[4df946]: / utils / slide.py

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"""
This class provides a unified interface decoding various slide formats.
Cancheng Liu
Email: liucancheng@thorough.ai
"""
import os.path
from openslide import OpenSlide
from utils import config
class Slide(object):
def __init__(self, image_path):
super(Slide, self).__init__()
self.image_path = image_path.strip()
self.image_file = os.path.basename(image_path)
self.image_name, self.suffix = self.image_file.split('.')
if not self.suffix in config.format_mapping.keys():
raise Exception('Error: File format ' + self.suffix + ' is supported yet.')
self._slide = OpenSlide(image_path)
self._level_downsamples = self._slide.level_downsamples
self._level_dimensions = self._slide.level_dimensions
self.width, self.height = self._level_dimensions[0]
@property
def dimensions(self):
return self._level_dimensions[0]
@property
def level_dimensions(self):
return self._level_dimensions
@property
def level_downsamples(self):
return self._level_downsamples
def read_region(self, level, location, size):
(x, y), (w, h) = location, size
try:
_ds = self._level_downsamples[level]
patch = self._slide.read_region(
level=level, location=(int(x * _ds), int(y * _ds)), size=size)
except Exception:
raise
else:
return patch
def get_thumbnail(self):
try:
image = self._slide.read_region(
location=(0, 0), level=0, size=(1000, 1000))
except Exception:
raise
else:
return image