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#!/usr/bin/env python
#
# deepzoom_multiserver - Example web application for viewing multiple slides
#
# Copyright (c) 2010-2015 Carnegie Mellon University
#
# This library is free software; you can redistribute it and/or modify it
# under the terms of version 2.1 of the GNU Lesser General Public License
# as published by the Free Software Foundation.
#
# This library is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
# License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
from collections import OrderedDict
from flask import Flask, abort, make_response, render_template, url_for
from io import BytesIO
import openslide
from openslide import OpenSlide, OpenSlideError
from openslide.deepzoom import DeepZoomGenerator
import os
from optparse import OptionParser
from threading import Lock
SLIDE_DIR = '.'
SLIDE_CACHE_SIZE = 10
DEEPZOOM_FORMAT = 'jpeg'
DEEPZOOM_TILE_SIZE = 254
DEEPZOOM_OVERLAP = 1
DEEPZOOM_LIMIT_BOUNDS = True
DEEPZOOM_TILE_QUALITY = 75
app = Flask(__name__)
app.config.from_object(__name__)
app.config.from_envvar('DEEPZOOM_MULTISERVER_SETTINGS', silent=True)
class PILBytesIO(BytesIO):
def fileno(self):
'''Classic PIL doesn't understand io.UnsupportedOperation.'''
raise AttributeError('Not supported')
class _SlideCache(object):
def __init__(self, cache_size, dz_opts):
self.cache_size = cache_size
self.dz_opts = dz_opts
self._lock = Lock()
self._cache = OrderedDict()
def get(self, path):
with self._lock:
if path in self._cache:
# Move to end of LRU
slide = self._cache.pop(path)
self._cache[path] = slide
return slide
osr = OpenSlide(path)
slide = DeepZoomGenerator(osr, **self.dz_opts)
try:
mpp_x = osr.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = osr.properties[openslide.PROPERTY_NAME_MPP_Y]
slide.mpp = (float(mpp_x) + float(mpp_y)) / 2
except (KeyError, ValueError):
slide.mpp = 0
with self._lock:
if path not in self._cache:
if len(self._cache) == self.cache_size:
self._cache.popitem(last=False)
self._cache[path] = slide
return slide
class _Directory(object):
def __init__(self, basedir, relpath=''):
self.name = os.path.basename(relpath)
self.children = []
for name in sorted(os.listdir(os.path.join(basedir, relpath))):
cur_relpath = os.path.join(relpath, name)
cur_path = os.path.join(basedir, cur_relpath)
if os.path.isdir(cur_path):
cur_dir = _Directory(basedir, cur_relpath)
if cur_dir.children:
self.children.append(cur_dir)
elif OpenSlide.detect_format(cur_path):
self.children.append(_SlideFile(cur_relpath))
class _SlideFile(object):
def __init__(self, relpath):
self.name = os.path.basename(relpath)
self.url_path = relpath
@app.before_first_request
def _setup():
app.basedir = os.path.abspath(app.config['SLIDE_DIR'])
config_map = {
'DEEPZOOM_TILE_SIZE': 'tile_size',
'DEEPZOOM_OVERLAP': 'overlap',
'DEEPZOOM_LIMIT_BOUNDS': 'limit_bounds',
}
opts = dict((v, app.config[k]) for k, v in config_map.items())
app.cache = _SlideCache(app.config['SLIDE_CACHE_SIZE'], opts)
def _get_slide(path):
path = os.path.abspath(os.path.join(app.basedir, path))
if not path.startswith(app.basedir + os.path.sep):
# Directory traversal
abort(404)
if not os.path.exists(path):
abort(404)
try:
slide = app.cache.get(path)
slide.filename = os.path.basename(path)
return slide
except OpenSlideError:
abort(404)
@app.route('/')
def index():
return render_template('files.html', root_dir=_Directory(app.basedir))
@app.route('/<path:path>')
def slide(path):
slide = _get_slide(path)
slide_url = url_for('dzi', path=path)
return render_template('slide-fullpage.html', slide_url=slide_url,
slide_filename=slide.filename, slide_mpp=slide.mpp)
@app.route('/<path:path>.dzi')
def dzi(path):
slide = _get_slide(path)
format = app.config['DEEPZOOM_FORMAT']
resp = make_response(slide.get_dzi(format))
resp.mimetype = 'application/xml'
return resp
@app.route('/<path:path>_files/<int:level>/<int:col>_<int:row>.<format>')
def tile(path, level, col, row, format):
slide = _get_slide(path)
format = format.lower()
if format != 'jpeg' and format != 'png':
# Not supported by Deep Zoom
abort(404)
try:
tile = slide.get_tile(level, (col, row))
except ValueError:
# Invalid level or coordinates
abort(404)
buf = PILBytesIO()
tile.save(buf, format, quality=app.config['DEEPZOOM_TILE_QUALITY'])
resp = make_response(buf.getvalue())
resp.mimetype = 'image/%s' % format
return resp
if __name__ == '__main__':
parser = OptionParser(usage='Usage: %prog [options] [slide-directory]')
parser.add_option('-B', '--ignore-bounds', dest='DEEPZOOM_LIMIT_BOUNDS',
default=True, action='store_false',
help='display entire scan area')
parser.add_option('-c', '--config', metavar='FILE', dest='config',
help='config file')
parser.add_option('-d', '--debug', dest='DEBUG', action='store_true',
help='run in debugging mode (insecure)')
parser.add_option('-e', '--overlap', metavar='PIXELS',
dest='DEEPZOOM_OVERLAP', type='int',
help='overlap of adjacent tiles [1]')
parser.add_option('-f', '--format', metavar='{jpeg|png}',
dest='DEEPZOOM_FORMAT',
help='image format for tiles [jpeg]')
parser.add_option('-l', '--listen', metavar='ADDRESS', dest='host',
default='127.0.0.1',
help='address to listen on [127.0.0.1]')
parser.add_option('-p', '--port', metavar='PORT', dest='port',
type='int', default=5000,
help='port to listen on [5000]')
parser.add_option('-Q', '--quality', metavar='QUALITY',
dest='DEEPZOOM_TILE_QUALITY', type='int',
help='JPEG compression quality [75]')
parser.add_option('-s', '--size', metavar='PIXELS',
dest='DEEPZOOM_TILE_SIZE', type='int',
help='tile size [254]')
(opts, args) = parser.parse_args()
# Load config file if specified
if opts.config is not None:
app.config.from_pyfile(opts.config)
# Overwrite only those settings specified on the command line
for k in dir(opts):
if not k.startswith('_') and getattr(opts, k) is None:
delattr(opts, k)
app.config.from_object(opts)
# Set slide directory
try:
app.config['SLIDE_DIR'] = args[0]
except IndexError:
pass
app.run(host=opts.host, port=opts.port, threaded=True)