Python3

anonymize-slide.py

@@ -22,9 +22,9 @@
 # Boston, MA 02110-1301 USA.
 #
 
-from __future__ import division
-from ConfigParser import RawConfigParser
-from cStringIO import StringIO
+
+from configparser import RawConfigParser
+import io
 from glob import glob
 from optparse import OptionParser
 import os
@@ -54,9 +54,9 @@
 NDPI_SOURCELENS = 65421
 
 # Format headers
-LZW_CLEARCODE = '\x80'
-JPEG_SOI = '\xff\xd8'
-UTF8_BOM = '\xef\xbb\xbf'
+LZW_CLEARCODE = b'\x80'
+JPEG_SOI = b'\xff\xd8'
+UTF8_BOM = b'\xef\xbb\xbf'
 
 # MRXS
 MRXS_HIERARCHICAL = 'HIERARCHICAL'
@@ -67,15 +67,20 @@ class UnrecognizedFile(Exception):
  pass
 
 
-class TiffFile(file):
+class TiffFile(object):
  def __init__(self, path):
- file.__init__(self, path, 'r+b')
+ mode = 'r+b'
+ self.file = io.open(path, mode)
+ self.close_file = (self.file is not path)
 
  # Check header, decide endianness
- endian = self.read(2)
- if endian == 'II':
+ endian = self.file.read(2)
+ endianII = bytes('II', 'utf-8')
+ endianMM = bytes('MM', 'utf-8')
+
+ if endian == endianII:
  self._fmt_prefix = '<'
- elif endian == 'MM':
+ elif endian == endianMM:
  self._fmt_prefix = '>'
  else:
  raise UnrecognizedFile
@@ -97,11 +102,11 @@ def __init__(self, path):
  # Read directories
  self.directories = []
  while True:
- in_pointer_offset = self.tell()
+ in_pointer_offset = self.file.tell()
  directory_offset = self.read_fmt('D')
  if directory_offset == 0:
  break
- self.seek(directory_offset)
+ self.file.seek(directory_offset)
  directory = TiffDirectory(self, len(self.directories),
  in_pointer_offset)
  if not self.directories and not self._bigtiff:
@@ -110,12 +115,33 @@ def __init__(self, path):
  # the first directory is beyond 4 GB.
  if NDPI_MAGIC in directory.entries:
  if DEBUG:
- print 'Enabling NDPI mode.'
+ print('Enabling NDPI mode.')
  self._ndpi = True
  self.directories.append(directory)
  if not self.directories:
  raise IOError('No directories')
 
+ def __enter__(self):
+ return self
+
+ def __exit__(self, *args, **kwargs):
+ if (not self.close_file):
+ return # do nothing
+ # clean up
+ exit = getattr(self.file, '__exit__', None)
+ if exit is not None:
+ return exit(*args, **kwargs)
+ else:
+ exit = getattr(self.file, 'close', None)
+ if exit is not None:
+ exit()
+
+ def __getattr__(self, attr):
+ return getattr(self.file, attr)
+
+ def __iter__(self):
+ return iter(self.file)
+
  def _convert_format(self, fmt):
  # Format strings can have special characters:
  # y: 16-bit signed on little TIFF, 64-bit signed on BigTIFF
@@ -124,11 +150,11 @@ def _convert_format(self, fmt):
  # Z: 32-bit unsigned on little TIFF, 64-bit unsigned on BigTIFF
  # D: 32-bit unsigned on little TIFF, 64-bit unsigned on BigTIFF/NDPI
  if self._bigtiff:
- fmt = fmt.translate(string.maketrans('yYzZD', 'qQqQQ'))
+ fmt = fmt.translate(str.maketrans('yYzZD', 'qQqQQ'))
  elif self._ndpi:
- fmt = fmt.translate(string.maketrans('yYzZD', 'hHiIQ'))
+ fmt = fmt.translate(str.maketrans('yYzZD', 'hHiIQ'))
  else:
- fmt = fmt.translate(string.maketrans('yYzZD', 'hHiII'))
+ fmt = fmt.translate(str.maketrans('yYzZD', 'hHiII'))
  return self._fmt_prefix + fmt
 
