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flimfit / FLIMfit

State of the art fluorescence lifetime imaging analysis software
http://flimfit.org
GNU General Public License v2.0
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Cannot load .sdt files #352

Closed pjmattei closed 5 years ago

pjmattei commented 5 years ago

Hello,

I am trying to use FLIMfit 5.1.1, but when attempting to load my data, the below message appears. I believe my configuration (MacOS HighSierra, 64bits, Matlab R2016b, java 1.8.0_191(jdk and jre updated)) may be responsible, since the same error occurs with other FLIMfit versions.

Thank you,

PJ

Error using flim_data_series/load_flim_cube (line 214) Java exception occurred: java.lang.NegativeArraySizeException at loci.formats.in.SDTReader.openBytes(SDTReader.java:204) at loci.formats.ImageReader.openBytes(ImageReader.java:460) at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:227) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:159) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:141)

Error in flim_data_series/load_selected_files (line 124) Error in flim_data_series/load_multiple (line 116) Error in flim_data_series/load_single (line 104) Error in flim_data_series_controller/load_single (line 168) Error in front_end_menu_controller/menu_file_load_single_callback (line 656) Error in front_end_menu_controller>@(varargin)obj.menu_file_load_single_callback(varargin{:}) Error in EC (line 7) Error in front_end_menu_controller>@(x,y)EC(fcn) (line 263)

seanwarren commented 5 years ago

Hi, please could you send a copy of a file that isn't working for you to s.warren@garvan.org.au

imunro commented 5 years ago

Hi Sean. Does this mean that there are .sdt files that bio-formats can't handle ? If so I should let the bio-formats team know.

seanwarren commented 5 years ago

@imunro, I haven't recieved a file to test yet, if you are able to send a file over please do @pjmattei

seanwarren commented 5 years ago

@pjmattei, please could you test the following version which I believe resolves this issue: https://storage.googleapis.com/flimfit-downloads/latest/5.1.1-22-gc63e3ac9/FLIMfit_5.1.1-22-gc63e3ac9_MACI64.zip

Would you be ok with us sharing this file with the OMERO team so they can look into the issue with bioformats?

seanwarren commented 5 years ago

@imunro - I have replaced the bioformats sdt reader with an implementation in FlimReader. This resolves this issue (which I believe is related to the size of the image - 256x2048x2048) and some other issues I've been having with multichannel and single-point sdt files not loading correctly using the bioformats reader. I'm open to switching back to bioformats at some point but this has become a blocking issue for a project at the moment.

imunro commented 5 years ago

@seanwarren if you could send me any examples of files which have shown issues then I can report them. Thanks.

pjmattei commented 5 years ago

@seanwarren please feel free to share. There are still errors with this version :

Invalid MEX-file '/Users/pj/Library/Application Support/.mcrCache9.1/FLIMfi1/Libraries/FlimReader.mexmaci64': dlopen(/Users/pj/Library/Application Support/.mcrCache9.1/FLIMfi1/Libraries/FlimReader.mexmaci64, 6): Library not loaded: @rpath/libmkl_rt.dylib Referenced from: /Users/pj/Library/Application Support/.mcrCache9.1/FLIMfi1/Libraries/FlimReader.mexmaci64
Reason: image not found.

Error in flim_data_series/get_image_dimensions (line 206)
Error in flim_data_series/load_multiple (line 30)
Error in flim_data_series/load_single (line 104)

Error in flim_data_series_controller/load_single (line 168)
Error in front_end_menu_controller/menu_file_load_single_callback (line 656)
Error in front_end_menu_controller>@(varargin)obj.menu_file_load_single_callback(varargin{:})
Error in EC (line 7)
Error in front_end_menu_controller>@(x,y)EC(fcn) (line 263)

seanwarren commented 5 years ago

@pjmattei - apologies, I didn't have access to a mac to test last night. This version resolves that issue.

https://storage.googleapis.com/flimfit-downloads/latest/5.1.1-24-ge5f33002/FLIMfit_5.1.1-24-ge5f33002_MACI64.zip

Let me know how you get on, cheers Sean