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

niwrap_afni/afni/v__align_centers.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__ALIGN_CENTERS_METADATA = Metadata(
-    id="33d48e001912a44e2935434b56014a343a7f22f0.boutiques",
+    id="1b932a373180cc531e4256c1ee969f9ced257aa4.boutiques",
     name="@Align_Centers",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V__ALIGN_CENTERS_METADATA = Metadata(
 
 
 VAlignCentersParameters = typing.TypedDict('VAlignCentersParameters', {
-    "__STYXTYPE__": typing.Literal["@Align_Centers"],
+    "@type": typing.NotRequired[typing.Literal["afni/@Align_Centers"]],
+    "base": InputPathType,
+    "dset": InputPathType,
+    "children": typing.NotRequired[list[InputPathType] | None],
+    "echo": bool,
+    "overwrite": bool,
+    "prefix": typing.NotRequired[str | None],
+    "matrix_only": bool,
+    "matrix_only_no_dset": bool,
+    "no_cp": bool,
+    "center_grid": bool,
+    "center_cm": bool,
+    "center_cm_no_amask": bool,
+    "shift_xform": typing.NotRequired[InputPathType | None],
+    "shift_xform_inv": typing.NotRequired[InputPathType | None],
+})
+VAlignCentersParametersTagged = typing.TypedDict('VAlignCentersParametersTagged', {
+    "@type": typing.Literal["afni/@Align_Centers"],
     "base": InputPathType,
     "dset": InputPathType,
     "children": typing.NotRequired[list[InputPathType] | None],
@@ -30,43 +47,11 @@ VAlignCentersParameters = typing.TypedDict('VAlignCentersParameters', {
     "shift_xform": typing.NotRequired[InputPathType | None],
     "shift_xform_inv": 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 {
-        "@Align_Centers": v__align_centers_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 {
-        "@Align_Centers": v__align_centers_outputs,
-    }.get(t)
 
 
 class VAlignCentersOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__align_centers(...)`.
+    Output object returned when calling `VAlignCentersParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +78,7 @@ def v__align_centers_params(
     center_cm_no_amask: bool = False,
     shift_xform: InputPathType | None = None,
     shift_xform_inv: InputPathType | None = None,
-) -> VAlignCentersParameters:
+) -> VAlignCentersParametersTagged:
     """
     Build parameters.
     
@@ -120,7 +105,7 @@ def v__align_centers_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@Align_Centers",
+        "@type": "afni/@Align_Centers",
         "base": base,
         "dset": dset,
         "echo": echo,
@@ -158,43 +143,43 @@ def v__align_centers_cargs(
     """
     cargs = []
     cargs.append("@Align_Centers")
-    cargs.append(execution.input_file(params.get("base")))
-    cargs.append(execution.input_file(params.get("dset")))
-    if params.get("children") is not None:
+    cargs.append(execution.input_file(params.get("base", None)))
+    cargs.append(execution.input_file(params.get("dset", None)))
+    if params.get("children", None) is not None:
         cargs.extend([
             "-child",
-            *[execution.input_file(f) for f in params.get("children")]
+            *[execution.input_file(f) for f in params.get("children", None)]
         ])
-    if params.get("echo"):
+    if params.get("echo", False):
         cargs.append("-echo")
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
-    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("matrix_only"):
+    if params.get("matrix_only", False):
         cargs.append("-1Dmat_only")
-    if params.get("matrix_only_no_dset"):
+    if params.get("matrix_only_no_dset", False):
         cargs.append("-1Dmat_only_nodset")
-    if params.get("no_cp"):
+    if params.get("no_cp", False):
         cargs.append("-no_cp")
-    if params.get("center_grid"):
+    if params.get("center_grid", False):
         cargs.append("-grid")
-    if params.get("center_cm"):
+    if params.get("center_cm", False):
         cargs.append("-cm")
-    if params.get("center_cm_no_amask"):
+    if params.get("center_cm_no_amask", False):
         cargs.append("-cm_no_amask")
-    if params.get("shift_xform") is not None:
+    if params.get("shift_xform", None) is not None:
         cargs.extend([
             "-shift_xform",
-            execution.input_file(params.get("shift_xform"))
+            execution.input_file(params.get("shift_xform", None))
         ])
-    if params.get("shift_xform_inv") is not None:
+    if params.get("shift_xform_inv", None) is not None:
         cargs.extend([
             "-shift_xform_inv",
-            execution.input_file(params.get("shift_xform_inv"))
+            execution.input_file(params.get("shift_xform_inv", None))
         ])
     return cargs
 
