dmlib

Python library for calibration and control of deformable mirrors (DM). This library implements the methods described in detail in this tutorial from aomicroscopy.org.

dmlib is meant to be used as an external library in a Python application that needs to control DMs. dmlib is not bound to particular hardware, and can be used with any kind of DM. To control actual hardware you can either use your own manufacturer-provided library or one of the existing wrappers found in the subpackage devwraps.

There are two possible use cases:

• Full calibration and control using dmlib. You can use dmlib's GUIs and embed them into your Python application. In this case your DM and scientific camera must be directly supported via the hardware wrappers subpackage devwraps. A guide explaining how to use the GUIs is found here.
• Calibration with dmlib and control using your own code. If your DM is directly supported by dmlib, then you can use dmlib's calibration GUI to collect the calibration data and to generate a calibration file. Subsequently you can load the control matrix from the calibration file and use it in your own code. Instead, if your hardware is not directly supported by dmlib, you can adjust the data collection script data_collection.py in the examples folder and collect the calibration data with this script. Afterwards, you can generate the calibration as shown in the examples/calibration.py script.

Installation

Hardware devices such as DMs and scientific cameras are only supported in Windows via the devwraps subpackage. You can still install dmlib under Linux and run the GUIs, but only in simulation mode (using dummy virtual devices).

To install dmlib in Windows, follow the steps below.

• You should first install the following software requirements:
  • Anaconda for Python 3. This includes Python as well as some necessary scientific libraries.
  • Build Tools for Visual Studio. Note that this is not Visual Studio itself, but just the command-line interface Build Tools for Visual Studio 2019. You can find that under Tools for Visual Studio.
  • Git. This is necessary for the automatic version numbering of this package. Also, make sure you choose Git from the command line and also 3rd-party software in Adjusting your PATH environment.
• Clone this repository using Git. From any folder in File Explorer, right-click and hit Git Bash here. Paste git clone --recurse-submodules https://github.com/jacopoantonello/dmlib and hit enter. Do not use GitHub's Download ZIP button above, as the installation script will not work in that case.
• Finally, double-click on install.bat. This script installs dmlib and its two subpackages zernike and devwraps.

Running dmlib GUIs

DM calibration GUI (dmlib.gui)

The calibration GUI dmlib.gui can be used to interferometrically calibrate and test a DM. You can start the GUI using a BAT script as outlined in the guide. Alternatively, open an Anaconda Prompt and query the available drivers with python -m dmlib.gui --help. Select the appropriate drivers flags and run the GUI again without the --help flag.

For example

python -m dmlib.gui --dm-driver bmc --dm-name DM_SERIAL_NUMBER --cam-driver
thorcam --cam-name CAM_SERIAL_NUMBER

would run dmlib.gui using the Boston Multi-DM with serial number DM_SERIAL_NUMBER and the Thorlabs camera with serial number CAM_SERIAL_NUMBER.

To run the calibration GUI in simulation mode without any hardware, use

python -m dmlib.gui --dm-driver sim --cam-driver sim

For convenience, you can create a BAT file with the correct parameters by modifying the examples/run_calibration_gui.bat.

DM control using Zernike modes (dmlib.zpanel)

The control GUI dmlib.zpanel can load a DM calibration file and control the DM in open-loop using Zernike modes. You can start the GUI using a BAT script as outlined in the guide. Alternatively, open an Anaconda Prompt and use the -m dmlib.zpanel flag to start this GUI. You can query the GUIs flags with --help as seen above.

References

[1] J. Antonello, J. Wang, C. He, M. Phillips, and M. Booth, "Interferometric calibration of a deformable mirror," 10.5281/zenodo.3714951.