SYD is a command-line environment and a python toolkit to perform image processing tasks on a database of medical images. It is initially developed to manage SPECT/CT images and perform tasks such as computing activity or integrated activity in various ROIs, in the field of Target Radionuclide Therapy and nuclear medicine.

use git clone --recursive or git submodule update --init. Warning: syd contains git submodules so you need to use --recursivethe first time you clone the repository.

Then, install with pip install -e . in the cloned folder. You can check that everything goes well with:

python -m unittest syd_test -v

From here, you can start using the syd module in your python scripts:

import syd

Some documentation here: https://syd.readthedocs.io/en/latest

Main API

Create a new empty DB.

db = syd.create_db('mydatabase.db')

Open a db.

db = syd.open_db('mydatabase.db')

Insert elements in a table. The patient variable is a dict.

syd.insert(db['Patient'], patients)
syd.insert_one(db['Patient'], patient)

Delete elements in a table. The input is id or an array of ids.

syd.delete(db['Patient'], ids)
syd.delete_one(db['Patient'], id)

Update element in a table, the input is a dict, with 'id' key.

syd.update_one(db['Patient'], patient)

Find elements. From syd.find, element is a Box (a kind of dictionnary that allow dot notation to retrieve the field value, elem.name instead of elem['name']).

element = syd.find_one(db['Patient'], id=12)
elements = syd.find(db['Patient'], id=[12,14])
elements = syd.find(db['Patient'], name=['toto', 'titi'])

for e in elements:
     print(e.name)

Dicom API

Search for all dicom series in the folder and add it to the db. Dicom are associated with patient_id (guess if == 0).

syd.insert_dicom(db, folder, patient_id)

Helper to get all files associated with a dicom serie.

syd.get_dicom_serie_files(db, dicom_serie)

Image API

Convert dicom series into image.

syd.insert_image_from_dicom(db, dicom_serie)

Examples of helpers functions.

patient = syd.get_image_patient(db, image)
filename = syd.get_image_filename(db, image)
itk_image = syd.read_itk_image(db, image)
new_image = syd.insert_new_image(db, image, itk_image)
new_image = syd.insert_write_new_image(db, image, itk_image, tags)