Bisque Module Generator

V2.0.0

Standardizes and automates the process of creating modules that can be integrated in the Bisque web application. This command line interface (CLI) supports multiple inputs and outputs of type image, table or file. Output images will be displayed in the module results section in Bisque while tables and file outputs will have links to their respective resource service where they can be downloaded and visualized.
Custom outputs or interactive parameters will require users to manually edit some files. Regardless of your application, it is a good idea to follow this guide and use the CLI to automate a big part of the process and avoid common bugs. Once you have reached the end of this guide, if you need more customization, please take a look at the Official Bisque Documentation for a full guide on how to build modules from scratch. The XML section will provide you with some common features that users might want to include in their module and how to define them in the xml. The vision for this project is for users to build their modules without the need to edit the module files which can be tedious and time consuming to write. I will continuously update this guide and the code to include as many features as possible.

Before cloning repo:

Before cloning this repo, structure your module in the following manner.

-- Modules
    -- {ModuleName}
        -- src
            -- {source_code}
            -- BQ_run_module.py

You should create a Modules folder which will only contain the modules that you wish to test in Bisque. You should name your {ModuleName} folder how you would like your module to appear in bisque, for ex. EdgeDetection. Create a folder named src and place all your source code inside it. Finally, create a python file named BQ_run_module.py inside the src folder.

BQ_run_module.py

Include all necessary data reading and pre-processing code in BQ_run_module.py as well as a function named run_module that will take input_path_dict and output_folder_path. Hyper parameters for running the module will have to be hardcoded for now but future releases will extend functionality for these as well. This function should load input resources from input_path_dict, do any preprocessing steps, run the algorithm, save all outputs to output_folder_path, AND return the outputs_path_dict.

input_path_dict

The input_path_dict parameter is a dictionary with input names as keys and their corresponding paths as values. It is important to note that these input names will be the labels that Bisque will display in your module web page.

These input names must also match the input names specified with the cli in a later step. This will become clear later, for now, just choose some descriptive and unique input names that you would like Bisque to display in the module web page. You will use these input names to index the input_path_dict dictionary and load each resource from its respective path. Ex:

input_img_path = input_path_dict['Input Image']
img = cv2.imread(input_img_path, 0)

output_folder_path

The output_folder_path parameter is a path to the directory where output results should be saved.

output_paths_dict

You should save all output result paths into a dictionary with descriptive and unique output names as keys. These output names will be used by Bisque as labels in your module results web page. Ex:

output_paths_dict = {}
output_paths_dict['Output Image'] = output_img_path

These output paths must also be the same names used to specify outputs with the cli at a later step. The run_module function must return this dictionary of output paths in order for Bisque to read and post results back to the module web page.

A sample BQ_run_module.py is shown below:

import cv2
import os
from detection import canny_detector

# input_path_dict will have input file paths with keys corresponding to the input names set in the cli.
def run_module(input_path_dict, output_folder_path, min_hysteresis=100, max_hysteresis=200):
    """
    This function should load input resources from input_path_dict, do any pre-processing steps, run the algorithm,
    save all outputs to output_folder_path, AND return the outputs_path_dict.
    
    :param input_path_dict: Dictionary of input resource paths indexed by input names. 
    :param output_folder_path: Directory where to save output results.
    :param min_hysteresis: Tunable parameter must have default values.
    :param max_hysteresis: Tunable parameter  must have default values.
    :return: Dictionary of output result paths.
    """
    
    ##### Preprocessing #####

    # Get input file paths from dictionary
    input_img_path = input_path_dict['Input Image'] # KEY MUST BE DESCRIPTIVE, UNIQUE, AND MATCH INPUT NAME SET IN CLI

    # Load data
    img = cv2.imread(input_img_path, 0)

    ##### Run algorithm #####

    edges_detected = canny_detector(img, min_hysteresis, max_hysteresis)


    ##### Save output #####

    # Get filename
    input_img_name = os.path.split(input_img_path)[-1][:-4]

    # Generate desired output file names and paths
    output_img_path = "%s/%s_out.jpg" % (output_folder_path, input_img_name) # CHECK FILE EXTENSION!

