Start the Application
After configuration is done and you have a good understanding of how things work, you are ready to turn it on! You have two options - using the watcher (better for on demand, streamed processing) or with a cached queue (better if many datasets are already present). For both, an important note is that each job added to the queue to do dicom import will also handle the complete processing for that job. This is so that we don’t have a tasks in the queue relevant to the same job (for example, imagine a queue of 1000, and adding the “next step” for the first item to the end. We wouldn’t process it until the other 999 are started! Our disk might run out of space.
This approach add jobs to a queue and they are processed when workers are available. This is a slightly longer process since it needs to read the filesystem, but it’s only run when the
previous set of folders found and queued is empty (meaning no Batch objects with status
A cached queue is NOT processed by way of the watcher, but instead the python manage.py start_queue.py script:
python manage.py start_queue
optionally you can provide the following arguments:
--number: a max count to add to the queue --subfolder: optionally, a subfolder to use assumed in /data, to take preference
without any arguments, it goes over the bases defined as subfolders to create the cache
DATA_INPUT_FOLDERS=['/data/1_%s' %s for x in range(8) ] # /data/1_0 through /data/1_7
The cache will not be generated until the current set is done and processed.
Streaming with Watcher
The watcher is intended to be used for streaming data. The folders will be looked for in the
DATA_BASE and optionally a specific subfolder, if defined:
# Optionally, parse a subfolder under /data, or set to None DATA_SUBFOLDER="1_6"
First, let’s learn about how to start and stop the watcher, and the kind of datasets and location that the watcher is expecting. It is up to you to plop these dataset folders into the application’s folder being watched.
1. Running the Watcher
This initial setup is stupid in that it’s going to be checking an input folder to find new images. We do this using the watcher application, which is started and stopped with a manage.py command:
python manage.py start_watcher python manage.py stop_watcher
And the default is to watch for files added to data, which is mapped to ‘/data’ in the container. Remember that you can change this mapping in the docker-compose.yml. In terms of the strategy for receiving the folders, this is currently up to you, but the high level idea is that the application should receive DICOM from somewhere. It should use an atomic download strategy, but with folders, into the application data input folder. This will mean that when it starts, the folder (inside the container) might look like:
/data ST-000001.tmp2343 image1.dcm image2.dcm image3.dcm
Only when all of the dicom files are finished copying will the driving function rename it to be like this:
/data ST-000001 image1.dcm image2.dcm image3.dcm
A directory is considered “finished” and ready for processing when it does not have an entension that starts with “tmp”. For more details about the watcher daemon, you can look at his docs. While many examples are provided, for this application we use the celery task
import_dicomdir in main/tasks.py to read in a finished dicom directory from the directory being watched, and this uses the class
DicomCelery in the event_processors file. Other examples are provided, in the case that you want to change or extend the watcher daemon. For complete details about the import of dicom files, see dicom_import.md
2. Database Models
The Dockerized application is constantly monitoring the folder to look for folders that are not in the process of being populated. When a folder is found:
- A new object in the database is created to represent the “Batch”
- Each “Image” is represented by an equivalent object
- Each “Image” is linked to its “Batch”
- Currently, all uids for each must be unique.
Generally, the query of interest will retrieve a set of images with an associated accession number, and the input folder will be named by the accession number. Since there is variance in the data with regard to
AccessionNumber and different series identifiers, for our batches we give them ids based on the folder name.
Now that the application is started, you can learn about usage, starting with the manager, or check out details about the simple interface.