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

niwrap_afni/afni/v__surf_to_vol_spackle.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SURF_TO_VOL_SPACKLE_METADATA = Metadata(
-    id="b6dc12ea2739e07bf96f46f96b9e18d749e7c831.boutiques",
+    id="f935e80f0e8c3a679fc91decb05be875ab2940b9.boutiques",
     name="@surf_to_vol_spackle",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V__SURF_TO_VOL_SPACKLE_METADATA = Metadata(
 
 
 VSurfToVolSpackleParameters = typing.TypedDict('VSurfToVolSpackleParameters', {
-    "__STYXTYPE__": typing.Literal["@surf_to_vol_spackle"],
+    "@type": typing.NotRequired[typing.Literal["afni/@surf_to_vol_spackle"]],
+    "maskset": InputPathType,
+    "spec": InputPathType,
+    "surfA": str,
+    "surfB": typing.NotRequired[str | None],
+    "surfset": InputPathType,
+    "prefix": str,
+    "normal_vector_length": typing.NotRequired[float | None],
+    "search_radius": typing.NotRequired[float | None],
+    "num_steps": typing.NotRequired[float | None],
+    "keep_temp_files": bool,
+    "max_iters": typing.NotRequired[float | None],
+    "use_mode": bool,
+    "datum_type": typing.NotRequired[str | None],
+    "ignore_unknown_options": bool,
+})
+VSurfToVolSpackleParametersTagged = typing.TypedDict('VSurfToVolSpackleParametersTagged', {
+    "@type": typing.Literal["afni/@surf_to_vol_spackle"],
     "maskset": InputPathType,
     "spec": InputPathType,
     "surfA": str,
@@ -30,43 +47,11 @@ VSurfToVolSpackleParameters = typing.TypedDict('VSurfToVolSpackleParameters', {
     "datum_type": typing.NotRequired[str | None],
     "ignore_unknown_options": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@surf_to_vol_spackle": v__surf_to_vol_spackle_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 {
-        "@surf_to_vol_spackle": v__surf_to_vol_spackle_outputs,
-    }.get(t)
 
 
 class VSurfToVolSpackleOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__surf_to_vol_spackle(...)`.
+    Output object returned when calling `VSurfToVolSpackleParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +74,7 @@ def v__surf_to_vol_spackle_params(
     use_mode: bool = False,
     datum_type: str | None = None,
     ignore_unknown_options: bool = False,
-) -> VSurfToVolSpackleParameters:
+) -> VSurfToVolSpackleParametersTagged:
     """
     Build parameters.
     
@@ -117,7 +102,7 @@ def v__surf_to_vol_spackle_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@surf_to_vol_spackle",
+        "@type": "afni/@surf_to_vol_spackle",
         "maskset": maskset,
         "spec": spec,
         "surfA": surf_a,
@@ -157,43 +142,43 @@ def v__surf_to_vol_spackle_cargs(
     """
     cargs = []
     cargs.append("@surf_to_vol_spackle")
-    cargs.append(execution.input_file(params.get("maskset")))
-    cargs.append(execution.input_file(params.get("spec")))
-    cargs.append(params.get("surfA"))
-    if params.get("surfB") is not None:
-        cargs.append(params.get("surfB"))
-    cargs.append(execution.input_file(params.get("surfset")))
-    cargs.append(params.get("prefix"))
-    if params.get("normal_vector_length") is not None:
+    cargs.append(execution.input_file(params.get("maskset", None)))
+    cargs.append(execution.input_file(params.get("spec", None)))
+    cargs.append(params.get("surfA", None))
+    if params.get("surfB", None) is not None:
+        cargs.append(params.get("surfB", None))
+    cargs.append(execution.input_file(params.get("surfset", None)))
+    cargs.append(params.get("prefix", None))
+    if params.get("normal_vector_length", None) is not None:
         cargs.extend([
             "-f_pn_mm",
-            str(params.get("normal_vector_length"))
+            str(params.get("normal_vector_length", None))
         ])
-    if params.get("search_radius") is not None:
+    if params.get("search_radius", None) is not None:
         cargs.extend([
             "-meanrad",
-            str(params.get("search_radius"))
+            str(params.get("search_radius", None))
         ])
-    if params.get("num_steps") is not None:
+    if params.get("num_steps", None) is not None:
         cargs.extend([
             "-nsteps",
-            str(params.get("num_steps"))
+            str(params.get("num_steps", None))
         ])
-    if params.get("keep_temp_files"):
+    if params.get("keep_temp_files", False):
         cargs.append("-keep_temp_files")
-    if params.get("max_iters") is not None:
+    if params.get("max_iters", None) is not None:
         cargs.extend([
             "-maxiters",
-            str(params.get("max_iters"))
+            str(params.get("max_iters", None))
         ])
-    if params.get("use_mode"):
+    if params.get("use_mode", False):
         cargs.append("-mode")
-    if params.get("datum_type") is not None:
+    if params.get("datum_type", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datum_type")
+            params.get("datum_type", None)
         ])
-    if params.get("ignore_unknown_options"):
+    if params.get("ignore_unknown_options", False):
         cargs.append("-ignore_unknown_options")
     return cargs
 