@@ -214,20 +199,22 @@ def v__align_centers_outputs(
     """
     ret = VAlignCentersOutputs(
         root=execution.output_file("."),
-        transform_matrix=execution.output_file(pathlib.Path(params.get("dset")).name + "_shft.1D"),
-        shifted_dset=execution.output_file(params.get("prefix") + "_shft+orig.BRIK") if (params.get("prefix") is not None) else None,
-        shifted_child_dsets=execution.output_file(params.get("prefix") + "_child_shft+orig.BRIK") if (params.get("prefix") is not None) else None,
+        transform_matrix=execution.output_file(pathlib.Path(params.get("dset", None)).name + "_shft.1D"),
+        shifted_dset=execution.output_file(params.get("prefix", None) + "_shft+orig.BRIK") if (params.get("prefix") is not None) else None,
+        shifted_child_dsets=execution.output_file(params.get("prefix", None) + "_child_shft+orig.BRIK") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v__align_centers_execute(
     params: VAlignCentersParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAlignCentersOutputs:
     """
-    Moves the center of a dataset (DSET) to the center of a base volume (BASE) and
-    optionally creates a transform matrix.
+    @Align_Centers
+    
+    Moves the center of a dataset (DSET) to the center of a base volume (BASE)
+    and optionally creates a transform matrix.
     
     Author: AFNI Developers
     
@@ -235,10 +222,12 @@ def v__align_centers_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAlignCentersOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ALIGN_CENTERS_METADATA)
     params = execution.params(params)
     cargs = v__align_centers_cargs(params, execution)
     ret = v__align_centers_outputs(params, execution)
@@ -264,8 +253,10 @@ def v__align_centers(
     runner: Runner | None = None,
 ) -> VAlignCentersOutputs:
     """
-    Moves the center of a dataset (DSET) to the center of a base volume (BASE) and
-    optionally creates a transform matrix.
+    @Align_Centers
+    
+    Moves the center of a dataset (DSET) to the center of a base volume (BASE)
+    and optionally creates a transform matrix.
     
     Author: AFNI Developers
     
@@ -294,8 +285,6 @@ def v__align_centers(
     Returns:
         NamedTuple of outputs (described in `VAlignCentersOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__ALIGN_CENTERS_METADATA)
     params = v__align_centers_params(
         base=base,
         dset=dset,
@@ -312,13 +301,13 @@ def v__align_centers(
         shift_xform=shift_xform,
         shift_xform_inv=shift_xform_inv,
     )
-    return v__align_centers_execute(params, execution)
+    return v__align_centers_execute(params, runner)
 
 
 __all__ = [
     "VAlignCentersOutputs",
-    "VAlignCentersParameters",
     "V__ALIGN_CENTERS_METADATA",
     "v__align_centers",
+    "v__align_centers_execute",
     "v__align_centers_params",
 ]

niwrap_afni/afni/v__align_partial_oblique.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__ALIGN_PARTIAL_OBLIQUE_METADATA = Metadata(
-    id="d0ac6388c730c43ce7683b59b4069417404eff3d.boutiques",
+    id="848c2d43f23ed079e10b11fc04e86a8910515626.boutiques",
     name="@align_partial_oblique",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V__ALIGN_PARTIAL_OBLIQUE_METADATA = Metadata(
 
