549 lines
19 KiB
Cython
549 lines
19 KiB
Cython
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# cython: language_level=3, initializedcheck=False
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# cython: warn.maybe_uninitialized=True, warn.unused=True
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from cython cimport Py_ssize_t
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from libc.stddef cimport size_t
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from libc.stdint cimport (
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int64_t,
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uint8_t,
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uint16_t,
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uint32_t,
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uint64_t,
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)
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from libc.stdlib cimport (
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calloc,
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free,
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)
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import numpy as np
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import pandas.io.sas.sas_constants as const
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cdef object np_nan = np.nan
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cdef struct Buffer:
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# Convenience wrapper for uint8_t data to allow fast and safe reads and writes.
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# We use this as a replacement for np.array(..., dtype=np.uint8) because it's
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# much slower to create NumPy arrays and we create Buffer instances many times
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# when reading a SAS7BDAT file (roughly once per row that is being read).
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uint8_t *data
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size_t length
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cdef uint8_t buf_get(Buffer buf, size_t offset) except? 255:
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assert offset < buf.length, "Out of bounds read"
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return buf.data[offset]
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cdef bint buf_set(Buffer buf, size_t offset, uint8_t value) except 0:
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assert offset < buf.length, "Out of bounds write"
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buf.data[offset] = value
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return True
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cdef bytes buf_as_bytes(Buffer buf, size_t offset, size_t length):
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assert offset + length <= buf.length, "Out of bounds read"
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return buf.data[offset:offset+length]
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cdef Buffer buf_new(size_t length) except *:
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cdef uint8_t *data = <uint8_t *>calloc(length, sizeof(uint8_t))
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if data == NULL:
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raise MemoryError(f"Failed to allocate {length} bytes")
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return Buffer(data, length)
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cdef buf_free(Buffer buf):
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if buf.data != NULL:
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free(buf.data)
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# rle_decompress decompresses data using a Run Length Encoding
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# algorithm. It is partially documented here:
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#
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# https://cran.r-project.org/package=sas7bdat/vignettes/sas7bdat.pdf
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cdef int rle_decompress(Buffer inbuff, Buffer outbuff) except? 0:
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cdef:
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uint8_t control_byte, x
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int rpos = 0
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int i, nbytes, end_of_first_byte
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size_t ipos = 0
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Py_ssize_t _
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while ipos < inbuff.length:
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control_byte = buf_get(inbuff, ipos) & 0xF0
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end_of_first_byte = <int>(buf_get(inbuff, ipos) & 0x0F)
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ipos += 1
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if control_byte == 0x00:
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nbytes = <int>(buf_get(inbuff, ipos)) + 64 + end_of_first_byte * 256
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ipos += 1
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for _ in range(nbytes):
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buf_set(outbuff, rpos, buf_get(inbuff, ipos))
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rpos += 1
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ipos += 1
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elif control_byte == 0x40:
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# not documented
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nbytes = <int>(buf_get(inbuff, ipos)) + 18 + end_of_first_byte * 256
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ipos += 1
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for _ in range(nbytes):
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buf_set(outbuff, rpos, buf_get(inbuff, ipos))
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rpos += 1
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ipos += 1
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elif control_byte == 0x60:
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nbytes = end_of_first_byte * 256 + <int>(buf_get(inbuff, ipos)) + 17
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ipos += 1
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for _ in range(nbytes):
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buf_set(outbuff, rpos, 0x20)
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rpos += 1
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elif control_byte == 0x70:
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nbytes = end_of_first_byte * 256 + <int>(buf_get(inbuff, ipos)) + 17
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ipos += 1
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for _ in range(nbytes):
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buf_set(outbuff, rpos, 0x00)
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rpos += 1
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elif control_byte == 0x80:
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nbytes = end_of_first_byte + 1
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for i in range(nbytes):
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buf_set(outbuff, rpos, buf_get(inbuff, ipos + i))
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rpos += 1
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ipos += nbytes
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elif control_byte == 0x90:
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nbytes = end_of_first_byte + 17
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for i in range(nbytes):
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buf_set(outbuff, rpos, buf_get(inbuff, ipos + i))
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rpos += 1
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ipos += nbytes
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elif control_byte == 0xA0:
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nbytes = end_of_first_byte + 33
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for i in range(nbytes):
