unet style image translation from image of hive entrance to bitmap of location of center of bees.
see this blog post for more info..
here's an example of predicting bee position on some held out data. the majority of examples trained had ~10 bees per image.
the ability to locate each bee means you can summarise with a count. note the spike around 4pm when the bees at this time of year come back to base.
run_sample_training_pipeline.sh for an executable end to end smoke test walkthrough of these steps (using sample data)
code depends in
sudo apt-get install python3-tk python3-pil python3-pil.imagetk sudo pip3 install -r requirements.txt
rasp_pi sub directory includes one method of collecting images on a raspberry pi.
start by using the
label_ui.py tool to manually label some images and create a sqlite
the following command starts the labelling tool for some already labelled (by me!) sample data provided with in this repro.
./label_ui.py \ --image-dir sample_data/training/ \ --label-db sample_data/labels.db \ --width 768 --height 1024
- left click to label the center of a bee
- right click to remove the closest label
- press up to toggle labels on / off. this can help in tricky cases.
- use left / right to move between images. it's often helpful when labelling to quickly switch back/forth between images to help distinguish background
- use whatever system your OS provides to zoom in; e.g. in ubuntu super+up / down
you can merge entries from
./merge_dbs.py --from-db a.db --into-db b.db
before training we materialise a
label.db (which is a database of x,y coords)
into black and white bitmaps using
./materialise_label_db.py \ --label-db sample_data/labels.db \ --directory sample_data/labels/ \ --width 768 --height 1024
we can visualise the training data with
data.py. this will generate a number of
test*png files with
the input data on the left (with data augmentation) and the output labels on the right.
./data.py \ --image-dir sample_data/training/ \ --label-dir sample_data/labels/ \ --width 768 --height 1024
run denotes the subdirectory for ckpts and tensorboard logs; e.g.
--run r12 checkpoints
ckpts/r12/ and logs under
--help to get complete list of options including model config, defining validation data and stopping conditions.
e.g. to train for a short time on
sample_data run the following... (for a more realistic result we'd want
to train for many more steps on much more data)
./train.py \ --run r12 \ --steps 300 \ --train-steps 50 \ --train-image-dir sample_data/training/ \ --test-image-dir sample_data/test/ \ --label-dir sample_data/labels/ \ --width 768 --height 1024
progress can be visualised with tensorboard (serves at localhost:6006)
tensorboard --log-dir tb
predictions can be run with
to specifiy what type of output set one of the following...
--output-label-dbto create a label db; this can be merged with a human labelled db, using
./merge_dbs.pyfor semi supervised learning
--export-pngs centroidsto export output bitmaps equivalent as those made by
--export-pngs predictionsto export explicit model output (i.e. before connected components post processing)
NOTE: given the above step that only runs a short period on a small dataset we DON'T expect this to give a great result; these instructions are more included to prove the plumbing works...
./predict.py \ --run r12 \ --image-dir sample_data/unlabelled \ --output-label-db sample_predictions.db \ --export-pngs predictions
output predictions can be compared to labelled data to calculate precision recall. (we deem a detection correct if it is within a thresholded distance from a label)
./compare_label_dbs.py --true-db ground_truth.db --predicted-db predictions.db precision 0.936 recall 0.797 f1 0.861
running on compute stick
[update] given how long ago this was, i'm hoping things are easier these days :D