def parse_binary_compressed_pc_data(f, dtype, metadata):
# compressed size of data (uint32)
# uncompressed size of data (uint32)
# compressed data
# junk
fmt = 'II'
compressed_size, uncompressed_size =\
struct.unpack(fmt, f.read(struct.calcsize(fmt)))
compressed_data = f.read(compressed_size)
# TODO what to use as second argument? if buf is None
# (compressed > uncompressed)
# should we read buf as raw binary?
buf = lzf.decompress(compressed_data, uncompressed_size)
if len(buf) != uncompressed_size:
raise Exception('Error decompressing data')
# the data is stored field-by-field
pc_data = np.zeros(metadata['width'], dtype=dtype)
ix = 0
for dti in range(len(dtype)):
dt = dtype[dti]
bytes = dt.itemsize * metadata['width']
column = np.fromstring(buf[ix:(ix+bytes)], dt)
pc_data[dtype.names[dti]] = column
ix += bytes
return pc_data
def pure_python_loads(data):
"convert a mummy string into the python object it represents"
if not data:
raise ValueError("no data from which to load")
if ord(data[0]) >> 7:
if not lzf:
raise RuntimeError("can't decompress without python-lzf")
kind, ucsize, data = (chr(ord(data[0]) & 0x7F), _load_int(data[1:5])[0], data[5:])
data = kind + lzf.decompress(data, ucsize + 1)
return _loads(string(data))[0]
def parseBINARY_COMPRESSED(self):
""" BROKEN!!! - There seem to be uncompatiblities
with pcl LZF and liblzf"""
max_size = 1024**3 # 1GB
fs = '<i'
compressed_len = struct.unpack('<i', self.file.read(4))[0]
decompressed_len = struct.unpack('<i', self.file.read(4))[0]
compressed_body = self.file.read(compressed_len)
decompressed_body = lzf.decompress(compressed_body, max_size)
fobj = io.BytesIO(decompressed_body)
self.parseBINARY(fobj)
def lzf_decompress(self, compressed, expected_length):
if HAS_PYTHON_LZF:
return lzf.decompress(compressed, expected_length)
else:
in_stream = bytearray(compressed)
in_len = len(in_stream)
in_index = 0
out_stream = bytearray()
out_index = 0
while in_index < in_len :
ctrl = in_stream[in_index]
if not isinstance(ctrl, int) :
raise Exception('lzf_decompress', 'ctrl should be a number %s for key %s' % (str(ctrl), self._key))
in_index = in_index + 1
if ctrl < 32 :
for x in range(0, ctrl + 1) :
out_stream.append(in_stream[in_index])
#sys.stdout.write(chr(in_stream[in_index]))
in_index = in_index + 1
out_index = out_index + 1
else :
length = ctrl >> 5
if length == 7 :
length = length + in_stream[in_index]
in_index = in_index + 1
ref = out_index - ((ctrl & 0x1f) << 8) - in_stream[in_index] - 1
in_index = in_index + 1
for x in range(0, length + 2) :
out_stream.append(out_stream[ref])
ref = ref + 1
out_index = out_index + 1
if len(out_stream) != expected_length :
raise Exception('lzf_decompress', 'Expected lengths do not match %d != %d for key %s' % (len(out_stream), expected_length, self._key))
return bytes(out_stream)
def read_pcd(filename):
""" Reads and pcd file and return the elements as pandas Dataframes.
Parameters
----------
filename: str
Path to the pcd file.
Returns
-------
pandas Dataframe.
"""
data = {}
with open(filename, 'rb') as f:
header = []
while True:
ln = f.readline().strip().decode()
header.append(ln)
if ln.startswith('DATA'):
metadata = parse_header(header)
dtype = build_dtype(metadata)
break
if metadata['data'] == 'ascii':
pc_data = np.loadtxt(f, dtype=dtype, delimiter=' ')
elif metadata['data'] == 'binary':
rowstep = metadata['points'] * dtype.itemsize
# for some reason pcl adds empty space at the end of files
buf = f.read(rowstep)
pc_data = np.fromstring(buf, dtype=dtype)
elif metadata['data'] == 'binary_compressed':
# compressed size of data (uint32)
# uncompressed size of data (uint32)
# compressed data
# junk
fmt = 'II'
compressed_size, uncompressed_size =\
struct.unpack(fmt, f.read(struct.calcsize(fmt)))
compressed_data = f.read(compressed_size)
