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Added support for anonymizing Philips TIFF slides #3

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Added support for anonymizing Philips TIFF slides #3

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37 changes: 36 additions & 1 deletion anonymize-slide.py
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Original file line number Diff line number Diff line change
Expand Up @@ -229,14 +229,19 @@ def value(self):
else:
# Out-of-line value
self._fh.seek(self._fh.near_pointer(self.start, self.value_offset))
self.realstart = self._fh.tell()
items = self._fh.read_fmt(fmt, force_list=True)
if self.type == ASCII:
if items[-1] != '\0':
raise ValueError('String not null-terminated')
return ''.join(items[:-1])
else:
return items


def spaceout(self, position, length):
self._fh.seek(self.realstart + position)
self._fh.write(' ' * length)


class MrxsFile(object):
def __init__(self, filename):
Expand Down Expand Up @@ -488,6 +493,35 @@ def do_aperio_svs(filename):
else:
raise IOError("No label in SVS file")

def do_philips_tif(filename):
with TiffFile(filename) as fh:
# Check for TIF file
try:
desc0 = fh.directories[0].entries[IMAGE_DESCRIPTION].value()
except KeyError:
raise UnrecognizedFile

# Find and delete labels
found=False
for directory in fh.directories:
desc = directory.entries[IMAGE_DESCRIPTION].value()
if desc.find("LABELIMAGE") != -1:
pos = desc.find('<DataObject ObjectType="DPScannedImage">')
while pos != -1:
endpos=desc.find("</DataObject", pos)+len("</DataObject>")
labelpos = desc.find("LABELIMAGE")
if (labelpos < endpos and labelpos > pos):
print "found it at %d"%pos
directory.entries[IMAGE_DESCRIPTION].spaceout(pos, endpos-pos)
found=True
pos = desc.find('<DataObject ObjectType="DPScannedImage">', endpos)
if desc == "Label":
print "found label"
directory.delete()
found=True
else:
if not found:
raise IOError("No label in Philips TIFF file")

def do_hamamatsu_ndpi(filename):
with TiffFile(filename) as fh:
Expand All @@ -514,6 +548,7 @@ def do_3dhistech_mrxs(filename):


format_handlers = [
do_philips_tif,
do_aperio_svs,
do_hamamatsu_ndpi,
do_3dhistech_mrxs,
Expand Down