slmsuite 0.0.1__tar.gz

slmsuite-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 slmsuite Developers.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

slmsuite-0.0.1/PKG-INFO

@@ -0,0 +1,61 @@
+Metadata-Version: 2.1
+Name: slmsuite
+Version: 0.0.1
+Summary: Package for high-performance spatial light modulator (SLM) control and holography.
+Author: MIT Quantum Photonics Group
+Author-email: qp-slm@mit.edu
+Project-URL: Homepage, https://github.com/QPG-MIT/slmsuite
+Project-URL: Documentation, https://slmsuite.readthedocs.io/en/latest/
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+<p align="center">
+<img alt="qp-slm" src="https://raw.githubusercontent.com/QPG-MIT/slmsuite/main/docs/source/static/qp-slm.svg" width="256">
+</p>
+
+<h2 align="center">High-Performance Spatial Light Modulator Control and Holography</h2>
+
+<p align="center">
+<a href="https://slmsuite.readthedocs.io/en/latest"><img alt="Documentation Status" src="https://readthedocs.org/projects/slmsuite/badge/?version=latest"></a>
+<a href="https://github.com/QPG-MIT/slmsuite/blob/main/LICENSE"><img alt="License: MIT" src="https://img.shields.io/github/license/QPG-MIT/slmsuite?color=purple"></a>
+<!--<a href="https://pepy.tech/project/slmsuite"><img alt="Downloads" src="https://pepy.tech/badge/slmsuite"></a>-->
+<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
+</p>
+
+## Installation
+
+Install the stable version of `slmsuite` from [PyPi](https://pypi.org/project/slmsuite/) using:
+
+```console
+$ pip install slmsuite
+```
+
+
+Install the latest version of `slmsuite` from GitHub using:
+
+```console
+$ pip install git+https://github.com/QPG-MIT/slmsuite
+```
+
+## Documentation and Examples
+
+Extensive
+[documentation](https://slmsuite.readthedocs.io/en/latest/)
+and
+[API reference](https://slmsuite.readthedocs.io/en/latest/api.html)
+are available through readthedocs.
+
+Examples can be found embedded in
+[documentation](https://slmsuite.readthedocs.io/en/latest/examples.html),
+live through
+[nbviewer](https://nbviewer.org/github/QPG-MIT/slmsuite-examples/tree/main/examples/),
+or directly in
+[source](https://github.com/QPG-MIT/slmsuite-examples).
+
+<p align="center">
+<img alt="qp-slm" src="https://raw.githubusercontent.com/QPG-MIT/slmsuite/main/docs/source/static/readme-example.png" width="256">
+</p>

slmsuite-0.0.1/README.md

@@ -0,0 +1,52 @@
+<p align="center">
+<picture>
+<source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/QPG-MIT/slmsuite/main/docs/source/static/qp-slm-dark.svg">
+<img alt="qp-slm" src="https://raw.githubusercontent.com/QPG-MIT/slmsuite/main/docs/source/static/qp-slm.svg" width="256">
+</picture>
+</p>
+
+<h2 align="center">High-Performance Spatial Light Modulator Control and Holography</h2>
+
+<p align="center">
+<a href="https://slmsuite.readthedocs.io/en/latest"><img alt="Documentation Status" src="https://readthedocs.org/projects/slmsuite/badge/?version=latest"></a>
+<a href="https://github.com/QPG-MIT/slmsuite/blob/main/LICENSE"><img alt="License: MIT" src="https://img.shields.io/github/license/QPG-MIT/slmsuite?color=purple"></a>
+<!--<a href="https://pepy.tech/project/slmsuite"><img alt="Downloads" src="https://pepy.tech/badge/slmsuite"></a>-->
+<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
+</p>
+
+## Installation
+
+Install the stable version of `slmsuite` from [PyPi](https://pypi.org/project/slmsuite/) using:
+
+```console
+$ pip install slmsuite
+```
+
+
+Install the latest version of `slmsuite` from GitHub using:
+
+```console
+$ pip install git+https://github.com/QPG-MIT/slmsuite
+```
+
+## Documentation and Examples
+
+Extensive
+[documentation](https://slmsuite.readthedocs.io/en/latest/)
+and
+[API reference](https://slmsuite.readthedocs.io/en/latest/api.html)
+are available through readthedocs.
+
+Examples can be found embedded in
+[documentation](https://slmsuite.readthedocs.io/en/latest/examples.html),
+live through
+[nbviewer](https://nbviewer.org/github/QPG-MIT/slmsuite-examples/tree/main/examples/),
+or directly in
+[source](https://github.com/QPG-MIT/slmsuite-examples).
+
+<p align="center">
+<picture>
+<source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/QPG-MIT/slmsuite/main/docs/source/static/readme-example-dark.png">
+<img alt="qp-slm" src="https://raw.githubusercontent.com/QPG-MIT/slmsuite/main/docs/source/static/readme-example.png" width="256">
+</picture>
+</p>

