You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
439 lines
15 KiB
439 lines
15 KiB
# cython: profile=False
|
|
# cython: boundscheck=False, initializedcheck=False
|
|
from cython import Py_ssize_t
|
|
import numpy as np
|
|
|
|
import pandas.io.sas.sas_constants as const
|
|
|
|
ctypedef signed long long int64_t
|
|
ctypedef unsigned char uint8_t
|
|
ctypedef unsigned short uint16_t
|
|
|
|
# rle_decompress decompresses data using a Run Length Encoding
|
|
# algorithm. It is partially documented here:
|
|
#
|
|
# https://cran.r-project.org/package=sas7bdat/vignettes/sas7bdat.pdf
|
|
cdef const uint8_t[:] rle_decompress(int result_length, const uint8_t[:] inbuff):
|
|
|
|
cdef:
|
|
uint8_t control_byte, x
|
|
uint8_t[:] result = np.zeros(result_length, np.uint8)
|
|
int rpos = 0
|
|
int i, nbytes, end_of_first_byte
|
|
Py_ssize_t ipos = 0, length = len(inbuff)
|
|
|
|
while ipos < length:
|
|
control_byte = inbuff[ipos] & 0xF0
|
|
end_of_first_byte = <int>(inbuff[ipos] & 0x0F)
|
|
ipos += 1
|
|
|
|
if control_byte == 0x00:
|
|
if end_of_first_byte != 0:
|
|
raise ValueError("Unexpected non-zero end_of_first_byte")
|
|
nbytes = <int>(inbuff[ipos]) + 64
|
|
ipos += 1
|
|
for _ in range(nbytes):
|
|
result[rpos] = inbuff[ipos]
|
|
rpos += 1
|
|
ipos += 1
|
|
elif control_byte == 0x40:
|
|
# not documented
|
|
nbytes = end_of_first_byte * 16
|
|
nbytes += <int>(inbuff[ipos])
|
|
ipos += 1
|
|
for _ in range(nbytes):
|
|
result[rpos] = inbuff[ipos]
|
|
rpos += 1
|
|
ipos += 1
|
|
elif control_byte == 0x60:
|
|
nbytes = end_of_first_byte * 256 + <int>(inbuff[ipos]) + 17
|
|
ipos += 1
|
|
for _ in range(nbytes):
|
|
result[rpos] = 0x20
|
|
rpos += 1
|
|
elif control_byte == 0x70:
|
|
nbytes = end_of_first_byte * 256 + <int>(inbuff[ipos]) + 17
|
|
ipos += 1
|
|
for _ in range(nbytes):
|
|
result[rpos] = 0x00
|
|
rpos += 1
|
|
elif control_byte == 0x80:
|
|
nbytes = end_of_first_byte + 1
|
|
for i in range(nbytes):
|
|
result[rpos] = inbuff[ipos + i]
|
|
rpos += 1
|
|
ipos += nbytes
|
|
elif control_byte == 0x90:
|
|
nbytes = end_of_first_byte + 17
|
|
for i in range(nbytes):
|
|
result[rpos] = inbuff[ipos + i]
|
|
rpos += 1
|
|
ipos += nbytes
|
|
elif control_byte == 0xA0:
|
|
nbytes = end_of_first_byte + 33
|
|
for i in range(nbytes):
|
|
result[rpos] = inbuff[ipos + i]
|
|
rpos += 1
|
|
ipos += nbytes
|
|
elif control_byte == 0xB0:
|
|
nbytes = end_of_first_byte + 49
|
|
for i in range(nbytes):
|
|
result[rpos] = inbuff[ipos + i]
|
|
rpos += 1
|
|
ipos += nbytes
|
|
elif control_byte == 0xC0:
|
|
nbytes = end_of_first_byte + 3
|
|
x = inbuff[ipos]
|
|
ipos += 1
|
|
for _ in range(nbytes):
|
|
result[rpos] = x
|
|
rpos += 1
|
|
elif control_byte == 0xD0:
|
|
nbytes = end_of_first_byte + 2
|
|
for _ in range(nbytes):
|
|
result[rpos] = 0x40
|
|
rpos += 1
|
|
elif control_byte == 0xE0:
|
|
nbytes = end_of_first_byte + 2
|
|
for _ in range(nbytes):
|
|
result[rpos] = 0x20
|
|
rpos += 1
|
|
elif control_byte == 0xF0:
|
|
nbytes = end_of_first_byte + 2
|
|
for _ in range(nbytes):
|
|
result[rpos] = 0x00
|
|
rpos += 1
|
|
else:
|
|
