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b72823e May 21, 2016
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#!/usr/bin/env python
#
# deepzoom_server - Example web application for serving whole-slide images
#
# 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 flask import Flask, abort, make_response, render_template, url_for
from io import BytesIO
import openslide
from openslide import ImageSlide, open_slide
from openslide.deepzoom import DeepZoomGenerator
from optparse import OptionParser
import re
from unicodedata import normalize
DEEPZOOM_SLIDE = None
DEEPZOOM_FORMAT = 'jpeg'
DEEPZOOM_TILE_SIZE = 254
DEEPZOOM_OVERLAP = 1
DEEPZOOM_LIMIT_BOUNDS = True
DEEPZOOM_TILE_QUALITY = 75
SLIDE_NAME = 'slide'
app = Flask(__name__)
app.config.from_object(__name__)
app.config.from_envvar('DEEPZOOM_TILER_SETTINGS', silent=True)
class PILBytesIO(BytesIO):
def fileno(self):
'''Classic PIL doesn't understand io.UnsupportedOperation.'''
raise AttributeError('Not supported')
@app.before_first_request
def load_slide():
slidefile = app.config['DEEPZOOM_SLIDE']
if slidefile is None:
raise ValueError('No slide file specified')
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())
slide = open_slide(slidefile)
app.slides = {
SLIDE_NAME: DeepZoomGenerator(slide, **opts)
}
app.associated_images = []
app.slide_properties = slide.properties
for name, image in slide.associated_images.items():
app.associated_images.append(name)
slug = slugify(name)
app.slides[slug] = DeepZoomGenerator(ImageSlide(image), **opts)
try:
mpp_x = slide.properties[openslide.PROPERTY_NAME_MPP_X]
mpp_y = slide.properties[openslide.PROPERTY_NAME_MPP_Y]
app.slide_mpp = (float(mpp_x) + float(mpp_y)) / 2
except (KeyError, ValueError):
app.slide_mpp = 0
@app.route('/')
def index():
slide_url = url_for('dzi', slug=SLIDE_NAME)
associated_urls = dict((name, url_for('dzi', slug=slugify(name)))
for name in app.associated_images)
return render_template('slide-multipane.html', slide_url=slide_url,
associated=associated_urls, properties=app.slide_properties,
slide_mpp=app.slide_mpp)
@app.route('/<slug>.dzi')
def dzi(slug):
format = app.config['DEEPZOOM_FORMAT']
try:
resp = make_response(app.slides[slug].get_dzi(format))
resp.mimetype = 'application/xml'
return resp
except KeyError:
# Unknown slug
abort(404)
@app.route('/<slug>_files/<int:level>/<int:col>_<int:row>.<format>')
def tile(slug, level, col, row, format):
format = format.lower()
if format != 'jpeg' and format != 'png':
# Not supported by Deep Zoom
abort(404)
try:
tile = app.slides[slug].get_tile(level, (col, row))
except KeyError:
# Unknown slug
abort(404)
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
def slugify(text):
text = normalize('NFKD', text.lower()).encode('ascii', 'ignore').decode()
return re.sub('[^a-z0-9]+', '-', text)
if __name__ == '__main__':
parser = OptionParser(usage='Usage: %prog [options] [slide]')
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 file
try:
app.config['DEEPZOOM_SLIDE'] = args[0]
except IndexError:
if app.config['DEEPZOOM_SLIDE'] is None:
parser.error('No slide file specified')
app.run(host=opts.host, port=opts.port, threaded=True)