[ImageJ-bugs] [Bug 862] New: Virtual stack of raw import becomes unusable after going beyond EOF

bugzilla at fiji.sc bugzilla at fiji.sc
Mon Jul 21 10:19:42 CDT 2014 

http://fiji.sc/bugzilla/show_bug.cgi?id=862

            Bug ID: 862
           Summary: Virtual stack of raw import becomes unusable after
                    going beyond EOF
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Linux
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: adrian.daerr at univ-paris-diderot.fr
                CC: adrian.daerr at univ-paris-diderot.fr

If a file is opened via File->Import->Raw... using the "Use Virtual Stack"
option, the "Number of Images" parameter is not checked against the file size,
and taken as the stack size (i.e. the maximum value for the slice slider at the
bottom of the image window). If the file underlying the Virtual Stack does not
contain this number of images (i.e. is smaller than Height*Width*NumberOfImages
pixels), then trying to access the last images of the Virtual Stack
unsurprisingly results in a "Read error or file not found (741)" (Log Window)
and a FileOpener error dialog "FileInfo parameter error: Offset+Image size >
file size". The dialog opens three times in a row, and after that (here comes
the bug) the slider in the image window does not update the visible slice
anymore, even if one goes back to the beginning of the stack. That is, the
Image Window appears to be frozen on one of the last loadable slices.

Work-around: calculate the correct number of images from the file size and the
image dimensions by hand before importing. This avoids the bug by never
creating too big a virtual stack, at the expense of being slightly cumbersome.

Expected/desired behaviour:
- at least return to a state where the image window showing the virtual stack
is usable
- if possible check the file size and update the virtual stack size accordingly
(either once on import, or upon trying to access an image beyond the end of the
backing file). If not desireable in all situations, add as a sub-option to "Use
Virtual Stack" in the raw import dialog.
- make the error dialog non modal to make this error less disruptive for the
workflow; or use only the log error, or display some text inside the virtual
image stack window (on the ImageCanvas) in lieu of a non-existing slice
(something like "Could not read slice number ###").

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.14-1-amd64
  java.version => 1.8.0_05
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_05-b13
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.5-b02
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /usr/lib/jvm/jdk-8-oracle-x64/jre
  imagej.dir => /home/adrian/bin/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140712000647)
Fiji: http://fiji.sc/update/ (last check:20140715020940)
Fijiplugins-AD: http://sites.imagej.net/Daerr/ (last check:20130606182917)

Files not up-to-date:
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  79a563c1 (LOCAL_ONLY) 20130424131314 plugins/vieux plugins
Maison/Remove_horizontal_Zebra.class
  5b6d5e01 (LOCAL_ONLY) 20130424131314 plugins/vieux plugins
Maison/Zap_Endpoints.class
  3d1d7d50 (LOCAL_ONLY) 20140508174402 scripts/Smooth_mask.py

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