@@ -213,18 +198,20 @@ def v__surf_to_vol_spackle_outputs(
     """
     ret = VSurfToVolSpackleOutputs(
         root=execution.output_file("."),
-        output_volume=execution.output_file(params.get("prefix") + ".nii.gz"),
+        output_volume=execution.output_file(params.get("prefix", None) + ".nii.gz"),
     )
     return ret
 
 
 def v__surf_to_vol_spackle_execute(
     params: VSurfToVolSpackleParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSurfToVolSpackleOutputs:
     """
-    Project data from a surface dataset into a volume primarily using 3dSurf2Vol but
-    then filling any holes with an iterative smoothing procedure.
+    @surf_to_vol_spackle
+    
+    Project data from a surface dataset into a volume primarily using 3dSurf2Vol
+    but then filling any holes with an iterative smoothing procedure.
     
     Author: AFNI Developers
     
@@ -232,10 +219,12 @@ def v__surf_to_vol_spackle_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSurfToVolSpackleOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SURF_TO_VOL_SPACKLE_METADATA)
     params = execution.params(params)
     cargs = v__surf_to_vol_spackle_cargs(params, execution)
     ret = v__surf_to_vol_spackle_outputs(params, execution)
@@ -261,8 +250,10 @@ def v__surf_to_vol_spackle(
     runner: Runner | None = None,
 ) -> VSurfToVolSpackleOutputs:
     """
-    Project data from a surface dataset into a volume primarily using 3dSurf2Vol but
-    then filling any holes with an iterative smoothing procedure.
+    @surf_to_vol_spackle
+    
+    Project data from a surface dataset into a volume primarily using 3dSurf2Vol
+    but then filling any holes with an iterative smoothing procedure.
     
     Author: AFNI Developers
     
@@ -292,8 +283,6 @@ def v__surf_to_vol_spackle(
     Returns:
         NamedTuple of outputs (described in `VSurfToVolSpackleOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SURF_TO_VOL_SPACKLE_METADATA)
     params = v__surf_to_vol_spackle_params(
         maskset=maskset,
         spec=spec,
@@ -310,13 +299,13 @@ def v__surf_to_vol_spackle(
         datum_type=datum_type,
         ignore_unknown_options=ignore_unknown_options,
     )
-    return v__surf_to_vol_spackle_execute(params, execution)
+    return v__surf_to_vol_spackle_execute(params, runner)
 
 
 __all__ = [
     "VSurfToVolSpackleOutputs",
-    "VSurfToVolSpackleParameters",
     "V__SURF_TO_VOL_SPACKLE_METADATA",
     "v__surf_to_vol_spackle",
+    "v__surf_to_vol_spackle_execute",
     "v__surf_to_vol_spackle_params",
 ]

niwrap_afni/afni/v__t1scale.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__T1SCALE_METADATA = Metadata(
-    id="89645e221a5cc9e1118b45d0730af83cf88ad32b.boutiques",
+    id="47d59aac1ea3196ec67f51d01cd720d77bd6e68c.boutiques",
     name="@T1scale",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V__T1SCALE_METADATA = Metadata(
 