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buf_set(outbuff, rpos, buf_get(inbuff, ipos + i))
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rpos += 1
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ipos += nbytes
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elif control_byte == 0xB0:
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nbytes = end_of_first_byte + 49
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for i in range(nbytes):
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buf_set(outbuff, rpos, buf_get(inbuff, ipos + i))
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rpos += 1
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ipos += nbytes
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elif control_byte == 0xC0:
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nbytes = end_of_first_byte + 3
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x = buf_get(inbuff, ipos)
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ipos += 1
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for _ in range(nbytes):
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buf_set(outbuff, rpos, x)
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rpos += 1
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elif control_byte == 0xD0:
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nbytes = end_of_first_byte + 2
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for _ in range(nbytes):
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buf_set(outbuff, rpos, 0x40)
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rpos += 1
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elif control_byte == 0xE0:
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nbytes = end_of_first_byte + 2
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for _ in range(nbytes):
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buf_set(outbuff, rpos, 0x20)
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rpos += 1
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elif control_byte == 0xF0:
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nbytes = end_of_first_byte + 2
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for _ in range(nbytes):
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buf_set(outbuff, rpos, 0x00)
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rpos += 1
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else:
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raise ValueError(f"unknown control byte: {control_byte}")
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return rpos
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# rdc_decompress decompresses data using the Ross Data Compression algorithm:
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#
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# http://collaboration.cmc.ec.gc.ca/science/rpn/biblio/ddj/Website/articles/CUJ/1992/9210/ross/ross.htm
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cdef int rdc_decompress(Buffer inbuff, Buffer outbuff) except? 0:
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cdef:
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uint8_t cmd
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uint16_t ctrl_bits = 0, ctrl_mask = 0, ofs, cnt
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int rpos = 0, k, ii
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size_t ipos = 0
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ii = -1
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while ipos < inbuff.length:
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ii += 1
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ctrl_mask = ctrl_mask >> 1
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if ctrl_mask == 0:
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ctrl_bits = ((<uint16_t>buf_get(inbuff, ipos) << 8) +
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<uint16_t>buf_get(inbuff, ipos + 1))
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ipos += 2
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ctrl_mask = 0x8000
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if ctrl_bits & ctrl_mask == 0:
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buf_set(outbuff, rpos, buf_get(inbuff, ipos))
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ipos += 1
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rpos += 1
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continue
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cmd = (buf_get(inbuff, ipos) >> 4) & 0x0F
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cnt = <uint16_t>(buf_get(inbuff, ipos) & 0x0F)
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ipos += 1
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# short RLE
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if cmd == 0:
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cnt += 3
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for k in range(cnt):
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buf_set(outbuff, rpos + k, buf_get(inbuff, ipos))
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rpos += cnt
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ipos += 1
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# long RLE
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elif cmd == 1:
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cnt += <uint16_t>buf_get(inbuff, ipos) << 4
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cnt += 19
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ipos += 1
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for k in range(cnt):
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buf_set(outbuff, rpos + k, buf_get(inbuff, ipos))
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rpos += cnt
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ipos += 1
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# long pattern
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elif cmd == 2:
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ofs = cnt + 3
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ofs += <uint16_t>buf_get(inbuff, ipos) << 4
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ipos += 1
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cnt = <uint16_t>buf_get(inbuff, ipos)
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ipos += 1
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cnt += 16
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for k in range(cnt):
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buf_set(outbuff, rpos + k, buf_get(outbuff, rpos - <int>ofs + k))
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rpos += cnt
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# short pattern
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else:
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ofs = cnt + 3
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ofs += <uint16_t>buf_get(inbuff, ipos) << 4
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ipos += 1
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for k in range(cmd):
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buf_set(outbuff, rpos + k, buf_get(outbuff, rpos - <int>ofs + k))
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rpos += cmd
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return rpos
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cdef enum ColumnTypes:
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column_type_decimal = 1
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column_type_string = 2
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# Const aliases
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assert len(const.page_meta_types) == 2
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cdef:
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int page_meta_types_0 = const.page_meta_types[0]
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int page_meta_types_1 = const.page_meta_types[1]
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int page_mix_type = const.page_mix_type
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int page_data_type = const.page_data_type
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int subheader_pointers_offset = const.subheader_pointers_offset
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# Copy of subheader_signature_to_index that allows for much faster lookups.
