Quickstart

This section assumes you have successfully installed zamba and are ready to train a model or identify species in your videos!

zamba can be used "out of the box" to generate predictions or train a model using your own videos. To perform inference, you simply need to run zamba predict followed by a set of arguments that let zamba know where your videos are located, which model you want to use, and where to save your output. To train a model, you can similarly run zamba train and specify your labels. The following sections provide details about these separate modules.

There are two ways to interact with the zamba package:

1. Use zamba as a command line interface tool. This page provides an overview of how to use the CLI.
2. Import zamba in Python and use it as a Python package. For instructions on using the Python package, see the user tutorial that corresponds to your use case.

Installation is the same for both the command line interface tool and the Python package.

All of the commands on this page should be run at the command line. On macOS, this can be done in the terminal (⌘+space, "Terminal"). On Windows, this can be done in a command prompt, or if you installed Anaconda an anaconda prompt (Start > Anaconda3 > Anaconda Prompt).

How do I organize my videos for zamba?

You can input the path to a directory of videos or specify a list of file paths. zamba supports the same video formats as FFmpeg, which are listed here. Any videos that fail a set of FFmpeg checks will be skipped during inference or training.

For example, say we have a directory of videos called example_vids that we want to generate predictions for using zamba. Let's list the videos:

$ ls example_vids/
blank.mp4
chimp.mp4
eleph.mp4
leopard.mp4

Here are some screenshots from those videos:

blank.mp4	chimp.mp4
eleph.mp4	leopard.mp4

In this example, the videos have meaningful names so that we can easily compare the predictions made by zamba. In practice, your videos will probably be named something much less useful!

Generating predictions

To generate and save predictions for your videos using the default settings, run:

$ zamba predict --data-dir example_vids/

zamba will output a .csv file with rows labeled by each video filename and columns for each class (ie. species). The default prediction will store all class probabilities, so that cell (i,j) is the probability that animal j is present in video i. Comprehensive predictions are helpful when a single video contains multiple species. Predictions will be saved to zamba_predictions.csv in the current working directory by default. You can save out predictions under a different name or in a different folder using the --save-path argument.

Adding the argument --output-class-names will simplify the predictions to return only the most likely animal in each video:

$ zamba predict --data-dir example_vids/ --output-class-names
$ cat zamba_predictions.csv
blank.mp4,blank
chimp.mp4,chimpanzee_bonobo
eleph.mp4,elephant
leopard.mp4,leopard

There are three pretrained models that ship with zamba: time_distributed, slowfast, and european. Which model you should use depends on your priorities and geography (see the Available Models page for more details). By default zamba will use the time_distributed model. Add the --model argument to specify one of other options:

$ zamba predict --data-dir example_vids/ --model slowfast

Training a model

You can continue training one of the models that ships with zamba by either:

• Fine-tuning with additional labeled videos where the species are included in the list of zamba class labels
• Fine-tuning with labeled videos that include new species

In either case, the commands for training are the same. Say that we have labels for the videos in the example_vids folder saved in example_labels.csv. To train a model, run:

$ zamba train --data-dir example_vids/ --labels example_labels.csv

The labels file must have columns for both filepath and label. The filepath column should contain either absolute paths or paths relative to the data-dir. Optionally, there can also be columns for split (train, val, or holdout) and site. Let's print the example labels:

$ cat example_labels.csv
filepath,label
blank.MP4,blank
chimp.MP4,chimpanzee_bonobo
eleph.MP4,elephant
leopard.MP4,leopard

By default, the trained model and additional training output will be saved to a folder in the current working directory called zamba_{model_name}. For example, a model finetuned from the provided time_distributed model will be saved in zamba_time_distributed.

$ zamba train --data-dir example_vids/ --labels example_labels.csv
$ ls zamba_time_distributed
time_distributed.ckpt 
...

Downloading model weights

zamba needs to download the "weights" files for the neural networks that it uses to make predictions. On first run it will download ~200-500 MB of files with these weights depending which model you choose. Once a model's weights are downloaded, the tool will use the local version and will not need to perform this download again. If you are not in the US, we recommend running the above command with the additional flag either --weight_download_region eu or --weight_download_region asia depending on your location. The closer you are to the server the faster the downloads will be.