slmsuite-0.0.1/README_PYPI.md

@@ -0,0 +1,46 @@
+<p align="center">
+<img alt="qp-slm" src="https://raw.githubusercontent.com/QPG-MIT/slmsuite/main/docs/source/static/qp-slm.svg" width="256">
+</p>
+
+<h2 align="center">High-Performance Spatial Light Modulator Control and Holography</h2>
+
+<p align="center">
+<a href="https://slmsuite.readthedocs.io/en/latest"><img alt="Documentation Status" src="https://readthedocs.org/projects/slmsuite/badge/?version=latest"></a>
+<a href="https://github.com/QPG-MIT/slmsuite/blob/main/LICENSE"><img alt="License: MIT" src="https://img.shields.io/github/license/QPG-MIT/slmsuite?color=purple"></a>
+<!--<a href="https://pepy.tech/project/slmsuite"><img alt="Downloads" src="https://pepy.tech/badge/slmsuite"></a>-->
+<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
+</p>
+
+## Installation
+
+Install the stable version of `slmsuite` from [PyPi](https://pypi.org/project/slmsuite/) using:
+
+```console
+$ pip install slmsuite
+```
+
+
+Install the latest version of `slmsuite` from GitHub using:
+
+```console
+$ pip install git+https://github.com/QPG-MIT/slmsuite
+```
+
+## Documentation and Examples
+
+Extensive
+[documentation](https://slmsuite.readthedocs.io/en/latest/)
+and
+[API reference](https://slmsuite.readthedocs.io/en/latest/api.html)
+are available through readthedocs.
+
+Examples can be found embedded in
+[documentation](https://slmsuite.readthedocs.io/en/latest/examples.html),
+live through
+[nbviewer](https://nbviewer.org/github/QPG-MIT/slmsuite-examples/tree/main/examples/),
+or directly in
+[source](https://github.com/QPG-MIT/slmsuite-examples).
+
+<p align="center">
+<img alt="qp-slm" src="https://raw.githubusercontent.com/QPG-MIT/slmsuite/main/docs/source/static/readme-example.png" width="256">
+</p>

slmsuite-0.0.1/pyproject.toml

@@ -0,0 +1,18 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "slmsuite"
+readme = "README_PYPI.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dynamic = ["version", "dependencies", "description", "authors"]
+
+[project.urls]
+"Homepage" = "https://github.com/QPG-MIT/slmsuite"
+"Documentation" = "https://slmsuite.readthedocs.io/en/latest/"

slmsuite-0.0.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

slmsuite-0.0.1/setup.py

@@ -0,0 +1,28 @@
+"""
+setup.py - this module makes the package installable
+"""
+
+from setuptools import setup
+
+NAME = "slmsuite"
+VERSION = "0.0.1"
+DEPENDENCIES = [
+    "numpy",
+    "scipy",
+    "opencv-python",
+    "matplotlib",
+    "h5py",
+    "tqdm"
+]
+DESCRIPTION = ("Package for high-performance spatial light "
+               "modulator (SLM) control and holography.")
+AUTHOR = "MIT Quantum Photonics Group"
+AUTHOR_EMAIL = "qp-slm@mit.edu"
+
+setup(author=AUTHOR,
+      author_email=AUTHOR_EMAIL,
+      description=DESCRIPTION,
+      install_requires=DEPENDENCIES,
+      name=NAME,
+      version=VERSION,
+)

slmsuite-0.0.1/slmsuite/__init__.py

@@ -0,0 +1 @@
+__version__ = '0.0.0'

slmsuite-0.0.1/slmsuite/hardware/__init__.py

@@ -0,0 +1 @@
+"""Interface to experimental devices."""