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# Lookups are done in get_subheader_index. The C structures are initialized
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# in _init_subheader_signatures().
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uint32_t subheader_signatures_32bit[13]
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int subheader_indices_32bit[13]
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uint64_t subheader_signatures_64bit[17]
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int subheader_indices_64bit[17]
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int data_subheader_index = const.SASIndex.data_subheader_index
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def _init_subheader_signatures():
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subheaders_32bit = [
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(sig, idx)
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for sig, idx in const.subheader_signature_to_index.items()
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if len(sig) == 4
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]
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subheaders_64bit = [
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(sig, idx)
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for sig, idx in const.subheader_signature_to_index.items()
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if len(sig) == 8
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]
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assert len(subheaders_32bit) == 13
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assert len(subheaders_64bit) == 17
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assert len(const.subheader_signature_to_index) == 13 + 17
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for i, (signature, idx) in enumerate(subheaders_32bit):
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subheader_signatures_32bit[i] = (<uint32_t *><char *>signature)[0]
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subheader_indices_32bit[i] = idx
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for i, (signature, idx) in enumerate(subheaders_64bit):
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subheader_signatures_64bit[i] = (<uint64_t *><char *>signature)[0]
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subheader_indices_64bit[i] = idx
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_init_subheader_signatures()
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def get_subheader_index(bytes signature):
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"""Fast version of 'subheader_signature_to_index.get(signature)'."""
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cdef:
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uint32_t sig32
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uint64_t sig64
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Py_ssize_t i
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assert len(signature) in (4, 8)
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if len(signature) == 4:
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sig32 = (<uint32_t *><char *>signature)[0]
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for i in range(len(subheader_signatures_32bit)):
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if subheader_signatures_32bit[i] == sig32:
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return subheader_indices_32bit[i]
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else:
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sig64 = (<uint64_t *><char *>signature)[0]
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for i in range(len(subheader_signatures_64bit)):
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if subheader_signatures_64bit[i] == sig64:
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return subheader_indices_64bit[i]
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return data_subheader_index
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cdef class Parser:
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cdef:
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int column_count
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int64_t[:] lengths
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int64_t[:] offsets
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int64_t[:] column_types
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uint8_t[:, :] byte_chunk
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object[:, :] string_chunk
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uint8_t *cached_page
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int cached_page_len
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int current_row_on_page_index
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int current_page_block_count
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int current_page_data_subheader_pointers_len
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int current_page_subheaders_count
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int current_row_in_chunk_index
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int current_row_in_file_index
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bint blank_missing
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int header_length
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int row_length
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int bit_offset
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int subheader_pointer_length
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int current_page_type
