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

niwrap_afni/afni/v__measure_in2out.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__MEASURE_IN2OUT_METADATA = Metadata(
-    id="12e4cb21b35db70d6b2ca1c1f10b19ffe465fb9d.boutiques",
+    id="2aaf2876f213e52543ed8cf4135338ef0c4ff428.boutiques",
     name="@measure_in2out",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ V__MEASURE_IN2OUT_METADATA = Metadata(
 
 
 VMeasureIn2outParameters = typing.TypedDict('VMeasureIn2outParameters', {
-    "__STYXTYPE__": typing.Literal["@measure_in2out"],
+    "@type": typing.NotRequired[typing.Literal["afni/@measure_in2out"]],
+    "maskset": InputPathType,
+    "surfset": InputPathType,
+    "outdir": str,
+    "resample": typing.NotRequired[str | None],
+    "increment": typing.NotRequired[float | None],
+    "surfsmooth": typing.NotRequired[float | None],
+    "maxthick": typing.NotRequired[float | None],
+    "depthsearch": typing.NotRequired[float | None],
+    "maskinoutvals": typing.NotRequired[list[float] | None],
+    "keep_temp_files": bool,
+    "surfsmooth_method": typing.NotRequired[str | None],
+    "fs_cort_dir": typing.NotRequired[str | None],
+})
+VMeasureIn2outParametersTagged = typing.TypedDict('VMeasureIn2outParametersTagged', {
+    "@type": typing.Literal["afni/@measure_in2out"],
     "maskset": InputPathType,
     "surfset": InputPathType,
     "outdir": str,
@@ -28,43 +43,11 @@ VMeasureIn2outParameters = typing.TypedDict('VMeasureIn2outParameters', {
     "surfsmooth_method": typing.NotRequired[str | None],
     "fs_cort_dir": 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 {
-        "@measure_in2out": v__measure_in2out_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 {
-        "@measure_in2out": v__measure_in2out_outputs,
-    }.get(t)
 
 
 class VMeasureIn2outOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__measure_in2out(...)`.
+    Output object returned when calling `VMeasureIn2outParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +82,7 @@ def v__measure_in2out_params(
     keep_temp_files: bool = False,
     surfsmooth_method: str | None = None,
     fs_cort_dir: str | None = None,
-) -> VMeasureIn2outParameters:
+) -> VMeasureIn2outParametersTagged:
     """
     Build parameters.
     
@@ -130,7 +113,7 @@ def v__measure_in2out_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@measure_in2out",
+        "@type": "afni/@measure_in2out",
         "maskset": maskset,
         "surfset": surfset,
         "outdir": outdir,
@@ -172,57 +155,57 @@ def v__measure_in2out_cargs(
     cargs.append("@measure_in2out")
     cargs.extend([
         "-maskset",
-        execution.input_file(params.get("maskset"))
+        execution.input_file(params.get("maskset", None))
     ])
     cargs.extend([
         "-surfset",
-        execution.input_file(params.get("surfset"))
+        execution.input_file(params.get("surfset", None))
     ])
     cargs.extend([
         "-outdir",
-        params.get("outdir")
+        params.get("outdir", None)
     ])
-    if params.get("resample") is not None:
+    if params.get("resample", None) is not None:
         cargs.extend([
             "-resample",
-            params.get("resample")
+            params.get("resample", None)
         ])
-    if params.get("increment") is not None:
+    if params.get("increment", None) is not None:
         cargs.extend([
             "-increment",
-            str(params.get("increment"))
+            str(params.get("increment", None))
         ])
-    if params.get("surfsmooth") is not None:
+    if params.get("surfsmooth", None) is not None:
         cargs.extend([
             "-surfsmooth",
-            str(params.get("surfsmooth"))
+            str(params.get("surfsmooth", None))
         ])
-    if params.get("maxthick") is not None:
+    if params.get("maxthick", None) is not None:
         cargs.extend([
             "-maxthick",
-            str(params.get("maxthick"))
+            str(params.get("maxthick", None))
         ])
-    if params.get("depthsearch") is not None:
+    if params.get("depthsearch", None) is not None:
         cargs.extend([
             "-depthsearch",
-            str(params.get("depthsearch"))
+            str(params.get("depthsearch", None))
         ])
-    if params.get("maskinoutvals") is not None:
+    if params.get("maskinoutvals", None) is not None:
         cargs.extend([
             "-maskinoutvals",
-            *map(str, params.get("maskinoutvals"))
+            *map(str, params.get("maskinoutvals", None))
         ])
-    if params.get("keep_temp_files"):
+    if params.get("keep_temp_files", False):
         cargs.append("-keep_temp_files")
-    if params.get("surfsmooth_method") is not None:
+    if params.get("surfsmooth_method", None) is not None:
         cargs.extend([
             "-surfsmooth_method",
-            params.get("surfsmooth_method")
+            params.get("surfsmooth_method", None)
         ])
-    if params.get("fs_cort_dir") is not None:
+    if params.get("fs_cort_dir", None) is not None:
         cargs.extend([
             "-fs_cort_dir",
-            params.get("fs_cort_dir")
+            params.get("fs_cort_dir", None)
         ])
     return cargs
 
