deepzoom_multiserver.py

#!/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)