params.get("bmax_ref") is not None:
+    if params.get("bmax_ref", None) is not None:
         cargs.extend([
             "-bmax_ref",
-            str(params.get("bmax_ref"))
+            str(params.get("bmax_ref", None))
         ])
-    if params.get("nonlinear"):
+    if params.get("nonlinear", False):
         cargs.append("-nonlinear")
-    if params.get("linear"):
+    if params.get("linear", False):
         cargs.append("-linear")
-    if params.get("reweight"):
+    if params.get("reweight", False):
         cargs.append("-reweight")
-    if params.get("max_iter") is not None:
+    if params.get("max_iter", None) is not None:
         cargs.extend([
             "-max_iter",
-            str(params.get("max_iter"))
+            str(params.get("max_iter", None))
         ])
-    if params.get("max_iter_rw") is not None:
+    if params.get("max_iter_rw", None) is not None:
         cargs.extend([
             "-max_iter_rw",
-            str(params.get("max_iter_rw"))
+            str(params.get("max_iter_rw", None))
         ])
-    if params.get("eigs"):
+    if params.get("eigs", False):
         cargs.append("-eigs")
-    if params.get("debug_briks"):
+    if params.get("debug_briks", False):
         cargs.append("-debug_briks")
-    if params.get("cumulative_wts"):
+    if params.get("cumulative_wts", False):
         cargs.append("-cumulative_wts")
-    if params.get("verbose") is not None:
+    if params.get("verbose", None) is not None:
         cargs.extend([
             "-verbose",
-            str(params.get("verbose"))
+            str(params.get("verbose", None))
         ])
-    if params.get("drive_afni") is not None:
+    if params.get("drive_afni", None) is not None:
         cargs.extend([
             "-drive_afni",
-            str(params.get("drive_afni"))
+            str(params.get("drive_afni", None))
         ])
-    if params.get("sep_dsets"):
+    if params.get("sep_dsets", False):
         cargs.append("-sep_dsets")
-    if params.get("csf_val") is not None:
+    if params.get("csf_val", None) is not None:
         cargs.extend([
             "-csf_val",
-            str(params.get("csf_val"))
+            str(params.get("csf_val", None))
         ])
-    if params.get("min_bad_md") is not None:
+    if params.get("min_bad_md", None) is not None:
         cargs.extend([
             "-min_bad_md",
-            str(params.get("min_bad_md"))
+            str(params.get("min_bad_md", None))
         ])
-    if params.get("csf_fa") is not None:
+    if params.get("csf_fa", None) is not None:
         cargs.extend([
             "-csf_fa",
-            str(params.get("csf_fa"))
+            str(params.get("csf_fa", None))
         ])
-    if params.get("opt") is not None:
+    if params.get("opt", None) is not None:
         cargs.extend([
             "-opt",
-            params.get("opt")
+            params.get("opt", None)
         ])
-    if params.get("mean_b0"):
+    if params.get("mean_b0", False):
         cargs.append("-mean_b0")
     return cargs
 
@@ -333,16 +328,17 @@ def v_3d_dwito_dt_outputs(
     """
     ret = V3dDwitoDtOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file("<PREFIX>.*"),
     )
     return ret
 
 
 def v_3d_dwito_dt_execute(
     params: V3dDwitoDtParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDwitoDtOutputs:
     """
+    3dDWItoDT
+    
     Computes 6 principal direction tensors from multiple gradient vectors and
     corresponding DTI image volumes.
     
@@ -352,10 +348,12 @@ def v_3d_dwito_dt_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDwitoDtOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DWITO_DT_METADATA)
     params = execution.params(params)
     cargs = v_3d_dwito_dt_cargs(params, execution)
     ret = v_3d_dwito_dt_outputs(params, execution)
@@ -393,6 +391,8 @@ def v_3d_dwito_dt(
     runner: Runner | None = None,
 ) -> V3dDwitoDtOutputs:
     """
+    3dDWItoDT
+    
     Computes 6 principal direction tensors from multiple gradient vectors and
     corresponding DTI image volumes.
     
@@ -446,8 +446,6 @@ def v_3d_dwito_dt(
     Returns:
         NamedTuple of outputs (described in `V3dDwitoDtOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DWITO_DT_METADATA)
     params = v_3d_dwito_dt_params(
         gradient_file=gradient_file,
         dataset=dataset,
@@ -476,13 +474,13 @@ def v_3d_dwito_dt(
         opt=opt,
         mean_b0=mean_b0,
     )
-    return v_3d_dwito_dt_execute(params, execution)
+    return v_3d_dwito_dt_execute(params, runner)
 
 
 __all__ = [
     "V3dDwitoDtOutputs",
-    "V3dDwitoDtParameters",
     "V_3D_DWITO_DT_METADATA",
     "v_3d_dwito_dt",
+    "v_3d_dwito_dt_execute",
     "v_3d_dwito_dt_params",
 ]

niwrap_afni/afni/v_3d_dwuncert.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_DWUNCERT_METADATA = Metadata(
-    id="36a7630a6addf3cde3da6dc8c065b0d3b2cad85a.boutiques",
+    id="cbde019605b90635102379e325a6defdacd645f6.boutiques",
     name="3dDWUncert",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_DWUNCERT_METADATA = Metadata(
 
