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

niwrap_afni/afni/sfim.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SFIM_METADATA = Metadata(
-    id="b0a8b5208cc61585402c5d268873f5a63b76a9e6.boutiques",
+    id="ad5768baaae7cebeadaf50152b4413144e7e8b36.boutiques",
     name="sfim",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,55 +14,29 @@ SFIM_METADATA = Metadata(
 
 
 SfimParameters = typing.TypedDict('SfimParameters', {
-    "__STYXTYPE__": typing.Literal["sfim"],
+    "@type": typing.NotRequired[typing.Literal["afni/sfim"]],
+    "input_images": list[InputPathType],
+    "sfint_file": typing.NotRequired[str | None],
+    "baseline_state": typing.NotRequired[str | None],
+    "local_base_option": bool,
+    "output_prefix": typing.NotRequired[str | None],
+})
+SfimParametersTagged = typing.TypedDict('SfimParametersTagged', {
+    "@type": typing.Literal["afni/sfim"],
     "input_images": list[InputPathType],
     "sfint_file": typing.NotRequired[str | None],
     "baseline_state": typing.NotRequired[str | None],
     "local_base_option": bool,
     "output_prefix": 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 {
-        "sfim": sfim_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 {
-        "sfim": sfim_outputs,
-    }.get(t)
 
 
 class SfimOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `sfim(...)`.
+    Output object returned when calling `SfimParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_files: OutputPathType | None
-    """Output image file for interval 'i' with task state name."""
 
 
 def sfim_params(
@@ -71,7 +45,7 @@ def sfim_params(
     baseline_state: str | None = None,
     local_base_option: bool = False,
     output_prefix: str | None = None,
-) -> SfimParameters:
+) -> SfimParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +65,7 @@ def sfim_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "sfim",
+        "@type": "afni/sfim",
         "input_images": input_images,
         "local_base_option": local_base_option,
     }
@@ -119,23 +93,23 @@ def sfim_cargs(
     """
     cargs = []
     cargs.append("sfim")
-    cargs.extend([execution.input_file(f) for f in params.get("input_images")])
-    if params.get("sfint_file") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("input_images", None)])
+    if params.get("sfint_file", None) is not None:
         cargs.extend([
             "-sfint",
-            params.get("sfint_file")
+            params.get("sfint_file", None)
         ])
-    if params.get("baseline_state") is not None:
+    if params.get("baseline_state", None) is not None:
         cargs.extend([
             "-base",
-            params.get("baseline_state")
+            params.get("baseline_state", None)
         ])
-    if params.get("local_base_option"):
+    if params.get("local_base_option", False):
         cargs.append("-localbase")
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
     return cargs
 
@@ -155,16 +129,17 @@ def sfim_outputs(
     """
     ret = SfimOutputs(
         root=execution.output_file("."),
-        output_files=execution.output_file(params.get("output_prefix") + ".*.i") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def sfim_execute(
     params: SfimParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SfimOutputs:
     """
+    sfim
+    
     Stepwise Functional IMages.
     
     Author: AFNI Developers
@@ -173,10 +148,12 @@ def sfim_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SfimOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SFIM_METADATA)
     params = execution.params(params)
     cargs = sfim_cargs(params, execution)
     ret = sfim_outputs(params, execution)
@@ -193,6 +170,8 @@ def sfim(
     runner: Runner | None = None,
 ) -> SfimOutputs:
     """
+    sfim
+    
     Stepwise Functional IMages.
     
     Author: AFNI Developers
@@ -215,8 +194,6 @@ def sfim(
     Returns:
         NamedTuple of outputs (described in `SfimOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SFIM_METADATA)
     params = sfim_params(
         input_images=input_images,
         sfint_file=sfint_file,
@@ -224,13 +201,13 @@ def sfim(
         local_base_option=local_base_option,
         output_prefix=output_prefix,
     )
-    return sfim_execute(params, execution)
+    return sfim_execute(params, runner)
 
