[OpenSPIM] Problems with Image Processing -> in my case seems linked to Switching to BigTIFF

[m.pawlowska at nencki.gov.pl]

Hi,

I noticed the following: when the TOTAL about of data (not a single 
stack, but the whole series) to be collected is large (>4 GB I think), a 
following line appears in the fiji console: "Switching to BigTIFF (by 
file size)" and then the files behave differently. For example, 
sometimes I have the behavious that Dylan described: the last displayed 
message in the Fiji status bar is "Import preparations complete", but no 
image ever appears. If the total amount of data is smaller, I have no 
problems opening files. So the BigTIFF behaviour is somehow different. 
But I thought BigTIFF should be only used if one file and not the whole 
series are >4GB...?

By the way, I also get now and then the 'Could not get 
charToByteConverterClass!', also coming from Fiji.

I realize that these are not really OpenSPIM problems, but I'm not sure 
where to look/how to understand it better.

Regards,
Monika


W dniu 2015-06-15 16:26, Windell, Dylan napisał(a):
> Hi Johannes,
> 
> Thank you for your email. I changed the settings to open the files
> without any prompts but it still seems to bring up all the different
> stacks every time I try to open a file or convert the file types. The
> files are actually converting now but they are taking >3 hours each
> and sometimes an error pops up telling me the file type incompatible
> and will not convert at all.
> 
> The macro only converts one at a time too, can it convert them all at
> once? Whenever I type in 'setBatchMode( true )' I get the attached
> error.
> 
> Furthermore, I also get this warning quite often: 'Could not get
> charToByteConverterClass!' Any idea what this is?
> 
> Thanks again,
> 
> Dylan
> 
> -----Original Message-----
> From: Johannes Schindelin [mailto:johannes.schindelin at gmx.de]
> Sent: 09 June 2015 14:02
> To: Windell, Dylan
> Cc: openspim at openspim.org
> Subject: Re: [OpenSPIM] Problems with Image Processing
> 
> Hi Dylan,
> 
> On 2015-06-09 14:45, Windell, Dylan wrote:
> 
>> I am very new to OpenSPIM and do not have previous experience with
>> regards to coding or ImageJ so I do apologise for all the basic
>> questions.
>> 
>> I have managed to take some practise stack image stacks at 6 angles
>> (300 images - ~2-4GB) but they do not open normally in Image J and the
>> program just says this:
>> 
>> Reading heading file header (Bio-Formats Import Options listing all
>> series), Cancelling thumbnail generation, Import preparations complete
>> - which is followed by nothing.
>> 
>> When I tried pre-processing the images using the macro I used the
>> following adaptions to the code as I only have 1 time-point:
>> 
>> for ( t = 1; t <= 1; t++ ) {
>>     for ( a = 0; a <= 5; a++ )
>> 
>> As I have Windows 7 64bit, I changed the directory to this:
>> open("E:\\SPIM_Images\\<file:///\\E:\SPIM_Images\>....spim_TL"
>> 
>> I also attached an exception message I received when trying to process
>> the files.
> 
> It appears as if the time lapse might have been interrupted (but this
> is just a wild guess).
> 
> You could try to open the files individually by using
> File>Import>Bio-Formats and then adjusting the setting so that it does
> *not* group the images.
> 
> Ciao,
> Johannes
> 
> _______________________________________________
> OpenSPIM mailing list
> OpenSPIM at openspim.org
> http://openspim.org/mailman/listinfo/openspim