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

niwrap_afni/afni/v__make_plug_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__MAKE_PLUG_DIFF_METADATA = Metadata(
-    id="d1ce49de5eb108e0627f42d6a6246b152634ab14.boutiques",
+    id="b2f0f17eb81cb2af9f53307b7c9521014f7908a4.boutiques",
     name="@make_plug_diff",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V__MAKE_PLUG_DIFF_METADATA = Metadata(
 
 
 VMakePlugDiffParameters = typing.TypedDict('VMakePlugDiffParameters', {
-    "__STYXTYPE__": typing.Literal["@make_plug_diff"],
+    "@type": typing.NotRequired[typing.Literal["afni/@make_plug_diff"]],
+    "vtk_dir": str,
+    "xm_dir": str,
+    "afni_src_dir": str,
+    "afni_bin_dir": str,
+    "comments": bool,
+    "linux": bool,
+    "diff_dir": str,
+})
+VMakePlugDiffParametersTagged = typing.TypedDict('VMakePlugDiffParametersTagged', {
+    "@type": typing.Literal["afni/@make_plug_diff"],
     "vtk_dir": str,
     "xm_dir": str,
     "afni_src_dir": str,
@@ -23,42 +33,11 @@ VMakePlugDiffParameters = typing.TypedDict('VMakePlugDiffParameters', {
     "linux": bool,
     "diff_dir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@make_plug_diff": v__make_plug_diff_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 VMakePlugDiffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__make_plug_diff(...)`.
+    Output object returned when calling `VMakePlugDiffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def v__make_plug_diff_params(
     diff_dir: str,
     comments: bool = False,
     linux: bool = False,
-) -> VMakePlugDiffParameters:
+) -> VMakePlugDiffParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +67,7 @@ def v__make_plug_diff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@make_plug_diff",
+        "@type": "afni/@make_plug_diff",
         "vtk_dir": vtk_dir,
         "xm_dir": xm_dir,
         "afni_src_dir": afni_src_dir,
@@ -117,27 +96,27 @@ def v__make_plug_diff_cargs(
     cargs.append("@make_plug_diff")
     cargs.extend([
         "-vtk",
-        params.get("vtk_dir")
+        params.get("vtk_dir", None)
     ])
     cargs.extend([
         "-xm",
-        params.get("xm_dir")
+        params.get("xm_dir", None)
     ])
     cargs.extend([
         "-asrc",
-        params.get("afni_src_dir")
+        params.get("afni_src_dir", None)
     ])
     cargs.extend([
         "-abin",
-        params.get("afni_bin_dir")
+        params.get("afni_bin_dir", None)
     ])
-    if params.get("comments"):
+    if params.get("comments", False):
         cargs.append("-comments")
-    if params.get("linux"):
+    if params.get("linux", False):
         cargs.append("-linux")
     cargs.extend([
         "-diff",
-        params.get("diff_dir")
+        params.get("diff_dir", None)
     ])
     return cargs
 
@@ -163,9 +142,11 @@ def v__make_plug_diff_outputs(
 
 def v__make_plug_diff_execute(
     params: VMakePlugDiffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VMakePlugDiffOutputs:
     """
+    @make_plug_diff
+    
     Compiles AFNI's diffusion plugin.
     
     Author: AFNI Developers
@@ -174,10 +155,12 @@ def v__make_plug_diff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VMakePlugDiffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MAKE_PLUG_DIFF_METADATA)
     params = execution.params(params)
     cargs = v__make_plug_diff_cargs(params, execution)
     ret = v__make_plug_diff_outputs(params, execution)
@@ -196,6 +179,8 @@ def v__make_plug_diff(
     runner: Runner | None = None,
 ) -> VMakePlugDiffOutputs:
     """
+    @make_plug_diff
+    
     Compiles AFNI's diffusion plugin.
     