 
 VAlignPartialObliqueParameters = typing.TypedDict('VAlignPartialObliqueParameters', {
-    "__STYXTYPE__": typing.Literal["@align_partial_oblique"],
+    "@type": typing.NotRequired[typing.Literal["afni/@align_partial_oblique"]],
+    "base": InputPathType,
+    "input": InputPathType,
+    "suffix": typing.NotRequired[str | None],
+    "keep_tmp": bool,
+    "clean": bool,
+    "dxyz": typing.NotRequired[float | None],
+    "dx": typing.NotRequired[float | None],
+    "dy": typing.NotRequired[float | None],
+    "dz": typing.NotRequired[float | None],
+})
+VAlignPartialObliqueParametersTagged = typing.TypedDict('VAlignPartialObliqueParametersTagged', {
+    "@type": typing.Literal["afni/@align_partial_oblique"],
     "base": InputPathType,
     "input": InputPathType,
     "suffix": typing.NotRequired[str | None],
@@ -25,43 +37,11 @@ VAlignPartialObliqueParameters = typing.TypedDict('VAlignPartialObliqueParameter
     "dy": typing.NotRequired[float | None],
     "dz": 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 {
-        "@align_partial_oblique": v__align_partial_oblique_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 {
-        "@align_partial_oblique": v__align_partial_oblique_outputs,
-    }.get(t)
 
 
 class VAlignPartialObliqueOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__align_partial_oblique(...)`.
+    Output object returned when calling `VAlignPartialObliqueParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def v__align_partial_oblique_params(
     dx: float | None = None,
     dy: float | None = None,
     dz: float | None = None,
-) -> VAlignPartialObliqueParameters:
+) -> VAlignPartialObliqueParametersTagged:
     """
     Build parameters.
     
@@ -101,7 +81,7 @@ def v__align_partial_oblique_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@align_partial_oblique",
+        "@type": "afni/@align_partial_oblique",
         "base": base,
         "input": input_,
         "keep_tmp": keep_tmp,
@@ -137,40 +117,40 @@ def v__align_partial_oblique_cargs(
     cargs.append("@align_partial_oblique")
     cargs.extend([
         "-base",
-        execution.input_file(params.get("base"))
+        execution.input_file(params.get("base", None))
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input"))
+        execution.input_file(params.get("input", None))
     ])
-    if params.get("suffix") is not None:
+    if params.get("suffix", None) is not None:
         cargs.extend([
             "-suffix",
-            params.get("suffix")
+            params.get("suffix", None)
         ])
-    if params.get("keep_tmp"):
+    if params.get("keep_tmp", False):
         cargs.append("-keep_tmp")
-    if params.get("clean"):
+    if params.get("clean", False):
         cargs.append("-clean")
-    if params.get("dxyz") is not None:
+    if params.get("dxyz", None) is not None:
         cargs.extend([
             "-dxyz",
-            str(params.get("dxyz"))
+            str(params.get("dxyz", None))
         ])
-    if params.get("dx") is not None:
+    if params.get("dx", None) is not None:
         cargs.extend([
             "-dx",
-            str(params.get("dx"))
+            str(params.get("dx", None))
         ])
-    if params.get("dy") is not None:
+    if params.get("dy", None) is not None:
         cargs.extend([
             "-dy",
-            str(params.get("dy"))
+            str(params.get("dy", None))
         ])
-    if params.get("dz") is not None:
+    if params.get("dz", None) is not None:
         cargs.extend([
             "-dz",
-            str(params.get("dz"))
+            str(params.get("dz", None))
         ])
     return cargs
 
