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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 io import BytesIO | |
from optparse import OptionParser | |
import os | |
import re | |
from unicodedata import normalize | |
from flask import Flask, abort, make_response, render_template, url_for | |
if os.name == 'nt': | |
_dll_path = os.getenv('OPENSLIDE_PATH') | |
if _dll_path is not None: | |
if hasattr(os, 'add_dll_directory'): | |
# Python >= 3.8 | |
with os.add_dll_directory(_dll_path): | |
import openslide | |
else: | |
# Python < 3.8 | |
_orig_path = os.environ.get('PATH', '') | |
os.environ['PATH'] = _orig_path + ';' + _dll_path | |
import openslide | |
os.environ['PATH'] = _orig_path | |
else: | |
import openslide | |
from openslide import ImageSlide, open_slide | |
from openslide.deepzoom import DeepZoomGenerator | |
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) | |
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 = {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 | |
def index(): | |
slide_url = url_for('dzi', slug=SLIDE_NAME) | |
associated_urls = { | |
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, | |
) | |
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) | |
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 = BytesIO() | |
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) |