     Author: AFNI Developers
@@ -214,8 +199,6 @@ def v__make_plug_diff(
     Returns:
         NamedTuple of outputs (described in `VMakePlugDiffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__MAKE_PLUG_DIFF_METADATA)
     params = v__make_plug_diff_params(
         vtk_dir=vtk_dir,
         xm_dir=xm_dir,
@@ -225,13 +208,13 @@ def v__make_plug_diff(
         linux=linux,
         diff_dir=diff_dir,
     )
-    return v__make_plug_diff_execute(params, execution)
+    return v__make_plug_diff_execute(params, runner)
 
 
 __all__ = [
     "VMakePlugDiffOutputs",
-    "VMakePlugDiffParameters",
     "V__MAKE_PLUG_DIFF_METADATA",
     "v__make_plug_diff",
+    "v__make_plug_diff_execute",
     "v__make_plug_diff_params",
 ]

niwrap_afni/afni/v__measure_bb_thick.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__MEASURE_BB_THICK_METADATA = Metadata(
-    id="1c250530ee036924f16cb74f8eac684773e85841.boutiques",
+    id="191428b333de802e70729f5b51e6bbe935e45cfd.boutiques",
     name="@measure_bb_thick",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ V__MEASURE_BB_THICK_METADATA = Metadata(
 
 
 VMeasureBbThickParameters = typing.TypedDict('VMeasureBbThickParameters', {
-    "__STYXTYPE__": typing.Literal["@measure_bb_thick"],
+    "@type": typing.NotRequired[typing.Literal["afni/@measure_bb_thick"]],
+    "maskset": InputPathType,
+    "surfset": InputPathType,
+    "outdir": typing.NotRequired[str | None],
+    "resample": typing.NotRequired[str | None],
+    "increment": typing.NotRequired[float | None],
+    "surfsmooth": typing.NotRequired[float | None],
+    "smoothmm": typing.NotRequired[float | None],
+    "maxthick": typing.NotRequired[float | None],
+    "depth_search": typing.NotRequired[float | None],
+    "keep_temp_files": bool,
+    "balls_only": bool,
+    "surfsmooth_method": typing.NotRequired[str | None],
+})
+VMeasureBbThickParametersTagged = typing.TypedDict('VMeasureBbThickParametersTagged', {
+    "@type": typing.Literal["afni/@measure_bb_thick"],
     "maskset": InputPathType,
     "surfset": InputPathType,
     "outdir": typing.NotRequired[str | None],
@@ -28,43 +43,11 @@ VMeasureBbThickParameters = typing.TypedDict('VMeasureBbThickParameters', {
     "balls_only": bool,
     "surfsmooth_method": 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_bb_thick": v__measure_bb_thick_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_bb_thick": v__measure_bb_thick_outputs,
-    }.get(t)
 
 
 class VMeasureBbThickOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__measure_bb_thick(...)`.
+    Output object returned when calling `VMeasureBbThickParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +84,7 @@ def v__measure_bb_thick_params(
     keep_temp_files: bool = False,
     balls_only: bool = False,
     surfsmooth_method: str | None = None,
-) -> VMeasureBbThickParameters:
+) -> VMeasureBbThickParametersTagged:
     """
     Build parameters.
     
@@ -130,7 +113,7 @@ def v__measure_bb_thick_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@measure_bb_thick",
+        "@type": "afni/@measure_bb_thick",
         "maskset": maskset,
         "surfset": surfset,
         "keep_temp_files": keep_temp_files,
@@ -172,55 +155,55 @@ def v__measure_bb_thick_cargs(
     cargs.append("@measure_bb_thick")
     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))
     ])
-    if params.get("outdir") is not None:
+    if params.get("outdir", None) is not 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("smoothmm") is not None:
+    if params.get("smoothmm", None) is not None:
         cargs.extend([
             "-smoothmm",
-            str(params.get("smoothmm"))
+            str(params.get("smoothmm", 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("depth_search") is not None:
+    if params.get("depth_search", None) is not None:
         cargs.extend([
             "-depthsearch",
-            str(params.get("depth_search"))
+            str(params.get("depth_search", None))
         ])
-    if params.get("keep_temp_files"):
+    if params.get("keep_temp_files", False):
         cargs.append("-keep_temp_files")
-    if params.get("balls_only"):
+    if params.get("balls_only", False):
         cargs.append("-balls_only")
-    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)
         ])
     return cargs
 