@@ -256,9 +239,11 @@ def v__measure_in2out_outputs(
 
 def v__measure_in2out_execute(
     params: VMeasureIn2outParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VMeasureIn2outOutputs:
     """
+    @measure_in2out
+    
     Compute thickness of mask using in2out method.
     
     Author: AFNI Developers
@@ -267,10 +252,12 @@ def v__measure_in2out_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VMeasureIn2outOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MEASURE_IN2OUT_METADATA)
     params = execution.params(params)
     cargs = v__measure_in2out_cargs(params, execution)
     ret = v__measure_in2out_outputs(params, execution)
@@ -294,6 +281,8 @@ def v__measure_in2out(
     runner: Runner | None = None,
 ) -> VMeasureIn2outOutputs:
     """
+    @measure_in2out
+    
     Compute thickness of mask using in2out method.
     
     Author: AFNI Developers
@@ -327,8 +316,6 @@ def v__measure_in2out(
     Returns:
         NamedTuple of outputs (described in `VMeasureIn2outOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__MEASURE_IN2OUT_METADATA)
     params = v__measure_in2out_params(
         maskset=maskset,
         surfset=surfset,
@@ -343,13 +330,13 @@ def v__measure_in2out(
         surfsmooth_method=surfsmooth_method,
         fs_cort_dir=fs_cort_dir,
     )
-    return v__measure_in2out_execute(params, execution)
+    return v__measure_in2out_execute(params, runner)
 
 
 __all__ = [
     "VMeasureIn2outOutputs",
-    "VMeasureIn2outParameters",
     "V__MEASURE_IN2OUT_METADATA",
     "v__measure_in2out",
+    "v__measure_in2out_execute",
     "v__measure_in2out_params",
 ]

niwrap_afni/afni/v__move_to_series_dirs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__MOVE_TO_SERIES_DIRS_METADATA = Metadata(
-    id="3258c3e5be037bd2af4e822c7e7ad229a6157990.boutiques",
+    id="27688027b086a8f3681feffe1acd7e006bb142e5.boutiques",
     name="@move.to.series.dirs",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V__MOVE_TO_SERIES_DIRS_METADATA = Metadata(
 
