def raw_tile(self, event, context):
uuid = event_path_param(event, 'uuid')
validate_uuid(uuid)
self._has_image_permission(self.user_uuid, uuid, 'Read')
x = int(event_path_param(event, 'x'))
y = int(event_path_param(event, 'y'))
z = int(event_path_param(event, 'z'))
t = int(event_path_param(event, 't'))
level = int(event_path_param(event, 'level'))
channel = int(event_path_param(event, 'channels'))
raw_format = self.get_raw_format(event)
tile_provider = S3TileProvider(
bucket.split(':')[-1],
missing_tile_callback=handle_missing_tile,
cache_client=redis_client_raw)
tile = tile_provider.get_tile(uuid, x, y, z, t, channel, level,
raw_format)
# Encode rendered image as PNG
img = BytesIO()
imagecodecs.imwrite(img, tile, codec="png", level=1)
img.seek(0)
return img.read()
def _render_tile(
self,
uuid,
x,
y,
z,
t,
level,
channels,
gamma=1,
codec="jpg",
raw_format="tiff",
tile_size=1024,
):
# Prepare for blending
args = [(uuid, x, y, z, t, channel["index"], level, raw_format)
for channel in channels]
# Fetch raw tiles in parallel
tile_provider = S3TileProvider(
bucket.split(":")[-1],
missing_tile_callback=handle_missing_tile,
cache_client=redis_client_raw,
tile_size=tile_size,
)
try:
images = pool.starmap(tile_provider.get_tile, args)
finally:
pass
# Update channel dictionary with image data
for channel, image in zip(channels, images):
channel["image"] = image
# Blend the raw tiles
composite = render.composite_channels(channels, gamma=gamma)
# Encode rendered image as JPG
img = BytesIO()
imagecodecs.imwrite(img, composite, codec=codec, level=85)
img.seek(0)
return img.read()
def imwrite(file_name, image, image_type='file-extension-default'):
'''
Save image
:param file_name:
File name and path in the disk that function save to.
:param image:
The image array that will be saved on disl as file_name.
:param image_type:
The type of image as:
'kitti-disparity', 'optical-flow', 'disparity', 'file-extension-default'
:return: None
'''
ext = os.path.splitext(file_name)[1].lower()[1:]
image_type = image_type.lower()
if not image_type in IMAGE_TYPES:
print(IMAGE_TYPES_ERR_MSG)
return
if image_type == 'file-extension-default':
if ext in NORMAL_IMAGE_FORMATS:
return write_image(file_name, image)
elif ext in ['flo']:
return save_flo(file_name, image)
elif ext in ['dpt']:
return save_dpt(file_name, image)
elif ext in ['pfm']:
return save_pfm(file_name, image)
elif ext in ['jxr']:
return imagecodecs.imwrite(file_name,
(image * (2**16 - 1)).astype(np.uint16),
codec='jpegxr')
elif ext in ['exr']:
return cv2.imwrite(file_name, image, [cv2.IMWRITE_EXR_TYPE_HALF])
else:
print("ERROR: The image type is unknown.")
elif image_type == 'optical-flow':
if len(image.shape) == 3 and image.shape[2] == 2:
return save_flo(file_name, image.astype(np.float32))
else:
print("ERROR: The image type is unknown.")
elif image_type == 'disparity':
return save_pfm(file_name, image)
elif image_type == 'depth':
return save_dpt(file_name, image)
elif image_type == 'kitti-disparity':
return write_image(file_name, (image * 256.).astype(np.uint16))
else:
print("This image type is not implemented.")
