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:
-
To provide a standardized and machine-readable way to access DICOM Standard information for software applications
-
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:
- New fields may be added
- Bugs or incorrect data will be fixed as the standard changes
- No fields are removed, maintaining backwards compatibility
- 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
idfield - JSON files containing relational data between tables contain "foreign keys" to the relevant table JSON file. These field names end with
Id(e.g.ciodIdandmoduleId)
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/FG | | Modules/ | | Sections | | |
| Modules | | Macros | | Macro Attrs | +--------+-+ v v
+----+----+ +----+-----+ +------+-----+ | sops.json attributes.json
| | | |
+-------------+ | +---------------+ +-----------+
| | | | | |
+-----v-----+ +----v----+ +----v------+ +-----v------+ +-----v------+ |
| Process | | Process | | Process | | Preprocess | | Preprocess | |
| CIOD/ | | CIODs | | CIOD/FG | | Modules/ | | Macros/ | |
| Module | +----+----+ | Macro | | Attributes | | Attributes | |
| Relations | | | Relations | +-----+------+ +-----+------+ |
+-----+-----+ | +----+------+ | | |
| v | +-------+ +-------+ |
| ciods.json | | | | | |
v | +----v----+ | +----v----+ | |
ciod_to_modules.json | | Process | | | Process | | |
v | Modules | | | Macros | | |
ciod_to_func_group_macros.json +----+----+ | +----+----+ | |
| | | | |
| | | | |
v | v | |
modules.json | macros.json | |
| | |
+-------v---+ +-------v---+ |
| Process | | Process | |
| Module | | Macro | |
| Attribute | | Attribute | |
| Relations | | Relations | |
+-------+---+ +-------+---+ |
| | |
+-v---------------v------v-+
| Postprocess |
| Add References |
+-----+-------+------+-----+
| | |
+--------+ | +--------+
| v |
| macros_to_attributes.json |
v v
modules_to_attributes.json references.json
To update the parser map, please use ASCIIFlow.
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.
