Pre Dicom Import

There is a process running on the server that uses based dcm4che command line tools to issue a C-MOVE command to download datasets to the application /data folder. The script that runs might look something like this:



mkdir $BASE/$NUM.tmp
dcmqr -L$CALLINGAE@$PORT $TARGETAE -qAccessionNumber=$NUM -cmove $CALLINGAE -cstoredest=$BASE/$NUM.tmp
mv $BASE/$NUM.tmp $BASE/$NUM

In the above, we see that dcmqr is used to call C-MOVE to dump a bunch of dicoms into a folder named based on a number, which is likely an accession number as it is a common query. The last line of the script renames the *.tmp folder by removing the extension, which then notifies the watcher that the folder is done.

Dicom Import

When the watcher detects a FINISHED session directory in the folder being watched (/data in the container, mapping to data in the application base folder on the host), the process of importing the images into the database is started. This means the following steps:

1. Adding Models to Database

Each dicom file is read, and during reading, added as an Image object to the database. The study and session are also extracted from the header, and these are added as Study and Session objects, respectively. The Series and Study Ids are extracted from these fields in the dicom header, for each file separately:


If we run into some case where the fields are not defined, I have put a check that will use the folder name instead, prefixed with series_ or study_. For example, a folder ST-1234 with a dicom missing header information would have study and session series_ST-1234 and study study_ST-1234.

2. Saving Dicoms

All files in the folder are assumed to be dicom, as it is the case the extensions may vary. If a file is attempted to be read as dicom fails, a warning is issued and the file skipped, but the process continued. The file is not removed, in case inspection is warranted later (is this how we want it?) (some notification?)

The dicom file itself, when saved to the model, is saved with the application’s media at /images.

3. Finishing Batch

All the images found in a folder are considered to be a “batch,” and when all files for a batch have been added, the function fires off the list to be anonymized. If there were no files in the batch, the function is not fired.