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bint is_little_endian
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int (*decompress)(Buffer, Buffer) except? 0
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object parser
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def __init__(self, object parser):
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cdef:
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int j
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char[:] column_types
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self.parser = parser
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self.blank_missing = parser.blank_missing
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self.header_length = self.parser.header_length
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self.column_count = parser.column_count
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self.lengths = parser.column_data_lengths()
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self.offsets = parser.column_data_offsets()
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self.byte_chunk = parser._byte_chunk
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self.string_chunk = parser._string_chunk
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self.row_length = parser.row_length
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self.bit_offset = self.parser._page_bit_offset
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self.subheader_pointer_length = self.parser._subheader_pointer_length
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self.is_little_endian = parser.byte_order == "<"
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self.column_types = np.empty(self.column_count, dtype="int64")
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# page indicators
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self.update_next_page()
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column_types = parser.column_types()
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# map column types
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for j in range(self.column_count):
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if column_types[j] == b"d":
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self.column_types[j] = column_type_decimal
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elif column_types[j] == b"s":
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self.column_types[j] = column_type_string
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else:
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raise ValueError(f"unknown column type: {self.parser.columns[j].ctype}")
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# compression
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if parser.compression == const.rle_compression:
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||
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|
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
|
||
|
|
Py_ssize_t i
|
||
|
|
|
||
|
|
for i 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) except? True:
|
||
|
|
cdef bint 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 = <uint8_t *>self.parser._cached_page
|
||
|
|
self.cached_page_len = len(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 bint readline(self) except? True:
|
||
|
|
|
||
|
|
cdef:
|
||
|
|
int offset, length, 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 in (page_meta_types_0, page_meta_types_1):
|
||
|
|
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
|
||
|
|
offset, length = self.parser._current_page_data_subheader_pointers[
|
||
|
|
self.current_row_on_page_index
|
||
|
|
]
|
||
|
|
self.process_byte_array_with_data(offset, length)
|
||
|
|
return False
|
||
|
|
elif self.current_page_type == page_mix_type:
|
||
|
|
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:
|
||
|
|
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) except *:
|
||
|
|
|
||
|
|
cdef:
|
||
|
|
Py_ssize_t j
|
||
|
|
int s, k, m, jb, js, current_row, rpos
|
||
|
|
int64_t lngt, start, ct
|
||
|
|
Buffer source, decompressed_source
|
||
|
|
int64_t[:] column_types
|
||
|
|
int64_t[:] lengths
|
||
|
|
int64_t[:] offsets
|
||
|
|
uint8_t[:, :] byte_chunk
|
||
|
|
object[:, :] string_chunk
|
||
|
|
bint compressed
|
||
|
|
|
||
|
|
assert offset + length <= self.cached_page_len, "Out of bounds read"
|
||
|
|
source = Buffer(&self.cached_page[offset], length)
|
||
|
|
|
||
|
|
compressed = self.decompress != NULL and length < self.row_length
|
||
|
|
if compressed:
|
||
|
|
decompressed_source = buf_new(self.row_length)
|
||
|
|
rpos = self.decompress(source, decompressed_source)
|
||
|
|
if rpos != self.row_length:
|
||
|
|
raise ValueError(
|
||
|
|
f"Expected decompressed line of length {self.row_length} bytes "
|
||
|
|
f"but decompressed {rpos} bytes"
|
||
|
|
)
|
||
|
|
source = decompressed_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] = buf_get(source, start + k)
|
||
|
|
jb += 1
|
||
|
|
elif column_types[j] == column_type_string:
|
||
|
|
# string
|
||
|
|
# Skip trailing whitespace. This is equivalent to calling
|
||
|
|
# .rstrip(b"\x00 ") but without Python call overhead.
|
||
|
|
while lngt > 0 and buf_get(source, start + lngt - 1) in b"\x00 ":
|
||
|
|
lngt -= 1
|
||
|
|
if lngt == 0 and self.blank_missing:
|
||
|
|
string_chunk[js, current_row] = np_nan
|
||
|
|
else:
|
||
|
|
string_chunk[js, current_row] = buf_as_bytes(source, start, lngt)
|
||
|
|
js += 1
|
||
|
|
|
||
|
|
self.current_row_on_page_index += 1
|
||
|
|
self.current_row_in_chunk_index += 1
|
||
|
|
self.current_row_in_file_index += 1
|
||
|
|
|
||
|
|
if compressed:
|
||
|
|
buf_free(decompressed_source)
|