# TODO what to use as second argument? if buf is None
# (compressed > uncompressed)
# should we read buf as raw binary?
buf = lzf.decompress(compressed_data, uncompressed_size)
if len(buf) != uncompressed_size:
raise Exception('Error decompressing data')
# the data is stored field-by-field
pc_data = np.zeros(metadata['width'], dtype=dtype)
ix = 0
for dti in range(len(dtype)):
dt = dtype[dti]
bytes = dt.itemsize * metadata['width']
column = np.fromstring(buf[ix:(ix + bytes)], dt)
pc_data[dtype.names[dti]] = column
ix += bytes
data["points"] = pd.DataFrame(pc_data)
return data
print("Uncompressed: {0}".format(len(uncompressed_blobs)))
for compressed_blob in compressed_blobs:
try:
print "Decompress {0}...".format(compressed_blob["compressed_filename"])
if False:
decompressor = zlib.decompressobj()
cs = hashlib.sha256()
with io.FileIO(DUMP_STORAGE_PATH + session_guid + "/" + compressed_blob["compressed_filename"], 'rb') as fd:
with io.FileIO(DUMP_STORAGE_PATH + session_guid + "/" + compressed_blob["decompressed_filename"], 'wb') as n_fd:
if True:
cd_data = fd.readall()
dc_data = lzf.decompress(cd_data, 1 * 1024 * 1024 * 1024)
n_fd.write(dc_data)
cs.update(dc_data)
else:
for data in iter(lambda: fd.read(8192), ''):
dc_data = decompressor.decompress(data)
n_fd.write(dc_data)
cs.update(dc_data)
dc_data = decompressor.flush()
n_fd.write(dc_data)
cs.update(dc_data)
def test_decompresses_correctly(self):
compressed = self.compress(self.VAL)
self.assertEqual(lzf.decompress(compressed, len(self.VAL)), self.VAL)
def test_selective(self):
compressed = self.compress(self.VAL)
self.assertEqual(lzf.decompress(compressed, len(self.VAL) - 1), None)
assert lzf.decompress(compressed, len(self.VAL))
def read_pcd(filename):
""" Reads and pcd file and return the elements as pandas Dataframes.
Parameters
----------
filename: str
Path to the obj file.
Returns
-------
pandas Dataframe.
"""
data = {}
with open(filename, 'rb') as f:
header = []
while True:
ln = f.readline().strip().decode()
header.append(ln)
if ln.startswith('DATA'):
metadata = parse_header(header)
dtype = build_dtype(metadata)
break
if metadata['data'] == 'ascii':
pc_data = np.loadtxt(f, dtype=dtype, delimiter=' ')
elif metadata['data'] == 'binary':
rowstep = metadata['points'] * dtype.itemsize
# for some reason pcl adds empty space at the end of files
buf = f.read(rowstep)
pc_data = np.fromstring(buf, dtype=dtype)
elif metadata['data'] == 'binary_compressed':
# compressed size of data (uint32)
# uncompressed size of data (uint32)
# compressed data
# junk
fmt = 'II'
compressed_size, uncompressed_size =\
struct.unpack(fmt, f.read(struct.calcsize(fmt)))
compressed_data = f.read(compressed_size)
# TODO what to use as second argument? if buf is None
# (compressed > uncompressed)
# should we read buf as raw binary?
buf = lzf.decompress(compressed_data, uncompressed_size)
if len(buf) != uncompressed_size:
raise Exception('Error decompressing data')
# the data is stored field-by-field
pc_data = np.zeros(metadata['width'], dtype=dtype)
ix = 0
for dti in range(len(dtype)):
dt = dtype[dti]
bytes = dt.itemsize * metadata['width']
column = np.fromstring(buf[ix:(ix + bytes)], dt)
pc_data[dtype.names[dti]] = column
ix += bytes
data["points"] = pd.DataFrame(pc_data)
return data