Autodetect NDPI in TIFF parser so we don't choke on SVS files

anonymize-slide.py

@@ -57,7 +57,7 @@ class UnrecognizedFile(Exception):
 
 
 class TiffFile(file):
- def __init__(self, path, ndpi=False):
+ def __init__(self, path):
  file.__init__(self, path, 'r+b')
 
  # Check header, decide endianness
@@ -74,7 +74,7 @@ def __init__(self, path, ndpi=False):
  self._ndpi = False
  version = self.read_fmt('H')
  if version == 42:
- self._ndpi = ndpi
+ pass
  elif version == 43:
  self._bigtiff = True
  magic2, reserved = self.read_fmt('HH')
@@ -93,6 +93,14 @@ def __init__(self, path, ndpi=False):
  self.seek(directory_offset)
  directory = TiffDirectory(self, len(self.directories),
  in_pointer_offset)
+ if not self.directories and not self._bigtiff:
+ # Check for NDPI. Because we don't know we have an NDPI file
+ # until after reading the first directory, we will choke if
+ # the first directory is beyond 4 GB.
+ if NDPI_MAGIC in directory.entries:
+ if DEBUG:
+ print 'Enabling NDPI mode.'
+ self._ndpi = True
  self.directories.append(directory)
  if not self.directories:
  raise IOError('No directories')
@@ -246,7 +254,7 @@ def do_aperio_svs(filename):
 
 
 def do_hamamatsu_ndpi(filename):
- with TiffFile(filename, ndpi=True) as fh:
+ with TiffFile(filename) as fh:
  # Check for NDPI file
  if NDPI_MAGIC not in fh.directories[0].entries:
  raise UnrecognizedFile
@@ -262,8 +270,8 @@ def do_hamamatsu_ndpi(filename):
 
 
 format_handlers = [
- do_hamamatsu_ndpi,
  do_aperio_svs,
+ do_hamamatsu_ndpi,
 ]