def read_fundus_image(self):
""" Reads fundus image.
Returns:
obj:FundusImageWithMetaData
"""
if b'@IMG_OBS' not in self.chunk_dict:
raise ValueError(
'Could not find OCT header @IMG_OBS in chunk list')
with open(self.filepath, 'rb') as f:
chunk_location, chunk_size = self.chunk_dict[b'@IMG_OBS']
f.seek(chunk_location)
raw = f.read(21)
fundus_header = self.fundus_header.parse(raw)
#number_pixels = fundus_header.width * fundus_header.height * fundus_header.number_slices
raw_image = np.fromstring(f.read(fundus_header.size),
dtype=np.uint8)
#raw_image = [struct.unpack('B', f.read(1)) for pixel in range(fundus_header.size)]
image = np.array(raw_image)
image = image.reshape(3,
fundus_header.width,
fundus_header.height,
order='F')
image = np.transpose(image, [2, 1, 0])
image = image.astype(np.float32)
fundus_image = FundusImageWithMetaData(image)
return fundus_image
def read_fundus_image(self):
""" Reads fundus image.
Returns:
obj:FundusImageWithMetaData
"""
if b'@IMG_FUNDUS' not in self.chunk_dict:
raise ValueError('Could not find fundus header @IMG_FUNDUS in chunk list')
with open(self.filepath, 'rb') as f:
chunk_location, chunk_size = self.chunk_dict[b'@IMG_FUNDUS']
f.seek(chunk_location)# Set the chunk’s current position.
raw = f.read(24)# skip 24 is important
fundus_header = self.fundus_header.parse(raw)
number_pixels = fundus_header.width * fundus_header.height * 3
raw_image = f.read(fundus_header.size)
image = decode(raw_image)
fundus_image = FundusImageWithMetaData(image)
return fundus_image
def read_fundus_image(self):
""" Reads fundus data.
Returns:
obj:FundusImageWithMetaData
"""
with open(self.filepath, 'rb') as f:
raw = f.read(36)
header = self.header_structure.parse(raw)
raw = f.read(52)
main_directory = self.main_directory_structure.parse(raw)
# traverse list of main directories in first pass
directory_stack = []
current = main_directory.current
while current != 0:
directory_stack.append(current)
f.seek(current)
raw = f.read(52)
directory_chunk = self.main_directory_structure.parse(raw)
current = directory_chunk.prev
# traverse in second pass and get all subdirectories
chunk_stack = []
for position in directory_stack:
f.seek(position)
raw = f.read(52)
directory_chunk = self.main_directory_structure.parse(raw)
for ii in range(directory_chunk.num_entries):
raw = f.read(44)
chunk = self.sub_directory_structure.parse(raw)
if chunk.start > chunk.pos:
chunk_stack.append([chunk.start, chunk.size])
# initalise dict to hold all the image volumes
image_array_dict = {}
# traverse all chunks and extract slices
for start, pos in chunk_stack:
f.seek(start)
raw = f.read(60)
chunk = self.chunk_structure.parse(raw)
if chunk.type == 11: # laterality data
raw = f.read(20)
try:
laterality_data = self.lat_structure.parse(raw)
if laterality_data.laterality == 82:
self.laterality = 'R'
elif laterality_data.laterality == 76:
self.laterality = 'L'
except:
self.laterality = None
if chunk.type == 1073741824: # image data
raw = f.read(20)
image_data = self.image_structure.parse(raw)
if chunk.ind == 0: # fundus data
raw_volume = np.frombuffer(f.read(image_data.height *
image_data.width),
dtype=np.uint8)
image = np.array(raw_volume).reshape(
image_data.height, image_data.width)
image_string = '{}_{}_{}'.format(
chunk.patient_id, chunk.study_id, chunk.series_id)
image_array_dict[image_string] = image
fundus_images = []
for key, image in image_array_dict.items():
fundus_images.append(
FundusImageWithMetaData(image=image,
patient_id=key,
laterality=self.laterality))
return fundus_images