@@ -190,16 +170,18 @@ def v__align_partial_oblique_outputs(
     """
     ret = VAlignPartialObliqueOutputs(
         root=execution.output_file("."),
-        aligned_output=execution.output_file(pathlib.Path(params.get("base")).name + "_alnd_" + pathlib.Path(params.get("input")).name + ".nii.gz"),
+        aligned_output=execution.output_file(pathlib.Path(params.get("base", None)).name + "_alnd_" + pathlib.Path(params.get("input", None)).name + ".nii.gz"),
     )
     return ret
 
 
 def v__align_partial_oblique_execute(
     params: VAlignPartialObliqueParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAlignPartialObliqueOutputs:
     """
+    @align_partial_oblique
+    
     A script to align a full coverage T1 weighted non-oblique dataset to match a
     partial coverage T1 weighted non-oblique dataset. Alignment is done with a
     rotation and shift (6 parameters) transform only.
@@ -210,10 +192,12 @@ def v__align_partial_oblique_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAlignPartialObliqueOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ALIGN_PARTIAL_OBLIQUE_METADATA)
     params = execution.params(params)
     cargs = v__align_partial_oblique_cargs(params, execution)
     ret = v__align_partial_oblique_outputs(params, execution)
@@ -234,6 +218,8 @@ def v__align_partial_oblique(
     runner: Runner | None = None,
 ) -> VAlignPartialObliqueOutputs:
     """
+    @align_partial_oblique
+    
     A script to align a full coverage T1 weighted non-oblique dataset to match a
     partial coverage T1 weighted non-oblique dataset. Alignment is done with a
     rotation and shift (6 parameters) transform only.
@@ -260,8 +246,6 @@ def v__align_partial_oblique(
     Returns:
         NamedTuple of outputs (described in `VAlignPartialObliqueOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__ALIGN_PARTIAL_OBLIQUE_METADATA)
     params = v__align_partial_oblique_params(
         base=base,
         input_=input_,
@@ -273,13 +257,13 @@ def v__align_partial_oblique(
         dy=dy,
         dz=dz,
     )
-    return v__align_partial_oblique_execute(params, execution)
+    return v__align_partial_oblique_execute(params, runner)
 
 
 __all__ = [
     "VAlignPartialObliqueOutputs",
-    "VAlignPartialObliqueParameters",
     "V__ALIGN_PARTIAL_OBLIQUE_METADATA",
     "v__align_partial_oblique",
+    "v__align_partial_oblique_execute",
     "v__align_partial_oblique_params",
 ]

niwrap_afni/afni/v__anaticor.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__ANATICOR_METADATA = Metadata(
-    id="a21b28f4b637e8294ef269d38d45d16815c41138.boutiques",
+    id="7812bf7600226fd27b9134757f2d604e2f65dc7a.boutiques",
     name="@ANATICOR",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V__ANATICOR_METADATA = Metadata(
 
 
 VAnaticorParameters = typing.TypedDict('VAnaticorParameters', {
-    "__STYXTYPE__": typing.Literal["@ANATICOR"],
+    "@type": typing.NotRequired[typing.Literal["afni/@ANATICOR"]],
+    "ts": InputPathType,
+    "polort": str,
+    "motion": InputPathType,
+    "aseg": InputPathType,
+    "prefix": str,
+    "radius": typing.NotRequired[float | None],
+    "view": typing.NotRequired[str | None],
+    "nuisance": typing.NotRequired[InputPathType | None],
+    "no_ventricles": bool,
+    "Rsq_WMe": bool,
+    "coverage": bool,
+    "verb": bool,
+    "dirty": bool,
+    "echo": bool,
+})
+VAnaticorParametersTagged = typing.TypedDict('VAnaticorParametersTagged', {
+    "@type": typing.Literal["afni/@ANATICOR"],
     "ts": InputPathType,
     "polort": str,
     "motion": InputPathType,
@@ -30,43 +47,11 @@ VAnaticorParameters = typing.TypedDict('VAnaticorParameters', {
     "dirty": bool,
     "echo": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@ANATICOR": v__anaticor_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 {
-        "@ANATICOR": v__anaticor_outputs,
-    }.get(t)
 
 
 class VAnaticorOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__anaticor(...)`.
+    Output object returned when calling `VAnaticorParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +74,7 @@ def v__anaticor_params(
     verb: bool = False,
     dirty: bool = False,
     echo: bool = False,
-) -> VAnaticorParameters:
+) -> VAnaticorParametersTagged:
     """
     Build parameters.
     