 
 VT1scaleParameters = typing.TypedDict('VT1scaleParameters', {
-    "__STYXTYPE__": typing.Literal["@T1scale"],
+    "@type": typing.NotRequired[typing.Literal["afni/@T1scale"]],
+    "t1_volume": InputPathType,
+    "pd_volume": typing.NotRequired[InputPathType | None],
+    "output_directory": typing.NotRequired[str | None],
+    "align": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "head_mask": bool,
+    "unmasked_uni": bool,
+    "masked_uni": bool,
+    "echo": bool,
+    "help": bool,
+    "h_web": bool,
+    "h_view": bool,
+    "all_opts": bool,
+    "h_find_word": typing.NotRequired[str | None],
+})
+VT1scaleParametersTagged = typing.TypedDict('VT1scaleParametersTagged', {
+    "@type": typing.Literal["afni/@T1scale"],
     "t1_volume": InputPathType,
     "pd_volume": typing.NotRequired[InputPathType | None],
     "output_directory": typing.NotRequired[str | None],
@@ -30,43 +47,11 @@ VT1scaleParameters = typing.TypedDict('VT1scaleParameters', {
     "all_opts": bool,
     "h_find_word": 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 {
-        "@T1scale": v__t1scale_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 {
-        "@T1scale": v__t1scale_outputs,
-    }.get(t)
 
 
 class VT1scaleOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__t1scale(...)`.
+    Output object returned when calling `VT1scaleParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +78,7 @@ def v__t1scale_params(
     h_view: bool = False,
     all_opts: bool = False,
     h_find_word: str | None = None,
-) -> VT1scaleParameters:
+) -> VT1scaleParametersTagged:
     """
     Build parameters.
     
@@ -120,7 +105,7 @@ def v__t1scale_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@T1scale",
+        "@type": "afni/@T1scale",
         "t1_volume": t1_volume,
         "align": align,
         "head_mask": head_mask,
@@ -160,45 +145,45 @@ def v__t1scale_cargs(
     cargs.append("@T1scale")
     cargs.extend([
         "-T1",
-        execution.input_file(params.get("t1_volume"))
+        execution.input_file(params.get("t1_volume", None))
     ])
-    if params.get("pd_volume") is not None:
+    if params.get("pd_volume", None) is not None:
         cargs.extend([
             "-PD",
-            execution.input_file(params.get("pd_volume"))
+            execution.input_file(params.get("pd_volume", None))
         ])
-    if params.get("output_directory") is not None:
+    if params.get("output_directory", None) is not None:
         cargs.extend([
             "-odir",
-            params.get("output_directory")
+            params.get("output_directory", None)
         ])
-    if params.get("align"):
+    if params.get("align", False):
         cargs.append("-align")
-    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("head_mask"):
+    if params.get("head_mask", False):
         cargs.append("-head_mask")
-    if params.get("unmasked_uni"):
+    if params.get("unmasked_uni", False):
         cargs.append("-unmasked_uni")
-    if params.get("masked_uni"):
+    if params.get("masked_uni", False):
         cargs.append("-masked_uni")
-    if params.get("echo"):
+    if params.get("echo", False):
         cargs.append("-echo")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("h_web"):
+    if params.get("h_web", False):
         cargs.append("-h_web")
-    if params.get("h_view"):
+    if params.get("h_view", False):
         cargs.append("-hview")
-    if params.get("all_opts"):
+    if params.get("all_opts", False):
         cargs.append("-all_opts")
-    if params.get("h_find_word") is not None:
+    if params.get("h_find_word", None) is not None:
         cargs.extend([
             "-h_find",
-            params.get("h_find_word")
+            params.get("h_find_word", None)
         ])
     return cargs
 
@@ -227,9 +212,11 @@ def v__t1scale_outputs(
 
 def v__t1scale_execute(
     params: VT1scaleParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VT1scaleOutputs:
     """
+    @T1scale
+    
     Fix bias field shading in T1 by scaling it with PD image. You can also get a
     decent result even without the PD volume.
     
@@ -239,10 +226,12 @@ def v__t1scale_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VT1scaleOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__T1SCALE_METADATA)
     params = execution.params(params)
     cargs = v__t1scale_cargs(params, execution)
     ret = v__t1scale_outputs(params, execution)
@@ -268,6 +257,8 @@ def v__t1scale(
     runner: Runner | None = None,
 ) -> VT1scaleOutputs:
     """
+    @T1scale
+    
     Fix bias field shading in T1 by scaling it with PD image. You can also get a
     decent result even without the PD volume.
     
