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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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Load FLIM dataset error, crashes halfway through loading using 4.11.1 #232

Closed natandrews closed 8 years ago

natandrews commented 8 years ago

Subscripted assignment dimension mismatch.

Error in flim_data_series/load_flim_cube (line 330)

Error in flim_data_series/load_selected_files (line 91)

Error in flim_data_series/load_multiple (line 126)

Error in flim_data_series/load_data_series (line 150)

Error in flim_data_series_controller/load_data_series (line 105)

Error in front_end_menu_controller/menu_file_load_widefield_callback (line 661)

Error in front_end_menu_controller>@(varargin)obj.menu_file_load_widefield_callback(varargin{:})

Error in escaped_callback (line 7)

Error in front_end_menu_controller>@(x,y)escaped_callback(x,y,fcn) (line 257)

imunro commented 8 years ago

Hi is it possible one image is a different size in any dimension? There should be checks but maybe something slipped through. If not can you point me at the data please?

natandrews commented 8 years ago

It could be possible… It does always stop in the same place but other than going through all the folders manually I’m not sure how to find out? The data is here: /Volumes/fogim_datastore/User data/Natalie Andrews/May/renamed data for flimfit

From: imunro notifications@github.com<mailto:notifications@github.com> Reply-To: imperial-photonics/FLIMfit reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, 19 May 2016 at 16:19 To: imperial-photonics/FLIMfit FLIMfit@noreply.github.com<mailto:FLIMfit@noreply.github.com> Cc: "Andrews, Natalie J" natalie.andrews11@imperial.ac.uk<mailto:natalie.andrews11@imperial.ac.uk>, Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [imperial-photonics/FLIMfit] Load FLIM dataset error, crashes halfway through loading using 4.11.1 (#232)

Hi is it possible one image is a different size in any dimension? There should be checks but maybe something slipped through. If not can you point me at the data please?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/imperial-photonics/FLIMfit/issues/232#issuecomment-220357651

imunro commented 8 years ago

Thanks I'll try and have a look tomorrow.

imunro commented 8 years ago

Hi Natalie I'm trying to load subsets of your data to see if I can pin down the problem. I had no problems loading Fish2 but after loading I did get the following:

Error using circshift Invalid shift type: must be a real finite integer vector.

I don't suppose you have any idea what might be causing that?

Error in flim_data_series/compute_tr_data (line 92) t_inc_perp = circshift(t_inc,[1 -coarse_shift]);

Error in flim_data_series/init_dataset (line 127) obj.compute_tr_data();

imunro commented 8 years ago

It turns out that the above error is generated when you load any of your data -( I can get it loading a single image via File-> Load Data) and that it's because there are no delays associated (they are all NaNs). This suggests that your file names do not adhere to the convention for tiff-stack data. I suggest renaming so that the names match a known-working data set. e.g INT_002300 T_01000.tif

imunro commented 8 years ago

I've had a quick look and it looks as if the "T_"bit might be critical and that the last 6 chars should contain the delay.

imunro commented 8 years ago

I've added some code to make it fail a bit more elegantly when it can't recognise filenames. Commit cb4ba5a should be in the next release.

natandrews commented 8 years ago

Sorry I missed all of this, I was imaging all day! I’ll try this but if it applies to all of my data will it still have problems?

From: imunro notifications@github.com<mailto:notifications@github.com> Reply-To: imperial-photonics/FLIMfit reply@reply.github.com<mailto:reply@reply.github.com> Date: Friday, 20 May 2016 at 16:27 To: imperial-photonics/FLIMfit FLIMfit@noreply.github.com<mailto:FLIMfit@noreply.github.com> Cc: "Andrews, Natalie J" natalie.andrews11@imperial.ac.uk<mailto:natalie.andrews11@imperial.ac.uk>, Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [imperial-photonics/FLIMfit] Load FLIM dataset error, crashes halfway through loading using 4.11.1 (#232)

I've added some code to make it fail a bit more elegantly when it can't recognise filenames. Commit cb4ba5a

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/imperial-photonics/FLIMfit/issues/232#issuecomment-220637353

imunro commented 8 years ago

Hi Nat

The extra bit of code that I added won't kick in until the next release so 4.11.1 will still crash I'm afraid. I'm afraid that I didn't quite follow "if it applies to all of my data will it still have problems?"?