# 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
