sqapi 0.2

A python package that simplifies interactions with the SQUIDLE+ API. It can be used to integrate automated labelling from machine learning algorithms and plenty other cool things.

SQAPI

sqapi is a python package that simplifies interactions with the SQUIDLE+ API. It can be used to integrate automated labelling from machine learning algorithms and plenty other cool things.

Installation

To install the sqapi module, you can use pip

pip install sqapi 

Why & how

The sqapi module helps to build the HTTP requests that are sent to the API. These are GET, POST, PATCH or DELETE requests. Setting verbosity=2 on the sqapi module will print the HTTP requests that are being made.

sqapi takes care of authentication, and simplifies the creation of API queries. For example:

from sqapi.api import SQAPI

sqapi = SQAPI(host=<HOST>,api_key=<API_KEY>, verbosity=2)  # instantiate the sqapi module
r=sqapi.get(<ENDPOINT>)              # define a get request using a specific endpoint
r.filter(<NAME>,<OPERATORE>,<VALUE>) # define a filter to compare a property with a value using an operator
data = r.execute().json()            # perform the request & return result as JSON dict (don't set template)

Instantiating sqapi without an API key argument will prompt for a user login, i.e.:

sqapi = SQAPI(host=<HOST>, verbosity=2)  # instantiate the sqapi module

You can also use it to apply templates to the data that comes out of the API:

r.template(<TEMPLATE>)               # format the output of the request using an inbuilt HTML template
html = r.execute().text              # perform the request & return result as text (eg: for html)

IMPORTANT: in order to proceed, you will need a user account on SQUIDLE+. You will also need to activate your API key.

Examples

Random annotation BOT

This is an example of an automated labelling bot that selects random class labels to assign to points. It provides terrible suggestions, however it provides a simple boiler-plate example of how to integrate a Machine Learning algorithm for label suggestions.

Set up the environment and a mini project

mkdir sqbot_demo && cd sqbot_demo   # make a directory
virtualenv -p python3 env           # create a virtual environment
source env/bin/activate             # activate it
pip install sqapi  # install sqapi

1. Create a bot class

In your project directory, create a file named run_bot.py:

# run_bot.py
import random
from sqapi.annotate import Annotator
from sqapi.request import query_filter as qf
from sqapi.helpers import cli_init, create_parser
from sqapi.media import SQMediaObject


class RandoBOT(Annotator):
    def __init__(self, user_group_id: int, **annotator_args):
        """
        Demo classifier that creates random class allocations and probabilities
        :param user_group_id: the ID of the user_group that you wish to classify
        """
        super().__init__(**annotator_args)  # calls base class with all required inputs
        self.user_group_id = user_group_id  # example of an extra parameter added to the init
        self.possible_codes = ["ECK", "ASC", "SUB"]

    def classify_point(self, mediaobj: SQMediaObject, x, y, t):
        """Overridden method: predict label for x-y point"""
        # image_data = mediaobj.data()            # cv2 image object containing media data
        # media_path = mediaobj.url               # path to media item
        classifier_code = random.sample(self.possible_codes, 1)[0]  # get a random code
        prob = round(random.random(), 2)  # generate a random probability
        # TODO: use the image_data, x and y point position to generate a real label and prob
        return classifier_code, prob


if __name__ == '__main__':
    # Get the cli arguments from the Class __init__ function signatures
    parser = create_parser(RandoBOT)  # convenient method to build a parser from the bot class
    
    # Add an extra argument to the parser to get an annotation_set id to classify
    parser.add_argument('--annotation_set_id', help="Process annotation_set with specific ID", type=int)
    
    # Instantiate the bot class
    args = parser.parse_args()
    bot = RandoBOT(**vars(args))
    
    # Initialise the request for the list of annotation_sets that you want classified
    # only consider annotation_sets that do not already have suggestions from this user
    r = bot.sqapi.get("/api/annotation_set")
    r.filter_not(qf("children", "any", val=qf("user_id", "eq", bot.sqapi.current_user.get("id"))))

    # filter annotation_sets within a nominated user_group 
    # as specified by the extra parameter added to RandoBot.__init__
    r.filter(name="id", op="in", val=args.annotation_set_id)

    bot.start(r)

The create_parser method is a convenience tool that allows you to build a command line parser from the
signature of the __init__ methods for the RandoBot class and all inherited base classes (eg: Annotator).

This allows you to pass arguments from the command line, and to use help on how to use it:

python run_bot.py --help

It will show you all the required parameters from the base class Annotator as well as any extra arguments added to the __init__ method of the RandoBot class. Parameter descriptions come from the comment block.

2. Create a Label Mapper File

Before you run it, you also need to create a label map file to pass into the --label_map_file argument. This maps the outputs from your classifier to real class labels in the system.

In your project directory, create a file named rando_bot_label_map.json with the following content:

{
  "ECK": [{"or":[{"name":"vocab_elements","op":"any","val":{"name":"key","op":"eq","val":"214344"}},{"name":"vocab_elements","op":"any","val":{"name":"key","op":"eq","val":"54079009"}}]}],
  "ASC": [{"or":[{"name":"vocab_elements","op":"any","val":{"name":"key","op":"eq","val":"1839"}},{"name":"vocab_elements","op":"any","val":{"name":"key","op":"eq","val":"35000000"}}]}],
  "SUB": [{"name":"vocab_elements","op":"any","val":{"name":"key","op":"eq","val":"82001000"}}]
}

3. Run your bot

Now you're ready to run your classifier RandoBot, by simply executing this from the command line:

python run_bot.py --label_map_file rando_bot_label_map.json --annotation_set_id=55 --poll_delay 5 --email_results

This will get the list of annotation_sets contained in the user_group with the id of 55 and attempt to provide automated suggestions on the labels it contains using random class allocations and probabilities. It will continue this indefinitely in a loop every 5s ( as defined by the --poll_delay parameter) until canceled. It will send an email to the owner of every annotation_set that it completes.

Now all that's left is for you to make the labels and probabilities real, and bob's your uncle, you've made an automated classifier.

The examples directory has some examples that you can use and/or adapt for your purposes. Specifically with regard to classifiers:

1. demo_randobot.py: same as example above, but with additional command line arguments for filtering annotation_sets
2. keras_cnn_bot.py: a real classifier that uses a tensor_flow/keras model for classifying points in images. The class received a number of additional parameters that can all be passed in as command line arguments. Run python keras_cnn_bot.py --help for more information. This shows an example of how to include additional model-specific arguments along with other parameters, as well as how to process the images and for a real classifier.