opticalib 2.1.3__tar.gz → 2.2.0__tar.gz

opticalib-2.2.0/CITATION.bib

@@ -0,0 +1,10 @@
+@misc{opticalib, 
+    doi = {10.20371/INAF/SW/2026_00013}, 
+    url = {https://openscience.inaf.it/?page_id=696}, 
+    author = {{Pietro Ferraiuolo} and {Marco Xompero} and {Runa Briguglio} and {Matteo Menessini}}, 
+    language = {en}, 
+    title = {OPTICALIB: A Python Framework for Adaptive Optics Experimentation}, 
+    publisher = {O.A. Arcetri}, 
+    year = {2025}, 
+    copyright = {MIT License}
+}

{opticalib-2.1.3 → opticalib-2.2.0}/MANIFEST.in

@@ -1,8 +1,9 @@
 include README.md
-include requirements.txt
+include LICENSE
+include CITATION.bib
 include opticalib/core/_configurations/configuration.yaml
-include setup_calpy.py
-include opticalib/__init_script__/initCalpy.py
 include opticalib/simulator/_API/alpao_conf.yaml
+include opticalib/__init_script__/initCalpy.py
 recursive-include opticalib/gui/resources *.svg *.png *.ico
-recursive-include labott *.py
+graft tests
+global-exclude __pycache__ *.py[cod]

{opticalib-2.1.3/opticalib.egg-info → opticalib-2.2.0}/PKG-INFO

@@ -1,14 +1,14 @@
 Metadata-Version: 2.4
 Name: opticalib
-Version: 2.1.3
+Version: 2.2.0
 Summary: This package is a python interface for laboratory adaptive optics systems, with a focus on the calibration of deformable mirrors (DMs) and the acquisition of wavefront data using wavefront sensors.
-Home-page: https://github.com/ArcetriAdaptiveOptics/opticalib
-Author: Adaptive Optics Group - INAF - Osservatorio Astrofisico di Arcetri
-Author-email: pietro.ferraiuolo@inaf.it
-Maintainer: Pietro Ferraiuolo
-License: MIT License
+Author-email: Adaptive Optics Group - INAF - Osservatorio Astrofisico di Arcetri <pietro.ferraiuolo@inaf.it>
+Maintainer-email: Pietro Ferraiuolo <pietro.ferraiuolo@inaf.it>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/ArcetriAdaptiveOptics/opticalib
+Project-URL: Repository, https://github.com/ArcetriAdaptiveOptics/opticalib
+Project-URL: Issues, https://github.com/ArcetriAdaptiveOptics/opticalib/issues
 Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX :: Linux
 Classifier: Operating System :: MacOS
@@ -24,37 +24,43 @@ Requires-Dist: pipython
 Requires-Dist: photutils
 Requires-Dist: scipy
 Requires-Dist: ruamel.yaml
+Requires-Dist: PyYAML
 Requires-Dist: Pyro4
 Requires-Dist: h5py
 Requires-Dist: jdcal
 Requires-Dist: tqdm
 Requires-Dist: matplotlib
-Requires-Dist: xupy
 Requires-Dist: numpy
-Requires-Dist: qtconsole
-Requires-Dist: PyYAML
-Requires-Dist: PySide6-Essentials
-Requires-Dist: QtPy
-Requires-Dist: ipykernel
-Requires-Dist: jupyter_client
-Requires-Dist: pyqtgraph
-Requires-Dist: qtawesome
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: license
+Requires-Dist: rbfgpu
+Requires-Dist: xupy>=2.0
+Requires-Dist: ipython
+Provides-Extra: gui
+Requires-Dist: PySide6-Essentials; extra == "gui"
+Requires-Dist: QtPy; extra == "gui"
+Requires-Dist: qtconsole; extra == "gui"
+Requires-Dist: ipykernel; extra == "gui"
+Requires-Dist: jupyter_client; extra == "gui"
+Requires-Dist: pyqtgraph; extra == "gui"
+Requires-Dist: qtawesome; extra == "gui"
+Requires-Dist: psutil; extra == "gui"
+Provides-Extra: cuda12
+Requires-Dist: xupy[cuda12]>=2.0; extra == "cuda12"
+Provides-Extra: cuda13
+Requires-Dist: xupy[cuda13]>=2.0; extra == "cuda13"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: dev
+Requires-Dist: opticalib[gui,test]; extra == "dev"
+Requires-Dist: flake8; extra == "dev"
 Dynamic: license-file
-Dynamic: maintainer
-Dynamic: requires-dist
-Dynamic: requires-python
-Dynamic: summary
 
