1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
|
#!/usr/bin/env python
#
# deepzoom_server - Example web application for serving whole-slide images
#
# 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 flask import Flask, abort, make_response, render_template, url_for
from io import BytesIO
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 = 256
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)
@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)
@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 [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 file
try:
app.config['DEEPZOOM_SLIDE'] = args[0]
except IndexError:
pass
app.run(host=opts.host, port=opts.port, threaded=True)
|
