from __future__ import division import os import openslide import multiprocessing import numpy as np from time import time from math import ceil from PIL import Image Image.MAX_IMAGE_PIXELS = None class SlideLoader: def __init__(self, dataPath, savePath, downsample, endsFormat='mrxs', patchsize=400, nProcs=4, overlap=1, default_overlap_size=300, removeBlankPatch=0, blankRange=[200, 255]): self.removeBlank = removeBlankPatch self.slidePath = dataPath self.savePath = savePath self.savePath_slide = '' self.slideName = '' self.downsample = downsample self.patchsize = patchsize self.nProcs = nProcs self.margin = overlap self.marginsize = default_overlap_size self.balnkRange = blankRange self.downsample_scale = -1 self.slidewidth = -1 self.slideheight = -1 self.rows = -1 self.columns = -1 self.marker = endsFormat self.tic = -1 self.slideList = [] self.slidePointer = None for root, _, fnames in os.walk(self.slidePath): for fname in fnames: if fname.endswith(self.marker): self.slideList.append(os.path.join(root, fname)) def getSlide(self, index): self.tic = self.time_() self.slideName = self.slideList[index].split('/')[-1][:-len(self.marker)-1] print(self.slideList[index]) self.slidePointer = openslide.open_slide(self.slideList[index]) [self.slidewidth, self.slideheight] = self.slidePointer.level_dimensions[self.downsample] # margin version if self.margin != 0: self.rows = (self.slidewidth // self.marginsize) self.columns = (self.slideheight // self.marginsize) else: self.rows = (self.slidewidth // self.patchsize) self.columns = (self.slideheight // self.patchsize) self.downsample_scale = int(self.slidePointer.level_downsamples[self.downsample]) self.savePath_slide = os.path.join(self.savePath, self.slideName + '_' + str(self.rows) + '_' + str(self.columns)) if not os.path.exists(self.savePath_slide): os.mkdir(self.savePath_slide) print('Loaded image: %s' % self.slideList[index]) print('Width: %d, Height: %d' % (self.slidewidth, self.slideheight)) def time_(self, tic=0.0): if tic == 0.0: return time() else: return time() - tic def getPatch(self, startIndex): # function for getting patch sz = (self.patchsize, self.patchsize) layer = self.downsample patch = self.slidePointer.read_region(startIndex, layer, sz) return patch def savePatch(self, patch, path): # function for saving patch if self.removeBlank == 1: if self.checkBlank(patch) != -1: patch.convert("RGB").save(path) else: patch.convert("RGB").save(path) def checkBlank(self, patch): patch = np.array(patch.convert("RGB")) m = patch.mean() if self.balnkRange[0] <= m <= self.balnkRange[1]: return -1 else: return Image.fromarray(patch) def checkLayers(self): for one in self.slideList: if one.level_count < 3: raise ValueError('Slide only contain 1 or 2 layer(s).') def threadTarget(self, startIndex, perThread): threadT = self.time_() for i in range(startIndex, min(startIndex + int(perThread), self.rows)): for j in range(self.columns): Num = i * self.columns + j if Num % self.columns == 0: # print('%s, batch %d/%d' % # (multiprocessing.current_process().name, i, perThread)) savepath_batch = os.path.join(self.savePath_slide, 'batch' + str(Num // self.columns)) if not os.path.exists(savepath_batch): os.mkdir(savepath_batch) # margin version if self.margin: startIndex = [self.marginsize * i * self.downsample_scale, self.marginsize * j * self.downsample_scale] else: startIndex = [self.patchsize * i * self.downsample_scale, self.patchsize * j * self.downsample_scale] patch = self.getPatch(startIndex) imgName = self.slideName + '_' + str(i) + '_' + str(j) + '.jpg' self.savePatch(patch, os.path.join(savepath_batch, imgName)) print('time: %.2f' % self.time_(threadT)) def cut_image(self): threadT = self.time_() for i in range(self.rows): for j in range(self.columns): Num = i * self.columns + j if Num % self.columns == 0: # print('%s, batch %d/%d' % # (multiprocessing.current_process().name, i, perThread)) savepath_batch = os.path.join(self.savePath_slide) if not os.path.exists(savepath_batch): os.mkdir(savepath_batch) # margin version if self.margin: startIndex = [self.marginsize * i * self.downsample_scale, self.marginsize * j * self.downsample_scale] else: startIndex = [self.patchsize * i * self.downsample_scale, self.patchsize * j * self.downsample_scale] patch = self.getPatch(startIndex) imgName = self.slideName + '_' + str(i) + '_' + str(j) + '.jpg' self.savePatch(patch, os.path.join(savepath_batch, imgName)) print('time: %.2f' % self.time_(threadT)) def threadProcessing(self): # seperate work perThread = ceil(self.rows / self.nProcs) startIndex = [one for one in range(self.rows) if one % perThread == 0] if len(startIndex) != self.nProcs: assert len(startIndex) < self.nProcs print('Self-Adaptive modification of nProcs, ' 'default: %d process, used: %d process, ' '%d columns per process.' % (self.nProcs, len(startIndex), perThread)) self.nProcs = len(startIndex) else: print('Use default settings, used %d process, %d columns per process.' % (self.nProcs, perThread)) assert len(startIndex) == self.nProcs p = [None] * self.nProcs for Proc in range(self.nProcs): p[Proc] = multiprocessing.Process(target=self.threadTarget, args=(startIndex[Proc], perThread,)) p[Proc].start() for Proc in range(self.nProcs): p[Proc].join() print('Process ending.') def mainProcess(self, skip=False, nskip=0): for index, oneslide in enumerate(self.slideList): if skip: if index < nskip: continue self.getSlide(index) self.cut_image() # windows # self.threadProcessing() # linux def check_python_version(): import sys if not sys.version_info > (3, ): raise EnvironmentError( 'Please use Python3 or uncomment __future__ import.') def main(): check_python_version() slidepath = 'D:/luhd/11257_14_A13_Scan1/' outPath = 'C:/Users/luhd/Desktop/out/' # 0: 40x, 1: 20x, 2: 10x, ... # loader = SlideLoader(slidepath, outPath, # downsample=2, patchsize=400, # nProcs=8, overlap=1, default_overlap_size=300, # removeBlankPatch=0) loader = SlideLoader(slidepath, outPath, downsample=0, endsFormat='tif', patchsize=512, nProcs=4, overlap=0, default_overlap_size=300, removeBlankPatch=0, blankRange=[225, 255]) loader.mainProcess(skip=False, nskip=17) if __name__ == "__main__": main()