|
| 1 | +#!/usr/bin/env python |
| 2 | +# |
| 3 | +# deepzoom_multiserver - Example web application for viewing multiple slides |
| 4 | +# |
| 5 | +# Copyright (c) 2010-2014 Carnegie Mellon University |
| 6 | +# |
| 7 | +# This library is free software; you can redistribute it and/or modify it |
| 8 | +# under the terms of version 2.1 of the GNU Lesser General Public License |
| 9 | +# as published by the Free Software Foundation. |
| 10 | +# |
| 11 | +# This library is distributed in the hope that it will be useful, but |
| 12 | +# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY |
| 13 | +# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public |
| 14 | +# License for more details. |
| 15 | +# |
| 16 | +# You should have received a copy of the GNU Lesser General Public License |
| 17 | +# along with this library; if not, write to the Free Software Foundation, |
| 18 | +# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. |
| 19 | +# |
| 20 | + |
| 21 | +from collections import OrderedDict |
| 22 | +from flask import Flask, abort, make_response, render_template, url_for |
| 23 | +from io import BytesIO |
| 24 | +from openslide import OpenSlide, OpenSlideError |
| 25 | +from openslide.deepzoom import DeepZoomGenerator |
| 26 | +import os |
| 27 | +from optparse import OptionParser |
| 28 | +from threading import Lock |
| 29 | + |
| 30 | +SLIDE_DIR = '.' |
| 31 | +SLIDE_CACHE_SIZE = 10 |
| 32 | +DEEPZOOM_FORMAT = 'jpeg' |
| 33 | +DEEPZOOM_TILE_SIZE = 256 |
| 34 | +DEEPZOOM_OVERLAP = 1 |
| 35 | +DEEPZOOM_LIMIT_BOUNDS = True |
| 36 | +DEEPZOOM_TILE_QUALITY = 75 |
| 37 | + |
| 38 | +app = Flask(__name__) |
| 39 | +app.config.from_object(__name__) |
| 40 | +app.config.from_envvar('DEEPZOOM_MULTISERVER_SETTINGS', silent=True) |
| 41 | + |
| 42 | + |
| 43 | +class _SlideCache(object): |
| 44 | + def __init__(self, cache_size, dz_opts): |
| 45 | + self.cache_size = cache_size |
| 46 | + self.dz_opts = dz_opts |
| 47 | + self._lock = Lock() |
| 48 | + self._cache = OrderedDict() |
| 49 | + |
| 50 | + def get(self, path): |
| 51 | + with self._lock: |
| 52 | + if path in self._cache: |
| 53 | + # Move to end of LRU |
| 54 | + slide = self._cache.pop(path) |
| 55 | + self._cache[path] = slide |
| 56 | + return slide |
| 57 | + slide = DeepZoomGenerator(OpenSlide(path), **self.dz_opts) |
| 58 | + with self._lock: |
| 59 | + if path not in self._cache: |
| 60 | + if len(self._cache) == self.cache_size: |
| 61 | + self._cache.popitem(last=False) |
| 62 | + self._cache[path] = slide |
| 63 | + return slide |
| 64 | + |
| 65 | + |
| 66 | +class _Directory(object): |
| 67 | + def __init__(self, basedir, relpath=''): |
| 68 | + self.name = os.path.basename(relpath) |
| 69 | + self.children = [] |
| 70 | + for name in sorted(os.listdir(os.path.join(basedir, relpath))): |
| 71 | + cur_relpath = os.path.join(relpath, name) |
| 72 | + cur_path = os.path.join(basedir, cur_relpath) |
| 73 | + if os.path.isdir(cur_path): |
| 74 | + cur_dir = _Directory(basedir, cur_relpath) |
| 75 | + if cur_dir.children: |
| 76 | + self.children.append(cur_dir) |
| 77 | + elif OpenSlide.detect_format(cur_path): |
| 78 | + self.children.append(_SlideFile(cur_relpath)) |
| 79 | + |
| 80 | + |
| 81 | +class _SlideFile(object): |
| 82 | + def __init__(self, relpath): |
| 83 | + self.name = os.path.basename(relpath) |
| 84 | + self.url_path = relpath |
| 85 | + |
| 86 | + |
| 87 | +@app.before_first_request |
| 88 | +def _setup(): |
| 89 | + app.basedir = os.path.abspath(app.config['SLIDE_DIR']) |
| 90 | + config_map = { |
| 91 | + 'DEEPZOOM_TILE_SIZE': 'tile_size', |
| 92 | + 'DEEPZOOM_OVERLAP': 'overlap', |
| 93 | + 'DEEPZOOM_LIMIT_BOUNDS': 'limit_bounds', |
| 94 | + } |
| 95 | + opts = dict((v, app.config[k]) for k, v in config_map.items()) |
| 96 | + app.cache = _SlideCache(app.config['SLIDE_CACHE_SIZE'], opts) |
| 97 | + |
| 98 | + |
| 99 | +def _get_slide(path): |
| 100 | + path = os.path.abspath(os.path.join(app.basedir, path)) |
| 101 | + if not path.startswith(app.basedir + os.path.sep): |