@@ -240,24 +223,26 @@ def v__measure_bb_thick_outputs(
     """
     ret = VMeasureBbThickOutputs(
         root=execution.output_file("."),
-        maxfill=execution.output_file(params.get("outdir") + "/maxfill.nii.gz") if (params.get("outdir") is not None) else None,
-        bb_thick=execution.output_file(params.get("outdir") + "/bb_thick.nii.gz") if (params.get("outdir") is not None) else None,
-        bb_thick_smooth=execution.output_file(params.get("outdir") + "/bb_thick_smooth.nii.gz") if (params.get("outdir") is not None) else None,
-        bb_thick_niml=execution.output_file(params.get("outdir") + "/bb_thick.niml.dset") if (params.get("outdir") is not None) else None,
-        bb_thick_smooth_niml=execution.output_file(params.get("outdir") + "/bb_thick_smooth.niml.dset") if (params.get("outdir") is not None) else None,
-        maskset_output=execution.output_file(params.get("outdir") + "/maskset.nii.gz") if (params.get("outdir") is not None) else None,
-        maskset_resampled=execution.output_file(params.get("outdir") + "/maskset_rs.nii.gz") if (params.get("outdir") is not None) else None,
-        anat_surface=execution.output_file(params.get("outdir") + "/anat.gii") if (params.get("outdir") is not None) else None,
-        quick_spec=execution.output_file(params.get("outdir") + "/quick.spec") if (params.get("outdir") is not None) else None,
+        maxfill=execution.output_file(params.get("outdir", None) + "/maxfill.nii.gz") if (params.get("outdir") is not None) else None,
+        bb_thick=execution.output_file(params.get("outdir", None) + "/bb_thick.nii.gz") if (params.get("outdir") is not None) else None,
+        bb_thick_smooth=execution.output_file(params.get("outdir", None) + "/bb_thick_smooth.nii.gz") if (params.get("outdir") is not None) else None,
+        bb_thick_niml=execution.output_file(params.get("outdir", None) + "/bb_thick.niml.dset") if (params.get("outdir") is not None) else None,
+        bb_thick_smooth_niml=execution.output_file(params.get("outdir", None) + "/bb_thick_smooth.niml.dset") if (params.get("outdir") is not None) else None,
+        maskset_output=execution.output_file(params.get("outdir", None) + "/maskset.nii.gz") if (params.get("outdir") is not None) else None,
+        maskset_resampled=execution.output_file(params.get("outdir", None) + "/maskset_rs.nii.gz") if (params.get("outdir") is not None) else None,
+        anat_surface=execution.output_file(params.get("outdir", None) + "/anat.gii") if (params.get("outdir") is not None) else None,
+        quick_spec=execution.output_file(params.get("outdir", None) + "/quick.spec") if (params.get("outdir") is not None) else None,
     )
     return ret
 
 
 def v__measure_bb_thick_execute(
     params: VMeasureBbThickParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VMeasureBbThickOutputs:
     """
+    @measure_bb_thick
+    
     Compute thickness of mask using ball and box method.
     
     Author: AFNI Developers
@@ -266,10 +251,12 @@ def v__measure_bb_thick_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VMeasureBbThickOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MEASURE_BB_THICK_METADATA)
     params = execution.params(params)
     cargs = v__measure_bb_thick_cargs(params, execution)
     ret = v__measure_bb_thick_outputs(params, execution)
@@ -293,6 +280,8 @@ def v__measure_bb_thick(
     runner: Runner | None = None,
 ) -> VMeasureBbThickOutputs:
     """
+    @measure_bb_thick
+    
     Compute thickness of mask using ball and box method.
     
     Author: AFNI Developers
@@ -324,8 +313,6 @@ def v__measure_bb_thick(
     Returns:
         NamedTuple of outputs (described in `VMeasureBbThickOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__MEASURE_BB_THICK_METADATA)
     params = v__measure_bb_thick_params(
         maskset=maskset,
         surfset=surfset,
@@ -340,13 +327,13 @@ def v__measure_bb_thick(
         balls_only=balls_only,
         surfsmooth_method=surfsmooth_method,
     )
-    return v__measure_bb_thick_execute(params, execution)
+    return v__measure_bb_thick_execute(params, runner)
 
 
 __all__ = [
     "VMeasureBbThickOutputs",
-    "VMeasureBbThickParameters",
     "V__MEASURE_BB_THICK_METADATA",
     "v__measure_bb_thick",
+    "v__measure_bb_thick_execute",
     "v__measure_bb_thick_params",
 ]

niwrap_afni/afni/v__measure_erosion_thick.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__MEASURE_EROSION_THICK_METADATA = Metadata(
-    id="0a17dd4546f4d28205dbdff108358d9b46fa5306.boutiques",
+    id="38a8daf5a4a8dae931166c9e1c03b44c10b6b8df.boutiques",
     name="@measure_erosion_thick",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ V__MEASURE_EROSION_THICK_METADATA = Metadata(
 
