Ticket #156 (closed defect: invalid)

Opened 11 years ago

Last modified 10 years ago

xuvtools: fails to load a multi-page tiff file

Reported by: emmenlau Owned by: emmenlau
Priority: minor Milestone: XuvTools-1.8.0-final
Component: xuvtools Version:
Keywords: xuvtools, xuvtools_gui, load, tiff, stacks, error Cc: developer@…, tallavajhula@…

Description

Adding the file works. When trying to load images from the tiff file (i.e. compute thumbnails), XuvTools? loads only the first timepoint. For all other timepoints, an error message is shown.

File ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff, from Abhinav Tallavajhula <tallavajhula@…>.

Reproduced with XuvTools? r3516 by ME.

GenFile::generatePreview(): generating preview from array type 2 from /data/xuvtools_img/BugListData/Bug0201-proposed/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff: 0-24,0
File format supported by bioimageformats library.
read image from startpage 0.
GenFile::loadArray(): loading stack of extents (24, 512, 512) from page 0 to page 24, channel 0
Array plane size is 262144 (in bytes 262144), img byte-size is 262144
img depth is 8
GenFile::loadArray() page 0: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 1: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 2: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 3: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 4: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 5: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 6: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 7: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 8: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 9: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 10: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 11: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 12: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 13: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 14: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 15: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 16: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 17: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 18: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 19: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 20: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 21: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 22: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFile::loadArray() page 23: img.width() = 512, img.height() = 512, img.numPixels() = 262144, img.depth() = 8, img.samples() = 1 succeeded.
GenFileMath::_generatePreview(): loaded data from file '/data/xuvtools_img/BugListData/Bug0201-proposed/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff', stackID '0-24,0'
File format supported by bioimageformats library.
GenFile::generatePreview(): generating preview from array type 2 from /data/xuvtools_img/BugListData/Bug0201-proposed/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff: 24-48,0
File format supported by bioimageformats library.
unable to read image from startpage 24.
File format supported by bioimageformats library.
GenFile::generatePreview(): generating preview from array type 2 from /data/xuvtools_img/BugListData/Bug0201-proposed/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff: 48-72,0
File format supported by bioimageformats library.
unable to read image from startpage 48.
File format supported by bioimageformats library.
GenFile::generatePreview(): generating preview from array type 2 from /data/xuvtools_img/BugListData/Bug0201-proposed/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff: 72-96,0
File format supported by bioimageformats library.
unable to read image from startpage 72.
File format supported by bioimageformats library.
GenFile::generatePreview(): generating preview from array type 2 from /data/xuvtools_img/BugListData/Bug0201-proposed/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff: 96-120,0
File format supported by bioimageformats library.
unable to read image from startpage 96.

Change History

Changed 11 years ago by emmenlau

Dataset uploaded as

BugListData/Bug0156/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff.rar

Changed 10 years ago by emmenlau

  • status changed from new to accepted
  • milestone set to XuvTools-1.8.0-final

Changed 10 years ago by emmenlau

  • cc tallavajhula@… added
  • status changed from accepted to closed
  • resolution set to invalid

The file is actually broken. File header suggests it would consist of 72 Z-planes, but reading planes higher than 24 crashes. The same error happens with ImageJ, both with the native TIFF reader and the Bio-Formats library. XuvTools? reports:

Constructed new BlitzBioImageReader().
BlitzBioImageReader::setId() called.
BlitzBioImageReader::setId() finished successfully.
Genfile::inspectFile(): finished, printing map:
/data/xuvtools_img/BugListData/Bug0156/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff_filetype 6
stack0001 0
stack0001_datatype 2
stack0001_element_size_um 1,1,1
stack0001_filename /data/xuvtools_img/BugListData/Bug0156/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff
stack0001_size_pix 24,512,512
stack0001_stack_file_id 0,0
stack0001_tile tile0001
stack0002 0
stack0002_datatype 2
stack0002_element_size_um 1,1,1
stack0002_filename /data/xuvtools_img/BugListData/Bug0156/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff
stack0002_size_pix 24,512,512
stack0002_stack_file_id 1,0
stack0002_tile tile0002
stack0003 0
stack0003_datatype 2
stack0003_element_size_um 1,1,1
stack0003_filename /data/xuvtools_img/BugListData/Bug0156/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff
stack0003_size_pix 24,512,512
stack0003_stack_file_id 2,0
stack0003_tile tile0003
stack0004 0
stack0004_datatype 2
stack0004_element_size_um 1,1,1
stack0004_filename /data/xuvtools_img/BugListData/Bug0156/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff
stack0004_size_pix 24,512,512
stack0004_stack_file_id 3,0
stack0004_tile tile0004
stack0005 0
stack0005_datatype 2
stack0005_element_size_um 1,1,1
stack0005_filename /data/xuvtools_img/BugListData/Bug0156/ngp40x_100Res_523G_250P_Zscan10min_C1_TP1.tiff
stack0005_size_pix 24,512,512
stack0005_stack_file_id 4,0
stack0005_tile tile0005
stackcounter 5
stacks stack0001,stack0002,stack0003,stack0004,stack0005
submit_usage_statistics 1
tile0001_channels stack0001
tile0002_channels stack0002
tile0003_channels stack0003
tile0004_channels stack0004
tile0005_channels stack0005
tilecounter 5
tiles tile0001,tile0002,tile0003,tile0004,tile0005
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