Monitoring Mammalian Herbivores via Convolutional Neural Networks implemented on Thermal UAV imagery

This repository provides the code, images, and annotations of the research "Monitoring Mammalian Herbivores via Convolutional Neural Networks implemented on Thermal UAV imagery" https://doi.org/10.1016/j.compag.2024.108713.

Research

In the algorithms folder, code for applying TrackR-CNN and PWC-Net to Multi Object Tracking and Segmentation (MOTS) is provided. PWC-Net is tested as an alternative tracking method to the association head used in TrackR-CNN.

The flowchart below illustrates the steps followed to conduct this research:

Models

Configuration files for the models can be found in algorithms/TrackR-CNN. We test two temporal components (3D convolutions and LSTM convolutions), and two tracking mechanisms (optical flow and an association head).

Video of TrackR-CNN results

Dataset

We created our own instance segmentation dataset, which we named COW_MOTS, in the fashion of the KITTI_MOTS dataset.

COW_MOTS consists of 7 video sequences depicting aerial thermal imagery of cattle collected with a UAV in two outdoor farms in the Netherlands. Data was acquired at three temperatures (10ºC, 19ºC, and 26.5ºC), under sunny and overcast weather conditions, at various angles of inclination (including nadir), and at heights ranging between 8-28 meters.

The COW_MOTS dataset consists of 959 frames, 20.647 masks, and 239 tracks. Ground truth was labeled manually with the Computer Vision Annotation Tool CVAT, run in a docker container. Go to the preprocessing folder for instructions on using the annotation tool.

The following images are examples of the seven datasets that comprise COW_MOTS. They illustrate data collected at different atmospheric conditions (temperature and sunlight), heights, and angles of inclination:

Images and annotations of COW_MOTS will be made publicly available soon.

Algorithms

TrackR-CNN

Here, we provide a tutorial for applying the TrackR-CNN algorithm for a Multi-Object Tracking and Segmentation (MOTS) task to the COW_MOTS dataset or to a custom dataset.

If you want to apply PWC-Net together with Track R-CNN, instructions are provided at the end of this README.

Video of results

Installation and setup

Hardware

TrackR-CNN has been implemented on a high performance computer and on the Anunna High Performance Cluster (HPC).

High performance computer specs:

• NVIDIA Titan RTX videocard
• 64 GB RAM memory
• Intel® Core™ i9-10940X CPU @ 3.30GHz × 28
• Ubuntu 20.04.1 LTS

High Performance Cluster specs:

• NVIDIA Tesla V100
• 64 GB RAM memory
• Scientific linux

Requirements

• Install Anaconda
• Set up a virtual environment
  • conda create --name myenv python=3.6.7
  • conda activate myenv
• Clone (or download as a zip file) this repository
  • git clone https://git.wur.nl/diego.barbulobarrios/TrackR-CNN.git
• Navigate to the TrackR-CNN directory and install the requirements
  • cd algorithms/TrackR-CNN
  • pip install -r requirements.txt

Folder structure

• Create the following folders in algorithms/TrackR-CNN:
  • mkdir, forwarded, models, summaries, logs, data
• After running the code, the algorithm's output will be stored in these folders:
  • forwarded will store the detection and tracking files and visualizations
  • models will store the trained models checkpoints. It also stores the models used for pre-training (COCO and Mapillary) and fine-tuning (KITTI MOTS).
  • logs will store a copy of the terminal's output during the training procedure.

Set your folder structure as follows:

data/
- COW_MOTS/
-- train/
--- images/
---- 0000/
----- 000000.png
----- 000001.png
----- ...
---- 0001/
---- ...
--- instances
---- 0000/
----- 000000.png
----- 000001.png
----- ...
---- 0001/
---- ...
models/
- conv3d_sep2/
-- conv3d_sep2-00000005.data-00000-of-00001
-- conv3d_sep2-00000005.index
-- conv3d_sep2-00000005.meta
- converted.data-00000-of-00001
- converted.meta
- converted.index
...
main.py

Training

To train a model, navigate to algorithms/TrackR-CNN and run main.py with the corresponding configuration file e.g., python main.py configs/3dconv4 (cd algorithms/TrackR-CNN). If you are running the algorithm in Windows, you may get an error stating that the key USER has not been found among the environment variables. In this case, add it to the dictionary by writing os.environ["USER"] = os.environ["USERNAME"] at the beginning of the main() function in main.py