  def fmt_size(self, fmt):
@@ -180,27 +206,28 @@ def delete(self, expected_prefix=None):
  for offset, length in zip(offsets, lengths):
  offset = self._fh.near_pointer(self._out_pointer_offset, offset)
  if DEBUG:
- print 'Zeroing', offset, 'for', length
+ print('Zeroing', offset, 'for', length)
  self._fh.seek(offset)
  if expected_prefix:
- buf = self._fh.read(len(expected_prefix))
+ buf = self._fh.file.read(len(expected_prefix))
  if buf != expected_prefix:
  raise IOError('Unexpected data in image strip')
- self._fh.seek(offset)
- self._fh.write('\0' * length)
+ self._fh.file.seek(offset)
+ write_byte = b'\0'
+ self._fh.file.write(write_byte * length)
 
  # Remove directory
  if DEBUG:
- print 'Deleting directory', self._number
- self._fh.seek(self._out_pointer_offset)
+ print('Deleting directory', self._number)
+ self._fh.file.seek(self._out_pointer_offset)
  out_pointer = self._fh.read_fmt('D')
- self._fh.seek(self._in_pointer_offset)
+ self._fh.file.seek(self._in_pointer_offset)
  self._fh.write_fmt('D', out_pointer)
 
 
 class TiffEntry(object):
  def __init__(self, fh):
- self.start = fh.tell()
+ self.start = fh.file.tell()
  self.tag, self.type, self.count, self.value_offset = \
  fh.read_fmt('HHZZ')
  self._fh = fh
@@ -225,15 +252,16 @@ def value(self):
  len = self._fh.fmt_size(fmt)
  if len <= self._fh.fmt_size('Z'):
  # Inline value
- self._fh.seek(self.start + self._fh.fmt_size('HHZ'))
+ self._fh.file.seek(self.start + self._fh.fmt_size('HHZ'))
  else:
  # Out-of-line value
- self._fh.seek(self._fh.near_pointer(self.start, self.value_offset))
+ self._fh.file.seek(self._fh.near_pointer(self.start, self.value_offset))
  items = self._fh.read_fmt(fmt, force_list=True)
  if self.type == ASCII:
- if items[-1] != '\0':
+ utf8_zero = bytes('\0', 'utf-8')
+ if items[-1] != utf8_zero:
  raise ValueError('String not null-terminated')
- return ''.join(items[:-1])
+ return b''.join(items[:-1])
  else:
  return items
 
@@ -250,11 +278,12 @@ def __init__(self, filename):
  self._dat = RawConfigParser()
  self._dat.optionxform = str
  try:
- with open(self._slidedatfile, 'rb') as fh:
+ with open(self._slidedatfile, 'rb') as fh_prewrapped:
+ fh = io.TextIOWrapper(fh_prewrapped)
  self._have_bom = (fh.read(len(UTF8_BOM)) == UTF8_BOM)
  if not self._have_bom:
  fh.seek(0)
- self._dat.readfp(fh)
+ self._dat.read_file(fh)
  except IOError:
  raise UnrecognizedFile
 
@@ -326,9 +355,9 @@ def _zero_record(self, record):
  do_truncate = (fh.tell() == offset + length)
  if DEBUG:
  if do_truncate:
- print 'Truncating', path, 'to', offset
+ print('Truncating', path, 'to', offset)
  else:
- print 'Zeroing', path, 'at', offset, 'for', length
+ print('Zeroing', path, 'at', offset, 'for', length)
  fh.seek(offset)
  buf = fh.read(len(JPEG_SOI))
  if buf != JPEG_SOI:
@@ -341,7 +370,7 @@ def _zero_record(self, record):
 
  def _delete_index_record(self, record):
  if DEBUG:
- print 'Deleting record', record
+ print('Deleting record', record)
  with open(self._indexfile, 'r+b') as fh:
  entries_to_move = len(self._level_list) - record - 1
  if entries_to_move == 0:
@@ -361,51 +390,57 @@ def _delete_index_record(self, record):
  def _hier_keys_for_level(self, level):
  ret = []
  for k, _ in self._dat.items(MRXS_HIERARCHICAL):
- if k == level.key_prefix or k.startswith(level.key_prefix + '_'):
+ k_bytes = bytes(k, 'utf-8')
+ level_key_prefix_bytes = bytes(level.key_prefix, 'utf-8')
+ level_key_prefix_underscore_bytes = bytes(level.key_prefix + '_', 'utf-8')
+ if k_bytes == level_key_prefix_bytes or k_bytes.startswith(level_key_prefix_underscore_bytes):
  ret.append(k)
  return ret
 
