Tags

v1.8.3

1. Add option to calculate distance to center automatically

v1.8.2

1. For posthoc tracking after v1.8.0 it became necessary to add 'pwm_range'
   and 'legacy_PWM_control_bool' to the experiment_settings.json.

   During posthoc, the LED_functions.update_PWM_dutycycle() is called but
   with the 'just_calculate=True' flag to properly display the precision
   of the stimulus to the user.

2. Background.tiff was not saved in correct folder after change from os.cwd to
   pathlib.Path

v1.8.1

1. Added error handling logic and check for valid stimulus intensities
   in macro editor.

v1.8.0

1. Updated High Power PiVR BOM to address discontinued LED (#106).

2. Simplify code to improve readability: common.system_utils to find OS/Raspberry.

3. Added 'Select analysis area (Circle)' which allows user to interactively  to
   exclude part of the trajectory of an animal of a given experiment. The idea is
   that when the animal is very close to the edge of the arena it's hard to faithfully
   track the animal and it might be safer to discard those timepoints.

4. Video conversion: if 'Save *.npy' file or 'Save *.mat' file selected it will be 
   saved as 'all_images.npy' and 'all_images.mat', respectively. Previous behavior was 
   to save with original video name. 

5. Addresses #108. cleaned up discrepancy in data.csv between video recording and tracking 
   where the first would save columns as 'Time [s]' and the later as 'Time'. Now both are 
   'Time [s]'. This change will break downstream code which is why the next release will be 1.8.0

6. Hind Al Ali fixed a new bug in "Display tracked experiment" -> "Video" by swapping `draw.circle` 
   with `draw.disk` (!124)(#121).

   This merge also makes the circles indicating body parts a bit smaller, makes colors for head/tail
   consistent with GUI colors, removes whitespace and increments video.mp4 filename to not
   overwrite older videos.

   Thank you, Hind!

7. Fixed a bug that made it impossible to use animal detection method 3. It's still hard to use
   because the animal must stand out clearly from the background during detection, though. So 
   mode 1 will likely be the easiest to use for most users! Also - it might not be working as well
   as expected. To be tested with larvae.

8. Added 'macro editor' to video recording (#113) - tested and seems to works on PiVR.

9. Added macro editor info to pivr.org website.

10. Allow ignore error message during posthoc tracking #115. 

11. Display tracked experiment now shows time taken from data.csv (and not only frame number). Addresses #118.

12. Display tracked experiment will now present the experienced stimulus at each timepoints. Addressed #118.

13. Animal specific head/tail classification (work in progress!)

14. Changed how to deal with the high-powered setup. Philosophy is still to avoid letting the user
    know that there is any difference. Addresses #116 and should automatically address #112 (work in progress, to be tested!)

15. Added 'Recording type' in experiment_settings.json which directly indicates for example if this was 
    a video recording or real-time tracking.

16. Distance to Source and Distance to VR max analysis: Column with distance to centroid is named 
    'Centroid distance to source [mm]' (addresses #75). Also added 'Frame' and 'Time [s]' column. In addition,
    data.csv file gets a new column named 'Centroid distance to source [mm]'.

17. Had to update skimage for regionprops.weighted_centroid using `pip install scikit-image==0.22.0`
    -> provide a new image file after updating to v1.8.0

18. Added option to show trace of centroid/head/tail in visualize tracked experiment #129

19. Added PiVR naming option: Give name to PiVR which is then saved in 'experiment_settings.json' when running
    an experiment. This should help keep track of where experiments were run and not all setups are exactly
    identical when it comes to light stimulus intensity #136.

20. #131 code written by Hind to decrease size of experimental folder significantly: After the experiment check 
    which of the pixels is 0 in all frames of the experiments and remove them to get the smallest possible image.
    Thank you, Hind! 

21. #137 online undistort when tracking yields floating point numbers for:
   centroids, midpoints, tails, heads, endpoints.

22. #132 added column to indicate failed head/tail assignment.

23. #135: tripwire to alert the user that there's not a lot of space left:
    It's quite annyoing to completely fill up the disk as PiVR will be unable
    to boot. When saving tracking experiment, alert user when not enough space
    to write numpy file.

    Also added a new widget next to the recording time indicating space left
    in folder selected next to 'Save in'

24. #144 BIG change! In order to address the flickering, the way the GPIOs are set is changed
    significantly: Instead of using the in-built 'set_PWM_dutycycle' function the PWM is now 
    constructed as desired and then synchronized with the already running wave. 

    In addition, the way the HP setup address the GPIO has been changed significantly. I 
    checked (with my eyes) what settings lead to these light flashes I saw sporadically. See 
    discussion in #144 for limits. PiVR now uses a lookup table with pre-calculated ON/OFF 
    settings. Importantly, it's not possible to use light intensities going from 0.01-4.99% 
    and 98.01-99.99%!
    If user tries to load a VR arena or time dependent stimulus file with those values they
    are shown an error (i.e. it won't load).
  
    Added a comparison table on the website to highlight this disadvantage of the HP version.

    Added new HP compatible VR arenas. Also re-did the standard gaussian center arenas for 
    1024x768 and 1295x972 to have identical scaling of sigma relative to size.

25. When exiting PiVR, all LEDs, including background, turn off automatically.

26. Got rid of annoying flickering when starting the HP setup.

v1.7.10

1. Updated transistor to currently available in both the standard and HP BOMs.

2. Add option to emboss stimulus in video during video conversion (#97).

3. Fix broken 640x480 undistort (See #95).

4. Addressed #96: Video recording and full frame image recording time
   dependent stimulus is now based on time (not index as was before 1.7.0).

5. Renamed stimulus file for video and full frame recording from 
   'data.csv' to 'stimulation_presented.csv' and 'stimulation_file_used.csv' (#40). 
   Also updated docs to reflect those changes. 

6. Fixed additional typos in docs and updated .readthedocs.yaml.

v1.7.9

1. Fixed #71 (fix typos and update of docs)

2. Update list of labs using PiVR on website

3. Add 'PiVR used for teaching' on website

v1.7.8

1. Fix bug introduced in 1.7.6. control_file in line 141,
470, 589 & 664 raspberry->RASPBERRY

2. Fix bug introduced in 1.7.6. pre_experiment in line 
183, 206, 364, 424, 484, 529, 888, 1447, 2123, 2255,
2442, 2940 raspberry->RASPBERRY

3. Fix bug introduced in 1.7.6. record_videos_and_image_sequences.py 
in line 507

v1.7.7

1. Typo (wrong indendation on website)

v1.7.6

1. Fixed #87: PiVR software doesn't work on MacOS.

2. Typos in visualize_tracked_experiment 

3. Wrote documentation for #88. Instead of cloning the PiVR repository
   and installing all packages we provide an OS image which can be used 
   by the user. 

4. Added missing info to Changelog.md from previous 2 commits

v1.7.5

updated missing information in doc about files that are saved

v1.7.4

Updated installation guide to solve problem described in #78 and fixed a few typos.

v1.7.3

v1.7.2

v1.7.1.1

v1.7.1

v1.7.0

v1.6.11

v1.6.9

v1.6.8

v1.6.7