Decode an LZW-compressed ViewStation DICOM image section

decode_proprietary_dicom_lzw.py

"""
The code below is part of pdfminer (http://pypi.python.org/pypi/pdfminer/)

Copyright (c) 2004-2010 Yusuke Shinyama <yusuke at cs dot nyu dot edu>

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 
"""

import sys
from io import BytesIO


class LZWDecoder(object):
    debug = 0

    def __init__(self, fp):
        self.fp = fp
        self.buff = 0
        self.bpos = 8
        self.nbits = 9
        self.table = None
        self.prevbuf = None

    def readbits(self, bits):
        v = 0
        while True:
            # the number of remaining bits we can get from the current buffer.
            r = 8 - self.bpos
            if bits <= r:
                # |-----8-bits-----|
                # |-bpos-|-bits-|  |
                # |      |----r----|
                v = (v << bits) | ((self.buff >> (r - bits)) & ((1 << bits) - 1))
                self.bpos += bits
                break
            else:
                # |-----8-bits-----|
                # |-bpos-|---bits----...
                # |      |----r----|
                v = (v << r) | (self.buff & ((1 << r) - 1))
                bits -= r
                x = self.fp.read(1)
                if not x:
                    raise EOFError
                self.buff = ord(x)
                self.bpos = 0
        return v

    def feed(self, code):
        x = bytearray()
        if code == 256:
            self.table = [bytearray([c]) for c in range(256)]  # 0-255
            self.table.append(None)  # 256
            self.table.append(None)  # 257
            self.prevbuf = bytearray()
            self.nbits = 9
        elif code == 257:
            pass
        elif not self.prevbuf:
            x = self.prevbuf = self.table[code]
        else:
            if code < len(self.table):
                x = self.table[code]
                self.table.append(self.prevbuf + x[:1])
            else:
                self.table.append(self.prevbuf + self.prevbuf[:1])
                x = self.table[code]
            l = len(self.table)
            if l == 511:
                self.nbits = 10
            elif l == 1023:
                self.nbits = 11
            elif l == 2047:
                self.nbits = 12
            self.prevbuf = x
        return x

    def run(self):
        while True:
            try:
                code = self.readbits(self.nbits)
            except EOFError:
                break
            x = self.feed(code)
            yield x
            if self.debug:
                print('nbits=%d, code=%d, output=%r, table=%r' % (self.nbits, code, x, self.table[258:]), file=sys.stderr)


def lzw_decode(data):
    fp = BytesIO(data)
    return b''.join(LZWDecoder(fp).run())

# ----------------


import struct
import numpy as np
import matplotlib.pyplot as plt

def crc16(data):
    msb = 0
    lsb = 0
    for c in data:
        x = c ^ msb
        x ^= (x >> 4)
        msb = (lsb ^ (x >> 3) ^ (x << 4)) & 0xFF
        lsb = (x ^ (x << 5)) & 0xFF
    return (msb << 8) + lsb


path = "/home/martin/Downloads/001B2978.org"
file_data = open(path, "rb").read()

header = file_data[:50]
body = file_data[50:]

info = {}
(
    info["patientID"],
    info["imageNum"],
    info["numBytes"],
    info["dataBits"],
    info["height"],
    info["width"],
    info["widthStored"],
    info["storageType"],
    info["version"],
    _,
    info["pixrep"],
    _,
    info["headerCRC"],
) = struct.unpack(">IIHHIIIH3scH14sI", header)
assert info["headerCRC"] == crc16(header[:-4])

(
    info["bodyLen"],
    info["numBands"],
) = struct.unpack(">II", body[:8])
info["bodyCRC"] = struct.unpack(">I", body[-4:])[0]
assert info["bodyLen"] == len(body) - 8
assert info["bodyCRC"] == crc16(body[:-4])

bands = []
pos = 8
for band_idx in range(info["numBands"]):
    orig_len, compr_len = struct.unpack(">II", body[pos:][:8])
    data = body[pos+8:][:compr_len]
    pos += 8 + compr_len
    bands.append((orig_len, compr_len, data))

dtype = np.dtype(np.uint16 if info["numBytes"] == 2 else np.uint8)
dtype = dtype.newbyteorder(">")
canvas = np.zeros((512, 512), dtype=dtype)
w = info["width"]
h = info["height"]
for i, (orig_len, compr_len, raw_data) in enumerate(bands):
    if orig_len != 0:
        raw_data = lzw_decode(raw_data)
    arr = np.frombuffer(raw_data, dtype=dtype)
    img = arr.reshape(-1, info["width"])
    canvas[i * (info["height"] // len(bands)):][:img.shape[0]] = img
fig, ax = plt.subplots()
ax.set_aspect(1)
ax.imshow(canvas, vmin=0, vmax=0xFFFF, cmap="gray")
plt.show()