diff --git a/desuto-slideproperties/slideviewer-openslide-properties-service/slide-properties-service.py b/desuto-slideproperties/slideviewer-openslide-properties-service/slide-properties-service.py
index fd96861..dfe664a 100755
--- a/desuto-slideproperties/slideviewer-openslide-properties-service/slide-properties-service.py
+++ b/desuto-slideproperties/slideviewer-openslide-properties-service/slide-properties-service.py
@@ -1,105 +1,111 @@
import web
import urllib
from slide import Slide
from web.wsgiserver import CherryPyWSGIServer
urls = (
'/slide_properties/microns_pixel_x/(.*)', 'mppx',
'/slide_properties/microns_pixel_y/(.*)', 'mppy',
'/slide_properties/pixels_mm/(.*)', 'pmm',
'/slide_properties/pixels_m/(.*)', 'pm',
'/slide_properties/bounds/(.*)', 'bounds',
'/slide_properties/nbr_levels/(.*)', 'nbrlevels',
'/slide_properties/level_downsamples/(.*)', 'leveldownsamples',
'/slide_properties/level_dimensions/(.*)', 'leveldimensions',
'/slide_properties/best_level_for_downsample/(.*)/(.*)', 'bestleveldownsample',
'/slide_properties/common_info/(.*)', 'commoninfo',
'/slide_properties/magnification/(.*)', 'magnification'
)
app = web.application(urls, globals())
def corshook():
web.header('Access-Control-Allow-Origin', '*')
web.header('Access-Control-Allow-Credentials', 'true')
+def contentType():
+ web.header('Content-Type', 'text/plain')
+
app.add_processor(web.loadhook(corshook))
+app.add_processor(web.loadhook(contentType))
class commoninfo:
def GET(self, imagepath):
+ web.header('Content-Type', 'application/json')
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.common_info()
class magnification:
def GET(self, imagepath):
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.magnification()
class mppx:
def GET(self, imagepath):
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.mpp_x()
class mppy:
def GET(self, imagepath):
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.mpp_y()
class pmm:
def GET(self, imagepath):
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.px_mm()
class pm:
def GET(self, imagepath):
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.px_m()
class vendor:
def GET(self, imagepath):
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.vendor()
class bounds:
def GET(self, imagepath):
+ web.header('Content-Type', 'application/json')
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.bounds()
class nbrlevels:
def GET(self, imagepath):
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.nbr_levels()
class leveldownsamples:
def GET(self, imagepath):
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.level_downsamples()
class leveldimensions:
def GET(self, imagepath):
imagepath = urllib.unquote(imagepath)
slide = Slide(imagepath)
return slide.level_dimensions()
class bestleveldownsample:
def GET(self, imagepath, downsample):
imagepath = urllib.unquote(imagepath)
print(imagepath)
print(downsample)
slide = Slide(imagepath)
return slide.best_level_for_downsample(downsample)
if __name__ == "__main__":
app.run()
diff --git a/desuto-slideproperties/slideviewer-openslide-properties-service/slide.py b/desuto-slideproperties/slideviewer-openslide-properties-service/slide.py
index 1384312..5692d55 100755
--- a/desuto-slideproperties/slideviewer-openslide-properties-service/slide.py
+++ b/desuto-slideproperties/slideviewer-openslide-properties-service/slide.py
@@ -1,91 +1,97 @@
import openslide
from openslide import OpenSlide, OpenSlideError
import os
import json
+
class Slide:
def __init__(self, imagepath):
- self.osr = OpenSlide(imagepath);
+ self.osr = OpenSlide(imagepath)
# Microns per pixel y
def mpp_y(self):
return self.osr.properties.get(openslide.PROPERTY_NAME_MPP_X)
# Microns per pixel x
def mpp_x(self):
return self.osr.properties.get(openslide.PROPERTY_NAME_MPP_Y)
# Pixels mer milimeter
def px_mm(self):
- return 1/(((float(self.mpp_x())+float(self.mpp_y()))/2)/1000)
+ if self.mpp_x() is not None and self.mpp_y() is not None:
+ return 1 / (((float(self.mpp_x()) + float(self.mpp_y())) / 2) / 1000)
+ else:
+ return None
# Pixels mer milimeter
def px_m(self):
- return self.px_mm()*1000;
+ if self.px_mm() is not None:
+ return self.px_mm() * 1000
+ else:
+ return None
# Vendor
def vendor(self):
return self.osr.properties.get(openslide.PROPERTY_NAME_VENDOR)
# X coordinate of the rectangle bounding the non-empty region of the slide, if available
def bounds_x(self):
return self.osr.properties.get(openslide.PROPERTY_NAME_BOUNDS_X)
# X coordinate of the rectangle bounding the non-empty region of the slide, if available
def bounds_y(self):
return self.osr.properties.get(openslide.PROPERTY_NAME_BOUNDS_Y)
# width of the rectangle bounding the non-empty region of the slide, if available.
def bounds_width(self):
return self.osr.properties.get(openslide.PROPERTY_NAME_BOUNDS_WIDTH)
# Height of the rectangle bounding the non-empty region of the slide, if available.
def bounds_height(self):
return self.osr.properties.get(openslide.PROPERTY_NAME_BOUNDS_HEIGHT)
# x, y and rectangle width & height bounding the non-empty region of the slide, if available. JSON
def bounds(self):
info = {}
- info['x'] = self.bounds_x()
+ info['x'] = self.bounds_x()
info['y'] = self.bounds_y()
info['width'] = self.bounds_width()
info['height'] = self.bounds_height()
return json.dumps(info)
# Number of magnification levels
def nbr_levels(self):
return self.osr.level_count
# A list of downsample factors for each level of the slide. level_downsamples[k] is the downsample factor of level k.
def level_downsamples(self):
return self.osr.level_downsamples
# A list of (width, height) tuples, one for each level of the slide. level_dimensions[k] are the dimensions of level k.
def level_dimensions(self):
return self.osr.level_dimensions
# Best level for displaying the given downsample.
def best_level_for_downsample(self, downsample):
return self.osr.get_best_level_for_downsample(float(downsample))
# Magnification level
def magnification(self):
return self.osr.properties.get(openslide.PROPERTY_NAME_OBJECTIVE_POWER)
def common_info(self):
info = {}
info['pmm'] = self.px_mm()
info['pm'] = self.px_m()
info['nbrlevels'] = self.nbr_levels()
info['leveldownsamples'] = self.level_downsamples()
info['leveldimensions'] = self.level_dimensions()
-
info['bounds'] = {}
- info['bounds']['x'] = self.bounds_x()
+ info['bounds']['x'] = self.bounds_x()
info['bounds']['y'] = self.bounds_y()
info['bounds']['width'] = self.bounds_width()
info['bounds']['height'] = self.bounds_height()
- return json.dumps(info);
+ return json.dumps(info)