@@ -298,8 +289,6 @@ def v__t1scale(
     Returns:
         NamedTuple of outputs (described in `VT1scaleOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__T1SCALE_METADATA)
     params = v__t1scale_params(
         t1_volume=t1_volume,
         pd_volume=pd_volume,
@@ -316,13 +305,13 @@ def v__t1scale(
         all_opts=all_opts,
         h_find_word=h_find_word,
     )
-    return v__t1scale_execute(params, execution)
+    return v__t1scale_execute(params, runner)
 
 
 __all__ = [
     "VT1scaleOutputs",
-    "VT1scaleParameters",
     "V__T1SCALE_METADATA",
     "v__t1scale",
+    "v__t1scale_execute",
     "v__t1scale_params",
 ]

niwrap_afni/afni/v__thickness_master.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__THICKNESS_MASTER_METADATA = Metadata(
-    id="16b2f3c5546e0b51fc57c90130ccb25d83ec244f.boutiques",
+    id="72bf9288b5e5a62c999168abfffc7a9e9622c84f.boutiques",
     name="@thickness_master",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,22 @@ V__THICKNESS_MASTER_METADATA = Metadata(
 
 
 VThicknessMasterParameters = typing.TypedDict('VThicknessMasterParameters', {
-    "__STYXTYPE__": typing.Literal["@thickness_master"],
+    "@type": typing.NotRequired[typing.Literal["afni/@thickness_master"]],
+    "maskset": InputPathType,
+    "surfset": InputPathType,
+    "outdir": typing.NotRequired[str | None],
+})
+VThicknessMasterParametersTagged = typing.TypedDict('VThicknessMasterParametersTagged', {
+    "@type": typing.Literal["afni/@thickness_master"],
     "maskset": InputPathType,
     "surfset": InputPathType,
     "outdir": 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 {
-        "@thickness_master": v__thickness_master_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 {
-        "@thickness_master": v__thickness_master_outputs,
-    }.get(t)
 
 
 class VThicknessMasterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__thickness_master(...)`.
+    Output object returned when calling `VThicknessMasterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +45,7 @@ def v__thickness_master_params(
     maskset: InputPathType,
     surfset: InputPathType,
     outdir: str | None = None,
-) -> VThicknessMasterParameters:
+) -> VThicknessMasterParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +59,7 @@ def v__thickness_master_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@thickness_master",
+        "@type": "afni/@thickness_master",
         "maskset": maskset,
         "surfset": surfset,
     }
@@ -111,16 +85,16 @@ def v__thickness_master_cargs(
     cargs.append("@thickness_master")
     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)
         ])
     return cargs
 
@@ -140,18 +114,20 @@ def v__thickness_master_outputs(
     """
     ret = VThicknessMasterOutputs(
         root=execution.output_file("."),
-        output_bb_dir=execution.output_file(params.get("outdir") + "_bb/") if (params.get("outdir") is not None) else None,
-        output_erode_dir=execution.output_file(params.get("outdir") + "_erode/") if (params.get("outdir") is not None) else None,
-        output_in2out_dir=execution.output_file(params.get("outdir") + "_in2out/") if (params.get("outdir") is not None) else None,
+        output_bb_dir=execution.output_file(params.get("outdir", None) + "_bb/") if (params.get("outdir") is not None) else None,
+        output_erode_dir=execution.output_file(params.get("outdir", None) + "_erode/") if (params.get("outdir") is not None) else None,
+        output_in2out_dir=execution.output_file(params.get("outdir", None) + "_in2out/") if (params.get("outdir") is not None) else None,
     )
     return ret
 
 
 def v__thickness_master_execute(
     params: VThicknessMasterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VThicknessMasterOutputs:
     """
+    @thickness_master
+    
     Compute cortical thickness using mask and surface datasets.
     
     Author: AFNI Developers
@@ -160,10 +136,12 @@ def v__thickness_master_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VThicknessMasterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__THICKNESS_MASTER_METADATA)
     params = execution.params(params)
     cargs = v__thickness_master_cargs(params, execution)
     ret = v__thickness_master_outputs(params, execution)
@@ -178,6 +156,8 @@ def v__thickness_master(
     runner: Runner | None = None,
 ) -> VThicknessMasterOutputs:
     """
+    @thickness_master
+    
     Compute cortical thickness using mask and surface datasets.
     
     Author: AFNI Developers
@@ -194,20 +174,18 @@ def v__thickness_master(
     Returns:
         NamedTuple of outputs (described in `VThicknessMasterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__THICKNESS_MASTER_METADATA)
     params = v__thickness_master_params(
         maskset=maskset,
         surfset=surfset,
         outdir=outdir,
     )
-    return v__thickness_master_execute(params, execution)
+    return v__thickness_master_execute(params, runner)
 
 
 __all__ = [
     "VThicknessMasterOutputs",
-    "VThicknessMasterParameters",
     "V__THICKNESS_MASTER_METADATA",
     "v__thickness_master",
+    "v__thickness_master_execute",
     "v__thickness_master_params",
 ]