 
 __all__ = [
     "SFIM_METADATA",
     "SfimOutputs",
-    "SfimParameters",
     "sfim",
+    "sfim_execute",
     "sfim_params",
 ]

niwrap_afni/afni/slow_surf_clustsim_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SLOW_SURF_CLUSTSIM_PY_METADATA = Metadata(
-    id="ddeecc1fb59992d9c9426870d78e92238ec8b21a.boutiques",
+    id="4536849b259e21d078656a34c845d549eaef3333.boutiques",
     name="slow_surf_clustsim.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ SLOW_SURF_CLUSTSIM_PY_METADATA = Metadata(
 
 
 SlowSurfClustsimPyParameters = typing.TypedDict('SlowSurfClustsimPyParameters', {
-    "__STYXTYPE__": typing.Literal["slow_surf_clustsim.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/slow_surf_clustsim.py"]],
+    "on_surface": typing.NotRequired[str | None],
+    "save_script": typing.NotRequired[str | None],
+    "print_script": bool,
+    "uvar": typing.NotRequired[list[str] | None],
+    "verbosity": typing.NotRequired[float | None],
+    "help": bool,
+    "hist": bool,
+    "show_default_cvars": bool,
+    "show_default_uvars": bool,
+    "show_valid_opts": bool,
+    "version": bool,
+})
+SlowSurfClustsimPyParametersTagged = typing.TypedDict('SlowSurfClustsimPyParametersTagged', {
+    "@type": typing.Literal["afni/slow_surf_clustsim.py"],
     "on_surface": typing.NotRequired[str | None],
     "save_script": typing.NotRequired[str | None],
     "print_script": bool,
@@ -27,42 +41,11 @@ SlowSurfClustsimPyParameters = typing.TypedDict('SlowSurfClustsimPyParameters',
     "show_valid_opts": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "slow_surf_clustsim.py": slow_surf_clustsim_py_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 SlowSurfClustsimPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `slow_surf_clustsim_py(...)`.
+    Output object returned when calling `SlowSurfClustsimPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -80,7 +63,7 @@ def slow_surf_clustsim_py_params(
     show_default_uvars: bool = False,
     show_valid_opts: bool = False,
     version: bool = False,
-) -> SlowSurfClustsimPyParameters:
+) -> SlowSurfClustsimPyParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +86,7 @@ def slow_surf_clustsim_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "slow_surf_clustsim.py",
+        "@type": "afni/slow_surf_clustsim.py",
         "print_script": print_script,
         "help": help_,
         "hist": hist,
@@ -138,39 +121,39 @@ def slow_surf_clustsim_py_cargs(
     """
     cargs = []
     cargs.append("slow_surf_clustsim.py")
-    if params.get("on_surface") is not None:
+    if params.get("on_surface", None) is not None:
         cargs.extend([
             "-on_surface",
-            params.get("on_surface")
+            params.get("on_surface", None)
         ])
-    if params.get("save_script") is not None:
+    if params.get("save_script", None) is not None:
         cargs.extend([
             "-save_script",
-            params.get("save_script")
+            params.get("save_script", None)
         ])
-    if params.get("print_script"):
+    if params.get("print_script", False):
         cargs.append("-print_script")
-    if params.get("uvar") is not None:
+    if params.get("uvar", None) is not None:
         cargs.extend([
             "-uvar",
-            *params.get("uvar")
+            *params.get("uvar", None)
         ])
-    if params.get("verbosity") is not None:
+    if params.get("verbosity", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity"))
+            str(params.get("verbosity", None))
         ])
-    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("show_default_cvars"):
+    if params.get("show_default_cvars", False):
         cargs.append("-show_default_cvars")
-    if params.get("show_default_uvars"):
+    if params.get("show_default_uvars", False):
         cargs.append("-show_default_uvars")
-    if params.get("show_valid_opts"):
+    if params.get("show_valid_opts", False):
         cargs.append("-show_valid_opts")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-ver")
     return cargs
 
@@ -196,9 +179,11 @@ def slow_surf_clustsim_py_outputs(
 
 def slow_surf_clustsim_py_execute(
     params: SlowSurfClustsimPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SlowSurfClustsimPyOutputs:
     """
+    slow_surf_clustsim.py
+    
     Generate a tcsh script to run clustsim on surface.
     
