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DECTRIS support; use PipelinedExecutor for live processing #51
Commits on Jul 28, 2022
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Record and replay ZMQ messages
A very simple file format: int64 length field followed by bytes of that length per message.
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- Add `lz4` dependency - Set `trigger_mode` explicitly, and ensure `nimages` and/or `ntrigger` is set according to the current `nav_shape` - Make the `trigger` function optional, as it is not needed unless you want to either set additional detector parameters, or automate acquisition with a microscope API
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Use own fork for now, see kiyo-masui/bitshuffle#120
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Simulator for Dectris detector
This simulator can replay an acquisition that was recorded with prototypes/zmq_record.py. Usage: `libertem-live-dectris-sim <file>` This is not a complete simulator, but implements just enough of the API to allow performance testing and run unit tests of the whole acquisition code. It reads the metadata from the recording and ensures that the user settings match the file. For exte and exts triggers it will assume to be triggered. For inte and ints it will wait for the 'trigger' command.
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Allow co-existence of Dectris acquisition objects
ZMQ sockets balance load, meaning several co-existing listeners will only receive part of the data. For that reason we only connect while an acquisition is running and destroy the context directly after. That closes all sockets.
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Drive-by: Deactivate debug print. Co-authored-by: Alexander Clausen <a.clausen@fz-juelich.de>
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WIP: Working prototyp for multiprocessing-based executor
Still needs to be extracted into an executor and probably an adjusted `UDFRunner`. - properly drain and close queues - use a single response queue - this simplifies result handling on the receiving side (might become bottleneck in many-core situations) - perform decoding in the worker processes - `ZeroMQReceiver`: zero-copy recv, at least for the payload - some hacks to inject the receiver into the partition
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The duplicated code for `StoppableThreadMixin` was modified to take a `stop_event`, which is now moved to `libertem_live.detectors.common`.
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merlin: simplify comparison test case
This should now continue to work, even if we change further details of the communication between acquisition and partition
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Follow-up renaming:
get_controller
->get_task_comm_handler
Also fixes tracing span names
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Allow running the Dectris simulator in pytest
* Restructure to make all relevant components of the simulator importable and runnable from other code * Run Flask app for API in separate process to make it killable * Allow running both API and data on random free port * Fixture and simple test case, FIXME integrate meaningful tests * FIXME the other Dectris test cases seem to be broken, not sure what to do there
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Disregard copyright notice, will be changed before merging (!)
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Commits on Aug 1, 2022
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Commits on Aug 3, 2022
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tox.ini: install dectris extras; remove hdbscan
hdbscan does not exist as an extra of LiberTEM-live
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Commits on Aug 4, 2022
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Caused a freeze in the pipelined executor before
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Commits on Aug 15, 2022
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DECTRIS sim: send multipart messages; misc fixes
* Ignore extra data at the beginning of the file * Add missing acquisition footer
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Otel instrumentation for Eiger client
Debug connection lag on Windows FYI it was DNS for localhost -- examples should use IP address instead
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Commits on Aug 16, 2022
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Update to libertem_dectris>=0.2
+ Clean up some now-unused code + Move mocking/offline receiver into `libertem_live.detectors.dectris.mock` + dectris sim: use Python sim when `data_filter` is used (not needed for performance tests)
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Require Python 3.7 for dectris support
Don't install libertem-dectris on Python 3.6
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Lazily import dectris dependencies
Throw a helpful error message when dependencies are missing
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Don't clobber the ctx_pipelined in test_frame_skip
Instead, pull up a new one which we can close at the end
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Commits on Aug 17, 2022
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dectris sim: fix for Python 3.6
To at least make it importable - this doesn't add full 3.6 support
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merlin: cleanup;
pool_size
is not used anymoreIgnore and warn. Also remove some unused commented code.
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Only run
test_frame_skip
on recent LiberTEM versionsOn older versions, it does still hang, so we can't run that test in CI.
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Commits on Aug 18, 2022
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* Switch to RTD theme * Run the dectris sim in docs-check to check the example code * Separate sections for API reference and user documentation * Add verbosity switch in dectris sim to make sphinx doctest happy (it's not yet possible to ignore output of testsetup / testcleanup directives) * dectris sim: catch StopException
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Commits on Aug 22, 2022
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Commits on Aug 24, 2022
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