 
 VMeasureErosionThickParameters = typing.TypedDict('VMeasureErosionThickParameters', {
-    "__STYXTYPE__": typing.Literal["@measure_erosion_thick"],
+    "@type": typing.NotRequired[typing.Literal["afni/@measure_erosion_thick"]],
+    "maskset": InputPathType,
+    "surfset": InputPathType,
+    "outdir": typing.NotRequired[str | None],
+    "resample": typing.NotRequired[str | None],
+    "surfsmooth": typing.NotRequired[float | None],
+    "smoothmm": typing.NotRequired[float | None],
+    "maxthick": typing.NotRequired[float | None],
+    "depthsearch": typing.NotRequired[float | None],
+    "keep_temp_files": bool,
+    "surfsmooth_method": typing.NotRequired[str | None],
+})
+VMeasureErosionThickParametersTagged = typing.TypedDict('VMeasureErosionThickParametersTagged', {
+    "@type": typing.Literal["afni/@measure_erosion_thick"],
     "maskset": InputPathType,
     "surfset": InputPathType,
     "outdir": typing.NotRequired[str | None],
@@ -26,43 +39,11 @@ VMeasureErosionThickParameters = typing.TypedDict('VMeasureErosionThickParameter
     "keep_temp_files": bool,
     "surfsmooth_method": 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_erosion_thick": v__measure_erosion_thick_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_erosion_thick": v__measure_erosion_thick_outputs,
-    }.get(t)
 
 
 class VMeasureErosionThickOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__measure_erosion_thick(...)`.
+    Output object returned when calling `VMeasureErosionThickParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -97,7 +78,7 @@ def v__measure_erosion_thick_params(
     depthsearch: float | None = None,
     keep_temp_files: bool = False,
     surfsmooth_method: str | None = None,
-) -> VMeasureErosionThickParameters:
+) -> VMeasureErosionThickParametersTagged:
     """
     Build parameters.
     
@@ -123,7 +104,7 @@ def v__measure_erosion_thick_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@measure_erosion_thick",
+        "@type": "afni/@measure_erosion_thick",
         "maskset": maskset,
         "surfset": surfset,
         "keep_temp_files": keep_temp_files,
@@ -162,48 +143,48 @@ def v__measure_erosion_thick_cargs(
     cargs.append("@measure_erosion_thick")
     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))
     ])
-    if params.get("outdir") is not None:
+    if params.get("outdir", None) is not 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("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("smoothmm") is not None:
+    if params.get("smoothmm", None) is not None:
         cargs.extend([
             "-smoothmm",
-            str(params.get("smoothmm"))
+            str(params.get("smoothmm", 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("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)
         ])
     return cargs
 
@@ -238,9 +219,11 @@ def v__measure_erosion_thick_outputs(
 
 def v__measure_erosion_thick_execute(
     params: VMeasureErosionThickParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VMeasureErosionThickOutputs:
     """
+    @measure_erosion_thick
+    
     Compute thickness of mask using erosion method.
     
     Author: AFNI Developers
@@ -249,10 +232,12 @@ def v__measure_erosion_thick_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VMeasureErosionThickOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MEASURE_EROSION_THICK_METADATA)
     params = execution.params(params)
     cargs = v__measure_erosion_thick_cargs(params, execution)
     ret = v__measure_erosion_thick_outputs(params, execution)
@@ -274,6 +259,8 @@ def v__measure_erosion_thick(
     runner: Runner | None = None,
 ) -> VMeasureErosionThickOutputs:
     """
+    @measure_erosion_thick
+    
     Compute thickness of mask using erosion method.
     
     Author: AFNI Developers
@@ -302,8 +289,6 @@ def v__measure_erosion_thick(
     Returns:
         NamedTuple of outputs (described in `VMeasureErosionThickOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__MEASURE_EROSION_THICK_METADATA)
     params = v__measure_erosion_thick_params(
         maskset=maskset,
         surfset=surfset,
@@ -316,13 +301,13 @@ def v__measure_erosion_thick(
         keep_temp_files=keep_temp_files,
         surfsmooth_method=surfsmooth_method,
     )
-    return v__measure_erosion_thick_execute(params, execution)
+    return v__measure_erosion_thick_execute(params, runner)
 
 
 __all__ = [
     "VMeasureErosionThickOutputs",
-    "VMeasureErosionThickParameters",
     "V__MEASURE_EROSION_THICK_METADATA",
     "v__measure_erosion_thick",
+    "v__measure_erosion_thick_execute",
     "v__measure_erosion_thick_params",
 ]