@@ -120,7 +105,7 @@ def v__anaticor_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@ANATICOR",
+        "@type": "afni/@ANATICOR",
         "ts": ts,
         "polort": polort,
         "motion": motion,
@@ -159,44 +144,44 @@ def v__anaticor_cargs(
     cargs.append("@ANATICOR")
     cargs.extend([
         "-ts",
-        execution.input_file(params.get("ts"))
+        execution.input_file(params.get("ts", None))
     ])
     cargs.extend([
         "-polort",
-        params.get("polort")
+        params.get("polort", None)
     ])
     cargs.extend([
         "-motion",
-        execution.input_file(params.get("motion"))
+        execution.input_file(params.get("motion", None))
     ])
-    cargs.append(execution.input_file(params.get("aseg")))
+    cargs.append(execution.input_file(params.get("aseg", None)))
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("radius") is not None:
+    if params.get("radius", None) is not None:
         cargs.extend([
             "-radius",
-            str(params.get("radius"))
+            str(params.get("radius", None))
         ])
-    if params.get("view") is not None:
-        cargs.append(params.get("view"))
-    if params.get("nuisance") is not None:
+    if params.get("view", None) is not None:
+        cargs.append(params.get("view", None))
+    if params.get("nuisance", None) is not None:
         cargs.extend([
             "-nuisance",
-            execution.input_file(params.get("nuisance"))
+            execution.input_file(params.get("nuisance", None))
         ])
-    if params.get("no_ventricles"):
+    if params.get("no_ventricles", False):
         cargs.append("-no_ventricles")
-    if params.get("Rsq_WMe"):
+    if params.get("Rsq_WMe", False):
         cargs.append("-Rsq_WMe")
-    if params.get("coverage"):
+    if params.get("coverage", False):
         cargs.append("-coverage")
-    if params.get("verb"):
+    if params.get("verb", False):
         cargs.append("-verb")
-    if params.get("dirty"):
+    if params.get("dirty", False):
         cargs.append("-dirty")
-    if params.get("echo"):
+    if params.get("echo", False):
         cargs.append("-echo")
     return cargs
 
@@ -216,16 +201,18 @@ def v__anaticor_outputs(
     """
     ret = VAnaticorOutputs(
         root=execution.output_file("."),
-        output_files=execution.output_file(params.get("prefix")),
+        output_files=execution.output_file(params.get("prefix", None)),
     )
     return ret
 
 
 def v__anaticor_execute(
     params: VAnaticorParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAnaticorOutputs:
     """
+    @ANATICOR
+    
     Script to produce a residual time series cleaned by ANATICOR model.
     
     Author: AFNI Developers
@@ -234,10 +221,12 @@ def v__anaticor_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAnaticorOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ANATICOR_METADATA)
     params = execution.params(params)
     cargs = v__anaticor_cargs(params, execution)
     ret = v__anaticor_outputs(params, execution)
@@ -263,6 +252,8 @@ def v__anaticor(
     runner: Runner | None = None,
 ) -> VAnaticorOutputs:
     """
+    @ANATICOR
+    
     Script to produce a residual time series cleaned by ANATICOR model.
     
     Author: AFNI Developers
@@ -296,8 +287,6 @@ def v__anaticor(
     Returns:
         NamedTuple of outputs (described in `VAnaticorOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__ANATICOR_METADATA)
     params = v__anaticor_params(
         ts=ts,
         polort=polort,
@@ -314,13 +303,13 @@ def v__anaticor(
         dirty=dirty,
         echo=echo,
     )
-    return v__anaticor_execute(params, execution)
+    return v__anaticor_execute(params, runner)
 
 
 __all__ = [
     "VAnaticorOutputs",
-    "VAnaticorParameters",
     "V__ANATICOR_METADATA",
     "v__anaticor",
+    "v__anaticor_execute",
     "v__anaticor_params",
 ]