def saveImage(self, data, series, frame):
"""
save image data as cbf
"""
path = os.path.join(
self.path,
self.basename + "_%05d_%05d%s" % (series, frame + 1, self.ftype))
if albula:
albula.DImageWriter.write(albula.DImage().fromData(data), path)
else:
cbf.write(path, data, header=self._createHeader(self.metadata))
print "[OK] wrote %s" % path
return path
def test_write(self):
for i in range(1000):
logging.info('start')
test_file = 'test.cbf'
# Ensure that file does not exist
try:
os.remove(test_file)
except OSError:
pass
# 65536
# 66600 cannot compress at all
min_number = 0
max_number = 66600
max_number = 600
max_number = 2147483647 # max value int32
# max_number = 2147483648 # max value + 1int32 # will fail
numpy_array = numpy.random.randint(min_number, max_number,
(500, 400)).astype('int32')
numpy_array[0][0] = max_number
# numpy_array[0][0] = -1
# numpy_array = numpy.empty((500, 400)).astype('int32')
# numpy_array.fill(max_number)
print(numpy_array[0][0])
cbf.write(test_file, numpy_array)
content = cbf.read(test_file)
if not (numpy_array == content.data).all():
print('NOT SAME')
print((numpy_array == content.data).sum())
print(content.data)
print(content.metadata)
print(content.metadata)
print(i)
self.assertTrue((numpy_array == content.data).all())
# Remove test file
os.remove(test_file)
def test_write(self):
for i in range(1000):
logging.info('start')
test_file = 'test.cbf'
# Ensure that file does not exist
try:
os.remove(test_file)
except OSError:
pass
# 65536
# 66600 cannot compress at all
min_number = 0
max_number = 66600
max_number = 600
max_number = 2147483647 # max value int32
# max_number = 2147483648 # max value + 1int32 # will fail
numpy_array = numpy.random.randint(min_number, max_number, (500, 400)).astype('int32')
numpy_array[0][0] = max_number
# numpy_array = numpy.empty((500, 400)).astype('int32')
# numpy_array.fill(max_number)
print(numpy_array[0][0])
cbf.write(test_file, numpy_array)
content = cbf.read(test_file)
if not (numpy_array == content.data).all():
print('SAME')
print((numpy_array == content.data).sum())
print(content.data)
print(content.metadata)
print(content.metadata)
print(i)
self.assertTrue((numpy_array == content.data).all())
def saveTable(self, frames, name="", ftype=".dat"):
"""
save pixel mask, flatfield or LUT
"""
path = os.path.join(
self.path,
self.basename + "_%05d_%s%s" % (self.series, name, ftype))
header = json.loads(frames[0].bytes)
dtype = np.dtype(header["type"])
data = np.reshape(np.fromstring(frames[1].bytes, dtype=dtype),
header["shape"][::-1])
if ftype == ".dat":
np.savetxt(path, data)
elif ftype == ".cbf":
cbf.write(path, data) # self.__getHeader__())
else:
raise IOError("file type %s not known. Allowed are .cbf|.dat" %
ftype)
print "[OK] wrote %s" % path
def savecbf(filename, data):
if not isfile(filename):
cbf.write(filename, data)
else:
print("file ", filename, " does already exist!")
return None
def readBSLZ4(datafile, headerfile):
"""
unpack bitshuffle-lz4 compressed frame and return np array image data
frame: zmq data blob frame
shape: image shape
dtype: image data type
"""
with open(datafile, "r") as f:
data = f.read()
with open(headerfile, "r") as f:
header = json.loads(f.read())
shape = header["shape"]
dtype = np.dtype(header["type"])
blob = np.fromstring(data[12:], dtype=np.uint8)
# blocksize is big endian uint32 starting at byte 8, divided by element size
blocksize = np.ndarray(shape=(), dtype=">u4",
buffer=data[8:12]) / dtype.itemsize
print blocksize, dtype.itemsize
imgData = bitshuffle.decompress_lz4(blob, shape[::-1], dtype, blocksize)
print "[OK] unpacked {0} bytes of bs-lz4 data".format(len(imgData))
return imgData
if __name__ == "__main__":
data = readBSLZ4("/Users/sascha.grimm/Downloads/lcp_100hz/000078_002.raw",
"/Users/sascha.grimm/Downloads/lcp_100hz/000078_001.raw")
tifffile.imsave("bslz4_16bit.tiff", data)
tifffile.imsave("bslz4_32bit.tiff", data.astype("uint32"))
cbf.write("bslz4_32bit.cbf", data.astype("uint32"))