Closed bill-connelly closed 6 years ago
This might have to do with the default master_file calling another make_db file, thus overwriting your initial call. We typically change the master_file to run the correct make_db, and make all our customizations in there.
I am also experiencing this issue, while debugging build_ops3.m
has the correct path to my .tif files but, it doesn't detect any tiff files in the directory.
Initially the issue was that the wrong make_db.m
file was being called but even after fixing that and confirming that db.expts and file path were correct it was still reporting "Could not find any tif"
@tvajtay I found that all those problems went away when I kept my file sizes below 4gigs. ImageJ does bad things when it saves files above that size. I don't know if this is your problem, but worth a try anyway.
@bill-connelly Ultimately the error was me not replacing one of the path strings in the master_file.m
.
So I was a bit of a dunce.
However after I fixed that it did crash again, but this time due to a memory overflow. I'm going to see if we can run it on a nicer machine or if we ultimately have to break apart the movies. Our movie sizes are about 2-3 GB but I think that's too much data for Matlab to load into memory.
We do use 2 GB tiffs routinely ourselves. If there is an issue, it's likely easily fixable, so please let me know,
@marius10p I was able to run Suite2p successfully using a small 19MB video. I tried running a tiff stack of 860MB and got the following error in Matlab.
>> master_file
running rigid registration
bi-directional scanning offset = 1 pixels
Error using fft
Out of memory. Type HELP MEMORY for your options.
Error in fft2 (line 24)
f = fft(fft(x,[],2),[],1);
Error in regoffKriging (line 92)
corrMap = fft2(bsxfun(@plus, maskOffset,
bsxfun(@times, maskMul, batchData)));
Error in GetRegOffsets (line 25)
[ds, Corr] = regoffKriging(dat, ops1{i,l}, 0);
Error in reg2P (line 214)
[dsall, ops1] = GetRegOffsets(data, k, j,
iplane0, ops, ops1);
Error in run_pipeline (line 57)
ops1 = reg2P(ops); % do registration
Error in master_file (line 89)
run_pipeline(db, ops0);
The tiff stack is 796x512 pixels and 1070 frames, 16 bit The machine has 8GB of RAM
*Edit- Closed down everything but Matlab and it looks like it is chugging along. It took about 20 minutes to do the rigid registration and bi-directional scanning. And then easily another 30-45 minutes to calculate the first ROI's at the lowest error. (471 ROI's) idk if this perhaps too many?
are you still having this issue? with the ROIs not converging?
Please reopen this issue if you are still having problems, thanks
My tiff is in the folder: G:\test\32645\2017-07-27\1 %i.e. G:\test\MouseName\Date\Exp
My make_db file is
i = 0; i = i+1; db(i).mouse_name = '32645'; db(i).date = '2017-07-27'; db(i).expts = [1]; db(i).diameter = 12;
The relevant parts of my master_file is:
% root paths for files and temporary storage (ideally an SSD drive. my SSD is C:/) ops0.RootStorage = 'G:/test/'; % Suite2P assumes a folder structure, check out README file ops0.temp_tiff = 'G:/temp/temp.tif'; % copies each remote tiff locally first, into this file ops0.RegFileRoot = 'G:/temp/'; % location for binary file ops0.DeleteBin = 1; % set to 1 for batch processing on a limited hard drive ops0.ResultsSavePath = 'G:/temp/F'; % a folder structure is created inside ops0.RegFileTiffLocation = 'G:/temp/'; % leave empty to NOT save registered tiffs (slow)
I then run:
And I get the error "could not find any tif or tiff"
What am I doing wrong?
Thanks