    # Save output files
    cv2.imwrite(output_img_path, edges_detected)

    # Create dictionary of output paths
    output_paths_dict = {}
    output_paths_dict['Output Image'] = output_img_path  # KEY MUST BE DESCRIPTIVE, UNIQUE, AND MATCH OUTPUT NAME SET IN CLI

    ##### Return output paths dictionary #####  -> IMPORTANT STEP
    return output_paths_dict

if __name__ == '__main__':
    # Place some code to test implementation
    
    # Define input_path_dict and output_folder_path
    input_path_dict = {}
    current_directory = os.getcwd()
    # Place test image in current directory
    input_path_dict['Input Image'] = os.path.join(current_directory,'test_image.jpg') # KEY MUST MATCH INPUT NAME SET IN CLI
    output_folder_path = current_directory
    
    # Run algorithm and return output_paths_dict
    output_paths_dict = run_module(input_path_dict, output_folder_path, min_hysteresis=100, max_hysteresis=200)
    
    # Get outPUT file path from dictionary
    output_img_path = output_paths_dict['Output Image'] # KEY MUST MATCH OUTPUT NAME SET IN CLI
    # Load data
    out_img = cv2.imread(output_img_path, 0)
    # Display output image and ensure correct output
    cv2.imshow("Results",out_img)

IT IS IMPORTANT TO TRIPLE CHECK OUTPUT FILE EXTENSIONS TO AVOID BUGS WHEN UPLOADING RESULTS BACK TO BISQUE!

Containerizing application

Test your BQ_run_module.py file by writing some test code in the if __name__ == '__main__': code block. A simple test implementation is shown above. Once BQ_run_module.py is working as expected, you can containerize your application with docker. Follow the instructions on downloading docker, creating a Dockerfile, and running a container. Here is an example of a Dockerfile for a simple edge detection module.

You must include the section Copy Source Code in your own Dockerfile.

# ==================================================================
# module list
# ------------------------------------------------------------------
# python        3.6    (apt)
# ==================================================================

FROM python:3.6.15-buster

ENV DEBIAN_FRONTEND noninteractive

RUN apt-get update
RUN apt-get install ffmpeg libsm6 libxext6 -y

# ===================Module Dependencies============================

RUN pip3 install cycler imageio kiwisolver matplotlib numpy opencv-python Pillow pyparsing python-dateutil scipy 

# ===================Copy Source Code===============================

RUN mkdir /module
WORKDIR /module

COPY src /module/src

Create your image by running docker build -t {modulemame}:v0.0.0 . in your {ModuleName} folder. Note that docker images are only allowed to have lowercase letters. Run your docker container with docker run -it {modulemame}:v0.0.0 bash and test your application inside the container by calling python BQ_run_module.py.

Generating Module Files

Now that you have containerized and tested your application, you are ready to pull this repo and create the Bisque module.

Installing the bqmod CLI

First step is to clone this repo and install the CLI. You can create a virtual environment in which to install the CLI if you wish.

# Go to a directory outside your Modules folder and clone the rep
ivan@bisque:~/Bisque/Modules$ cd ~/Bisque
ivan@bisque:~/Bisque$ git clone https://github.com/ivanfarevalo/BQ_module_generator.git

# Go into the BQ_module_generator folder
ivan@bisque:~/Bisque$ cd BQ_module_generator

# This is optional
ivan@bisque:~/Bisque/BQ_module_generator$ virtualenv bqvenv
ivan@bisque:~/Bisque/BQ_module_generator$ . bqvenv/bin/activate

# This is required
(bqvenv) ivan@bisque:~/Bisque/BQ_module_generator$ pip3 install --editable .

Test the installation by running bqmod --help. You should get a help message. Remember to activate your virtual environment if you used one during installation, otherwise you wont be able to run the commands.

