#!/usr/bin/env python # # deepzoom_multiserver - Example web application for viewing multiple slides # # Copyright (c) 2010-2014 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 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 = 256 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 slide = DeepZoomGenerator(OpenSlide(path), **self.dz_opts) 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('/') 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) @app.route('/.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('/_files//_.') 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 [256]') (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)