raise ValueError(f"unknown control byte: {control_byte}")
|
|
|
|
# In py37 cython/clang sees `len(outbuff)` as size_t and not Py_ssize_t
|
|
if <Py_ssize_t>len(result) != <Py_ssize_t>result_length:
|
|
raise ValueError(f"RLE: {len(result)} != {result_length}")
|
|
|
|
return np.asarray(result)
|
|
|
|
|
|
# rdc_decompress decompresses data using the Ross Data Compression algorithm:
|
|
#
|
|
# http://collaboration.cmc.ec.gc.ca/science/rpn/biblio/ddj/Website/articles/CUJ/1992/9210/ross/ross.htm
|
|
cdef const uint8_t[:] rdc_decompress(int result_length, const uint8_t[:] inbuff):
|
|
|
|
cdef:
|
|
uint8_t cmd
|
|
uint16_t ctrl_bits = 0, ctrl_mask = 0, ofs, cnt
|
|
int rpos = 0, k
|
|
uint8_t[:] outbuff = np.zeros(result_length, dtype=np.uint8)
|
|
Py_ssize_t ipos = 0, length = len(inbuff)
|
|
|
|
ii = -1
|
|
|
|
while ipos < length:
|
|
ii += 1
|
|
ctrl_mask = ctrl_mask >> 1
|
|
if ctrl_mask == 0:
|
|
ctrl_bits = ((<uint16_t>inbuff[ipos] << 8) +
|
|
<uint16_t>inbuff[ipos + 1])
|
|
ipos += 2
|
|
ctrl_mask = 0x8000
|
|
|
|
if ctrl_bits & ctrl_mask == 0:
|
|
outbuff[rpos] = inbuff[ipos]
|
|
ipos += 1
|
|
rpos += 1
|
|
continue
|
|
|
|
cmd = (inbuff[ipos] >> 4) & 0x0F
|
|
cnt = <uint16_t>(inbuff[ipos] & 0x0F)
|
|
ipos += 1
|
|
|
|
# short RLE
|
|
if cmd == 0:
|
|
cnt += 3
|
|
for k in range(cnt):
|
|
outbuff[rpos + k] = inbuff[ipos]
|
|
rpos += cnt
|
|
ipos += 1
|
|
|
|
# long RLE
|
|
elif cmd == 1:
|
|
cnt += <uint16_t>inbuff[ipos] << 4
|
|
cnt += 19
|
|
ipos += 1
|
|
for k in range(cnt):
|
|
outbuff[rpos + k] = inbuff[ipos]
|
|
rpos += cnt
|
|
ipos += 1
|
|
|
|
# long pattern
|
|
elif cmd == 2:
|
|
ofs = cnt + 3
|
|
ofs += <uint16_t>inbuff[ipos] << 4
|
|
ipos += 1
|
|
cnt = <uint16_t>inbuff[ipos]
|
|
ipos += 1
|
|
cnt += 16
|
|
for k in range(cnt):
|
|
outbuff[rpos + k] = outbuff[rpos - <int>ofs + k]
|
|
rpos += cnt
|
|
|
|
# short pattern
|
|
elif (cmd >= 3) & (cmd <= 15):
|
|
ofs = cnt + 3
|
|
ofs += <uint16_t>inbuff[ipos] << 4
|
|
ipos += 1
|
|
for k in range(cmd):
|
|
outbuff[rpos + k] = outbuff[rpos - <int>ofs + k]
|
|
rpos += cmd
|
|
|
|
else:
|
|
raise ValueError("unknown RDC command")
|
|
|
|
# In py37 cython/clang sees `len(outbuff)` as size_t and not Py_ssize_t
|
|
if <Py_ssize_t>len(outbuff) != <Py_ssize_t>result_length:
|
|
raise ValueError(f"RDC: {len(outbuff)} != {result_length}\n")
|
|
|
|
return np.asarray(outbuff)
|
|
|
|
|
|
cdef enum ColumnTypes:
|
|
column_type_decimal = 1
|
|
column_type_string = 2
|
|
|
|
|
|
# type the page_data types
|
|
cdef:
|
|
int page_meta_type = const.page_meta_type
|
|
int page_mix_types_0 = const.page_mix_types[0]
|
|
int page_mix_types_1 = const.page_mix_types[1]
|
|
int page_data_type = const.page_data_type
|
|
int subheader_pointers_offset = const.subheader_pointers_offset
|
|
|
|
|
|
cdef class Parser:
|
|
|
|
cdef:
|
|
int column_count
|
|
int64_t[:] lengths
|
|
int64_t[:] offsets
|
|
int64_t[:] column_types
|
|
uint8_t[:, :] byte_chunk
|
|
object[:, :] string_chunk
|
|
char *cached_page
|
|
int current_row_on_page_index
|
|
int current_page_block_count
|
|
int current_page_data_subheader_pointers_len
