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* Add info to log about using default log path, if log path in config does not work. * Fix bugs.
* Fix the pattern for the glob search function. * Add try...except when reading images.
* Make imaging-dir required argument. * Change default first-job argument to 2. This argument is used to determine the first experiment job in the experiment patterns. This is important to know when renaming images. * Fix default log level and change it to INFO. * Remove working-dir argument. This is not needed anymore. * Do not calculate max projections unless saving histograms or images. * Fix csv file save path. * Never save max projection images. * Fix getting path to initial gain csv file. Check final objective argument and use appropriate initial gain csv file. * Check if reply from server is None, before adding reply. * Fix using format_new_name.
* Make sure X01--Y01 is always checked as last field in a gain scan. * Remove last-field as start argument and instead compute it from x-fields and y-fields, which are arguments.
* Fork contains fix for receive method in cam module.
* Monkeypatch socket. * Remove setup of real socket in test package. * Add requirements_test.txt for tests. * Test with pytest.
* Reset gain_dict between each gainjob run. Refactor the concerned methods in Gain class. * Simplify getting field and well path. Don't search for all compartments with glob. Path is already available from server reply. * Simplify check of which images to include for max projection calculation.
* Add receive call after stop command to catch two out of the three replies after stop command. * Tweak some sleep times between commands. These are needed to let the microscope settle. * Clean some stale comments and debug log calls.
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Fix bugs after refactor
work.