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

niwrap_afni/afni/v__fast_roi.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__FAST_ROI_METADATA = Metadata(
-    id="d18cbef8d851f59f23b93093ca933ae2433a09f2.boutiques",
+    id="be9840e265ca2a4c3bef07aff8593f44a38ea15a.boutiques",
     name="@fast_roi",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ V__FAST_ROI_METADATA = Metadata(
 
 
 VFastRoiParameters = typing.TypedDict('VFastRoiParameters', {
-    "__STYXTYPE__": typing.Literal["@fast_roi"],
+    "@type": typing.NotRequired[typing.Literal["afni/@fast_roi"]],
+    "region": list[str],
+    "drawn_roi": typing.NotRequired[InputPathType | None],
+    "anat": InputPathType,
+    "anat_ns": typing.NotRequired[InputPathType | None],
+    "base": InputPathType,
+    "roi_grid": InputPathType,
+    "prefix": str,
+    "time": bool,
+    "twopass": bool,
+    "help": bool,
+})
+VFastRoiParametersTagged = typing.TypedDict('VFastRoiParametersTagged', {
+    "@type": typing.Literal["afni/@fast_roi"],
     "region": list[str],
     "drawn_roi": typing.NotRequired[InputPathType | None],
     "anat": InputPathType,
@@ -26,43 +39,11 @@ VFastRoiParameters = typing.TypedDict('VFastRoiParameters', {
     "twopass": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@fast_roi": v__fast_roi_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 {
-        "@fast_roi": v__fast_roi_outputs,
-    }.get(t)
 
 
 class VFastRoiOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__fast_roi(...)`.
+    Output object returned when calling `VFastRoiParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +62,7 @@ def v__fast_roi_params(
     time_: bool = False,
     twopass: bool = False,
     help_: bool = False,
-) -> VFastRoiParameters:
+) -> VFastRoiParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +87,7 @@ def v__fast_roi_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@fast_roi",
+        "@type": "afni/@fast_roi",
         "region": region,
         "anat": anat,
         "base": base,
@@ -140,39 +121,39 @@ def v__fast_roi_cargs(
     cargs.append("@fast_roi")
     cargs.extend([
         "-region",
-        *params.get("region")
+        *params.get("region", None)
     ])
-    if params.get("drawn_roi") is not None:
+    if params.get("drawn_roi", None) is not None:
         cargs.extend([
             "-drawn_roi",
-            execution.input_file(params.get("drawn_roi"))
+            execution.input_file(params.get("drawn_roi", None))
         ])
     cargs.extend([
         "-anat",
-        execution.input_file(params.get("anat"))
+        execution.input_file(params.get("anat", None))
     ])
-    if params.get("anat_ns") is not None:
+    if params.get("anat_ns", None) is not None:
         cargs.extend([
             "-anat_ns",
-            execution.input_file(params.get("anat_ns"))
+            execution.input_file(params.get("anat_ns", None))
         ])
     cargs.extend([
         "-base",
-        execution.input_file(params.get("base"))
+        execution.input_file(params.get("base", None))
     ])
     cargs.extend([
         "-roi_grid",
-        execution.input_file(params.get("roi_grid"))
+        execution.input_file(params.get("roi_grid", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("time"):
+    if params.get("time", False):
         cargs.append("--time")
-    if params.get("twopass"):
+    if params.get("twopass", False):
         cargs.append("--twopass")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -192,16 +173,18 @@ def v__fast_roi_outputs(
     """
     ret = VFastRoiOutputs(
         root=execution.output_file("."),
-        roi_output=execution.output_file("ROI." + params.get("prefix") + "+orig"),
+        roi_output=execution.output_file("ROI." + params.get("prefix", None) + "+orig"),
     )
     return ret
 
 
 def v__fast_roi_execute(
     params: VFastRoiParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VFastRoiOutputs:
     """
+    @fast_roi
+    
     Creates Atlas-based ROI masked in ANAT's original space. The script executes
     rapidly for realtime fMRI applications.
     