Configuration files

In the configuration files:

Point KITTI_segtrack_data_dir to your train folder; e.g., "KITTI_segtrack_data_dir": "/home/saidlab/Thesis_DiegoBarbuloBarrios/MOTS/algorithms/TrackR-CNN/data/COW_MOTS/train/"

Point load_init to the model pre-trained on COCO & Mapillary, e.g., "load_init": "/home/saidlab/Thesis_DiegoBarbuloBarrios/MOTS/algorithms/TrackR-CNN/models/converted", or to the KITTI MOTS checkpoint used for fine-tuning, e.g., "load_init": "/home/saidlab/Thesis_DiegoBarbuloBarrios/MOTS/algorithms/TrackR-CNN/models/conv3d_sep2-00000005". For pre-training and fine-tuning, you can download the models here.

Optimal values for the hyperparameters (epochs and batch size) used to train each model have to be found experimentally. On COW MOTS, 23 epochs and a small batch size of 4 give the best results.

As a temporal component, three models (3dconv) use two 3D convolutional layers and one model (lstm8) uses two stacked LSTM layers. The number at the end of the models' names refers to the batch size.

COW_MOTS

There are two possibilities to train TrackR-CNN on COW_MOTS.

1. Train a model pre-trained on COCO and Mapillary:

• Change in a config file:
  • Model name
  • Point load_init to the model pre-trained on COCO and Mapillary ("converted") in the "models" folder e.g., "load_init": "/home/saidlab/Thesis_DiegoBarbuloBarrios/MOTS/algorithms/TrackR-CNN/models/converted".
  • Run python main.py configs/<config_file_name>

2. Train a model pre-trained on COCO and Mapillary and fine-tuned on KITTI MOTS:

• Change in a config file:
  • Model name
  • Point load init to the KITTI MOTS checkpoint in the "models" folder e.g., "load_init": "/home/saidlab/Thesis_DiegoBarbuloBarrios/MOTS/algorithms/TrackR-CNN/models/conv3d_sep2-00000005"
  • Run python main.py configs/<config_file_name>

If you want to use the best performing model (trained on COW_MOTS), you can download it here.

Custom dataset

To train TrackR-CNN on a custom dataset:

• Change in a config file:
  • Model name
  • Point load init to the model pre-trained on COCO and Mapillary or to the KITTI MOTS checkpoint in the "models" folder (see how in previous section "COW_MOTS").
  • Point KITTI_segtrack_data_dir to your train folder e.g., "KITTI_segtrack_data_dir": "/home/saidlab/Thesis_DiegoBarbuloBarrios/MOTS/algorithms/TrackR-CNN/data/<your_datasaet>/train/".
  • Experimentally, find the optimal values for the batch size and the number of epochs.
  • Set "input_size_train" and "input_size_val" to your images' resolution.
• Change the maximum number of detections:
  • Navigate to algorithms/TrackR-CNN/datasets/KITTI/segtrack/KITTI_segtrack.py and change the variable N_MAX_DETECTIONS to the maximum number of detections (frame with highest number of targets) in your dataset. A higher value than the highest number would also work.

Forwarding and tracking

First, make sure to add the datasets on which you want to apply forwarding and tracking to the train folder before running the respective procedures.

To obtain the models' detections, run the following command on the terminal:

python main.py configs/CONFIG_FILE_NAME "{\"task\":\"forward_tracking\",\"dataset\":\"KITTI_segtrack_feed\",\"load_epoch_no\":5,\"batch_size\":5,\"export_detections\":true,\"do_tracking\":false,\"video_tags_to_load\":[\"0000\",\"0001\",\"0002\",\"0003\",\"0004\",\"0005\",\"0006\"]}"

Use video_tags_to_load to choose on which datasets you want the predictions to be made. Make sure to set load_epoch_no to the number of epochs on which the model has been trained. In case you have saved several versions of the model at different points of the training procedure, keep in mind that the value you input in load_epoch_no is used to find the models' version with which you want to make predictions. The command's output will be written to the forwarded folder.