 
 VMoveToSeriesDirsParameters = typing.TypedDict('VMoveToSeriesDirsParameters', {
-    "__STYXTYPE__": typing.Literal["@move.to.series.dirs"],
+    "@type": typing.NotRequired[typing.Literal["afni/@move.to.series.dirs"]],
+    "action": typing.NotRequired[typing.Literal["copy", "move"] | None],
+    "dprefix": typing.NotRequired[str | None],
+    "tag": typing.NotRequired[str | None],
+    "test": bool,
+    "help": bool,
+    "hist": bool,
+    "ver": bool,
+    "dicom_files": list[InputPathType],
+})
+VMoveToSeriesDirsParametersTagged = typing.TypedDict('VMoveToSeriesDirsParametersTagged', {
+    "@type": typing.Literal["afni/@move.to.series.dirs"],
     "action": typing.NotRequired[typing.Literal["copy", "move"] | None],
     "dprefix": typing.NotRequired[str | None],
     "tag": typing.NotRequired[str | None],
@@ -24,42 +35,11 @@ VMoveToSeriesDirsParameters = typing.TypedDict('VMoveToSeriesDirsParameters', {
     "ver": bool,
     "dicom_files": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@move.to.series.dirs": v__move_to_series_dirs_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 VMoveToSeriesDirsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__move_to_series_dirs(...)`.
+    Output object returned when calling `VMoveToSeriesDirsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def v__move_to_series_dirs_params(
     help_: bool = False,
     hist: bool = False,
     ver: bool = False,
-) -> VMoveToSeriesDirsParameters:
+) -> VMoveToSeriesDirsParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +74,7 @@ def v__move_to_series_dirs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@move.to.series.dirs",
+        "@type": "afni/@move.to.series.dirs",
         "test": test,
         "help": help_,
         "hist": hist,
@@ -125,30 +105,30 @@ def v__move_to_series_dirs_cargs(
     """
     cargs = []
     cargs.append("@move.to.series.dirs")
-    if params.get("action") is not None:
+    if params.get("action", None) is not None:
         cargs.extend([
             "-action",
-            params.get("action")
+            params.get("action", None)
         ])
-    if params.get("dprefix") is not None:
+    if params.get("dprefix", None) is not None:
         cargs.extend([
             "-dprefix",
-            params.get("dprefix")
+            params.get("dprefix", None)
         ])
-    if params.get("tag") is not None:
+    if params.get("tag", None) is not None:
         cargs.extend([
             "-tag",
-            params.get("tag")
+            params.get("tag", None)
         ])
-    if params.get("test"):
+    if params.get("test", False):
         cargs.append("-test")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("hist"):
+    if params.get("hist", False):
         cargs.append("-hist")
-    if params.get("ver"):
+    if params.get("ver", False):
         cargs.append("-ver")
-    cargs.extend([execution.input_file(f) for f in params.get("dicom_files")])
+    cargs.extend([execution.input_file(f) for f in params.get("dicom_files", None)])
     return cargs
 
 
@@ -173,11 +153,13 @@ def v__move_to_series_dirs_outputs(
 
 def v__move_to_series_dirs_execute(
     params: VMoveToSeriesDirsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VMoveToSeriesDirsOutputs:
     """
-    Partition DICOM files into series directories by copying or moving them to new
-    series directories.
+    @move.to.series.dirs
+    
+    Partition DICOM files into series directories by copying or moving them to
+    new series directories.
     
     Author: AFNI Developers
     
@@ -185,10 +167,12 @@ def v__move_to_series_dirs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VMoveToSeriesDirsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MOVE_TO_SERIES_DIRS_METADATA)
     params = execution.params(params)
     cargs = v__move_to_series_dirs_cargs(params, execution)
     ret = v__move_to_series_dirs_outputs(params, execution)
@@ -208,8 +192,10 @@ def v__move_to_series_dirs(
     runner: Runner | None = None,
 ) -> VMoveToSeriesDirsOutputs:
     """
-    Partition DICOM files into series directories by copying or moving them to new
-    series directories.
+    @move.to.series.dirs
+    
+    Partition DICOM files into series directories by copying or moving them to
+    new series directories.
     
