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feat(nbia): add prefix option to get Collections methods
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@jjjermiah
jjjermiah committed Jan 21, 2024
1 parent f0f3781 commit 0f95c89
Showing 1 changed file with 51 additions and 41 deletions.
92 changes: 51 additions & 41 deletions src/nbiatoolkit/nbia.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
from typing import Union
import io
import zipfile

from tqdm import tqdm

class NBIAClient:
"""
Expand Down Expand Up @@ -101,22 +101,29 @@ def query_api(self, endpoint: NBIA_ENDPOINTS, params: dict = {}) -> dict:

return response_data

def getCollections(self) -> list:
def getCollections(self, prefix: str = ""
) -> list[dict[str]]:
response = self.query_api(NBIA_ENDPOINTS.GET_COLLECTIONS)
collections = []
for collection in response:
collections.append(collection["Collection"])
name = collection["Collection"]
if name.lower().startswith(prefix.lower()):
collections.append(name)
return collections

def getCollectionPatientCount(self) -> list:
# returns a list of dictionaries with the collection name and patient count
def getCollectionPatientCount(self, prefix: str = ""
) -> list[dict[str, int]]:
response = self.query_api(NBIA_ENDPOINTS.GET_COLLECTION_PATIENT_COUNT)
patientCount = []
patientCounts = []
for collection in response:
patientCount.append({
"Collection": collection["criteria"],
"PatientCount": collection["count"]})
name = collection["criteria"]
if name.lower().startswith(prefix.lower()):
patientCounts.append({
"Collection": collection["criteria"],
"PatientCount": int(collection["count"])})

return patientCount
return patientCounts

def getBodyPartCounts(
self, Collection: str = "", Modality: str = "") -> list:
Expand Down Expand Up @@ -172,9 +179,6 @@ def getSeries(self,

return response


from tqdm import tqdm

def downloadSeries(
self,
SeriesInstanceUID: Union[str, list],
Expand Down Expand Up @@ -277,39 +281,45 @@ def parsePARAMS(self, params: dict) -> dict:
from pprint import pprint
import os
client = NBIAClient(log_level='info')

all = client.getCollections()
pprint(all)

sub = client.getCollections(prefix="aCrin")
pprint(sub)
# collections = client.getCollections()
# pprint(collections[0:5])
# seriesJSON = client.getSeries(Collection="4D-Lung")
# # first get a list of the SeriesInstanceUIDs
# seriesUIDS = [series['SeriesInstanceUID'] for series in seriesJSON]
# pprint(seriesUIDS[0:5])

seriesUIDS = [
'1.3.6.1.4.1.14519.5.2.1.6834.5010.189721824525842725510380467695',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.336250251691987239290048605884',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.227929163446067537882961857921',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.925990093742075237571072608963',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.139116724721865252687455544825',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.364787732307640672278270360328',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.384197169742944248273003912317',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.149750833495190982103087204448',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.300347070051003027185063750283',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.317831614083862743715273480521',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.736089011729021729851027177073',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.133381852562664457904201355429',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.909088026336573109170906532418',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.953079890279542310843831057254',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.427052348021168186336245283790',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.295010883410722294053941635303',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.263257070197787007872578860295',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.672179203515231442641005032212',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.184961274239908956209701869504',
'1.3.6.1.4.1.14519.5.2.1.6834.5010.797307942821711099898506950104']

downloadDir = "./data"
os.makedirs(downloadDir, exist_ok=True)

client.downloadSeries(
seriesUIDS, downloadDir, overwrite=True, nParallel=8)

pprint(os.listdir(downloadDir))
# seriesUIDS = [
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.189721824525842725510380467695',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.336250251691987239290048605884',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.227929163446067537882961857921',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.925990093742075237571072608963',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.139116724721865252687455544825',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.364787732307640672278270360328',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.384197169742944248273003912317',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.149750833495190982103087204448',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.300347070051003027185063750283',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.317831614083862743715273480521',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.736089011729021729851027177073',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.133381852562664457904201355429',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.909088026336573109170906532418',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.953079890279542310843831057254',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.427052348021168186336245283790',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.295010883410722294053941635303',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.263257070197787007872578860295',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.672179203515231442641005032212',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.184961274239908956209701869504',
# '1.3.6.1.4.1.14519.5.2.1.6834.5010.797307942821711099898506950104']

# downloadDir = "./data"
# os.makedirs(downloadDir, exist_ok=True)

# client.downloadSeries(
# seriesUIDS, downloadDir, overwrite=True, nParallel=8)

# pprint(os.listdir(downloadDir))

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