def render_region(self, event, context):
from minerva_db.sql.api import Client as db_client
self._open_session()
client = db_client(self.session)
'''Render the specified region with the given settings'''
uuid = event_path_param(event, 'uuid')
validate_uuid(uuid)
self._has_image_permission(self.user_uuid, uuid, 'Read')
x = int(event_path_param(event, 'x'))
y = int(event_path_param(event, 'y'))
width = int(event_path_param(event, 'width'))
height = int(event_path_param(event, 'height'))
z = int(event_path_param(event, 'z'))
t = int(event_path_param(event, 't'))
# Split the channels path parameters
channel_path_params = event['pathParameters']['channels'].split('/')
# Read the path parameter for the channels and convert
channels = [
_parse_channel_params(param) for param in channel_path_params
]
# Read the optional query parameters for output shape
output_width = event['queryStringParameters'].get('output-width')
output_height = event['queryStringParameters'].get('output-height')
output_width = int(output_width) if output_width is not None else None
output_height = (int(output_height)
if output_height is not None else None)
# Set prefer_higher_resolution from query parameter
prefer_higher_resolution = (
event['queryStringParameters'].get('prefer-higher-resolution'))
prefer_higher_resolution = (prefer_higher_resolution.lower() == 'true'
if prefer_higher_resolution is not None
else False)
# Query the shape of the full image
image = client.get_image(uuid)
fileset_uuid = image['data']['fileset_uuid']
fileset = client.get_fileset(fileset_uuid)
if fileset['data']['complete'] is not True:
raise ValueError(
f'Fileset has not had metadata extracted yet: {fileset_uuid}')
obj = boto3.resource('s3').Object(
bucket.split(':')[-1], f'{fileset_uuid}/metadata.xml')
body = obj.get()['Body']
data = body.read()
stream = BytesIO(data)
import xml.etree.ElementTree as ET
e_root = ET.fromstring(stream.getvalue().decode('UTF-8'))
e_image = e_root.find('ome:Image[@ID="Image:{}"]'.format(uuid),
{'ome': OME_NS})
e_pixels = e_image.find('ome:Pixels', {'ome': OME_NS})
image_shape = (int(e_pixels.attrib['SizeX']),
int(e_pixels.attrib['SizeY']))
# Query the number of levels available
level_count = image['data']['pyramid_levels']
# Create shape tuples
tile_shape = (1024, 1024)
target_shape = (height, width)
# Get the optimum level of the pyramid from which to use tiles
try:
output_max = max(
[d for d in (output_height, output_width) if d is not None])
level = render.get_optimum_pyramid_level(image_shape, level_count,
output_max,
prefer_higher_resolution)
except ValueError:
level = 0
# Transform origin and shape of target region into that required for
# the pyramid level being used
origin = render.transform_coordinates_to_level((x, y), level)
shape = render.transform_coordinates_to_level(target_shape, level)
# Calculate the scaling factor
if output_width is not None:
if output_height is not None:
# Use both supplied scaling factors
scaling_factor = (output_height / shape[0],
output_width / shape[1])
else:
# Calculate scaling factor from output_width only
scaling_factor = output_width / shape[1]
else:
if output_height is not None:
# Calcuate scaling factor from output_height only
scaling_factor = output_height / shape[0]
else:
# No scaling
scaling_factor = 1
args = []
tiles = []
for channel in channels:
color = channel['color']
_id = channel['index']
_min = channel['min']
_max = channel['max']
for indices in render.select_grids(tile_shape, origin, shape):
(i, j) = indices
# Disallow negative tiles
if i < 0 or j < 0:
continue
# Add to list of tiles to fetch
args.append((uuid, j, i, z, t, _id, level))
# Add to list of tiles
tiles.append({
'grid': (i, j),
'color': color,
'min': _min,
'max': _max
})
# Fetch raw tiles in parallel
s3_tile_provider = S3TileProvider(
bucket.split(':')[-1], missing_tile_callback=handle_missing_tile)
try:
pool = ThreadPool(len(args))
images = pool.starmap(s3_tile_provider.get_tile, args)
finally:
pool.close()
# Update tiles dictionary with image data
for image_tile, image in zip(tiles, images):
image_tile['image'] = image
# Blend the raw tiles
composite = render.composite_subtiles(tiles, tile_shape, origin, shape)
#Rescale for desired output size
if scaling_factor != 1:
scaled = render.scale_image_nearest_neighbor(
composite, scaling_factor)
else:
scaled = composite
# requires 0 - 255 values
scaled *= 255
scaled = scaled.astype(np.uint8, copy=False)
# Encode rendered image as JPG
img = BytesIO()
imagecodecs.imwrite(img, scaled, codec="jpg")
img.seek(0)
return img.read()
def _write_test_jpg(
pth: os.PathLike[str],
size: tuple[int, int],
):
arr = np.random.randint(0, 255, size=(size[0], size[1], 3), dtype=np.uint8)
imwrite(pth, arr)