Getting help

Once zamba is installed, you can see more details of each function with --help.

To get help with zamba predict:

$ zamba predict --help

Usage: zamba predict [OPTIONS]

  Identify species in a video.

  This is a command line interface for prediction on camera trap footage.
  Given a path to camera trap footage, the predict function use a deep
  learning model to predict the presence or absense of a variety of species of
  common interest to wildlife researchers working with camera trap data.

  If an argument is specified in both the command line and in a yaml file, the
  command line input will take precedence.

Options:
  --data-dir PATH                 Path to folder containing videos.
  --filepaths PATH                Path to csv containing `filepath` column
                                  with videos.
  --model [time_distributed|slowfast|european]
                                  Model to use for inference. Model will be
                                  superseded by checkpoint if provided.
                                  [default: time_distributed]
  --checkpoint PATH               Model checkpoint path to use for inference.
                                  If provided, model is not required.
  --gpus INTEGER                  Number of GPUs to use for inference. If not
                                  specifiied, will use all GPUs found on
                                  machine.
  --batch-size INTEGER            Batch size to use for training.
  --save / --no-save              Whether to save out predictions to a csv
                                  file. If you want to specify the location of
                                  the csv, use save_path instead.
  --save-path PATH                Full path for prediction CSV file. Any
                                  needed parent directories will be created.
  --dry-run / --no-dry-run        Runs one batch of inference to check for
                                  bugs.
  --config PATH                   Specify options using yaml configuration
                                  file instead of through command line
                                  options.
  --proba-threshold FLOAT         Probability threshold for classification
                                  between 0 and 1. If specified binary
                                  predictions are returned with 1 being
                                  greater than the threshold, 0 being less
                                  than or equal to. If not specified,
                                  probabilities between 0 and 1 are returned.
  --output-class-names / --no-output-class-names
                                  If True, we just return a video and the name
                                  of the most likely class. If False, we
                                  return a probability or indicator (depending
                                  on --proba_threshold) for every possible
                                  class.
  --num-workers INTEGER           Number of subprocesses to use for data
                                  loading.
  --weight-download-region [us|eu|asia]
                                  Server region for downloading weights.
  --skip-load-validation / --no-skip-load-validation
                                  Skip check that verifies all videos can be
                                  loaded prior to inference. Only use if
                                  you're very confident all your videos can be
                                  loaded.
  -y, --yes                       Skip confirmation of configuration and
                                  proceed right to prediction.
  --help                          Show this message and exit.

To get help with zamba train:

$ zamba train --help

Usage: zamba train [OPTIONS]

  Train a model on your labeled data.

  If an argument is specified in both the command line and in a yaml file, the
  command line input will take precedence.

Options:
  --data-dir PATH                 Path to folder containing videos.
  --labels PATH                   Path to csv containing video labels.
  --model [time_distributed|slowfast|european]
                                  Model to train. Model will be superseded by
                                  checkpoint if provided.  [default:
                                  time_distributed]
  --checkpoint PATH               Model checkpoint path to use for training.
                                  If provided, model is not required.
  --config PATH                   Specify options using yaml configuration
                                  file instead of through command line
                                  options.
  --batch-size INTEGER            Batch size to use for training.
  --gpus INTEGER                  Number of GPUs to use for training. If not
                                  specifiied, will use all GPUs found on
                                  machine.
  --dry-run / --no-dry-run        Runs one batch of train and validation to
                                  check for bugs.
  --save-dir PATH                 Directory in which to save model checkpoint
                                  and configuration file. If not specified,
                                  will save to a folder called
                                  'zamba_{model_name}' in your working
                                  directory.
  --num-workers INTEGER           Number of subprocesses to use for data
                                  loading.
  --weight-download-region [us|eu|asia]
                                  Server region for downloading weights.
  --skip-load-validation / --no-skip-load-validation
                                  Skip check that verifies all videos can be
                                  loaded prior to training. Only use if you're
                                  very confident all your videos can be
                                  loaded.
  -y, --yes                       Skip confirmation of configuration and
                                  proceed right to training.
  --help                          Show this message and exit.