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2010.03.05 13:57 "Re: Problem with multipage .stk tiff file", by Shafiq Abedin
Great source! I apologize if I sound arrogant but I am trying to accomplish this with libtiff and c. We already process our data with Matlab. Thank you though :) Shafiq Abedin sha33@pitt.edu On Mar 5, 2010, at 7:46 AM, Ashish Uthama wrote: > Information in this thread might be useful: > http://www.mathworks.com/matlabcentral/newsreader/view_thread/265330 > > points to: http://support.meta.moleculardevices.com/docs/t10243.pdf and > ftp://ftp.meta.moleculardevices.com/support/stack/STK.doc > > > > From: tiff-bounces@lists.maptools.org > [mailto:tiff-bounces@lists.maptools.org] On Behalf Of Shafiq Abedin > Sent: Thursday, March 04, 2010 10:37 PM > To: tiff@lists.maptools.org > Subject: [Tiff] Problem with multipage .stk tiff file > > Hello All: > > I am writing this post after pulling my hair multiple times (I am bald > now!) and doing many many google searches (all the webpages related to > libtiff is now imprinted in my brain). I have failed to find a post on > this mailing list that solves the problem or anywhere for that matter. I > hate to be repetitive but I have the same problem described in this post > (http://www.asmail.be/msg0054982856.html). Solution given here is too > vague for me to pick up on (is it really like a linked list?). I didn't > find any post related to reading the .stk file (I wish I could give you a > sample right now but they are extremely big - 2gb ). I can read the first > in the stack but cant go beyond that. This particular image has 7400 > slices but whenever i do a tiffdump, this is what I get: > > test.stk: > Magic: 0x4949 <little-endian> Version: 0x2a > Directory 0: offset 1342567917 (0x5005f5ed) next 0 (0) > SubFileType (254) LONG (4) 1<0> > ImageWidth (256) LONG (4) 1<348> > ImageLength (257) LONG (4) 1<260> > BitsPerSample (258) SHORT (3) 1<16> > Compression (259) SHORT (3) 1<1> > Photometric (262) SHORT (3) 1<1> > ImageDescription (270) ASCII (2) 2545600<Acquired from Photometri ...> > StripOffsets (273) LONG (4) 24<8 7664 15320 22976 30632 38288 45944 53600 > 61256 68912 76568 84224 91880 99536 107192 114848 122504 130160 137816 > 145472 153128 160784 168440 176096> > SamplesPerPixel (277) SHORT (3) 1<1> > RowsPerStrip (278) LONG (4) 1<11> > StripByteCounts (279) LONG (4) 24<7656 7656 7656 7656 7656 7656 7656 7656 > 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 > 4872> > XResolution (282) RATIONAL (5) 1<72> > YResolution (283) RATIONAL (5) 1<72> > PlanarConfig (284) SHORT (3) 1<1> > ResolutionUnit (296) SHORT (3) 1<2> > Software (305) ASCII (2) 18<MetaMorph 7.1.7.0\0> > DateTime (306) ASCII (2) 21<2009:09:08 17:54:57\0\0> > Predictor (317) SHORT (3) 1<1> > 33628 (0x835c) LONG (4) 7435<0 0 1 0 2 4095 3 0 4 1341649855 5 1341649863 > 6 1341649871 7 1341649880 8 0 9 255 11 128 12 64 ...> > 33629 (0x835d) RATIONAL (5) 7400<0 0.0383822 0.0380645 0 0.0383822 > 0.0380645 0 0.0383821 0.0380645 0 0.0383821 0.0380645 0 0.038382 0.0380645 > 0 0.038382 0.0380645 0 0.038382 0.0380645 0 0.0383819 0.0380645 ...> > 33630 (0x835e) RATIONAL (5) 7400<0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > 0 0 0 ...> > 33631 (0x835f) LONG (4) 7400<28 65536 0 65536 0 65536 0 65536 0 65536 0 > 65536 0 65536 0 65536 0 65536 0 65536 0 65536 0 65536 ...> > > My attempt to get the the read Strip or Tile have failed because the > libtiff TIFFTAG_TILEBYTECOUNTS and TIFFTAG_STRIPBYTECOUNTS returns only > 24. Although I can see the offset info in the dump, I dont know actually > how to get to the next image and read (using TIFFReadScanline) it so that > I can manipulate it. I should also mention that the directory count is > useless here because it returns 1 . This problem might be too trivial for > you but I need help finding a way to read these images. If you please > provide examples, it would be most helpful. Thanks in advance. > > -- > Shafiq > > University Of Pittsburgh > McGowan Institute for Regenerative Medicine > _______________________________________________ > Tiff mailing list: Tiff@lists.maptools.org > http://lists.maptools.org/mailman/listinfo/tiff > http://www.remotesensing.org/libtiff/