Using the bqmod CLI

For Python3 modules, you must copy the bqapi folder from the BQ_module_generator folder into your {ModuleName} folder. Your folder structure should look like this so far:

-- Modules
    -- {ModuleName}
        -- bqapi (Only for python3 modules)
        -- Dockerfile
        -- src
            -- {source_code}
            -- BQ_run_module.py

The bqmod CLI uses simple commands to populate a .json file with the configurations details of your module. All commands must be ran in your {ModuleName} folder and are preceded with the bqmod command.

Command	Options	Description
bqmod	--help	Shows help information on how to use the CLI
bqmod init		Initializes configuration file for your module and pulls necessary files from repo. If one already exists, it wills ask whether you would like to overwrite it.
bqmod set	-n --name	Sets or changes the {ModuleName} field. This must match the {ModuleName} of your module folder and should not have spaces. Ex: bqmod set -n "EdgeDetection"
	-a --authors	Sets or changes the name of the authors. Ex: bqmod set -a "Ivan"
	-d --description	Sets or changes a short description of the module. Must be in quotations. Ex: bqmod set -d "This module finds edges in images"
bqmod inputs	--remove	Flag to remove input specified by --name flag
	-i --image	Flag that sets an input of type image.
	-t --table	Flag that sets an input of type table.
	-f --file	Flag that sets an input of type file.
	-n --name	Required parameter. Sets the name of the input as will be shown in Bisque module page. Input names MUST match input_path_dict keys in BQ_module_run.py.
bqmod outputs	--remove	Flag to remove output specified by --name flag.
	-i --image	Flag that sets and output of type image.
	-t --table	Flag that sets and output of type table.
	-f --file	Flag that sets and output of type file.
	-n --name	Required parameter. Sets the name of the output as will be shown in Bisque results section. Output names MUST match output_paths_dict keys in BQ_module_run.py.
bqmod summary		Prints out the current module configurations.
bqmod gen_help_html		Generates help.html from help.md.
bqmod create_module		Generates the module .xml.

It is crucial to note that the names for inputs and outputs MUST match the dictionary keys of input_path_dict and output_paths_dict respectively! Failure to ensure this will result in an error at runtime.

Here's an example of creating a simple Edge Detection module:

ivan@bisque:~/Bisque/Modules$ cd EdgeDetection
ivan@bisque:~/Bisque/Modules/EdgeDetection$ bqmod init
ivan@bisque:~/Bisque/Modules/EdgeDetection$ bqmod set -n "EdgeDetection"
ivan@bisque:~/Bisque/Modules/EdgeDetection$ bqmod set -a "Ivan"
ivan@bisque:~/Bisque/Modules/EdgeDetection$ bqmod set -d "This module finds edges in images"
ivan@bisque:~/Bisque/Modules/EdgeDetection$ bqmod inputs --image -n "Input Image"   # THIS MUST MATCH DICTIONARY KEYS in input_path_dict
ivan@bisque:~/Bisque/Modules/EdgeDetection$ bqmod outputs --image -n "Output Image"   # THIS MUST MATCH DICTIONARY KEYS in output_paths_dict
ivan@bisque:~/Bisque/Modules/EdgeDetection$ bqmod summary
Name: EdgeDetection
Author: Ivan
Description: This module finds edges in images
Inputs: {'Input Image': 'image'}
Outputs: {'Output Image': 'image'}
ivan@bisque:~/Bisque/Modules/EdgeDetection bqmod create_module
EdgeDetection.xml created

Generating help html file

Edit the help.md markdown file in the public folder to include any documentation and examples you want to provide users. When you are done, generate the html file by running bqmod gen_help_html from the {ModuleName} folder. Please do a hard refresh on your browser every time you make changes to help.html. If not, it's possible that the browser is just showing the old version of the file because it was cached.

Module Folder Structure

This should be the resulting folder structure after creating the module.

-- Modules
    -- {ModuleName}
        -- bqapi (Only for python3 modules)
        -- bqconfig.json
        -- public
            -- thumbnail.png (module icon for bisque)
            -- help.md (Help markdown)
            -- help.html (Help html)
        -- Dockerfile
        -- PythonScriptWrapper.py
        -- runtime-module.cfg
        -- src
            -- {source_code}
            -- BQ_run_module.py
        -- {ModuleName}.xml
        -- xml_template.xml

Testing Module

You can now start testing your module in Bisque. The first step is to edit your Dockerfile to create a new image that will include all the extra layers required for Bisque communication.