| 102 | + # Directory traversal |
| 103 | + abort(404) |
| 104 | + if not os.path.exists(path): |
| 105 | + abort(404) |
| 106 | + try: |
| 107 | + slide = app.cache.get(path) |
| 108 | + slide.filename = os.path.basename(path) |
| 109 | + return slide |
| 110 | + except OpenSlideError: |
| 111 | + abort(404) |
| 112 | + |
| 113 | + |
| 114 | +@app.route('/') |
| 115 | +def index(): |
| 116 | + return render_template('files.html', root_dir=_Directory(app.basedir)) |
| 117 | + |
| 118 | + |
| 119 | +@app.route('/<path:path>') |
| 120 | +def slide(path): |
| 121 | + slide = _get_slide(path) |
| 122 | + slide_url = url_for('dzi', path=path) |
| 123 | + return render_template('slide-fullpage.html', slide_url=slide_url, |
| 124 | + slide_filename=slide.filename) |
| 125 | + |
| 126 | + |
| 127 | +@app.route('/<path:path>.dzi') |
| 128 | +def dzi(path): |
| 129 | + slide = _get_slide(path) |
| 130 | + format = app.config['DEEPZOOM_FORMAT'] |
| 131 | + resp = make_response(slide.get_dzi(format)) |
| 132 | + resp.mimetype = 'application/xml' |
| 133 | + return resp |
| 134 | + |
| 135 | + |
| 136 | +@app.route('/<path:path>_files/<int:level>/<int:col>_<int:row>.<format>') |
| 137 | +def tile(path, level, col, row, format): |
| 138 | + slide = _get_slide(path) |
| 139 | + format = format.lower() |
| 140 | + if format != 'jpeg' and format != 'png': |
| 141 | + # Not supported by Deep Zoom |
| 142 | + abort(404) |
| 143 | + try: |
| 144 | + tile = slide.get_tile(level, (col, row)) |
| 145 | + except ValueError: |
| 146 | + # Invalid level or coordinates |
| 147 | + abort(404) |
| 148 | + buf = BytesIO() |
| 149 | + tile.save(buf, format, quality=app.config['DEEPZOOM_TILE_QUALITY']) |
| 150 | + resp = make_response(buf.getvalue()) |
| 151 | + resp.mimetype = 'image/%s' % format |
| 152 | + return resp |
| 153 | + |
| 154 | + |
| 155 | +if __name__ == '__main__': |
| 156 | + parser = OptionParser(usage='Usage: %prog [options] [slide-directory]') |
| 157 | + parser.add_option('-B', '--ignore-bounds', dest='DEEPZOOM_LIMIT_BOUNDS', |
| 158 | + default=True, action='store_false', |
| 159 | + help='display entire scan area') |
| 160 | + parser.add_option('-c', '--config', metavar='FILE', dest='config', |
| 161 | + help='config file') |
| 162 | + parser.add_option('-d', '--debug', dest='DEBUG', action='store_true', |
| 163 | + help='run in debugging mode (insecure)') |
| 164 | + parser.add_option('-e', '--overlap', metavar='PIXELS', |
| 165 | + dest='DEEPZOOM_OVERLAP', type='int', |
| 166 | + help='overlap of adjacent tiles [1]') |
| 167 | + parser.add_option('-f', '--format', metavar='{jpeg|png}', |
| 168 | + dest='DEEPZOOM_FORMAT', |
| 169 | + help='image format for tiles [jpeg]') |
| 170 | + parser.add_option('-l', '--listen', metavar='ADDRESS', dest='host', |
| 171 | + default='127.0.0.1', |
| 172 | + help='address to listen on [127.0.0.1]') |
| 173 | + parser.add_option('-p', '--port', metavar='PORT', dest='port', |
| 174 | + type='int', default=5000, |
| 175 | + help='port to listen on [5000]') |
| 176 | + parser.add_option('-Q', '--quality', metavar='QUALITY', |
| 177 | + dest='DEEPZOOM_TILE_QUALITY', type='int', |
| 178 | + help='JPEG compression quality [75]') |
| 179 | + parser.add_option('-s', '--size', metavar='PIXELS', |
| 180 | + dest='DEEPZOOM_TILE_SIZE', type='int', |
| 181 | + help='tile size [256]') |
| 182 | + |
| 183 | + (opts, args) = parser.parse_args() |
| 184 | + # Load config file if specified |
| 185 | + if opts.config is not None: |
| 186 | + app.config.from_pyfile(opts.config) |
| 187 | + # Overwrite only those settings specified on the command line |
| 188 | + for k in dir(opts): |
| 189 | + if not k.startswith('_') and getattr(opts, k) is None: |
| 190 | + delattr(opts, k) |
| 191 | + app.config.from_object(opts) |
| 192 | + # Set slide directory |
| 193 | + try: |
| 194 | + app.config['SLIDE_DIR'] = args[0] |
| 195 | + except IndexError: |
| 196 | + pass |
| 197 | + |
| 198 | + app.run(host=opts.host, port=opts.port, threaded=True) |
0 commit comments