dicom-standard 0.1.dev202004071759

Parse the DICOM Standard into a human-friendly JSON format.

DICOM Standard Parser

This program parses the web version of the DICOM Standard into human and machine-friendly JSON files. The purpose of these JSON files is twofold:

1. To provide a standardized and machine-readable way to access DICOM Standard information for software applications

2. To provide a logical model for the relationships between cross-referenced sections in the DICOM Standard

The finalized JSON output of this program is in the standard directory at the top level of this project.

These JSON files are used to make the DICOM Standard Browser.

JSON Data Guarantees

The JSON generated by this program adheres to the following four rules:

1. New fields may be added
2. Bugs or incorrect data will be fixed as the standard changes
3. No fields are removed, maintaining backwards compatibility
4. The shape and organization of the JSON files will remain the same

The JSON files can be viewed here.

JSON Data Format

The generated JSON files conform to these formatting rules:

• JSON files representing tables are lists of objects, each object containing a unique id field
• JSON files containing relational data between tables contain "foreign keys" to the relevant table JSON file. These field names end with Id (e.g. ciodId and moduleId)

Occasionally, files may deviate from this format when there is a very compelling reason. For example, references.json should be a list of reference objects where the href is the id for each object. However, since almost every use case for references.json will use the href as a lookup, it makes more sense for the file to be set up as an object containing href to HTML pairs.

Applications that use the JSON files from this repository may need to re-organize data. A separate script must be written to join data from multiple tables into one file or prune out unnecessary fields.

Current Status

This program currently parses the DICOM Standard sections related to Information Object Definitions, modules, and attributes, as well as cross-referenced sections in other parts of the standard. This translates to the following sections:

Completely processed:

• PS3.3
• PS3.6

Processed for references:

• PS3.4
• PS3.15
• PS3.16
• PS3.17
• PS3.18

Development Setup

The python scripts used to generate the JSON files are designed to be as extensible as possible. If you want to run the code yourself or configure your own custom parsing stage, you'll need the following system-level dependencies:

• Python 3.7
• Make + Unix tools

You will probably also want to setup a "virtual environment" (e.g. using Conda, or Pyenv + Virtualenv) to install the project dependencies into. Once you are in your "virtual environment", you can run:

$ make

to install and compile everything. Add the -j flag to speed this process up significantly.

Updating the Standard

To download and parse the most up-to-date web version of the DICOM Standard, run the following commands:

$ make clean
$ make updatestandard
$ make

Using the Library

Parsing stages are indicated by prefixed names (i.e. extract_xxx.py or process_xxx.py) and use a variety of utility functions from parse_lib.py and other *_utils.py modules.

Design Philosophy

The overall data flow of this program takes the following form:

          extract                      (post)process
Raw HTML ---------> JSON intermediate ---------------> JSON final

During this process, the following invariants are maintained:

• Each step in the parsing process is classified as either an "extract" stage, or a "process" stage.
• Stages are python scripts that take one or more files as inputs, and write their output to standard out.
• "Extract" stages takes one more more HTML input files and print out JSON.
• "Process" stages take one or more JSON files as inputs and print out JSON.

In this way, raw HTML is not touched by any stage other than extract_*.py, and successive processing steps use increasingly refined JSON.

Parser Stages

A map of all extraction and processing pathways is shown below:

                                      +-------+             +----------+    +-------+     +-------+
                                      | PS3.3 |             | Other    |    | PS3.4 |     | PS3.6 |
                                      +---+---+             | DICOM    |    +---+---+     +---+---+
                                          |                 | Sections |        |             |
                                          |                 +-----+----+        |             |
                                          |                       |        +----v----+  +-----v------+
                   +-------------+--------+------+-------------+  |        | Extract |  | Extract    |
                   |             |               |             |  |        | SOPs    |  | Attributes |
               +---v-----+  +----v----+   +------v------+  +---v--v---+    +----+----+  +-----+------+
               | Extract |  | Extract |   | Extract     |  | Extract  |         |             |
               | CIODs/  |  | CIODs/  |   | Modules/    |  | Sections |         |             |
               | Modules |  | Macros  |   | Macro Attrs |  +--------v-+         v             v
               +----+----+  +----+----+   +------v-----+            |       sops.json   attributes.json
                    |            |               |                  |
      +-------------+            |               +---------------+  +-----------|
      |             |            |               |               |              |
+-----v-----+  +----v----+  +----v------+  +-----v------+  +-----v------+       |
| Process   |  | Process |  | Process   |  | Preprocess |  | Preprocess |       |
| CIOD/     |  | CIODs   |  | CIOD/     |  | Modules/   |  | Macros/    |       |
| Module    |  +----+----+  | Macro     |  | Attributes |  | Attributes |       |
| Relations |       |       | Relations |  +-----v------+  +-----v------+       |
+-----+-----+       |       +----+------+        |               |              |
      |             v            |               +-------+       +-------+      |
      |        ciods.json        |               |       |       |       |      |
      v                          v          +----v----+  |  +----v----+  |      |
ciod_to_modules.json   ciod_to_macros.json  | Process |  |  | Process |  |      |
                                            | Modules |  |  | Macros  |  |      |
                                            +----+----+  |  +----+----+  |      |
                                                 |       |       |       |      |
                                                 |       |       |       |      |
                                                 v       |       v       |      |
                                            modules.json |  macros.json  |      |
                                                         |               |      |
                                                 +-------v---+   +-------v---+  |
                                                 | Process   |   | Process   |  |
                                                 | Module    |   | Macro     |  |
                                                 | Attribute |   | Attribute |  |
                                                 | Relations |   | Relations |  |
                                                 +-------+---+   +-------v---+  |
                                                         |               |      |
                                                       +-v---------------v------v-+
                                                       |        Postprocess       |
                                                       |      Add References      |
                                                       +-----+-------+------+-----+
                                                             |       |      |
                                                    +--------+       |      +--------+
                                                    |                v               |
                                                    |    macros_to_attributes.json   |
                                                    v                                v
                                         modules_to_attributes.json           references.json

Contact

Find a bug? JSON files missing a piece of information? We welcome pull requests! Feel free to make a PR or make a GitHub issue for any bugs you may find.