Editing Dockerfile

It is necessary to append a few commands to your Dockerfile. These commands will install dependencies needed for python 3 modules, create the necessary folder structure, and copy the required files and folders into your module container. If your module is written in Python 3, you need to make sure to copy the bqapi folder from this repo in your {ModuleName} folder as described above.

Here is the updated Dockerfile for a simple Edge Detection module: Remeber to change the .xml file name to your {ModuleName}.xml file

# ==================================================================
# module list
# ------------------------------------------------------------------
# python        3.6    (apt)
# ==================================================================

FROM python:3.6.15-buster

ENV DEBIAN_FRONTEND noninteractive

RUN apt-get update
RUN apt-get install ffmpeg libsm6 libxext6 -y

# ===================Module Dependencies============================

RUN pip3 install cycler imageio kiwisolver matplotlib numpy opencv-python Pillow pyparsing python-dateutil scipy 

# ===================Copy Source Code===============================

RUN mkdir /module
WORKDIR /module

COPY src /module/src

####################################################################
######################## Append From Here Down #####################
####################################################################

# ===============bqapi for python3 Dependencies=====================
# pip install in this exact order
RUN pip3 install six
RUN pip3 install lxml
RUN pip3 install requests==2.18.4
RUN pip3 install requests-toolbelt

# =====================Build Directory Structure====================

COPY PythonScriptWrapper.py /module/
COPY bqapi/ /module/bqapi

# Replace the following line with your {ModuleName}.xml
COPY EdgeDetection.xml /module/EdgeDetection.xml

ENV PATH /module:$PATH:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
ENV PYTHONPATH $PYTHONPATH:/module/src

Creating Module Image

Once you update the Dockerfile, create a new Docker image by running the following command from your {ModuleName} folder. Note that docker images must have lowercase names and tags. The biodev.ece.ucsb.edu:5000/ prefix is needed for Bisque to pull the image. Once you are ready to deploy your application to production, you will push this image to the specified repo.

docker build -t biodev.ece.ucsb.edu:5000/{modulename}:{tagname} .

It is good practice to specify a {tagname} that identifies the image versions. As you add functionalities and customize your module, it is a good idea to keep track of the various stable images of your module. By default, Docker will tag the image latest if a tag is not provided. The following are a few example of how you could tag your images:

# First stable module image
docker build -t biodev.ece.ucsb.edu:5000/edgedetection:v1.0.0 .

# Small bugs fixed
docker build -t biodev.ece.ucsb.edu:5000/edgedetection:v1.0.4 .

# Implementing some interactive parameters
docker build -t biodev.ece.ucsb.edu:5000/edgedetection:v1.2.0 .

# Second stable module image with all features implemented
docker build -t biodev.ece.ucsb.edu:5000/edgedetection:v2.0.0 .

You can also overwrite images by building with same {modulename}:{tagname} until you get to a point in which you want to keep that specific image as reference.

Updating runtime-module-cfg

The runtime module configuration file specifies the image that Bisque will pull when a user runs your module.

The only line that should be updated is docker.image = {modulename}:{tagname}. This should specify the Docker image and tag name that you wish to test or deploy on Bisque. This file will be called when a user hits the Run button in your module's page on Bisque. Note that the prefix biodev.ece.ucsb.edu:5000/ is not included in this line, Bisque will prepend it before pulling your local image.

IMPORTANT: It is very important to update the runtime-module.cfg each time you build an image with a different name or tag so Bisque pulls the correct image you want to test.

