Big TIFF problem

Engineering
22

Do you have git installed? Are you behind a proxy? What is your OS?

23

I do have git installed, and use it to store software on github. I am using Windows 7, and no proxy as far as I know.

24

Can you try:

git clone https://github.com/scifio/scifio-imageio.git delete_me_scifio

just to check if it is a cmake problem or git…

25

When I try the clone from the command line I get this:
D:>git clone https://github.com/scifio/scifio-imageio.git
Cloning into ‘scifio-imageio’…
fatal: unable to access ‘https://github.com/scifio/scifio-imageio.git/’: error:1
407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version

26

With delete_me_scifio I get the same error.

27

Umm reading from here. It seems that might be worthy try to reinstall git for windows, get the latest version.

28

I’ll do that.

29

That fixed it. I’m now rebuilding ITK.

30

I was able to add the SCIFIO code to my program and build it.
But running it gives an odd result. An error popup “Java Virtual Machine Launcher” appears with:
Could not find the main class: loci.scifio.itk.SCIFIOITKBridge. Program will exit.

By the way without the SCIFIO code the program behaved just as before, finding only one slice.

31

That seems like a java problem. Do you have it installed system wide?
Can you type java -version in the console?

Or maybe JAVA_HOME is unset.

32

@Gib There have been many fixes to the SCIFIO module in recent ITK. It is best to try ITK 4.13 or ITK 5.

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33

I can see java system-wide:
java version “1.8.0_151”
Java™ SE Runtime Environment (build 1.8.0_151-b12)
Java HotSpot™ 64-Bit Server VM (build 25.151-b12, mixed mode)

but java_home is not set. I will explore setting that,

But the problem may be solved at the other end. The person who creates these tiffs with ImageJ has just informed me that he has found a way to export them with BioFormats that generates big tiffs readable by my program.

Thanks for all the help, Pablo.

1 Like
34

@Gib Sorry for the late reply. You can install Cygwin, which enables usage of many *nix-based tools on Windows. I recommend using Chocolatey to install packages on Windows. Alternately, you could try the Windows Subsystem for Linux on a Windows 10 system.

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