Import movies for eer: "RuntimeError: unable to open tiff file"

Import and Export
1

Hi everyone,

I’m running CryoSPARC v4.1.2 to import eer movies, and after ~2h of work (not all movies processed) get an error:

Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 96, in cryosparc_compute.run.main
  File "/opt/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 1080, in run_import_movies_or_micrographs
    mov_raw = eer.read_eer(abs_path, num_fractions, upsampfactor=1)
  File "/opt/cryosparc/cryosparc_master/cryosparc_compute/blobio/eer.py", line 86, in read_eer
    eer = open_eer(fname)
  File "/opt/cryosparc/cryosparc_master/cryosparc_compute/blobio/eer.py", line 15, in open_eer
    return eerdecompressor.ElectronCountedFramesDecompressor(str(fname))
RuntimeError: unable to open tiff file

when I run the same job for a smaller subset of files, it works just fine. So I assume there’s a problem with one of the eer files, fut I have no idea which one :slight_smile:

Is there a way to detect damaged file externally, or (better) have them stored under “Failed movies” in the future?

2

Hi,

I wonder if the corruption would be evident in the tiff header?

If so, given an examplar output from IMOD’s header:

$ header FoilHole_14869372_Data_14822102_14822104_20230316_032125_EER.eer
 RO image file on unit   1 : FoilHole_14869372_Data_14822102_14822104_20230316_032125_EER.eer     Size=     582827 K

                    This is a TIFF file.

 Number of columns, rows, sections .....   16384   16384    1148
 Map mode ..............................    0   (byte)
 Start cols, rows, sects, grid x,y,z ...    0     0     0   16384  16384   1148
 Pixel spacing (Angstroms)..............   1.000      1.000      1.000
 Cell angles ...........................   90.000   90.000   90.000
 Fast, medium, slow axes ...............    X    Y    Z
 Origin on x,y,z .......................    0.000       0.000       0.000
 Minimum density .......................   0.0000
 Maximum density .......................   1.0000
 Mean density ..........................  0.14068E-02
 tilt angles (original,current) ........   0.0   0.0   0.0   0.0   0.0   0.0
 Space group,# extra bytes,idtype,lens .        0        0        0        0

…one could iterate as such:

for file in *.eer; do header ${file} | grep -e eer -e Number; done

…and scan for anomalies either in file size or number of frames (or if the command returns an error), for instance.

Cheers,
Yang