To link over time the detections obtained by the previous command, run:

python main.py configs/CONFIG_FILE_NAME
"{\"build_networks\":false,\"import_detections\":true,\"task\":\"forward_tracking\",\"dataset\":\"KITTI_segtrack_feed\",\"do_tracking\":true,\"visualize_detections\":false,\"visualize_tracks\":false,\"load_epoch_no\":5,\"video_tags_to_load\":[\"0000\",\"0001\",\"0002\",\"0003\",\"0004\",\"0005\",\"0006\"]}"

Visualizations will be stored in forwarded/<model_name>/vis/tracks.

Visualization

To change the class assigned to the detections (e.g., cow), go to TrackR-CNN/mots_tools/mots_vis/visualize_mots.py and change the category_name from "Cow" to the desired class. In case you want to detect and track more than one class, also change the second category_name from "Pedestrian" to the desired class and, if needed, add more classes.

Tuning

The tuning procedure is used to find the best detection and tracking parameters for the model on a specific dataset. It relies on a random search approach on the training dataset, after which the best parameters are tested on the test dataset and the metrics are calculated.

Before running the tuning procedure, make sure to add both training and testing datasets to the train folder. In order to specify the training and testing sequences, follow this procedure:

• Navigate to algorithms/TrackR-CNN/mots-tools/mots_eval/
• Add the sequences for training to train.seqmap and the sequences for testing to val.seqmap in the following format:
  • <seq_id> empty <start_frame> <end_frame>

To conduct the tuning procedure, run:

python scripts/eval/segtrack_tune_experiment.py /path/to/detections/ /path/to/groundtruth/ /path/to/precomputed_optical_flow/ /path/to/output_file /path/to/tmp_folder/ /path/to/mots_eval/ association_type num_iterations

where /path/to/detections/ is the folder containing the detections obtained by running the "forwarding" command above; /path/to/mots_eval/ refers to the "mots eval" folder contained in the "mots tools" directory; association_type determines the method (association head or optical flow) for associating detections into tracks and is either reid (relying on the association head), mask (using optical flow), bbox_iou (using bounding box warping with median optical flow) or bbox_center (using nearest neighbor matching); num_iterations is the number of random trials (1000 in this study); /path/to/groundtruth/ refers to the instances or instances_txt folder containing the annotations; /path/to/precomputed_optical_flow has to be set to a folder containing the optical flow images - namely when setting association_type to mask or bbox_iou but if you set it to something else, then the flow path is ignored; at /path/to/output_file, a file will be created containing the results of the individual tuning iterations, please make sure this path is writable; at /path/to/tmp_folder a lot of intermediate folders will be stored, you can delete these afterwards.

Evaluation

The code from the mots_tools repository has been included in this respository to make the evaluation of the results easier and faster.

To obtain all the metrics for your model on the testing dataset, run eval.py in mots_tools/mots_eval. Before running the script, set the right path to the "mots_tools" folder e.g., sys.path.append(/home/saidlab/Thesis_DiegoBarbuloBarrios/MOTS/algorithms/TrackR-CNN/mots_tools/).

Counting

In order to get the counting results of the model on your dataset, run eval.py and look at the TR Trk metric results (i.e., number of tracks predicted by the model). To test the model's counting efficiency, compare it with the ground truth tracks, which you can find under the metric GT Trk.

Optical Flow

To use optical flow as a tracking mechanism, follow the instructions below for generating optical flow images from the COW_MOTS dataset and naming them according to the format required by TrackR-CNN.

Video of results

PWC-Net detects pixel motion between consecutive frames, so only the cows in movement are detected by the algorithm.

PWC-Net

We use a simpler reimplementation of the official repository that provides the same results.

Setup

• Install Anaconda
• Create an environment
  • conda create --name myenv python=3.6.7
  • conda activate myenv
• Navigate to pytorch-pwc directory and install the requirements
  • cd algorithms/PWC-Net/flow_files/pytorch-pwc
  • pip install -r requirements.txt

Flow-files

To get a flow file from every pair of adjacent images in your dataset, follow these steps:

• Go to algorithms/PWC-Net/flow_files/pytorch-pwc/ and, in the estimate() function, insert your images' resolution values in intWidth and intHeight.
• Store the dataset's images in the images folder.
  • Make sure to either name your images according to the format used for TrackR-CNN (e.g., 000000.png, 000001.png, etc.) or to change the code in the script to fit the format you are using.
• Navigate to algorithms/PWC-Net/flow_files and run the flow_files_generator.py script.

The flow_files_generator.py script will produce a flow file from every pair of consecutive images and write it to the out folder.

