def decode(filedata, encoding, shape=None, dtype=None, block_size=None):
if (shape is None or dtype is None) and encoding not in ('npz', 'fpzip',
'kempressed'):
raise ValueError(
"Only npz encoding can omit shape and dtype arguments. {}".format(
encoding))
if filedata is None or len(filedata) == 0:
return np.zeros(shape=shape, dtype=dtype)
elif encoding == "raw":
return decode_raw(filedata, shape=shape, dtype=dtype)
elif encoding == "kempressed":
return decode_kempressed(filedata)
elif encoding == "fpzip":
return fpzip.decompress(filedata, order='F')
elif encoding == "compressed_segmentation":
return decode_compressed_segmentation(filedata,
shape=shape,
dtype=dtype,
block_size=block_size)
elif encoding == "jpeg":
return decode_jpeg(filedata, shape=shape, dtype=dtype)
elif encoding == "npz":
return decode_npz(filedata)
else:
raise NotImplementedError(encoding)
def decode(filedata: bytes,
encoding: str,
shape: Optional[Sequence[int]] = None,
dtype: Any = None,
block_size: Optional[Sequence[int]] = None,
background_color: int = 0) -> np.ndarray:
if (shape is None or dtype is None) and encoding not in ('npz', 'fpzip',
'kempressed'):
raise ValueError(
"Only npz encoding can omit shape and dtype arguments. {}".format(
encoding))
if filedata is None or len(filedata) == 0:
return np.full(shape=shape, fill_value=background_color, dtype=dtype)
elif encoding == "raw":
return decode_raw(filedata, shape=shape, dtype=dtype)
elif encoding == "kempressed":
return decode_kempressed(filedata)
elif encoding == "fpzip":
return fpzip.decompress(filedata, order='F')
elif encoding == "compressed_segmentation":
return decode_compressed_segmentation(filedata,
shape=shape,
dtype=dtype,
block_size=block_size)
elif encoding == "compresso":
return compresso.decompress(filedata).reshape(shape)
elif encoding == "jpeg":
return decode_jpeg(filedata, shape=shape, dtype=dtype)
elif encoding == "png":
return decode_png(filedata, shape=shape, dtype=dtype)
elif encoding == "npz":
return decode_npz(filedata)
else:
raise NotImplementedError(encoding)
def test_noncontiguous_memory():
x = np.random.random_sample(size=(15, 15, 15, 1)).astype(np.float32)
x_broken = x[2::2, ::3, ::2]
for order in ('C', 'F'):
y = fpzip.compress(x_broken, order=order)
z = fpzip.decompress(y, order=order)
assert np.all(x_broken == z)
def load_compressed_inf(file):
COR_SIZE = 4
FUR_SIZE = 4
POS = 0
with open(file, 'rb') as f:
compressed_bytes = f.read()
data_again = fpzip.decompress(compressed_bytes, order='C')
data_again = np.squeeze(data_again)
return data_again
def fpzip_decompress(c_bitstring):
"""
uses fpzip's decompress method to decompress a numpy array and return only the given array.
INPUT
c_bitstring: compressed bitstring
OUTPUT
np_arry = numpy array of data (converted to 1D list)
"""
np_arr = fpzip.decompress(c_bitstring)
return np_arr.tolist()[0][0][0]
def test_basic_conformation():
# corresponds to the base64 encoded compression of
# np.array([[[1]]], dtype=np.float32).tobytes()
# Was compressed by fpzip C program.
one_fpz = b'ZnB5KYcO8R7gAP8AAAD/AAAA/wAAAP8A8zvT3FAAAAA=\n'
one_fpz = base64.decodestring(one_fpz) # decodebytes is the modern name, but py27 doesn't have it
one_array = np.array([[[1]]], dtype=np.float32)
compressed = fpzip.compress(one_array)
assert len(one_fpz) == len(compressed)
assert np.all(
fpzip.decompress(compressed) == fpzip.decompress(one_fpz)
)
# encoded np.array([[[1,2,3], [4,5,6]]], dtype=np.float32)
# with open("six.raw", 'wb') as f:
# f.write(six_array.tobytes('C'))
#
# ./fpzip -i six.raw -3 3 2 1 -o six.fpz
# >> outbytes=44 ratio=0.55
#
# with open('six.fpz', 'rb') as f:
# encoded = f.read()
# six_fpz = base64.encodestring(encoded)
six_fpz = b'ZnB5KYcO8R7gAv0AAAH+AAAA/wAAAP8A8zvT3GsIJgDRE0yNUZgAHeZbgAA=\n' # 3 2 1
six_fpz = base64.decodestring(six_fpz)
six_array = np.array([[[1,2,3], [4,5,6]]], dtype=np.float32)
compressed = fpzip.compress(six_array)
assert len(six_fpz) == len(compressed)
assert np.all(
fpzip.decompress(six_fpz) == fpzip.decompress(compressed)[0,:,:,:]
)
def test_doubles():
size = (128, 127, 126, 2)
for dims in range(4):
print(dims)
x = np.random.random_sample(size=size[:dims]).astype(np.float64)
x = np.ascontiguousarray(x)
y = fpzip.compress(x, order='C')
z = fpzip.decompress(y, order='C')
assert np.all(x == z)
x = np.asfortranarray(x)
y = fpzip.compress(x, order='F')
z = fpzip.decompress(y, order='F')
z = np.squeeze(z)
assert np.all(x == z)
x = np.random.random_sample(size=[0] * dims).astype(np.float64)
y = fpzip.compress(x)
z = fpzip.decompress(y)
assert np.all(x == z)
def test_floats():
size = (128, 127, 126, 2)
for dims in range(4):
print(dims)
x = np.random.random_sample(size=size[:dims]).astype(np.float64)
x = np.ascontiguousarray(x)
y = fpzip.compress(x)
z = fpzip.decompress(y, order='C')
assert np.all(x == z)
x = np.asfortranarray(x)
y = fpzip.compress(x, order='F')
z = fpzip.decompress(y, order='F')
z = np.squeeze(z)
assert np.all(x == z)
x = np.random.random_sample(size=(128, 128, 128)).astype(np.float32)
x = np.ascontiguousarray(x)
y = fpzip.compress(x)
z = fpzip.decompress(y)
z = np.squeeze(z, axis=0) # is3d logic
assert np.all(x == z)
x = np.asfortranarray(x)
y = fpzip.compress(x, order='F')
z = fpzip.decompress(y, order='F')
z = np.squeeze(z, axis=3)
assert np.all(x == z)
x = np.random.random_sample(size=(0, 0, 0, 0)).astype(np.float32)
x = np.ascontiguousarray(x)
y = fpzip.compress(x, order='C')
z = fpzip.decompress(y, order='C')
assert np.all(x == z)
x = np.asfortranarray(x)
y = fpzip.compress(x, order='F')
z = fpzip.decompress(y, order='F')
assert np.all(x == z)
def decode_kempressed(bytestring):
"""subvol not bytestring since numpy conversion is done inside fpzip extension."""
subvol = fpzip.decompress(bytestring, order='F')
return np.swapaxes(subvol, 3, 2) - 2.0