     Author: AFNI Developers
@@ -207,10 +192,12 @@ def slow_surf_clustsim_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SlowSurfClustsimPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SLOW_SURF_CLUSTSIM_PY_METADATA)
     params = execution.params(params)
     cargs = slow_surf_clustsim_py_cargs(params, execution)
     ret = slow_surf_clustsim_py_outputs(params, execution)
@@ -233,6 +220,8 @@ def slow_surf_clustsim_py(
     runner: Runner | None = None,
 ) -> SlowSurfClustsimPyOutputs:
     """
+    slow_surf_clustsim.py
+    
     Generate a tcsh script to run clustsim on surface.
     
     Author: AFNI Developers
@@ -258,8 +247,6 @@ def slow_surf_clustsim_py(
     Returns:
         NamedTuple of outputs (described in `SlowSurfClustsimPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SLOW_SURF_CLUSTSIM_PY_METADATA)
     params = slow_surf_clustsim_py_params(
         on_surface=on_surface,
         save_script=save_script,
@@ -273,13 +260,13 @@ def slow_surf_clustsim_py(
         show_valid_opts=show_valid_opts,
         version=version,
     )
-    return slow_surf_clustsim_py_execute(params, execution)
+    return slow_surf_clustsim_py_execute(params, runner)
 
 
 __all__ = [
     "SLOW_SURF_CLUSTSIM_PY_METADATA",
     "SlowSurfClustsimPyOutputs",
-    "SlowSurfClustsimPyParameters",
     "slow_surf_clustsim_py",
+    "slow_surf_clustsim_py_execute",
     "slow_surf_clustsim_py_params",
 ]

niwrap_afni/afni/spharm_deco.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SPHARM_DECO_METADATA = Metadata(
-    id="17ed1e33cae4fff9df92d0adb8f450d2e0de7d46.boutiques",
+    id="136eb925672dddd41ae7dc46f8b5ae5e6222005b.boutiques",
     name="SpharmDeco",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ SPHARM_DECO_METADATA = Metadata(
 
 
 SpharmDecoParameters = typing.TypedDict('SpharmDecoParameters', {
-    "__STYXTYPE__": typing.Literal["SpharmDeco"],
+    "@type": typing.NotRequired[typing.Literal["afni/SpharmDeco"]],
+    "i_type_s": InputPathType,
+    "unit_sph_label": str,
+    "order_l": float,
+    "i_type_sd": typing.NotRequired[list[InputPathType] | None],
+    "data_d": typing.NotRequired[InputPathType | None],
+    "bases_prefix": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "o_type_sdr": typing.NotRequired[list[InputPathType] | None],
+    "debug": typing.NotRequired[float | None],
+    "sigma": typing.NotRequired[float | None],
+})
+SpharmDecoParametersTagged = typing.TypedDict('SpharmDecoParametersTagged', {
+    "@type": typing.Literal["afni/SpharmDeco"],
     "i_type_s": InputPathType,
     "unit_sph_label": str,
     "order_l": float,
@@ -26,51 +39,15 @@ SpharmDecoParameters = typing.TypedDict('SpharmDecoParameters', {
     "debug": typing.NotRequired[float | None],
     "sigma": 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 {
-        "SpharmDeco": spharm_deco_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 {
-        "SpharmDeco": spharm_deco_outputs,
-    }.get(t)
 
 
 class SpharmDecoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `spharm_deco(...)`.
+    Output object returned when calling `SpharmDecoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    harmonics_file: OutputPathType
-    """File for harmonics of each order l."""
-    beta_coefficients: OutputPathType
-    """Beta coefficients for each data column."""
-    reconstructed_data: OutputPathType
+    reconstructed_data: OutputPathType | None
     """Reconstructed data or surface files named based on PREFIX."""
 
 
@@ -85,7 +62,7 @@ def spharm_deco_params(
     o_type_sdr: list[InputPathType] | None = None,
     debug: float | None = None,
     sigma: float | None = None,
-) -> SpharmDecoParameters:
+) -> SpharmDecoParametersTagged:
     """
     Build parameters.
     