@@ -211,10 +194,12 @@ def v__fast_roi_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VFastRoiOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FAST_ROI_METADATA)
     params = execution.params(params)
     cargs = v__fast_roi_cargs(params, execution)
     ret = v__fast_roi_outputs(params, execution)
@@ -236,6 +221,8 @@ def v__fast_roi(
     runner: Runner | None = None,
 ) -> VFastRoiOutputs:
     """
+    @fast_roi
+    
     Creates Atlas-based ROI masked in ANAT's original space. The script executes
     rapidly for realtime fMRI applications.
     
@@ -264,8 +251,6 @@ def v__fast_roi(
     Returns:
         NamedTuple of outputs (described in `VFastRoiOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__FAST_ROI_METADATA)
     params = v__fast_roi_params(
         region=region,
         drawn_roi=drawn_roi,
@@ -278,13 +263,13 @@ def v__fast_roi(
         twopass=twopass,
         help_=help_,
     )
-    return v__fast_roi_execute(params, execution)
+    return v__fast_roi_execute(params, runner)
 
 
 __all__ = [
     "VFastRoiOutputs",
-    "VFastRoiParameters",
     "V__FAST_ROI_METADATA",
     "v__fast_roi",
+    "v__fast_roi_execute",
     "v__fast_roi_params",
 ]

niwrap_afni/afni/v__fat_tract_colorize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__FAT_TRACT_COLORIZE_METADATA = Metadata(
-    id="52600b9abdebebf0fd475c3cbed6752a3fa87572.boutiques",
+    id="8d8b3aaa35758a6a6a78e0730ac40b3f96234ac2.boutiques",
     name="@fat_tract_colorize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V__FAT_TRACT_COLORIZE_METADATA = Metadata(
 
 
 VFatTractColorizeParameters = typing.TypedDict('VFatTractColorizeParameters', {
-    "__STYXTYPE__": typing.Literal["@fat_tract_colorize"],
+    "@type": typing.NotRequired[typing.Literal["afni/@fat_tract_colorize"]],
+    "in_fa": InputPathType,
+    "in_v1": InputPathType,
+    "in_tracts": str,
+    "prefix": str,
+    "in_ulay": typing.NotRequired[InputPathType | None],
+    "no_view": bool,
+    "only_view": bool,
+})
+VFatTractColorizeParametersTagged = typing.TypedDict('VFatTractColorizeParametersTagged', {
+    "@type": typing.Literal["afni/@fat_tract_colorize"],
     "in_fa": InputPathType,
     "in_v1": InputPathType,
     "in_tracts": str,
@@ -23,43 +33,11 @@ VFatTractColorizeParameters = typing.TypedDict('VFatTractColorizeParameters', {
     "no_view": bool,
     "only_view": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@fat_tract_colorize": v__fat_tract_colorize_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 {
-        "@fat_tract_colorize": v__fat_tract_colorize_outputs,
-    }.get(t)
 
 
 class VFatTractColorizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__fat_tract_colorize(...)`.
+    Output object returned when calling `VFatTractColorizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -82,7 +60,7 @@ def v__fat_tract_colorize_params(
     in_ulay: InputPathType | None = None,
     no_view: bool = False,
     only_view: bool = False,
-) -> VFatTractColorizeParameters:
+) -> VFatTractColorizeParametersTagged:
     """
     Build parameters.
     
