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import hashlib | |
import pprint | |
import sys | |
import tifftools | |
def hash_ifd(idx, ifd, tagSet=tifftools.Tag, collect=None): | |
if collect is None: | |
collect = {} |
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export GIRDER_PORT=8080 | |
export VUE_PORT=8081 | |
SCREEN_NAME=nimbusimage_docker | |
DOCKER_NAME=girder | |
SERVICE_NAME="NimbusImage Docker" | |
pushd /home/ubuntu/UPennContrast | |
case "$1" in | |
install) |
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import json | |
import os | |
import tempfile | |
from pathlib import Path | |
from .datastore import datastore | |
class TestNucleiDetection: |
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import os | |
from collections import defaultdict | |
import configurations.importer | |
import django | |
from django.apps import apps | |
from django.db import models | |
os.environ['DJANGO_SETTINGS_MODULE'] = 'shapeworks_cloud.settings' | |
os.environ.setdefault('DJANGO_CONFIGURATION', 'DevelopmentConfiguration') |
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import logging | |
import sys | |
import dicomslide | |
import dicomweb_client | |
import pydicom | |
dslog = logging.getLogger('dicomslide') | |
# dslog.addHandler(logging.StreamHandler(sys.stderr)) | |
# dslog.setLevel(logging.WARN) |
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--- | |
version: '3' | |
services: | |
# To use a mongo container, uncomment this block and the links in the girder | |
# block. In the Dockerfile, disable starting mongo and enable the sysctl and | |
# iptables commands. | |
# mongodb: | |
# image: mongo:4.4 | |
# command: bash -c "mkdir /dev/shm/mongo && mongod --nojournal --dbpath=/dev/shm/mongo --noauth --bind_ip_all --quiet --logpath /var/log/mongodb/mongod.log" | |
# # command: bash -c "mongod --nojournal --noauth --bind_ip_all --quiet --logpath /var/log/mongodb/mongod.log" |
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#!/usr/bin/env python3 | |
import sys | |
list1 = set(entry for entry in sys.argv[1].strip().replace('\n', ',').split(',') if '==' in entry) | |
list2 = set(entry for entry in sys.argv[2].strip().replace('\n', ',').split(',') if '==' in entry) | |
diff1 = list1 - list2 | |
diff2 = list2 - list1 | |
print(sorted(list1)) | |
print(diff1, diff2) |
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import sys | |
import time | |
import girder_client | |
# Your instance of girder with the api/v1 path | |
apiUrl = 'http://abc.kitware.com:8085/api/v1' | |
# An authentication token that has permission to run jobs | |
apiToken = '64characterGirderTokenString' | |
# This is the directory where all of the images to process are located |
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import argparse | |
import base64 | |
import io | |
import json | |
import math | |
import os | |
import subprocess | |
import sys | |
import tempfile |
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