item removed. solved.
Comments and questions about movie processing with Unblur and Summovie.
item removed. solved.
I'm running 32 unblur movie alignments on a single machine (128 vCPUs on AWS instance x1.32xlarge) and I keep running into errors that pop up randomly related to the temporary files written out by unblur.
An example of the error message:
2017-10-10 15:28:51: Fatal error (UsefulFunctions::FileCopy): File exists but cannot be opened: .UnBlur_S6XFugQHyDU7jmnv ; file not found, unit 20, file /data/.UnBlur_S6XFugQHyDU7jmnv
I use FoilHole_18051246_Data_18043800_18043801_20170519_0130_Fractions.mrc as a input file. which have 39 frames. The result show there is a very big shift between each frame. I am not sure if I did wrong or the data is too poor?
Input stack filename [my_movie.mrc] : ./FoilHole_18051246_Data_18043800_18043801_20170519_0130_Fractions.mrc
Number of frames per movie  :
Output aligned sum file [my_aligned_sum.mrc] :
Output shifts file [my_shifts.txt] :
Pixel size of images (A)  :
I am now trying unblur_openmp_7_17_15.exe and sum_movie_openmp_7_17_15.exe for motion correction. After process my image movie stack (test_movie.mrc as input),I can get four sum images:
#1:sum image without dose-filter from unblur: test_movie_ubl_sum.mrc
#2:sum image with dose-filter from unblur: test_movie_ubl_DF.mrc
#3:dose-filter image from sum_movie: test_movie_ubl_sum_DF.mrc
#4:restore-noise-power image from sum_movie after dose-filter: test_movie_ubl_sum_RNP.mrc
Hi, we are trying to re-compile unblur from source in order to get the drift_filter option mentioned by Alexis some time ago in the ccpem forum. However, we run into error message (attached the full log file). We tried to use both F77=ifort F77=gfortran compilers but without success. Could you please let me know if a specific compiler is required or there something else that is not working properly?
Many thanks in advance,
module load gsl/1.16
I've used unblur for whole frame alignment, and I'd like to try polishing in relion (but I only generated the aligned sums initially, not aligned stacks).
I still have the shifts files, so I'd like to use them with sum_movie to generate aligned stacks, to speed up the process and ensure that the overall alignment is identical (which I am not 100% sure is guaranteed if I run unblur again to do so).
We are collecting some test data on new samples at home on our TF20 with
a CMOS 4K camera, and I wondered if there is software available that will
do dose correction on single micrographs, as opposed to movie frames in a
stack file? For smaller particles, it is useful to collect images with
about 30-35 e/A2, for better contrast and alignment, but can I dose correct
We recently ran into trouble with long input/output path names, so I made a quick test to reproduce the problem.
I used Unblur 1.0.2 on CentOS releaser 6.5 (Final)
When I use an input file name of >= 178 characters and an output file name of >= 201 characters it fails,
but with an input file name of <= 177 characters and an output file name of <= 200 characters it works quite nice.
I attached the last working and the first failing log file of the test.
I wonder if there is a length limitiation for the filenames in unblur and
I was wondering if there is any further reading for the expert options that are used during full-frame motion correction . I would like to understand the definitions
of these options as I am new to using Unblur
I'm using unblur (by itself, not with summovie) to output aligned averages. I have encountered a dataset that seems particularly problematic where a lot of the stacks seem like they get a couple of misaligned frames (example attached), but when I check the shifts file, all the shifts seem reasonable... Is this artifact not due to frame misalignment?
# Unblur shifts file for input stack : /tmp/unblurumn099wn/input.mrc
# Shifts below are given in Angstroms
# Number of micrographs: 1
# Number of frames per movie: 20
# Pixel size (A): .6650