[BUG] IMOD 4.10 download not available anymore and 4.9.12 and 4.11.24 give errors

[wlugmayr]

Describe the bug

You recommend imod 4.10.42 or earlier on your install instructions. imod 4.11.24 gives the error described in bug #18 and imod 4.9.12 gives an autofidseed error as described below.

Project JSON file

ribosome_empiar_10064_dynamo.json

Error message : Making coarse aligned stack (running prenewst.com) [brt2] Successfully finished prenewst.com in 00:07.2 [brt3]

Finding seed points for fiducial model (running autofidseed.com) [brt2] processchunks ERROR: autofidseed.com has given processing error 1 times - giving up ERROR: autofidseed -StandardInput: exited with status 1

ABORT SET: An error occurred running autofidseed.com :+1:

$ cat output/5_BatchRunTomo_1/tomogram_001/autofidseed.log

Entries to program autofidseed TrackCommandFile = track.com MinSpacing = 0.85 AdjustSizes = 1 PeakStorageFraction = 1.0 TwoSurfaces = 0 TargetNumberOfBeads = 20 End of entries

RUNNING IMODFINDBEADS on views 30, 31, and 32

Scaling down by 1.07 for Sobel filter; box size = 32, scaled size = 29

Analyzing group of sections starting with 29, ending with 31 Dips found in 3 groups based on bkg mean, means 161.86 to 165.37 Pass 1: 16382 peaks found. 13225 eliminated as too weak, 174 too close, 2983 remaining Histogram smoothed with H = 0.200 has dip at 0.307, peaks at 0.064 and 0.544 Histogram smoothed with H = 0.050 has lowest dip at 0.323 Threshold for averaging set to 0.378 Diameter of average bead at zero-crossing = 9.19 Adjusted parameters based on a new bead size of 9.19 Scaling down by 1.15 for Sobel filter; box size = 34, scaled size = 29 Adding another pass because size changed more than 5% Dips found in 4 groups based on bkg mean, means 155.84 to 165.24 Pass 2: 20917 peaks found. 15861 eliminated as too weak, 926 too close, 4130 remaining Histogram smoothed with H = 0.141 has dip at 0.494, peaks at 0.068 and 0.572 Histogram smoothed with H = 0.050 has lowest dip at 0.533 Threshold for averaging set to 0.543 Diameter of average bead at zero-crossing = 9.40 Adjusted parameters based on a new bead size of 9.40 Scaling down by 1.18 for Sobel filter; box size = 34, scaled size = 28 Dips found in 4 groups based on bkg mean, means 155.82 to 165.26 Pass 3: 20067 peaks found. 14911 eliminated as too weak, 999 too close, 4157 remaining Histogram smoothed with H = 0.141 has dip at 0.549, peaks at 0.069 and 0.567 Histogram smoothed with H = 0.050 has lowest dip at 0.550 11 peaks are above histogram dip at 0.550 11 total peaks being stored in model down to value of 0.553

REDOING IMODFINDBEADS with more views to try to get more points Traceback (most recent call last): File "/gpfs/cssb/software/centos7/x86_64/imod/4.9.12/bin/autofidseed", line 801, in seedViews = selectSeedViews(numSeedViews) File "/gpfs/cssb/software/centos7/x86_64/imod/4.9.12/bin/autofidseed", line 196, in selectSeedViews viewTry = fillFirstGap(seedViews, checkDir, midZ) File "/gpfs/cssb/software/centos7/x86_64/imod/4.9.12/bin/autofidseed", line 52, in fillFirstGap trackRange = rangeLo + rangeHi TypeError: unsupported operand type(s) for +: 'range' and 'range' ERROR: autofidseed -StandardInput: exited with status 1

To Reproduce Run the ribosome tutorial in MATLAB.

Additional context This step runs with imod 4.11.24 but it fails like on #18

[ArtsemiY]

@wlugmayr thanks for pointing to this! We will check the reason for this issue in the nearest time.

[ArtsemiY]

@wlugmayr I installed imod-4.9.12 and re-runned tutorial, but could not reproduce the issue. Please, let me know whether you have changed the path to the full one as in #18 and tried to reprocess from zero (since otherwise relative path which might cause the issue here as well could be saved in intermediate configuration files).

P.S. Please, let me know as well whether you are generally interested in resolving this issue after #18 was resolved or it might be withdrawn.

[wlugmayr]

After solving #18 this issue did not happen in recent stable imod 4.11.24. I think this issue can be closed.

[ArtsemiY]

Glad to hear! Thanks!