slmsuite-0.0.1/slmsuite/hardware/cameras/__init__.py

@@ -0,0 +1,31 @@
+# The first line of the docstring might read awkward alone,
+# but it's meant to parallel the slms module description.
+"""
+The sensor arrays used to measure results.
+Computer vision hardware is connected to python by a myriad of SDKs, often provided by hardware
+vendors. However, these SDKs likewise have a myriad of function names and hardware-specific
+quirks. Thus, cameras in :mod:`slmsuite` are integrated as subclasses of
+the abstract class :class:`.Camera`, which requires subclasses to implement a number of methods
+relevant for SLM feedback (see below).
+These subclasses are effectively wrappers for the given SDK, but also include
+quality-of-life features such as image transformations (flips, rotates) and useful common methods.
+A number of SDKs are supported, including:
+
+ - :class:`.AlliedVision`, for AlliedVision cameras, through :mod:`vimba`
+   (`GitHub <https://github.com/alliedvision/VimbaPython>`_),
+ - :class:`.Cheetah640`, for Xenics Cheetah cameras, through the
+   `Xenics SDK <https://www.xenics.com/software/>`_,
+ - :class:`.FLIR`, for Teledyne FLIR cameras, through the :mod:`PySpin`
+   interface of the `Spinnaker SDK <https://www.flir.com/products/spinnaker-sdk/>`_,
+ - :class:`.MMCore`, for the general microscope control package Micro-Manager,
+   through :mod:`pymmcore` (`GitHub <https://github.com/micro-manager/pymmcore>`_), and
+ - :class:`.ThorCam`, for Thorlabs scientific cameras, through :mod:`thorlabs_tsi_sdk`
+   and the `ThorCam SDK <https://www.thorlabs.com/software_pages/ViewSoftwarePage.cfm?Code=ThorCam>`_.
+
+Tip
+~~~~~~~~
+While the superclass :class:`.Camera` only requires a small number of features to
+be implemented as class functions, any further control of a camera interface can be
+accessed by using the given SDK object directly (usually the attribute :attr:`cam` of
+the subclass) or writing additional functions into the subclass.
+"""

