def read_png_images(path_prefix: str, bbox: BoundingBox,
volume_offset: tuple = (0, 0, 0),
voxel_size: tuple = (1, 1, 1),
digit_num: int = 5,
dtype: np.dtype = np.uint8):
chunk = Chunk.from_bbox(
bbox, dtype=dtype,
pattern='zero',
voxel_size=voxel_size
)
assert len(bbox.minpt) == 3
assert len(volume_offset) == 3
for z in tqdm( range(bbox.minpt[0], bbox.maxpt[0]) ):
file_name = f'{path_prefix}{z:0>{digit_num}d}.png'
file_name = path.expanduser(file_name)
if path.exists(file_name):
with open(file_name, "rb") as f:
img = pyspng.load(f.read())
img = np.expand_dims(img, axis=0)
img_chunk = Chunk(
img,
voxel_offset=(
z+volume_offset[0], volume_offset[1], volume_offset[2]),
voxel_size=voxel_size
)
chunk.blend(img_chunk)
else:
logging.warning(f'image file do not exist: {file_name}')
return chunk
def _load_raw_image(self, raw_idx):
fname = self._image_fnames[raw_idx]
with self._open_file(fname) as f:
if pyspng is not None and self._file_ext(fname) == '.png':
image = pyspng.load(f.read())
else:
image = np.array(PIL.Image.open(f))
if image.ndim == 2:
image = image[:, :, np.newaxis] # HW => HWC
image = image.transpose(2, 0, 1) # HWC => CHW
return image
def benchmark(title='',
content='noise',
width=1024,
height=1024,
compress_level=0,
loader='spng',
num_repeats=10,
num_calls=10):
if content == 'noise':
img = np.random.randint(0,
256,
size=[height, width, 3],
dtype=np.uint8)
if content == 'gradient':
x, y, _c = np.mgrid[:height, :width, :1]
img = np.concatenate([y * 255 / height, x * 255 / width, x * 0],
axis=2).astype(np.uint8)
stream = io.BytesIO()
PIL.Image.fromarray(img, 'RGB').save(stream,
format='png',
compress_level=compress_level)
bytes = stream.getvalue()
lowest_ms = float('inf')
for _repeat_idx in range(num_repeats):
start_time = time.time()
for _call_idx in range(num_calls):
if loader == 'pil':
out = np.asarray(PIL.Image.open(io.BytesIO(bytes)))
if loader == 'spng':
out = pyspng.load(bytes)
cur_ms = (time.time() - start_time) * 1e3
lowest_ms = min(lowest_ms, cur_ms)
print(f'{title} {lowest_ms:.2f}ms')
assert np.all(out == img)
def decode_png(bytestring: bytes, shape, dtype):
img = pyspng.load(bytestring).reshape(-1)
img = img.astype(dtype, copy=False)
return img.reshape(shape, order='F')