Getting error 'fl:filesystem:SystemError' when trying to read a file

Question

Gregory Vigil 2018-10-24

0
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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/425915-getting-error-fl-filesystem-systemerror-when-trying-to-read-a-file

Hi, I'm trying to read in data and separate it into discrete files using matlab running on linux. I've done this before when I've written code for every data set, but I was hoping I could get it so that I could write one piece of code that would iterate through all my files. However, it fails with the above error at the fifth line (data = h5read...) and i'm not sure why. I'm attaching my code and a picture of my file structure since I think the issue is coming from there, I just don't know why. I appreciate any help anyone might offer.

clear, clc
for j = 4:16
    batch_path = strcat('2018-07-05-video-', num2str(j, '%02d'), '/2018-07-05-video-', num2str(j, '%02d'), '-hdf5/');
    batch_filename = strcat('2018-07-05-video-', num2str(j, '%02d'), '/2018-07-05-video-', num2str(j, '%02d'), '-hdf5/2018-07-05-video-', num2str(j, '%02d'), '-batch.h5');
    disp('test1');
    data = h5read(batch_filename, '/data');
    disp('test2');
      mask = ones(1920,1080);
      mask(780:1150, 70:1080) = 1;
      mask = uint8(mask);
      one = uint8(1);
      % scale in pixels/millimeter as determined by fiji
      scale = 1808/144.6;
      bounds_all = [0; 1920/scale; 0; 1080/scale];
      deltaTime = .00104;
      for i = 1:1:size(data,3)
          filename = strcat(batch_path, '2018-07-05-video-', num2str(j, '%02d'), '-frame-', num2str(i,'%03d'), '.h5');
          % The next block creates and empty hdf5 file and initialized empty datasets
          % required by ACCIV. Four datasets are required: /data, /mask, /bounds, and
          % /time. /data is a 2-dimensional array with columns and rows equal to the
          % resolution of the image to be imported. The data for /data is required to
          % be a double datatype for ACCIV to read it. /mask is the same as /data,
          % except it needs to be entered as a uint8 and possibly with a chunksize
          % equal to the dimensions (unknown what was causing the error, I just made
          % every aspect match the Galileo source file). The /mask matrix has two
          % values, 0 where the data should be ignored and 1 where the data needs to
          % be analyzed. It's currently set to read everything, I need to explore how
          % to set the mask correctly. Finally, /time is the timestamp of the frame.
          % I set the first image to a time of 0 and increment it by 104.167
          % microseconds. So the ith image would have a time of 104.167*i
          % microseconds. The time datatype must be a uint8 to work.
          h5create(filename, '/data', [1920 1080]);
          h5create(filename, '/mask', [1920 1080], 'Datatype', 'uint8', 'ChunkSize', [1920 1080], 'FillValue', one);
          h5create(filename, '/bounds', 4);
          h5create(filename, '/time', 1);
          h5disp(filename);
          % The last block writes data into the empty datasets created in the
          % previous block. /data is the data created in imagej casted to a double
          % type, mask and bounds are extracted from datasets i created in hdfview,
          % and time is a uint8 that represents the total time since the first image
          % (i.e. for us it will be 0, 104.167, 208.333, ..., 104.167*i, ...)
          % recorded in microseconds.
          h5write(filename, '/data', double(data(:,:,i)));
          h5write(filename, '/mask', mask);
          h5write(filename, '/bounds', bounds_all);
          h5write(filename, '/time', (i-1)*deltaTime);
      end
  end