Scripts to generate DICOM files and insert them in MongoDB instance

This project is composed by two scripts:

• generator.py: generates DICOM objects or files (Computed Tomographies)
• insert.py: generates CT files in DICOM format and inserts them in a MongoDB endpoint

Requirements

• Python3
• Installation of requirements.txt

Instructions

1. Clone this repository

   git clone https://github.com/rlebre/dicoogle-mongodb-test-scripts.git

2. Install virtual environment

   virtualenv -p python3 venv

3. Activate virtual environment

   source venv/bin/activate

4. Install requirements.py

   pip install -r requirements.txt

5. Edit your configuration

Insert

6. Run generator.py and `insertion.py

   python generator.py -n 1000 -o ./dataset -j #generates 1000 files in the directory './dataset' 
   python insertion.py -c 50 -j ./dataset # reads database directory and inserts each 50 in database

   Usage: generator.py -n <number_to_generate> -o <output_directory> -d|-d <dicom_format | json_format>

7. Run simply generate objects in runtime insertion.py

   python insertion.py -n 1000 -c 50 # generates 1000 objects and inserts each 50 in database

   Usage: insertion.py -n <number_of_objects_to_insert -c <chunk_size> -j/-d <dicom|json_directory>

Query

8. Or run querying.py

   python querying.py [-i] [-d] [-q <query>] #generates 1000 DICOM files in directory ./dataset

   -i - create indexes
   -d - drop indexes
   -q - query
   

Configuration

You must configure your MongoDB instance first and provide the configurations in local_settings.py. Example:

MONGO_HOST='localhost'
MONGO_PORT=27017
MONGO_USER='dicoogle'
MONGO_PASSWORD='dicoogle'

Acknowledgments

• Thank you to the contributors of pydicom
• Thank you to Sjoerd for dicomgenerator
• Thank you to the contributors of pymongo

Disclaimer

This work received support from FCT, Fundação para a Ciência e a Tecnologia, under the project UID/CEC/00127/2019 and POCI-01-0145-FEDER-016385 (NETDIAMOND)