slmsuite-0.0.1/slmsuite/hardware/cameras/alliedvision.py

@@ -0,0 +1,289 @@
+"""
+Hardware control for AlliedVision cameras via the :mod:`vimba` interface.
+Install :mod:`vimba` by following the
+`provided instructions <https://github.com/alliedvision/VimbaPython>`_.
+Include the ``numpy-export`` flag in the ``pip install`` command,
+as the :class:`AlliedVision` class makes use of these features. See especially the
+`vimba python manual <https://github.com/alliedvision/VimbaPython/blob/master/Documentation/Vimba%20Python%20Manual.pdf>`_
+for reference.
+"""
+
+import time
+import numpy as np
+
+from slmsuite.hardware.cameras.camera import Camera
+
+try:
+    import vimba
+except ImportError:
+    print("alliedvision.py: vimba not installed. Install to use AlliedVision cameras.")
+
+
+class AlliedVision(Camera):
+    r"""
+    AlliedVision camera.
+
+    Attributes
+    ----------
+    sdk : vimba.Vimba
+        AlliedVision SDK. Shared among instances of :class:`AlliedVision`.
+    cam : vimba.Camera
+        Object to talk with the desired camera.
+
+    Caution
+    ~~~~~~~~
+    The AlliedVision SDK :mod:`vimba` includes protections to maintain camera connectivity:
+    specifically, the SDK :class:`vimba.Vimba` and cameras :class:`vimba.Camera` are designed
+    to be used in concert with ``with`` statements. Unfortunately, this does not mesh with the
+    architecture of :mod:`slmsuite`, where notebook-style operation is desired.
+    Using ``with`` statements inside :class:`.AlliedVision` methods is likewise not an option,
+    as the methods to :meth:`__enter__()` and :meth:`__exit__()` the ``with`` are time-consuming
+    due to calls to :meth:`_open()` and :meth:`_close()` the objects, to the point of
+    :math:`\mathcal{O}(\text{s})` overhead. :class:`.AlliedVision` disables these protections by
+    calling :meth:`__enter__()` and :meth:`__exit__()` directly during :meth:`.__init__()` and
+    :meth:`.close()`, instead of inside ``with`` statements.
+    """
+
+    sdk = None
+
+    def __init__(self, serial="", verbose=True, **kwargs):
+        """
+        Initialize camera and attributes.
+
+        Parameters
+        ----------
+        serial : str
+            Serial number of the camera to open. If empty, defaults to the first camera in the list
+            returned by :meth:`vimba.get_all_cameras()`.
+        verbose : bool
+            Whether or not to print extra information.
+        kwargs
+            See :meth:`.Camera.__init__` for permissible options.
+        """
+        if AlliedVision.sdk is None:
+            if verbose:
+                print("vimba initializing... ", end="")
+            AlliedVision.sdk = vimba.Vimba.get_instance()
+            AlliedVision.sdk.__enter__()
+            if verbose:
+                print("success")
+
+        if verbose:
+            print("Looking for cameras... ", end="")
+        camera_list = AlliedVision.sdk.get_all_cameras()
+        if verbose:
+            print("success")
+
+        serial_list = [cam.get_serial() for cam in camera_list]
+        if serial == "":
+            if len(camera_list) == 0:
+                raise RuntimeError("No cameras found by vimba.")
+            if len(camera_list) > 1 and verbose:
+                print("No serial given... Choosing first of ", serial_list)
+
+            self.cam = camera_list[0]
+            serial = self.cam.get_serial()
+        else:
+            if serial in serial_list:
+                self.cam = camera_list[serial_list.index(serial)]
+            else:
+                raise RuntimeError(
+                    "Serial " + serial + " not found by vimba. Available: ", serial_list
+                )
+
+        if verbose:
+            print("vimba sn " "{}" " initializing... ".format(serial), end="")
+        self.cam.__enter__()
+        if verbose:
+            print("success")
+
+        super().__init__(
+            self.cam.SensorWidth.get(),
+            self.cam.SensorHeight.get(),
+            bitdepth=int(self.cam.PixelSize.get()),
+            dx_um=None,
+            dy_um=None,
+            name=serial,
+            **kwargs
+        )
+
+        self.cam.BinningHorizontal.set(1)
+        self.cam.BinningVertical.set(1)
+
+        self.cam.GainAuto.set("Off")
+
+        self.cam.ExposureAuto.set("Off")
+        self.cam.ExposureMode.set("Timed")
+
+        self.cam.AcquisitionMode.set("SingleFrame")
+
+        # Future: triggered instead of SingleFrame.
+        self.cam.TriggerSelector.set("AcquisitionStart")
+        self.cam.TriggerMode.set("Off")
+        self.cam.TriggerActivation.set("RisingEdge")
+        self.cam.TriggerSource.set("Software")
+
+    def close(self, close_sdk=True):
+        """
+        See :meth:`.Camera.close`
+
+        Parameters
+        ----------
