dicomselect 0.8.9

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dicomselect: DICOM database and conversion software

dicomselect is a Python tool that simplifies the process of creating SQLite databases from directories containing .dcm files or from .zip archives containing .dcm files at the root of the zip file. Once the database is created, you can easily perform SQL-like queries on the data directly within Python. Additionally, dicomselect allows you to convert query results into various file formats supported by SimpleITK, providing flexibility in working with your DICOM data.

Installation

Python 3.10 or higher. You can install this project using pip. If you haven't already, it's recommended to create a virtual environment to isolate project dependencies.

pip install dicomselect

Example

Clone this repo, install dicomselect, then run this example in the repo.

from dicomselect import Database
from pathlib import Path

db_path = Path('tests/output/example.db')
db_path.parent.mkdir(exist_ok=True)

# initialize the Database object with a path to the to-be-created SQLite database file
db = Database(db_path)

# create the .db file, using test data as the input directory.
db.create('tests/input/ProstateX', max_workers=4)

with (db as query):
    # we only want to convert images with patient_id "ProstateX-0000" and image_direction "transverse"
    query_0000 = query.where('patient_id', '=', 'ProstateX-0000'
                             ).where('image_direction', '=', 'transverse')

    # print out a detailed extraction of our query
    print(query_0000.info())

# initialize the Plan object, with a template of DICOM headers for our conversion
# (note: dcm to dcm conversion is possible, if you only need restructuring of your data)
plan = db.plan('{patient_id}/prostateX_{series_description}_{instance_creation_time}', query_0000)

# ensure these properties are set
plan.target_dir = 'tests/output/example'
plan.extension = '.mha'
plan.max_workers = 4

# print out a detailed structure of our intended conversion
print(plan.to_string())

plan.execute()

Check out the results in tests/output/example

===========================================================================

Create a new database

from pathlib import Path
from dicomselect.database import Database

db_path = Path("/path/to/dicomselect_archive.db")
archive_path = Path("/path/to/archive")
db_path.parent.mkdir(parents=True, exist_ok=True)
db = Database(db_path)
db.create(archive_path, max_workers=4)

Select scans

1. Simple matching of values

from dicomselect.database import Database

mapping = {
    "t2w": {
        "SeriesDescription": [
            "t2_tse_tra_snel_bij bewogen t2 tra",
            "t2_tse_tra",        
            "t2_tse_tra_prostate",
            "t2_tse_tra_snel",
            "t2_tse_tra_Grappa3"
        ]
    },
}

db_path = Path("/path/to/dicomselect_archive.db")
db = Database(db_path)
cursor = db.open()
query = cursor.where("series_description", "in", mapping["t2w"]["SeriesDescription"])
print(query)
db.close()

2. Pattern matching and combining queries

from dicomselect.database import Database

mapping = {
    "hbv": {
        "SeriesDescription": [
            "ep2d_diff_tra%CALC_BVAL",
            "diffusie-3Scan-4bval_fsCALC_BVAL"
        ],
        "ImageType": [
            r"DERIVED\PRIMARY\DIFFUSION\CALC_BVALUE\TRACEW\DIS2D\DFC",
            r"DERIVED\PRIMARY\DIFFUSION\CALC_BVALUE\TRACEW\DIS2D",
            r"DERIVED\PRIMARY\DIFFUSION\CALC_BVALUE\TRACEW\ND\DFC",
            r"DERIVED\PRIMARY\DIFFUSION\CALC_BVALUE\TRACEW\NORM\DIS2D",
        ]
    }
}

db_path = Path("/path/to/dicomselect_archive.db")
db = Database(db_path)
cursor = db.open()
query1 = cursor.where("series_description", "LIKE", mapping["hbv"]["SeriesDescription"])
query2 = cursor.where("image_type", "LIKE", mapping["hbv"]["ImageType"])
query = query1.union(query2)
print(query)
db.close()

Show info

# print a default overview of the query result
print(query)

# for more fine-grained control of the reporting, use the Info object
# print a summary of series_description given the query
print(query.info().include("series_description"))

# print a summary of everything but series_description given the query
# note: some recommended columns are excluded, such as columns referring to some UID.
print(query.info().exclude("series_description", recommended=True))

Convert

from dicomselect.database import Database

db_path = Path("/path/to/dicomselect_archive.db")
db = Database(db_path)
plan = db.plan("{patient_id}/{series_description}_{patients_age}", query)
plan.target_dir = "/path/to/target_dir"
plan.extension = ".mha"
print(plan)
plan.execute(max_workers=4)