     Author: AFNI Developers
     
@@ -231,8 +217,6 @@ def v__move_to_series_dirs(
     Returns:
         NamedTuple of outputs (described in `VMoveToSeriesDirsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__MOVE_TO_SERIES_DIRS_METADATA)
     params = v__move_to_series_dirs_params(
         action=action,
         dprefix=dprefix,
@@ -243,13 +227,13 @@ def v__move_to_series_dirs(
         ver=ver,
         dicom_files=dicom_files,
     )
-    return v__move_to_series_dirs_execute(params, execution)
+    return v__move_to_series_dirs_execute(params, runner)
 
 
 __all__ = [
     "VMoveToSeriesDirsOutputs",
-    "VMoveToSeriesDirsParameters",
     "V__MOVE_TO_SERIES_DIRS_METADATA",
     "v__move_to_series_dirs",
+    "v__move_to_series_dirs_execute",
     "v__move_to_series_dirs_params",
 ]

niwrap_afni/afni/v__no_ext.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__NO_EXT_METADATA = Metadata(
-    id="aa54ce64e9dd0f5ee3b7a0897d18c2e03cd5cd84.boutiques",
+    id="74a67fecd0b092c695e69d2570c50eb30c42f685.boutiques",
     name="@NoExt",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,20 @@ V__NO_EXT_METADATA = Metadata(
 
 
 VNoExtParameters = typing.TypedDict('VNoExtParameters', {
-    "__STYXTYPE__": typing.Literal["@NoExt"],
+    "@type": typing.NotRequired[typing.Literal["afni/@NoExt"]],
+    "inputfile": str,
+    "extensions": typing.NotRequired[list[str] | None],
+})
+VNoExtParametersTagged = typing.TypedDict('VNoExtParametersTagged', {
+    "@type": typing.Literal["afni/@NoExt"],
     "inputfile": str,
     "extensions": typing.NotRequired[list[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 {
-        "@NoExt": v__no_ext_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 {
-        "@NoExt": v__no_ext_outputs,
-    }.get(t)
 
 
 class VNoExtOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__no_ext(...)`.
+    Output object returned when calling `VNoExtParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class VNoExtOutputs(typing.NamedTuple):
 def v__no_ext_params(
     inputfile: str,
     extensions: list[str] | None = None,
-) -> VNoExtParameters:
+) -> VNoExtParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def v__no_ext_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@NoExt",
+        "@type": "afni/@NoExt",
         "inputfile": inputfile,
     }
     if extensions is not None:
@@ -99,9 +72,9 @@ def v__no_ext_cargs(
     """
     cargs = []
     cargs.append("@NoExt")
-    cargs.append(params.get("inputfile"))
-    if params.get("extensions") is not None:
-        cargs.extend(params.get("extensions"))
+    cargs.append(params.get("inputfile", None))
+    if params.get("extensions", None) is not None:
+        cargs.extend(params.get("extensions", None))
     return cargs
 
 
@@ -127,9 +100,11 @@ def v__no_ext_outputs(
 
 def v__no_ext_execute(
     params: VNoExtParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VNoExtOutputs:
     """
+    @NoExt
+    
     Tool for removing specified extensions from filenames.
     
     Author: AFNI Developers
@@ -138,10 +113,12 @@ def v__no_ext_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VNoExtOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__NO_EXT_METADATA)
     params = execution.params(params)
     cargs = v__no_ext_cargs(params, execution)
     ret = v__no_ext_outputs(params, execution)
@@ -155,6 +132,8 @@ def v__no_ext(
     runner: Runner | None = None,
 ) -> VNoExtOutputs:
     """
+    @NoExt
+    
     Tool for removing specified extensions from filenames.
     
     Author: AFNI Developers
@@ -168,19 +147,17 @@ def v__no_ext(
     Returns:
         NamedTuple of outputs (described in `VNoExtOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__NO_EXT_METADATA)
     params = v__no_ext_params(
         inputfile=inputfile,
         extensions=extensions,
     )
-    return v__no_ext_execute(params, execution)
+    return v__no_ext_execute(params, runner)
 
 
 __all__ = [
     "VNoExtOutputs",
-    "VNoExtParameters",
     "V__NO_EXT_METADATA",
     "v__no_ext",
+    "v__no_ext_execute",
     "v__no_ext_params",
 ]