  def _rename_section(self, old, new):
  if self._dat.has_section(old):
  if DEBUG:
- print '[%s] -> [%s]' % (old, new)
+ print('[%s] -> [%s]' % (old, new))
  self._dat.add_section(new)
  for k, v in self._dat.items(old):
  self._dat.set(new, k, v)
  self._dat.remove_section(old)
  elif DEBUG:
- print '[%s] does not exist' % old
+ print('[%s] does not exist' % old)
 
  def _delete_section(self, section):
  if DEBUG:
- print 'Deleting [%s]' % section
+ print('Deleting [%s]' % section)
  self._dat.remove_section(section)
 
  def _set_key(self, section, key, value):
  if DEBUG:
  prev = self._dat.get(section, key)
- print '[%s] %s: %s -> %s' % (section, key, prev, value)
+ print('[%s] %s: %s -> %s' % (section, key, prev, value))
  self._dat.set(section, key, value)
 
  def _rename_key(self, section, old, new):
  if DEBUG:
- print '[%s] %s -> %s' % (section, old, new)
+ print('[%s] %s -> %s' % (section, old, new))
  v = self._dat.get(section, old)
  self._dat.remove_option(section, old)
  self._dat.set(section, new, v)
 
  def _delete_key(self, section, key):
  if DEBUG:
- print 'Deleting [%s] %s' % (section, key)
+ print('Deleting [%s] %s' % (section, key))
  self._dat.remove_option(section, key)
 
  def _write(self):
- buf = StringIO()
+ buf = io.StringIO()
  self._dat.write(buf)
- with open(self._slidedatfile, 'wb') as fh:
+ with open(self._slidedatfile, 'wb') as fh_prewrapped:
+ fh = io.TextIOWrapper(fh_prewrapped)
  if self._have_bom:
  fh.write(UTF8_BOM)
- fh.write(buf.getvalue().replace('\n', '\r\n'))
+ buf_replaced = buf.getvalue().replace('\n', '\r\n')
+ fh.write(buf_replaced)
+ fh.close()
 
  def delete_level(self, layer_name, level_name):
  level = self._levels[(layer_name, level_name)]
@@ -465,15 +500,16 @@ def __init__(self, dat, layer_id, level_id, record):
 
 def accept(filename, format):
  if DEBUG:
- print filename + ':', format
+ print(filename + ':', format)
 
 
 def do_aperio_svs(filename):
  with TiffFile(filename) as fh:
  # Check for SVS file
  try:
  desc0 = fh.directories[0].entries[IMAGE_DESCRIPTION].value()
- if not desc0.startswith('Aperio'):
+ aperio_bytes = bytes('Aperio', 'utf-8')
+ if not desc0.startswith(aperio_bytes):
  raise UnrecognizedFile
  except KeyError:
  raise UnrecognizedFile
@@ -482,8 +518,11 @@ def do_aperio_svs(filename):
  # Find and delete label
  for directory in fh.directories:
  lines = directory.entries[IMAGE_DESCRIPTION].value().splitlines()
- if len(lines) >= 2 and lines[1].startswith('label '):
- directory.delete(expected_prefix=LZW_CLEARCODE)
+ label_bytes = b'label '
+ if len(lines) >= 2:
+ line1_bytes = bytes(lines[1], 'utf-8')
+ if line1_bytes.startswith(label_bytes):
+ directory.delete(expected_prefix=LZW_CLEARCODE)
  break
  else:
  raise IOError("No label in SVS file")
@@ -551,10 +590,10 @@ def _main():
  pass
  else:
  raise IOError('Unrecognized file type')
- except Exception, e:
+ except Exception as e:
  if DEBUG:
  raise
- print >>sys.stderr, '%s: %s' % (filename, str(e))
+ sys.stderr.write('%s: %s %s' % (filename, str(e), os.linesep))
  exit_code = 1
  sys.exit(exit_code)