This is an example of a runtime-module.cfg for the EdgeDetection module:

#  Module configuration file for local execution of modules

module_enabled = True
runtime.platforms = command

[command]
docker.image = edgedetection:v2.0.0     # Only edit this line
environments = Staged,Docker
executable = python PythonScriptWrapper.py
files = pydist, PythonScriptWrapper.py

Running Bisque Container

Download the latest Bisque module development image by running:

docker pull amilworks/bisque-module-dev:git

The following command will launch a container named bisque on http://{your.private.ip.address}:8080/. The option --v $(pwd):/source/modules will mount your local module located in your current directory $(pwd) to your container at /source/modules. The -v /var/run/docker.sock:/var/run/docker.sock option will enable access to your local docker containers within the BisQue dev container. This is crucial because modules are ran as containers themselves so if you cannot run a container within a container, you will get an error.

# Navigate to the 'Modules' parent directory that holds your {ModuleName} folder.

ivan@bisque:~/Bisque$ cd ~/Bisque/Modules

# It should only contain the modules you intend to test on bisque, for Ex:

ivan@bisque:~/Bisque/Modules$ ls
EdgeDetection

# Run container
ivan@bisque:~/Bisque/Modules$ docker run --name bisque --rm -p 8080:8080 -v $(pwd):/source/modules -v /var/run/docker.sock:/var/run/docker.sock amilworks/bisque-module-dev:git

Logging Into Bisque

Navigate to http://{your.private.ip.address}:8080/ on any web browser and Bisque should be up and running. For example, if my ip address is 192.168.181.345, you would navigate to http://192.168.181.345:8080/. You can find your private ip address by running:

ifconfig | grep "inet.*broadcast.*" | awk '{print $2}'

or

ifconfig | grep "inet.*Bcast.*" | awk '{print $2}'

It will be the address that has twelve digits with a period after every third digit. You can also read the following article (Windows, Mac) or article (Linux) to find your private ip address if the previous commands didn't work.

If Bisque is not up, go into the container with docker run -it amilworks/bisque-module-dev:git bash and check the bisque_8080.log to debug. Report any issues on the Bisque GitHub.

Login as admin using the credentials:

Username: admin
Password: admin

Upload Data

You can now upload any data that you need to test your module. In the top menu bar, go to Upload -> Choose files -> Upload (at the bottom). Exit out of the pop-up window and move on to register your module.

Register Module

In the top right hand corner, go to Bisque admin -> Module Manager. In the right panel, Engine Modules, fill in the Engine URL with:

http://{your.private.ip.address}:8080/engine_service

You can find your private ip address as mentioned above.

Click Load to show all the modules that are in the Modules folder you mounted when running the Bisque docker image. Drag and drop the module you want to test from the right panel to the left and exit out of the setting window.

If you don't see any modules on this list, go throught the following debug process:

• Check that the Engine URL is correct. If your ip address is 192.168.181.345 for example, your engine url should be http://192.168.181.345:8080/engine_service.
• Make sure that the mounted folder -v $(pwd):/source/modules contains the {ModuleName} folders of the modules you want to test. You should be in your Modules folder when running the docker container.
• Make sure that the .xml file in your {ModuleName} folder and the {ModuleName} folder have the same name. For example, for the EdgeDetection module, {ModuleName} should be EdgeDetection and the .xml should be named EdgeDetection.xml.
• Make sure that your {ModuleName} folder has a runtime-module.cfg file.

Running Module

To run your module, click the Analyse button from the top menu bar and choose your module. If you don't see your module, refresh the page and try again.

Debug Steps

Follow the steps to run your module and verify that the result is as expected. If Bisque reports any errors or seems to be frozen, you can debug it by checking the logs in the Bisque container.

Log files

Every time you hit the Run button, Bisque starts a new container of your module and saves their corresponding logs in /source/staging/{mex_id}. Mex id's start with 00- followed by 22 alphanumeric characters, Ex: 00-fMqFvjiHRjUfaff6GRy73M. This folder will have all the logs needed to debug your module. To get to this folder, run the following:

docker exec -it amilworks/bisque-module-dev:git bash
cd /source/staging/{mex_id}

The docker_run.log logs information regarding the pulling, starting, and stopping of your module container. The PythonScript.log logs information regarding the communication between Bisque and your module. As mentioned at the beginning of these guide, if you would like to add custom outputs or interactive parameters, follow the in depth guide on creating modules.