@@ -109,7 +86,7 @@ def spharm_deco_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SpharmDeco",
+        "@type": "afni/SpharmDeco",
         "i_type_s": i_type_s,
         "unit_sph_label": unit_sph_label,
         "order_l": order_l,
@@ -146,28 +123,28 @@ def spharm_deco_cargs(
     """
     cargs = []
     cargs.append("SpharmDeco")
-    cargs.append(execution.input_file(params.get("i_type_s")))
-    cargs.append(params.get("unit_sph_label"))
-    cargs.append(str(params.get("order_l")))
-    if params.get("i_type_sd") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("i_type_sd")])
-    if params.get("data_d") is not None:
-        cargs.append(execution.input_file(params.get("data_d")))
-    if params.get("bases_prefix") is not None:
-        cargs.append(params.get("bases_prefix"))
-    if params.get("prefix") is not None:
-        cargs.append(params.get("prefix"))
-    if params.get("o_type_sdr") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("o_type_sdr")])
-    if params.get("debug") is not None:
+    cargs.append(execution.input_file(params.get("i_type_s", None)))
+    cargs.append(params.get("unit_sph_label", None))
+    cargs.append(str(params.get("order_l", None)))
+    if params.get("i_type_sd", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("i_type_sd", None)])
+    if params.get("data_d", None) is not None:
+        cargs.append(execution.input_file(params.get("data_d", None)))
+    if params.get("bases_prefix", None) is not None:
+        cargs.append(params.get("bases_prefix", None))
+    if params.get("prefix", None) is not None:
+        cargs.append(params.get("prefix", None))
+    if params.get("o_type_sdr", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("o_type_sdr", None)])
+    if params.get("debug", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug"))
+            str(params.get("debug", None))
         ])
-    if params.get("sigma") is not None:
+    if params.get("sigma", None) is not None:
         cargs.extend([
             "-sigma",
-            str(params.get("sigma"))
+            str(params.get("sigma", None))
         ])
     return cargs
 
@@ -187,18 +164,18 @@ def spharm_deco_outputs(
     """
     ret = SpharmDecoOutputs(
         root=execution.output_file("."),
-        harmonics_file=execution.output_file("BASES_PREFIX.sph*.1D"),
-        beta_coefficients=execution.output_file("PREFIX.beta.col*.1D.dset"),
-        reconstructed_data=execution.output_file("<PREFIX>_reconstructed"),
+        reconstructed_data=execution.output_file(params.get("prefix", None) + "_reconstructed") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def spharm_deco_execute(
     params: SpharmDecoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SpharmDecoOutputs:
     """
+    SpharmDeco
+    
     Spherical Harmonics Decomposition of a surface's coordinates or data.
     
     Author: AFNI Developers
@@ -207,10 +184,12 @@ def spharm_deco_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SpharmDecoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SPHARM_DECO_METADATA)
     params = execution.params(params)
     cargs = spharm_deco_cargs(params, execution)
     ret = spharm_deco_outputs(params, execution)
@@ -232,6 +211,8 @@ def spharm_deco(
     runner: Runner | None = None,
 ) -> SpharmDecoOutputs:
     """
+    SpharmDeco
+    
     Spherical Harmonics Decomposition of a surface's coordinates or data.
     
     Author: AFNI Developers
@@ -258,8 +239,6 @@ def spharm_deco(
     Returns:
         NamedTuple of outputs (described in `SpharmDecoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SPHARM_DECO_METADATA)
     params = spharm_deco_params(
         i_type_s=i_type_s,
         unit_sph_label=unit_sph_label,
@@ -272,13 +251,13 @@ def spharm_deco(
         debug=debug,
         sigma=sigma,
     )
-    return spharm_deco_execute(params, execution)
+    return spharm_deco_execute(params, runner)
 
 
 __all__ = [
     "SPHARM_DECO_METADATA",
     "SpharmDecoOutputs",
-    "SpharmDecoParameters",
     "spharm_deco",
+    "spharm_deco_execute",
     "spharm_deco_params",
 ]