+        close_sdk : bool
+            Whether or not to close the :mod:`vimba` instance.
+        """
+        self.cam.__exit__(None, None, None)
+
+        if close_sdk:
+            self.close_sdk()
+
+    @staticmethod
+    def info(verbose=True):
+        """
+        Discovers all Thorlabs scientific cameras.
+
+        Parameters
+        ----------
+        verbose : bool
+            Whether to print the discovered information.
+
+        Returns
+        --------
+        list of str
+            List of AlliedVision serial numbers.
+        """
+        if AlliedVision.sdk is None:
+            AlliedVision.sdk = vimba.Vimba.get_instance()
+            AlliedVision.sdk.__enter__()
+            close_sdk = True
+        else:
+            close_sdk = False
+
+        camera_list = AlliedVision.sdk.get_all_cameras()
+        serial_list = [cam.get_serial() for cam in camera_list]
+
+        if verbose:
+            print("AlliedVision serials:")
+            for serial in serial_list:
+                print("\"{}\"".format(serial))
+
+        if close_sdk:
+            AlliedVision.close_sdk()
+
+        return serial_list
+
+    @classmethod
+    def close_sdk(cls):
+        """
+        Close the :mod:`vimba` instance.
+        """
+        if cls.sdk is not None:
+            cls.sdk.__exit__(None, None, None)
+            cls.sdk = None
+
+    ### Property Configuration ###
+
+    def get_properties(self, properties=None):
+        """
+        Print the list of camera properties.
+
+        Parameters
+        ----------
+        properties : dict or None
+            The target camera's property dictionary. If ``None``, the property
+            dictionary is fetched from the camera associated with the calling instance.
+        """
+        if properties is None:
+            properties = self.cam.__dict__.keys()
+
+        for key in properties:
+            prop = self.cam.__dict__[key]
+            try:
+                print(prop.get_name(), end="\t")
+            except BaseException as e:
+                print("Error accessing property dictionary, '{}':{}".format(key, e))
+                continue
+
+            try:
+                print(prop.get(), end="\t")
+            except:
+                pass
+
+            try:
+                print(prop.get_unit(), end="\t")
+            except:
+                pass
+
+            try:
+                print(prop.get_description(), end="\n")
+            except:
+                print("")
+
+    def set_adc_bitdepth(self, bitdepth):
+        """
+        Set the digitization bitdepth.
+
+        Parameters
+        ----------
+        bitdepth : int
+            Desired digitization bitdepth.
+        """
+        bitdepth = int(bitdepth)
+
+        for entry in self.cam.SensorBitDepth.get_all_entries():
+            value = entry.as_tuple()  # (name : str, value : int)
+            if str(bitdepth) in value[0]:
+                self.cam.SensorBitDepth.set(value[1])
+                break
+            raise RuntimeError("ADC bitdepth {} not found.".format(bitdepth))
+
+    def get_adc_bitdepth(self):
+        """
+        Get the digitization bitdepth.
+
+        Returns
+        -------
+        int
+            The digitization bitdepth.
+        """
+        value = str(self.cam.SensorBitDepth.get())
+        bitdepth = int("".join(char for char in value if char.isdigit()))
+        return bitdepth
+
+    def get_exposure(self):
+        """See :meth:`.Camera.get_exposure`."""
+        return float(self.cam.ExposureTime.get()) / 1e6
+
+    def set_exposure(self, exposure_s):
+        """See :meth:`.Camera.set_exposure`."""
+        self.cam.ExposureTime.set(float(exposure_s * 1e6))
+
+    def set_woi(self, woi=None):
+        """See :meth:`.Camera.set_woi`."""
+        return
+
+    def get_image(self, timeout_s=1):
+        """See :meth:`.Camera.get_image`."""
+        t = time.time()
+
+        # Convert timeout_s to ms
+        frame = self.cam.get_frame(timeout_ms=int(1e3 * timeout_s))
+        frame = frame.as_numpy_ndarray()
+
+        # We have noticed that sometimes the camera gets into a state where
+        # it returns a frame of all zeros apart from one pixel with value of 31.
+        # This method is admittedly a hack to try getting a frame a few more times.
+        # We welcome contributions to fix this.
+        while np.sum(frame) == np.amax(frame) == 31 and time.time() - t < timeout_s:
+            frame = self.cam.get_frame(timeout_ms=int(1e3 * timeout_s))
+            frame = frame.as_numpy_ndarray()
+
+        return self.transform(np.squeeze(frame))
+
+    def flush(self, timeout_s=1e-3):
+        """See :meth:`.Camera.flush`."""
+        pass
+
+    def reset(self):
+        """See :meth:`.Camera.reset`."""
+        raise NotImplementedError()