|
|
int current_page_subheaders_count
|
|
int current_row_in_chunk_index
|
|
int current_row_in_file_index
|
|
int header_length
|
|
int row_length
|
|
int bit_offset
|
|
int subheader_pointer_length
|
|
int current_page_type
|
|
bint is_little_endian
|
|
const uint8_t[:] (*decompress)(int result_length, const uint8_t[:] inbuff)
|
|
object parser
|
|
|
|
def __init__(self, object parser):
|
|
cdef:
|
|
int j
|
|
char[:] column_types
|
|
|
|
self.parser = parser
|
|
self.header_length = self.parser.header_length
|
|
self.column_count = parser.column_count
|
|
self.lengths = parser.column_data_lengths()
|
|
self.offsets = parser.column_data_offsets()
|
|
self.byte_chunk = parser._byte_chunk
|
|
self.string_chunk = parser._string_chunk
|
|
self.row_length = parser.row_length
|
|
self.bit_offset = self.parser._page_bit_offset
|
|
self.subheader_pointer_length = self.parser._subheader_pointer_length
|
|
self.is_little_endian = parser.byte_order == "<"
|
|
self.column_types = np.empty(self.column_count, dtype='int64')
|
|
|
|
# page indicators
|
|
self.update_next_page()
|
|
|
|
column_types = parser.column_types()
|
|
|
|
# map column types
|
|
for j in range(self.column_count):
|
|
if column_types[j] == b'd':
|
|
self.column_types[j] = column_type_decimal
|
|
elif column_types[j] == b's':
|
|
self.column_types[j] = column_type_string
|
|
else:
|
|
raise ValueError(f"unknown column type: {self.parser.columns[j].ctype}")
|
|
|
|
# compression
|
|
if parser.compression == const.rle_compression:
|
|
self.decompress = rle_decompress
|
|
elif parser.compression == const.rdc_compression:
|
|
self.decompress = rdc_decompress
|
|
else:
|
|
self.decompress = NULL
|
|
|
|
# update to current state of the parser
|
|
self.current_row_in_chunk_index = parser._current_row_in_chunk_index
|
|
self.current_row_in_file_index = parser._current_row_in_file_index
|
|
self.current_row_on_page_index = parser._current_row_on_page_index
|
|
|
|
def read(self, int nrows):
|
|
cdef:
|
|
bint done
|
|
int i
|
|
|
|
for _ in range(nrows):
|
|
done = self.readline()
|
|
if done:
|
|
break
|
|
|
|
# update the parser
|
|
self.parser._current_row_on_page_index = self.current_row_on_page_index
|
|
self.parser._current_row_in_chunk_index = self.current_row_in_chunk_index
|
|
self.parser._current_row_in_file_index = self.current_row_in_file_index
|
|
|
|
cdef bint read_next_page(self):
|
|
cdef done
|
|
|
|
done = self.parser._read_next_page()
|
|
if done:
|
|
self.cached_page = NULL
|
|
else:
|
|
self.update_next_page()
|
|
return done
|
|
|
|
cdef update_next_page(self):
|
|
# update data for the current page
|
|
|
|
self.cached_page = <char *>self.parser._cached_page
|
|
self.current_row_on_page_index = 0
|
|
self.current_page_type = self.parser._current_page_type
|
|
self.current_page_block_count = self.parser._current_page_block_count
|
|
self.current_page_data_subheader_pointers_len = len(
|
|
self.parser._current_page_data_subheader_pointers
|
|
)
|
|
self.current_page_subheaders_count = self.parser._current_page_subheaders_count
|
|
|
|
cdef readline(self):
|
|
|
|
cdef:
|
|
int offset, bit_offset, align_correction
|
|
int subheader_pointer_length, mn
|
|
bint done, flag
|
|
|
|
bit_offset = self.bit_offset
|
|
subheader_pointer_length = self.subheader_pointer_length
|
|
|
|
# If there is no page, go to the end of the header and read a page.
|
|
if self.cached_page == NULL:
|
|
self.parser._path_or_buf.seek(self.header_length)
|
|
done = self.read_next_page()
|
|
if done:
|
|
return True
|
|
|
|
# Loop until a data row is read
|
|
while True:
|
|
if self.current_page_type == page_meta_type:
|
|
flag = self.current_row_on_page_index >=\
|
|
self.current_page_data_subheader_pointers_len
|
|
if flag:
|
|
done = self.read_next_page()
|
|
if done:
|
|
return True
|
|
continue
|
|
current_subheader_pointer = (
|
|
self.parser._current_page_data_subheader_pointers[
|
|
self.current_row_on_page_index])
|
|
self.process_byte_array_with_data(
|
|
current_subheader_pointer.offset,
|
|
current_subheader_pointer.length)
|
|
return False
|
|
elif (self.current_page_type == page_mix_types_0 or
|
|
self.current_page_type == page_mix_types_1):
|
|
align_correction = (
|
|
bit_offset
|
|
+ subheader_pointers_offset
|
|
+ self.current_page_subheaders_count * subheader_pointer_length
|
|
)
|
|
align_correction = align_correction % 8
|
|
offset = bit_offset + align_correction
|
|
offset += subheader_pointers_offset
|
|
offset += self.current_page_subheaders_count * subheader_pointer_length
|
|
offset += self.current_row_on_page_index * self.row_length
|
|
self.process_byte_array_with_data(offset, self.row_length)
|
|
mn = min(self.parser.row_count, self.parser._mix_page_row_count)
|
|
if self.current_row_on_page_index == mn:
|
|
done = self.read_next_page()
|
|
if done:
|
|
return True
|
|
return False
|
|
elif self.current_page_type & page_data_type == page_data_type:
|
|
self.process_byte_array_with_data(
|
|
bit_offset
|
|
+ subheader_pointers_offset
|
|
+ self.current_row_on_page_index * self.row_length,
|
|
self.row_length,
|
|
)
|
|
flag = self.current_row_on_page_index == self.current_page_block_count
|
|
if flag:
|
|
done = self.read_next_page()
|
|
if done:
|
|
return True
|
|
return False
|
|
else:
|
|
raise ValueError(f"unknown page type: {self.current_page_type}")
|
|
|
|
cdef void process_byte_array_with_data(self, int offset, int length):
|
|
|
|
cdef:
|
|
Py_ssize_t j
|
|
int s, k, m, jb, js, current_row
|
|
int64_t lngt, start, ct
|
|
const uint8_t[:] source
|
|
int64_t[:] column_types
|
|
int64_t[:] lengths
|
|
int64_t[:] offsets
|
|
uint8_t[:, :] byte_chunk
|
|
object[:, :] string_chunk
|
|
|
|
source = np.frombuffer(
|
|
self.cached_page[offset:offset + length], dtype=np.uint8)
|
|
|
|
if self.decompress != NULL and (length < self.row_length):
|
|
source = self.decompress(self.row_length, source)
|
|
|
|
current_row = self.current_row_in_chunk_index
|
|
column_types = self.column_types
|
|
lengths = self.lengths
|
|
offsets = self.offsets
|
|
byte_chunk = self.byte_chunk
|
|
string_chunk = self.string_chunk
|
|
s = 8 * self.current_row_in_chunk_index
|
|
js = 0
|
|
jb = 0
|
|
for j in range(self.column_count):
|
|
lngt = lengths[j]
|
|
if lngt == 0:
|
|
break
|
|
start = offsets[j]
|
|
ct = column_types[j]
|
|
if ct == column_type_decimal:
|
|
# decimal
|
|
if self.is_little_endian:
|
|
m = s + 8 - lngt
|
|
else:
|
|
m = s
|
|
for k in range(lngt):
|
|
byte_chunk[jb, m + k] = source[start + k]
|
|
jb += 1
|
|
elif column_types[j] == column_type_string:
|
|
# string
|
|
string_chunk[js, current_row] = np.array(source[start:(
|
|
start + lngt)]).tobytes().rstrip(b"\x00 ")
|
|
js += 1
|
|
|
|
self.current_row_on_page_index += 1
|
|
self.current_row_in_chunk_index += 1
|
|
self.current_row_in_file_index += 1
|
|
|