 # OptiCalib : python framework for OPTical CALibration of deformable mirrors and AO experimentation
 
 ![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/ArcetriAdaptiveOptics/opticalib/tests.yml)
+[![PyPI version](https://img.shields.io/pypi/v/opticalib.svg)](https://pypi.org/project/opticalib/)
+[![Python versions](https://img.shields.io/pypi/pyversions/opticalib.svg)](https://pypi.org/project/opticalib/)
+[![License: MIT](https://img.shields.io/pypi/l/opticalib.svg)](LICENSE)
 
 `Adaptive Optics Group, INAF - Osservatorio Astrofisico di Arcetri`
 
@@ -86,6 +92,14 @@ The latests, stable, version can be installed from pypi:
 pip install opticalib
 ```
 
+The base install contains everything needed to talk to the hardware, run the simulators and the calibration routines, and use the `calpy` shell. Two optional extras add the rest:
+
+```bash
+pip install "opticalib[gui]"      # the graphical interface (calpy --gui / OptiCalib)
+pip install "opticalib[cuda13]"   # GPU backend (CuPy, via xupy); use cuda12 for CUDA 12.x
+pip install "opticalib[gui,cuda13]"  # extras can be combined
+```
+
 The in-development version can be installed directly from this repository:
 
 ```bash

{opticalib-2.1.3 → opticalib-2.2.0}/README.md

@@ -1,6 +1,9 @@
 # OptiCalib : python framework for OPTical CALibration of deformable mirrors and AO experimentation
 
 ![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/ArcetriAdaptiveOptics/opticalib/tests.yml)
+[![PyPI version](https://img.shields.io/pypi/v/opticalib.svg)](https://pypi.org/project/opticalib/)
+[![Python versions](https://img.shields.io/pypi/pyversions/opticalib.svg)](https://pypi.org/project/opticalib/)
+[![License: MIT](https://img.shields.io/pypi/l/opticalib.svg)](LICENSE)
 
 `Adaptive Optics Group, INAF - Osservatorio Astrofisico di Arcetri`
 
@@ -32,6 +35,14 @@ The latests, stable, version can be installed from pypi:
 pip install opticalib
 ```
 
+The base install contains everything needed to talk to the hardware, run the simulators and the calibration routines, and use the `calpy` shell. Two optional extras add the rest:
+
+```bash
+pip install "opticalib[gui]"      # the graphical interface (calpy --gui / OptiCalib)
+pip install "opticalib[cuda13]"   # GPU backend (CuPy, via xupy); use cuda12 for CUDA 12.x
+pip install "opticalib[gui,cuda13]"  # extras can be combined
+```
+
 The in-development version can be installed directly from this repository:
 
 ```bash

{opticalib-2.1.3 → opticalib-2.2.0}/opticalib/__init__.py

@@ -5,20 +5,15 @@ OPTICALIB: adaptive OPTIcs package for dm CALIBration
 Author(s)
 ---------
 - Pietro Ferraiuolo : pietro.ferraiuolo@inaf.it
+- Runa Briguglio: runa.briguglio@inaf.it
+- Marco Xompero: marco.xompero@inaf.it
+- Matteo Menessini: matteo.menessini@inaf.it
 
 Description
 -----------
 OptiCalib is a package for the control of laboratory instrumentations, like
 Interferometers and Deformable Mirrors. It also provides tools for the
 analysis of wavefronts and images.
-
-How to Use:
------------
-```python
-> import opticalib
-> interf = opticalib.PhaseCam('193.206.155.218', 8011)
-> img = interf.acquire_map()
-```
 """
 
 from __future__ import annotations
@@ -34,13 +29,6 @@ from .core.root import (
 from .core import config
 from .core import _types as typings
 from .core.fitsarray import fits_array
-from .devices import *
-from .devices.interferometer import _4DInterferometer
-
-get_camera_settings = _4DInterferometer.get_camera_settings
-get_frame_rate = _4DInterferometer.get_frame_rate
-
-del _4DInterferometer
 
 from . import (
     analyzer,
@@ -51,6 +39,14 @@ from . import (
     visualization,
 )
 
+from .devices.interferometer import _4DInterferometer
+
+get_camera_settings = _4DInterferometer.get_camera_settings
+get_frame_rate = _4DInterferometer.get_frame_rate
+del _4DInterferometer
+
+from .devices import *
+
 vis = visualization
 