@@ -104,7 +82,7 @@ def v__fat_tract_colorize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@fat_tract_colorize",
+        "@type": "afni/@fat_tract_colorize",
         "in_fa": in_fa,
         "in_v1": in_v1,
         "in_tracts": in_tracts,
@@ -134,28 +112,28 @@ def v__fat_tract_colorize_cargs(
     cargs.append("@fat_tract_colorize")
     cargs.extend([
         "-in_fa",
-        execution.input_file(params.get("in_fa"))
+        execution.input_file(params.get("in_fa", None))
     ])
     cargs.extend([
         "-in_v1",
-        execution.input_file(params.get("in_v1"))
+        execution.input_file(params.get("in_v1", None))
     ])
     cargs.extend([
         "-in_tracts",
-        params.get("in_tracts")
+        params.get("in_tracts", None)
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("in_ulay") is not None:
+    if params.get("in_ulay", None) is not None:
         cargs.extend([
             "-in_ulay",
-            execution.input_file(params.get("in_ulay"))
+            execution.input_file(params.get("in_ulay", None))
         ])
-    if params.get("no_view"):
+    if params.get("no_view", False):
         cargs.append("-no_view")
-    if params.get("only_view"):
+    if params.get("only_view", False):
         cargs.append("-only_view")
     return cargs
 
@@ -175,19 +153,21 @@ def v__fat_tract_colorize_outputs(
     """
     ret = VFatTractColorizeOutputs(
         root=execution.output_file("."),
-        output_hue_volume=execution.output_file(params.get("prefix") + "_RGB_HUE.nii.gz"),
-        output_iso_surface=execution.output_file(params.get("prefix") + "_RGB_iso.ply"),
-        output_iso_spec=execution.output_file(params.get("prefix") + "_RGB_iso.spec"),
-        output_proj_surface=execution.output_file(params.get("prefix") + "_RGB.niml.dset"),
+        output_hue_volume=execution.output_file(params.get("prefix", None) + "_RGB_HUE.nii.gz"),
+        output_iso_surface=execution.output_file(params.get("prefix", None) + "_RGB_iso.ply"),
+        output_iso_spec=execution.output_file(params.get("prefix", None) + "_RGB_iso.spec"),
+        output_proj_surface=execution.output_file(params.get("prefix", None) + "_RGB.niml.dset"),
     )
     return ret
 
 
 def v__fat_tract_colorize_execute(
     params: VFatTractColorizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VFatTractColorizeOutputs:
     """
+    @fat_tract_colorize
+    
     Visualize tractographic output from 3dTrackID, particularly in probabilistic
     mode.
     
@@ -197,10 +177,12 @@ def v__fat_tract_colorize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VFatTractColorizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FAT_TRACT_COLORIZE_METADATA)
     params = execution.params(params)
     cargs = v__fat_tract_colorize_cargs(params, execution)
     ret = v__fat_tract_colorize_outputs(params, execution)
@@ -219,6 +201,8 @@ def v__fat_tract_colorize(
     runner: Runner | None = None,
 ) -> VFatTractColorizeOutputs:
     """
+    @fat_tract_colorize
+    
     Visualize tractographic output from 3dTrackID, particularly in probabilistic
     mode.
     
@@ -244,8 +228,6 @@ def v__fat_tract_colorize(
     Returns:
         NamedTuple of outputs (described in `VFatTractColorizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__FAT_TRACT_COLORIZE_METADATA)
     params = v__fat_tract_colorize_params(
         in_fa=in_fa,
         in_v1=in_v1,
@@ -255,13 +237,13 @@ def v__fat_tract_colorize(
         no_view=no_view,
         only_view=only_view,
     )
-    return v__fat_tract_colorize_execute(params, execution)
+    return v__fat_tract_colorize_execute(params, runner)
 
 
 __all__ = [
     "VFatTractColorizeOutputs",
-    "VFatTractColorizeParameters",
     "V__FAT_TRACT_COLORIZE_METADATA",
     "v__fat_tract_colorize",
+    "v__fat_tract_colorize_execute",
     "v__fat_tract_colorize_params",
 ]

niwrap_afni/afni/v__find_afni_dset_path.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__FIND_AFNI_DSET_PATH_METADATA = Metadata(
-    id="d33aa66f6df6fbc7fea6bf4750fec389976226bb.boutiques",
+    id="d98bb30ec2ffc8ff869e699815600ee516e0604e.boutiques",
     name="@FindAfniDsetPath",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,24 @@ V__FIND_AFNI_DSET_PATH_METADATA = Metadata(
 
