Merge development into master to do a release #142
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…ation classes. Also I'de changed makefile.OSX, TODO add description in README.md file
Merge latest
New simplified 3D scene configuration file including only worm body (with improved muscular cells geometry)
Add files via upload
Fixes README sentence duplication and formatting
Big significant update which includes the following key features and improvements:
1. Writing log file containing the coordinates of worm body midline, from head to tail. Works when “–l_to logstep=...” flag is used.
Default file path and name: sibernetic/buffers/worm_motion_log.txt.
Function responsible for this is called update_worm_motion_log_file(...)
2. Writing log file containing activity of worm body muscles. Works when “–l_to logstep=...” flag is used.
Default file path and name: sibernetic/buffers/muscles_activity_buffer.txt.
update_muscles_activity_signals_log_file(...)
3. Replaying previously recorded simulation (obtained using “–l_to logstep=...” flag) using “–l_from” flag – now with displaying muscular activity, as in ordinary simulation.
Function responsible for this is called read_muscle_activity_signals_from_log_file(...)
4. Finally I’ve fixed the annoying problem - changing of brightness of scene elements, which happened in case of scene rotation.
5. More convenient initial scene initial view (scale and camera settings). If necessary, they can be changed by user. Lines of code which are responsible for this are located in owWormSimulation.cpp (line 47 – “float camera_rot[] = {60, -90, 0};” and line 50 – “float sc = 0.025f;”.
6. Elastic matter “agar” particles which were in contact with the worm body at least once are highlighted with another color.
7. Three new low-resolution (and faster working) scenes - worm_swim_half_resolution (worm + volume of water), worm_crawl_half_resolution (worm on a layer of agar) and worm_alone_half_resolution (worm on a flat plane; works fast due to small number of particles). Current main_sim.py is configured to generate muscle activation patterns for crawling (after 6 seconds of simulation time it will change to swimming). For swimming at start and crawling after 6 seconds please change “<” to “>” at lines 56 and 66 of main_sim.py.
WARNING 1: simulation is quite stable both for using normal and low resolutions (I didn’t noticed anything strange yet), due to some compromise in physics-related parameters. But locomotion (swimming and/or crawling) might be not so efficient as usually. I expect that new forthcoming version will include two sets of physics-related parameters, each optimized for its own resolution.
WARNING 2: All previous versions of worm body (and the actual one as well) contain 24x4 body wall muscle cells, which are completely symmetrical. First 24 (in muscle_activation_signal_cpp[] array) correspond to MDR muscle bundle, next 24 – to MVR, then to MVL and finally to MDL. This was done for simplicity and convenience. If it is important to take into account that actually one muscle bundle contains 23 cells, let’s create an issue for this and discuss the details.
Enjoy!
Feedback is welcome!
Latest development
sibernetic_c302.py: Change naming template of simulation directories. now: paramset_ref_year-month-day_hour-minute-second.
…onsole each time step Updated wcon script, better graphs generated (angle calculated over endpoints/centre of 5 adjacent points)
Moving plot_positions to root for now... Allows setting logstep in sibernetic_c302.py Updates sibernetic version to 0.0.6 Addresses #129, uses pure muscle activation signal from Python class Removes some use of "Pyramidal"
Updated linux build instructions
…into development
…into openworm-development22 * 'development' of https://github.com/openworm/sibernetic: small changes, swimming & crawling parameters tuning Small update fixing a few issues Update README.md Update README.md
* openworm-development22: small changes, swimming & crawling parameters tuning Small update fixing a few issues Update README.md Update README.md
…ne generators, but save simulations in same way
…into openworm-development_m19 * 'development' of https://github.com/openworm/sibernetic: Update README.md Add to gitignore file path to .idea folder Delete ide files. Pass dt to C302NRNSimulation instance after initialization Fix skip_display_connections Add skip_display params
* openworm-development_m19: Update README.md Add to gitignore file path to .idea folder Delete ide files. Pass dt to C302NRNSimulation instance after initialization Fix skip_display_connections Add skip_display params
* test_dev2: Lots more versions Save sibernetic version Minor addition to report Update README.md Add to gitignore file path to .idea folder Delete ide files. Pass dt to C302NRNSimulation instance after initialization Fix skip_display_connections Add skip_display params
Minor additions to sibernetic_c302.py
- Also, making some fixes in Python code both for Python 3 and just so the code works
Use pythonX.Y-config for python build flags
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Do you guys see any reason not to merge to master?