 
 V3dDwuncertParameters = typing.TypedDict('V3dDwuncertParameters', {
-    "__STYXTYPE__": typing.Literal["3dDWUncert"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dDWUncert"]],
+    "input_file": InputPathType,
+    "input_prefix": str,
+    "output_prefix": str,
+    "grad_file": typing.NotRequired[InputPathType | None],
+    "bmatrix_file": typing.NotRequired[InputPathType | None],
+    "num_iters": typing.NotRequired[float | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "calc_thr_fa": typing.NotRequired[float | None],
+    "csf_fa": typing.NotRequired[float | None],
+})
+V3dDwuncertParametersTagged = typing.TypedDict('V3dDwuncertParametersTagged', {
+    "@type": typing.Literal["afni/3dDWUncert"],
     "input_file": InputPathType,
     "input_prefix": str,
     "output_prefix": str,
@@ -25,43 +37,11 @@ V3dDwuncertParameters = typing.TypedDict('V3dDwuncertParameters', {
     "calc_thr_fa": typing.NotRequired[float | None],
     "csf_fa": 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 {
-        "3dDWUncert": v_3d_dwuncert_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 {
-        "3dDWUncert": v_3d_dwuncert_outputs,
-    }.get(t)
 
 
 class V3dDwuncertOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_dwuncert(...)`.
+    Output object returned when calling `V3dDwuncertParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def v_3d_dwuncert_params(
     mask_file: InputPathType | None = None,
     calc_thr_fa: float | None = None,
     csf_fa: float | None = None,
-) -> V3dDwuncertParameters:
+) -> V3dDwuncertParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +78,7 @@ def v_3d_dwuncert_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dDWUncert",
+        "@type": "afni/3dDWUncert",
         "input_file": input_file,
         "input_prefix": input_prefix,
         "output_prefix": output_prefix,
@@ -135,45 +115,45 @@ def v_3d_dwuncert_cargs(
     cargs.append("3dDWUncert")
     cargs.extend([
         "-inset",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-input",
-        params.get("input_prefix")
+        params.get("input_prefix", None)
     ])
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
-    if params.get("grad_file") is not None:
+    if params.get("grad_file", None) is not None:
         cargs.extend([
             "-grads",
-            execution.input_file(params.get("grad_file"))
+            execution.input_file(params.get("grad_file", None))
         ])
-    if params.get("bmatrix_file") is not None:
+    if params.get("bmatrix_file", None) is not None:
         cargs.extend([
             "-bmatrix_FULL",
-            execution.input_file(params.get("bmatrix_file"))
+            execution.input_file(params.get("bmatrix_file", None))
         ])
-    if params.get("num_iters") is not None:
+    if params.get("num_iters", None) is not None:
         cargs.extend([
             "-iters",
-            str(params.get("num_iters"))
+            str(params.get("num_iters", None))
         ])
-    if params.get("mask_file") is not None:
+    if params.get("mask_file", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_file"))
+            execution.input_file(params.get("mask_file", None))
         ])
-    if params.get("calc_thr_fa") is not None:
+    if params.get("calc_thr_fa", None) is not None:
         cargs.extend([
             "-calc_thr_FA",
-            str(params.get("calc_thr_fa"))
+            str(params.get("calc_thr_fa", None))
         ])
-    if params.get("csf_fa") is not None:
+    if params.get("csf_fa", None) is not None:
         cargs.extend([
             "-csf_fa",
-            str(params.get("csf_fa"))
+            str(params.get("csf_fa", None))
         ])
     return cargs
 
@@ -193,16 +173,18 @@ def v_3d_dwuncert_outputs(
     """
     ret = V3dDwuncertOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_prefix") + "+*.HEAD/" + params.get("output_prefix") + "+*.BRIK"),
+        output_file=execution.output_file(params.get("output_prefix", None) + "+.HEAD/" + params.get("output_prefix", None) + "+.BRIK"),
     )
     return ret
 
 
 def v_3d_dwuncert_execute(
     params: V3dDwuncertParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dDwuncertOutputs:
     """
+    3dDWUncert
+    
     Use jackknifing to estimate uncertainty of DTI parameters, important for
     probabilistic tractography.
     
@@ -212,10 +194,12 @@ def v_3d_dwuncert_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dDwuncertOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DWUNCERT_METADATA)
     params = execution.params(params)
     cargs = v_3d_dwuncert_cargs(params, execution)
     ret = v_3d_dwuncert_outputs(params, execution)
@@ -236,6 +220,8 @@ def v_3d_dwuncert(
     runner: Runner | None = None,
 ) -> V3dDwuncertOutputs:
     """
+    3dDWUncert
+    
     Use jackknifing to estimate uncertainty of DTI parameters, important for
     probabilistic tractography.
     
@@ -258,8 +244,6 @@ def v_3d_dwuncert(
     Returns:
         NamedTuple of outputs (described in `V3dDwuncertOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_DWUNCERT_METADATA)
     params = v_3d_dwuncert_params(
         input_file=input_file,
         input_prefix=input_prefix,
@@ -271,13 +255,13 @@ def v_3d_dwuncert(
         calc_thr_fa=calc_thr_fa,
         csf_fa=csf_fa,
     )
-    return v_3d_dwuncert_execute(params, execution)
+    return v_3d_dwuncert_execute(params, runner)
 
 
 __all__ = [
     "V3dDwuncertOutputs",
-    "V3dDwuncertParameters",
     "V_3D_DWUNCERT_METADATA",
     "v_3d_dwuncert",
+    "v_3d_dwuncert_execute",
     "v_3d_dwuncert_params",
 ]