 __all__ = [

{opticalib-2.1.3 → opticalib-2.2.0}/opticalib/__version__.py

@@ -9,7 +9,7 @@ Pietro Ferraiuolo
 __title__ = "opticalib"
 __long_title__ = "OPTICALIB : python framework for OPTIcal CALIBration of deformable mirrors and adaptive optics experimentation"
 __description__ = "This package is a python interface for laboratory adaptive optics systems, with a focus on the calibration of deformable mirrors (DMs) and the acquisition of wavefront data using wavefront sensors."
-__version__ = "2.1.3"
+__version__ = "2.2.0"
 __author__ = "Adaptive Optics Group - INAF - Osservatorio Astrofisico di Arcetri"
 __maintainer__ = "Pietro Ferraiuolo"
 __author_email__ = "pietro.ferraiuolo@inaf.it"

opticalib-2.2.0/opticalib/analyzer/__init__.py

@@ -0,0 +1,13 @@
+from .image_processing import *
+from .signals import *
+from .timeseries import *
+
+
+def _get_safe_interf_fullframe():
+    from ..devices.interferometer import _4DInterferometer
+
+    func = _4DInterferometer.into_full_frame
+    return func
+
+
+into_4d_full_frame = _get_safe_interf_fullframe()

{opticalib-2.1.3 → opticalib-2.2.0}/opticalib/analyzer/image_processing.py

@@ -20,6 +20,38 @@ from ..ground import osutils as osu, modal_decomposer as _md
 from scipy import stats as _stats, fft as _fft, ndimage as _ndimage
 
 
+def pad_image_to_shape(
+    img: _ot.ImageData,
+    shape: tuple[int, int],
+    offset: tuple[int, int],
+    fill_value: float = 0.0,
+) -> _ot.ImageData:
+    """
+    Pads an image to a specified shape with a given offset and fill value.
+
+    Parameters
+    ----------
+    img : _ot.ImageData
+        The image to be padded.
+    shape : tuple[int, int]
+        The target shape (height, width) for the padded image.
+    offset : tuple[int, int]
+        The (y, x) offset at which to place the original image in the padded image.
+    fill_value : float, optional
+        The value to fill the padded areas with. Default is 0.
+
+    Returns
+    -------
+    padded_img : _ot.ImageData
+        The padded image.
+    """
+    padded_img = _np.full(shape, fill_value)
+    y, x = offset
+    h, w = _np.shape(img)
+    padded_img[y : y + h, x : x + w] = img.data
+    return padded_img
+
+
 def frame(idx: int, mylist: list[_ot.ImageData] | _ot.CubeData) -> _ot.ImageData:
     """
     Returns a single frame from a list of files or from a cube.
@@ -225,7 +257,7 @@ def push_pull_reduction_algorithm(
     # Template weights computation
     w = _xp.asarray(
         template.astype(_np.result_type(template, imagelist[0].data), copy=True),
-        dtype=_xp.float,
+        dtype=_ot.compute_float(),
     )
     if n_images > 2:
         w[1:-1] *= 2.0
@@ -233,9 +265,9 @@ def push_pull_reduction_algorithm(
     master_mask = _np.logical_or.reduce([ima.mask for ima in imagelist])
     # Compute weighted sum over realizations on raw data
     stack = _xp.stack(
-        [_xp.asarray(ima.data, dtype=_xp.float) for ima in imagelist],
+        [_xp.asarray(ima.data, dtype=_ot.compute_float()) for ima in imagelist],
         axis=0,
-        dtype=_xp.float,
+        dtype=_ot.compute_float(),
     )  # (n, H, W)
     image = _xp.asnumpy(_xp.tensordot(w, stack, axes=(0, 0)))  # (H, W)
 
@@ -860,6 +892,8 @@ def rebin2_d_array(
 
 
 __all__ = [
+    "pad_image_to_shape",
+    # "into_4d_full_frame",
     "frame",
     "unwrap_piston",
     "unwrap_image",

{opticalib-2.1.3 → opticalib-2.2.0}/opticalib/core/_types.py

@@ -162,7 +162,7 @@ class _DMProtocol(Protocol):
     def set_shape(self, cmd: MatrixLike, differential: bool) -> None: ...
     def get_shape(self) -> ArrayLike: ...
     def upload_cmd_history(
-        self, cmdhist: MatrixLike, *, slave: bool | str = False
+        self, cmdhist: MatrixLike, *, slaving: bool | str = False
     ) -> None: ...
     def run_cmd_history(
         self,
@@ -453,3 +453,18 @@ def get_device_type(device: object) -> str:
     elif isinstance_(device, "CameraDevice"):
         return "camera"
     return device._name
+
+
+def compute_float():
+    """
+    Floating dtype for numerical work on the active xupy backend.
+
+    ``float32`` on GPU (CuPy) for speed, ``float64`` on CPU (NumPy). This is
+    what the removed ``xupy.float`` alias used to resolve to; it is evaluated
+    at call time, so it follows ``xupy.use_cpu()`` / ``xupy.use_gpu()``.
+    """
+    import xupy as xp
+
+    dtype = xp.float32 if xp.on_gpu else xp.float64
+    del xp
+    return dtype

