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Updating Motioncor2 package in Scipion

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Jose Miguel de la Rosa Trevin edited this page May 8, 2018 · 2 revisions

Updating Motioncor2

Recently (2018-05-07) there was announced a new version of the Motioncor2 program in ccpem list. One of the most important updates was speed-up: 5 to 6 times faster! So we wanted to update the protocol in Scipion as soon as possible to integrated it for the v1.2.1 upcoming release. Following are some notes about the update of the binaries, that I hope will be useful in the future to someone (probably myself).

Updating the binary

  • Download the binary from: here
  • Create the folder to put the binaries in Scipion: mkdir -p ~/scipion/software/em/motioncor2-1.1.0/bin
  • Copy the zipped file: cp ~/Download/MotionCor2-1.1.0.zip ~/scipion/software/em/motioncor2-1.1.0/bin/
  • Unzip the file:
cd ~/scipion/software/em/motioncor2-1.1.0/bin/
unzip MotionCor2-1.1.0.zip

Then you should have the following files (or equivalent, depending on the version of Motioncor2):

drwxr-xr-x 2 josem ipausers    4096 May  8 11:07 ./
drwxr-xr-x 3 josem ipausers    4096 May  8 10:46 ../
-rw-r--r-- 1 josem ipausers 2331768 May  3 10:19 MotionCor2_1.1.0-Cuda80
-rw-r--r-- 1 josem ipausers 2361120 May  3 10:19 MotionCor2_1.1.0-Cuda90
-rw-r--r-- 1 josem ipausers 2557720 May  3 10:19 MotionCor2_1.1.0-Cuda91
-rw-r--r-- 1 josem ipausers 1814037 May  8 11:07 MotionCor2-1.1.0.zip
-rw-r--r-- 1 josem ipausers   97865 May  3 12:29 MotionCor2-UserManual-05-03-2018.pdf

Then we can remove the zip and the pdf manual (probably you will have it in another place) and given execution permission to the binaries.

rm MotionCor2-1.1.0.zip 
rm MotionCor2-UserManual-05-03-2018.pdf
chmod u+x MotionCor2_1.1.0-Cuda*

Updating the user config file

Now the next step is to edit your config file to point to the new Motioncor2 binaries

Use your favorite text editor to change your configuration file at: ~/.config/scipion/scipion.conf The following variables should be updated with the new version and binary depending also in your CUDA version:

MOTIONCOR2_BIN = MotionCor2_1.1.0-Cuda80
MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.1.0

Passing the tests

After the previous steps, the new Motioncor2 should be in use, so we can proceed to pass the test to check if the protocol still works as expected:

./scipion test --grep motioncor2 --show
./scipion test tests.em.protocols.test_protocols_motioncor2.TestMotioncor2AlignMovies

Updating the protocol

This has been the easiest protocol to update ever: just adding the new options in to the Advanced parameters:

+    Since version *1.1.0*:
+        -GpuMemUsage 0.5      Specify how much GPU memory is used to buffer movie frames.
+                              It is recommended when running side by side processes in
+                              the same card. By default is 50% (i. e 0.5)
+        -InFmMotion 1         Takes into account of motion-induced blurring of
+                              each frame. It has shown resolution improvement
+                              in some test cases. By default this option is off.
+        -Bft 500 150          Since version 1.1.0 this option can take two arguments.
+                              First one is used in global-motion measurement and the
+                              second one is for local-motion. (default 500 150).

Well, still some testing will need to be done...but first things first.

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