manthey

#!/usr/bin/env python

import argparse
import girder_client
import girder_client.cli
import os
import re


def get_girder_client(opts):

manthey

FROM ubuntu:18.04

# Prerequisites and runtimes
RUN apt-get update && apt-get upgrade -y && apt-get install -y --no-install-recommends \
    build-essential \
    git \
    python-dev \
    python-pip \
    python-setuptools \
    python-wheel \

manthey

import argparse
import base64
import io
import json
import math
import os
import subprocess
import sys
import tempfile

manthey

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

manthey

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)

manthey

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')

manthey

import json
import os
import tempfile
from pathlib import Path

from .datastore import datastore


class TestNucleiDetection:

manthey

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)

manthey

import hashlib
import pprint
import sys

import tifftools


def hash_ifd(idx, ifd, tagSet=tifftools.Tag, collect=None):
    if collect is None:
        collect = {}