Support for New Device
Before starting the work of adding a new device, check the issue tracker first. It is likely that someone already requested it and maybe someone is already working on it. Even if they are not working on it they might have a slightly different model and willing to test your implementation on it. Sometimes there is already a half-working implementation that needs testing. If there is no related issue on the tracker, open one. If there is one, comment that you’re working on it. This ensures that there is no duplication of work.
Adding support for a new device is often a relatively straightforward job. Doing so means:
Identify the correct device type and the corresponding abstract base class in the
microscope.abcmodule. For example,
Read the documentation for that class which lists the abstract methods and properties that need to be implemented.
Create a concrete class that implement those abstract methods and properties using the documentation provided by the device vendor.
As one can imagine, this apparently simple 3 step process hides a lot of complexity, most of it in the last step. Surprisingly, the difficulty is not in writing the actual code, which is often really simple, but in decoding the device documentation.
Besides the different device types, which define what methods need to be implemented, devices can also be grouped by their communication method. When it comes to this, most devices fall under two categories: serial connection or C library.
Most microscope devices will provide a RS-232 serial interface, sometimes with USB to serial bridges. Typical exceptions are devices that need to transfer large amounts of data such as cameras or deformable mirrors. Devices with serial interface are the easiest to control, one only needs to find the correct commands in the manual. Here’s some tips to create a new device using serial communication:
Create a class that wraps the serial connection and provides the different commands as Python methods. The device object then “has a” device connection object, and the device connection object “has a” serial connection object. This will greatly simplify the code reducing most methods to 1-2 lines of code.
Beware of multiple threads controlling the device and note that GUIs will often have multiple threads. Consider using
microscope._utils.SharedSerialor roll your own synchronisation logic to ensure thread safety.
The first argument to the class initialiser should be the port number which identifies the device. Beware that the assigned port number might change each time the computer is restarted or even when the device itself is restarted. Checks your OS documentation to assign fixed port number/name.
Beware that indexing a single byte from a byte array returns an int and not a byte, i.e.:
b"CMD" == b"C" # False b"CMD" == 65 # True b"CMD" == ord(b"C") # True b"CMD"[0:1] == b"C" # True
However, typically the goal often is to compare the character at a specific position with a specific character that signals error or success. Note only do we know the exact character this will be done pretty much every time a command is sent to the device. So declare the value in the module globals and use it internally, like so:
_K_CODE = ord(b"K")
C libraries / SDKs
When a device is not controlled via serial it is most likely controlled via some vendor provided SDK. In these cases, adding support for such device means:
find the C library for the SDK;
ctypeswrapper to it under microscope._wrappers;
use the wrapper to add support for the new device, possibly with an intermediary wrapper.
Some vendors provide Python bindings to their SDKs which may or may not be worth using. Often they are undocumented thin wrappers to their C library and if you use them, not only will you have to deal with undocumented behaviour from their C library you will also have to deal with the undocumented idiosyncrasies of their wrapper.
Finding the C library
The first thing to do is to identify the correct shared library file. i.e., the C libraries. On Windows, these are often called dll files. Sometimes the SDK is in C++ and there will be C bindings available. Other times, there are SDKs in many different languages and one needs to get the “low level libraries” for those SDKs. It may be required to contact the vendor directly.
There may be more than one C library required for a single device.
For example, Andor’s SDK3 requires the DLLs
For each library file create one Python file with the same name under microscope._wrappers. Each of those files should load the library, declare required constants and structures, and finally declare the function prototypes with the required argument types and return values. Take a look at the existing wrappers for examples but here’s some tips to write a new one:
Keep the wrapper as thinner as possible. Namely, do not have functions automatically check the return value or convert types. The wrapper should provide the exact same interface provided by the C library but callable from Python. That said, do specify the required arguments and return type by setting the
Wrap only the symbols required by Python-microscope and not every single symbol declared in the header file. Wrapping only the required functions ensures that it will work with any version of the library that has the required functions. On the other hand, wrapping all the symbols may lead to failures with older library versions because they miss something that is not even required.
Use the exact same names as in the C header files even if they don’t follow Python naming conventions. However, it is very common for C libraries to use a prefix for all their functions, e.g. the
BMClibraries prefix all their functions with
BMCrespectively. In such case, remove that prefix.
Typedefs are often used for function arguments, e.g.,
RESULTis the return type for all functions which is a typedef for
HANDLEwhich is a pointer for some forwarded declared struct. Do declare those typedefs and use them when declaring the arguments and return types of functions. This eases the comparison with the header files and the long-term maintenance.
Importing the wrapper should load the library, i.e., will call
ctypes.CDLLor similar. This ensures that if Python fails to find the library this will fail as soon as possible. However, some libraries need to be “manually” initialised. Importing the wrapper should not initialise the library, leave it to the user of the library.
Not all Window’s DLLs use
stdcallso don’t assume that you need to use
ctypes.WinDLLjust because you are in Windows. Also, using
WinDLLincorrectly instead of
CDLLwill not fail but may lead to issues later. So check the header files and look for
Different structs may have different packing alignment. Check it, i.e., look for
__atribute__((packed, aligned(X))), and set it appropriately via the
Do not do wildcard imports, i.e., no
from ctypes import *.
Actual device class
Because the thin wrapper should only declare the symbols required by the concrete device class these two should be implemented in parallel. Details on how to implement this devices are mainly device type specific.
Tips to implement support for a new device
Only use named arguments and keyword arguments for the class
__init__. This is required by the device server and also makes things simpler when there’s multiple parent classes.
Avoid using the
FloatingDeviceMixinif possible. Some devices really need it, namely cameras, but these cause issues when there are multiple such devices available but only a subset is to be used.
While often the end goal is to use the devices via the device server, avoid using it during development since it adds an extra layer of complexity. Do test that it works via the device server in the end though.
Make use of the
microscope.guimodule which provides simple widgets to quickly test the device during development. For example, if one was testing the implementation of a deformable mirror, they could do this on a Python shell:
from microscope.mirrors.my_new_dm import MyNewDM dm = MyNewDM() from microscope.gui import DeformableMirrorWidget, MainWindow from qtpy import QtWidgets app = QtWidgets.QApplication() widget = DeformableMirrorWidget(dm) window = MainWindow(widget) window.show() app.exec()
When documenting support for the device, use the class docstring and not the module docstring. Use the module docstring if there are multiple device classes in the module and they share documentation.
Use type annotations.
When all is done and support for a new device is merged, do not forget to make reference to it on the NEWS.rst and doc/architecture/supported-devices.rst files.
More often than not a device does not really perform according to their documentation. The documentation rarely includes all of the available commands, the description or arguments in the documentation is wrong, different models behave slightly different despite using the same SDK, and changing settings have surprising side effects. Despite all this defects, vendors tend to be very protective of their documentation and can be complicated to get a copy of it — it’s almost as if they don’t want us to use it.
Anyone implementing support for a new device is bound to find issues with the vendor interface. In that case, please be a good citizen and report it back to them so that they can improve. In addition, open an issue on Python-Microscope tracker for vendor issues.