Getting Started

Before you can run dicom_wsi, you first need to gather some input data necessary for creating a valid DICOM file. There are to ways to do this: 1.) Create a YAML file or 2.) Build a dictionary yourself.

Create a YAML file

The YAML file contains two sections: General and BaseAttributes. The General section contains a fixed number of required fields that are used by dicom_wsi, whereas the BaseAttributes are restricted key words from the DICOM standard. These are cross-referenced with the pydicom dictionary.

General section

Definitions

Term Definition
WSIFile Path to whole slide image file
OutFilePrefix What prefix to use when saving the DICOM output file
NumberOfLevels How many levels should be extracted (in powers of 2)
OrgUIDRoot Your organizations UID root prefix
FrameSize How many pixels should be used for DICOM frames
MaxFrames Number of frames allowed before writing to a new file

BaseAttributes section

Most of the terms in this section are defined in the DICOM standard. Many will not need to be changed, but some always will. Below, I highlight those terms that will likely need to be manually set. Definitions

Term Definition
PatientName LastName^FirstName
PatientBirthDate Date format (i.e. 20000101)
PatientSex M: Male, F: Female, O: Other
PatientID Unique identifier for the patient
ReferringPhysicianName LastName^FirstName
StudyDate Date format
StudyID Human readable study name

A full example can be found in yaml/base.yaml.

Without a YAML file

While a YAML file is recommended, you don’t actually need one. You could choose to make the dictionary yourself. The dictionary has two nested components, General and BaseAttributes, each of which has the elements defined in yaml/base.yaml.

Using in existing code

To use dicom-wsi in a project:

from yaml import load, BaseLoader
from dicom_wsi import create_dicom
from parse_wsi import get_wsi

# Define your YAML file
my_yaml = '/path/to/yaml'
# Load your YAML file
cfg = load(open(my_yaml), Loader=BaseLoader)
# Read the WSI, updating the config with information contained in the slide
cfg, wsi = get_wsi(cfg)
# Create DICOM files
create_dicom(cfg)

Sample RUN

This Step will download the sample svs file python ./tests/__init__.py

This is sample execution python cli.py -y ./tests/testfiles/base.yaml