{opticalib-2.1.3 → opticalib-2.2.0}/opticalib/core/config.py

@@ -558,8 +558,8 @@ def get_cmd_delay(bpath: str = _cfold):
         sub_section="DM",
         path=bpath,
     )
-    if "sequentialDelay" in dm_config:
-        cmdDelay = float(dm_config["sequentialDelay"])
+    if "sequential_delay" in dm_config:
+        cmdDelay = float(dm_config["sequential_delay"])
     elif "delay" in dm_config:
         cmdDelay = float(dm_config["delay"])
     elif "triggeredMode" in dm_config and "cmdDelay" in dm_config["triggeredMode"]:

{opticalib-2.1.3 → opticalib-2.2.0}/opticalib/core/root.py

@@ -351,7 +351,7 @@ class ConfSettingReader4D:
     defined object:
 
     >>> cr = ConfSettingReader4D(file_path)
-    >>> cr.get_image_widht_in_pixels()
+    >>> cr.get_image_width_in_pixels()
     2000
     >>> cr.get_image_height_in_pixels()
     2000
@@ -382,13 +382,13 @@ class ConfSettingReader4D:
         frame_rate = self.config.get(self.camera_section, "FrameRate")
         return float(frame_rate)
 
-    def get_image_widht_in_pixels(self):
+    def get_image_width_in_pixels(self):
         """
-        Returns the image widht in pixel scale
+        Returns the image width in pixel scale
 
         Returns
         -------
-        image_wight_in_pixels : int
+        image_width_in_pixels : int
             Image pixel width.
         """
         image_width_in_pixels = self.config.get(

{opticalib-2.1.3 → opticalib-2.2.0}/opticalib/devices/_API/alpaoAPI.py

@@ -5,6 +5,7 @@ from opticalib.core import _types as _t
 
 import weakref
 
+
 def _shutdown_dm(dm, reset: bool, logger, name: str) -> None:
     """Stop (and optionally Reset) a raw SDK handle. Module-level so it
     holds no reference to the wrapper object."""
@@ -112,12 +113,15 @@ class BaseAlpaoMirror:
         self._resolve_init(sdk_params, plico_params)
         self._is_plico = bool(plico_params[0])
 
-        self.n_acts = int(
-            self._plico_dm.get_number_of_actuators()
-        ) if self._is_plico else int(self._sdk_dm.Get("NbOfActuator"))
-        
+        self.n_acts = (
+            int(self._plico_dm.get_number_of_actuators())
+            if self._is_plico
+            else int(self._sdk_dm.Get("NbOfActuator"))
+        )
+
         if self.n_acts != int(nacts):
             import warnings
+
             warnings.warn(
                 f"Number of actuators reported by the SDK ({self.n_acts}) "
                 f"does not match the called number ({nacts}). Verify your BAX files",
@@ -131,7 +135,7 @@ class BaseAlpaoMirror:
             self._name
         ].get("diameter", None)
         self.mirrorModes = None
-        self.cmdHistory = None
+        self._cmd_history = None
         self.refAct = None
         self.ff = None
 
@@ -194,12 +198,14 @@ class BaseAlpaoMirror:
         if not self._is_plico:
             return int(self._sdk_dm.Get("VersionInfo"))
         else:
-            raise AttributeError("Version information is not available for PLICO devices.")
+            raise AttributeError(
+                "Version information is not available for PLICO devices."
+            )
 
     def close(self) -> None:
         """
         Stop the DM (and Reset it if ``reset_on_close``) and release the hardware
-        resources. 
+        resources.
 