UV-files

Setup

• Create an environment in Anaconda
• Clone (or download as a zip file) this repository
  • git clone https://github.com/georgegach/flowiz.git
• Install requirements

Running the code

To generate a pair of UV images from each flow file (previously generated from the datasets' images), follow these steps:

• Go to algorithms/PWC-Net/UV_files/flowiz/flowiz and open the UV_files_generator.py script.
• Change the string in variable a to a path pointing to the flow-files' folder, and those of variables b and c to paths pointing to the output folders to which images representing U V channels will be written.
• Run UV_files_generator.py

Minimum flow values

To obtain the minimum flow value of each flow file (a requirement to run optical flow within TrackR-CNN), this repository provides code from the Middlebury evaluation under the color_files_&_minimum_flow folder.

Runing the code

Follow these steps:

• Navigate to algorithms/PWC-Net/color_files_&_minimum_flow/Middlebury_evaluation and open the colorimage_&_minflow.py script.
• Modify the strings within the os.system() method so that it points to the folder containing the flow files.
• The minimum and maximum flow values for each flow file's U V channels are part of the terminal output. Make sure to save this output to a log to later extract the minimum-flow values.
• Run the script

Renaming

Running the code

As a final step for using optical flow as a tracking mechanism in TrackR-CNN, you will have to rename the U V files in accordance with the format required by TrackR-CNN. To do so, follow these steps:

• Go to algorithms/PWC-Net/rename_UV/Optical-flow and open the Renaming_UV_images script.
• Point log_path to the logs containing the minimum-flow values and point path to a folder containing the UV images.
• Run the script

The script renames UV images with the format required by TrackR-CNN (e.g., 000000_x_minimal-4.png, 000000_y_minimal-2.png, etc.); where the terminations "x" and "y" denote, respectively, the U and V channels, and the number is the rounded minimum flow value. For example, 000006_x_minimal-3.png describes the flow in x direction for frame 6.

After generating the optical flow images, change the following in the tuning procedure:

• Point the /path/to/precomputed_optical_flow to the location where the optical flow images are stored.
• Set association type either to mask or to bbox_iou so that optical flow is used as a tracking mechanism.

Now, you can run the tuning procedure with optical flow, instead of the association head, as a tracking mechanism.

Using Optical flow as a tracking mechanism

After generating the optical flow images and renaming them according to the format required by Track R-CNN, change the following in the tuning procedure:

• Point the /path/to/precomputed_optical_flow to the location where the optical flow images are stored.
• Set association type either to mask or to bbox_iou so that optical flow is used as a tracking mechanism.

Now, you can run the tuning procedure with optical flow, instead of the association head, as a tracking mechanism.

References

The TrackR-CNN code and parts of the README come from TrackR-CNN. The PWC-Net and flowiz code have been obtained from PWC-Net and flowiz. Code for obtaining the minimum flow values comes from the Middlebury evaluation.

Citation

If you use this code, please cite:

@misc{pytorch-pwc,
author = {Simon Niklaus},
title = {A Reimplementation of {PWC-Net} Using {PyTorch}},
year = {2018},
howpublished = {\url{https://github.com/sniklaus/pytorch-pwc}}
}
@inproceedings{Sun_CVPR_2018,
author = {Deqing Sun and Xiaodong Yang and Ming-Yu Liu and Jan Kautz},
title = {{PWC-Net}: {CNNs} for Optical Flow Using Pyramid, Warping, and Cost Volume},
booktitle = {IEEE Conference on Computer Vision and Pattern Recognition},
year = {2018}
}
@inproceedings{Voigtlaender19CVPR_MOTS,
 author = {Paul Voigtlaender and Michael Krause and Aljosa Osep and Jonathon Luiten and Berin Balachandar Gnana Sekar and Andreas Geiger and Bastian Leibe},
 title = {{MOTS}: Multi-Object Tracking and Segmentation},
 booktitle = {CVPR},
 year = {2019},
}
GitHub - georgegach/flowiz: Converts Optical Flow files to images and optionally compiles them to a video. Flow viewer GUI is also available. Check out mockup right from Github Pages: https://github.com/georgegach/flowiz.
vision.middlebury.edu/flow/submit. https://vision.middlebury.edu/flow/submit/.

Contact

If you encounter problems when running the code or have any questions, please open an issue or contact [email protected]