# timeID) #if caseID != '032': # continue filenameE2E = '*{0}_*{1}*.E2E'.format(caseID, timeID) filepathE2ESearch = os.path.join(E2EIN, Tiff2E2EDir[folder], filenameE2E) filepathsE2E2 = glob(filepathE2ESearch) if (len(filepathsE2E2)==0): continue mindiff = 9e99 mindifffname='' for filepathE2E in filepathsE2E2: print(filepathE2E) file = E2E(filepathE2E) cslo_imgs = file.read_clso_image() # returns an cslo volume with additional metadata if available single_cslo = cslo_imgs[0] if imgTiff.shape != single_cslo.shape: continue diff = np.sum(cv2.absdiff(imgTiff, single_cslo)) allbasefname = os.path.basename(filepathE2E) outf = os.path.join(E2EOUTBASE, 'test', allbasefname.upper().replace('.E2E', '_all_e2e.png')) os.makedirs(os.path.dirname(outf), exist_ok=True) print('Write png:{0}'.format(outf)) cv2.imwrite(outf, single_cslo) tiffbase = os.path.basename(filepathTIFF)
from oct_converter.readers import E2E filepath = '/Users/mark/Downloads/Sample/001_O01S.E2E' file = E2E(filepath) oct_volumes = file.read_oct_volume() # returns a list of all OCT volumes with additional metadata if available for volume in oct_volumes: volume.peek() # plots a montage of the volume volume.save('{}.avi'.format(volume.patient_id)) fundus_images = file.read_fundus_image() #returns a list of all fundus images with additional metadata if available for image in fundus_images: image.save('{}.png'.format(image.patient_id))
imgTiff = cv2.imread(filepathTIFF, cv2.IMREAD_GRAYSCALE) filenameSplit = os.path.splitext(filename)[0].split('_') filenameE2E = '{0}_{1}_{2}_*_{3}_{4}_*.E2E'.format( filenameSplit[0], filenameSplit[1], filenameSplit[2], filenameSplit[4], filenameSplit[5]) filepathE2ESearch = os.path.join(E2EIN, filenameE2E) filepathsE2E2 = glob(filepathE2ESearch) if (len(filepathsE2E2) == 0): continue mindiff = 9e9 mindifffname = '' for filepathE2E in filepathsE2E2: print(filepathE2E) file = E2E(filepathE2E) cslo_imgs = file.read_clso_image( ) # returns an cslo volume with additional metadata if available single_cslo = cslo_imgs[0] diff = np.sum(cv2.absdiff(imgTiff, single_cslo)) allbasefname = os.path.basename(filepathE2E) cv2.imwrite( os.path.join(E2EOUT, 'test', allbasefname.replace('.E2E', '_all_e2e.png')), single_cslo) if diff < mindiff: mindiff = diff