 
 VFindAfniDsetPathParameters = typing.TypedDict('VFindAfniDsetPathParameters', {
-    "__STYXTYPE__": typing.Literal["@FindAfniDsetPath"],
+    "@type": typing.NotRequired[typing.Literal["afni/@FindAfniDsetPath"]],
+    "dsetname": str,
+    "append_file": bool,
+    "full_path": bool,
+    "help": bool,
+})
+VFindAfniDsetPathParametersTagged = typing.TypedDict('VFindAfniDsetPathParametersTagged', {
+    "@type": typing.Literal["afni/@FindAfniDsetPath"],
     "dsetname": str,
     "append_file": bool,
     "full_path": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@FindAfniDsetPath": v__find_afni_dset_path_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 VFindAfniDsetPathOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__find_afni_dset_path(...)`.
+    Output object returned when calling `VFindAfniDsetPathParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def v__find_afni_dset_path_params(
     append_file: bool = False,
     full_path: bool = False,
     help_: bool = False,
-) -> VFindAfniDsetPathParameters:
+) -> VFindAfniDsetPathParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def v__find_afni_dset_path_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@FindAfniDsetPath",
+        "@type": "afni/@FindAfniDsetPath",
         "dsetname": dsetname,
         "append_file": append_file,
         "full_path": full_path,
@@ -103,12 +79,12 @@ def v__find_afni_dset_path_cargs(
     """
     cargs = []
     cargs.append("@FindAfniDsetPath")
-    cargs.append(params.get("dsetname"))
-    if params.get("append_file"):
+    cargs.append(params.get("dsetname", None))
+    if params.get("append_file", False):
         cargs.append("-append_file")
-    if params.get("full_path"):
+    if params.get("full_path", False):
         cargs.append("-full_path")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -134,10 +110,13 @@ def v__find_afni_dset_path_outputs(
 
 def v__find_afni_dset_path_execute(
     params: VFindAfniDsetPathParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VFindAfniDsetPathOutputs:
     """
-    Searches various AFNI directories for a specified dataset and returns its path.
+    @FindAfniDsetPath
+    
+    Searches various AFNI directories for a specified dataset and returns its
+    path.
     
     Author: AFNI Developers
     
@@ -145,10 +124,12 @@ def v__find_afni_dset_path_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VFindAfniDsetPathOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FIND_AFNI_DSET_PATH_METADATA)
     params = execution.params(params)
     cargs = v__find_afni_dset_path_cargs(params, execution)
     ret = v__find_afni_dset_path_outputs(params, execution)
@@ -164,7 +145,10 @@ def v__find_afni_dset_path(
     runner: Runner | None = None,
 ) -> VFindAfniDsetPathOutputs:
     """
-    Searches various AFNI directories for a specified dataset and returns its path.
+    @FindAfniDsetPath
+    
+    Searches various AFNI directories for a specified dataset and returns its
+    path.
     
     Author: AFNI Developers
     
@@ -179,21 +163,19 @@ def v__find_afni_dset_path(
     Returns:
         NamedTuple of outputs (described in `VFindAfniDsetPathOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__FIND_AFNI_DSET_PATH_METADATA)
     params = v__find_afni_dset_path_params(
         dsetname=dsetname,
         append_file=append_file,
         full_path=full_path,
         help_=help_,
     )
-    return v__find_afni_dset_path_execute(params, execution)
+    return v__find_afni_dset_path_execute(params, runner)
 
 
 __all__ = [
     "VFindAfniDsetPathOutputs",
-    "VFindAfniDsetPathParameters",
     "V__FIND_AFNI_DSET_PATH_METADATA",
     "v__find_afni_dset_path",
+    "v__find_afni_dset_path_execute",
     "v__find_afni_dset_path_params",
 ]