         Should be called when the DM object is no longer needed to
         ensure a clean shutdown of the Alpao SDK connection.
@@ -311,15 +317,13 @@ class BaseAlpaoMirror:
 
     def _resolve_init(
         self,
-        sdk_params: tuple[str|None, str|None, str|None],
-        plico_params: tuple[str|None, str|None, int|None]
+        sdk_params: tuple[str | None, str | None, str | None],
+        plico_params: tuple[str | None, str | None, int | None],
     ):
         sn, sdk_fold, acfg_p = sdk_params
         plico, plico_ip, plico_port = plico_params
 
-        config = get_section_config(
-            "DEVICES", "DEFORMABLE.MIRRORS"
-        ).get(self._name, {})
+        config = get_section_config("DEVICES", "DEFORMABLE.MIRRORS").get(self._name, {})
 
         if plico:
             self._plico_ip = config.get("plico_ip", plico_ip)
@@ -396,9 +400,13 @@ class BaseAlpaoMirror:
             os.environ["ACECFG"] = self.acfg_path
 
         try:
-            sdk_path = self.sdk_folder_path or os.path.join(CONFIGURATION_FOLDER, "alpao_sdk")
+            sdk_path = self.sdk_folder_path or os.path.join(
+                CONFIGURATION_FOLDER, "alpao_sdk"
+            )
 
-            if self.sdk_folder_path is not None and not os.path.exists(self.sdk_folder_path):
+            if self.sdk_folder_path is not None and not os.path.exists(
+                self.sdk_folder_path
+            ):
                 sdk_path = os.path.join(CONFIGURATION_FOLDER, self.sdk_folder_path)
 
             if not os.path.exists(sdk_path):

{opticalib-2.1.3 → opticalib-2.2.0}/opticalib/devices/_API/base_devices.py

@@ -36,6 +36,26 @@ class BaseDeformableMirror(ABC):
     Base class for all deformable mirror devices.
     """
 
+    @property
+    def slave_ids(self):
+        return self._slaveIds
+
+    @property
+    def border_ids(self):
+        return self._borderIds
+    
+    @property
+    def cmd_history(self) -> _ot.Optional[_ot.MatrixLike]:
+        """
+        Get the command history of the simulated deformable mirror (DM).
+
+        Returns
+        -------
+        cmd_history : _ot.Optional[_ot.MatrixLike]
+            The command history of the DM, or None if no history has been uploaded.
+        """
+        return self._cmd_history
+
     @abstractmethod
     def set_shape(self, cmd):
         """
@@ -97,24 +117,17 @@ class BaseDeformableMirror(ABC):
             return None
         return "minimum-rms" if (s and b) else "zero-force"
 
-    def _apply_slaving(self, cmd: _ot.ArrayLike, slave: bool | str) -> _ot.ArrayLike:
+    def _apply_slaving(self, cmd: _ot.ArrayLike|_ot.MatrixLike, slave: bool | str) -> _ot.ArrayLike|_ot.MatrixLike:
         """
         Apply actuator slaving to a command when requested.
         """
         method = self._get_slaving_method(slave)
         if method is None:
             return cmd
+        if _ot.isinstance_(cmd, "MatrixLike"):
+            return compute_slaved_command_matrix(self, cmdmat=cmd, method=slave)
         return compute_slave_cmd(self, cmd, method=method)
 
-    def _slave_cmdmat(self, cmdmat: _ot.ArrayLike, slave: bool | str) -> _ot.MatrixLike:
-        """
-        Apply actuator slaving to a command matrix when requested.
-        """
-        method = self._get_slaving_method(slave)
-        if method is None:
-            return cmdmat
-        return compute_slaved_command_matrix(self, cmdmat, method=method)
-
 
 class BaseCamera(ABC):
 

{opticalib-2.1.3 → opticalib-2.2.0}/opticalib/devices/_API/piAPI.py

@@ -31,9 +31,9 @@ class BasePetalMirror:
 
         self._had_error = False
         self.is_segmented = True
-        self.nSegments = 6
-        self.nActsPerSegment = 3
-        self.n_acts = self.nSegments * self.nActsPerSegment
+        self.n_segments = 6
+        self.n_acts_per_segment = 3
+        self.n_acts = self.n_segments * self.n_acts_per_segment
         self._slaveIds = ptl_config.get("slave_ids", [])
         self._borderIds = ptl_config.get("border_ids", [])
 
@@ -213,7 +213,7 @@ class BasePetalMirror:
         CommandError
             If any command is outside the allowed limits.
         """
-        for k in self.nSegments:
+        for k in range(self.n_segments):
             for ax, c in enumerate(cmd[k * 3 : k * 3 + 3]):
                 if not (_CMDLIMITS[ax][0] <= c <= _CMDLIMITS[ax][1]):
                     raise CommandError(f"Command for actuator {ax} out of bounds: {c}")
@@ -326,4 +326,4 @@ class BasePetalMirror:
             raise RuntimeError("Failed to check/enable axes") from err
 
     def __repr__(self):
-        return f"PetalMirror(nSegments={self.nSegments}, nActsPerSegment={self.nActsPerSegment})"
+        return f"PetalMirror(n_segments={self.n_segments}, n_acts_per_segment={self.n_acts_per_segment})"