rivassh / BodyPartIndex.py

Python wrapper library for standard set of anatomic location tags.

BodyPartIndex.py

Python wrapper library for standard set of body parts for tagging artifacts in medical imaging informatics (see https://www.anatomiclocations.org).

Installation

Pending

Will soon be possible to install from PyPI:

pip install body_part_index

BodyPartIndex (Scenarios)

How to open the library?

To open the library, you first need to import it into your project. Then, you can use the BodyPartIndex object.

import requests, json
from body_part_index import BodyPartIndex, BodyPart, BODY_PART_INDEX_DATA_URL

# Import data distributed with the package
index = BodyPartIndex()


# OR import data from the latest version on the web
if (r := requests.get(BODY_PART_INDEX_DATA_URL)).status_code == requests.codes.ok:
    index = BodyPartIndex(json_data=json.loads(r.text))

# OR Open a local data file
index = BodyPartIndex(json_filename='body_parts.json')

How to use a local JSON file of body parts?

pending

How to get a particular body part by RadLex ID, SNOMED, or another code?

index = BodyPartIndex(json_filename='body_parts.json')
bodyPart = index.get('RID294')
bodyPart2 = index.get('265256') # FMA code
# TODO: bodyPart3 = index.get('THX1138') # Local code

The function returns a BodyPart object.

How to get a particular body part by system/code?

index = BodyPartIndex(json_filename='body_parts.json')
body_part: BodyPart = index.get_by_code(Code('SNOMED', '818983003'))

How to search for body parts based on names or synonyms?

The search function will return all the BodyParts that match a specific search value.

index = BodyPartIndex(json_filename='body_parts.json')
bodyPart = index.search('adnexa')

BodyPart (Scenarios)

What can you get from a BodyPart?

index = BodyPartIndex(json_filename='body_parts.json')
bodyPart = index.get('RID294')
bodyPart.description    # "uterine adnexa"
bodyPart.sex_specific   # "Female"
bodyPart.synonyms       # ["adnexa"]
bodyPart.contained_by   # BodyPart(radlex_id='RID2507', description='pelvis', ...)
bodyPart.part_of        # BodyPart(radlex_id='RID270', description='female genital system', ...)
bodyPart.codes          # [ Code(system='SNOMED', 'code=''), Code(...), Code(...) ]

How to deal with sided body parts?

For cases where the body part is sided, the index contains three versions: an unsided version, a left-sided version, and a right-sided version. All of these are aware of each other.

index = BodyPartIndex(json_filename='body_parts.json')
bodyPart = index.get('RID294') # uterine adnexa (side not specified)
# From the unsided version, get the right- and left-sided versions
right = bodyPart.right     # BodyPart(radlex_id='RID294_RID5825', description='right uterine adnexa', ...)
left  = bodyPart.left      # BodyPart(radlex_id='RID294_RID5824', description='left uterine adnexa', ...)
# From either sided versions, can get back to the unsided or to the other side
right.unsided == body_part # True
left.right    == right     # True

How to determine if one body part is contained by another?

To determine if a one body part is contained by another, use the is_contained function.

index = BodyPartIndex(json_filename='body_parts.json')
bodyPart1 = index.get('RID294') # uterine adnexa (side not specified)
bodyPart2 = index.get('RID39569') # whole body
is_contained = bodyPart1.is_contained(bodyPart2)

How to get the contained children of a body part?