K2 alignment timing test

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Name	K2 alignment timing test
Permalink	https://serialemscripts.nexperion.net/script/10
Category	Testing
Language	SerialEM Scripting
Description	This script measures time for aligning K2 frames. Its main purpose is to compare timing with and without a GPU, but the use of the GPU is optional. It tests all variations of counting versus superresolution, 8 or 14 frames, simple or more complex alignment, and saving frames or not. Results can be extracted from the log with: grep '^Mean\\|filter.*,'
Author	David Mastronarde

Version History

Version 1 (January 28, 2017; 718 download(s); SerialEM version ≥ 3.6)

Version 1

Download

Upload date	January 28, 2017
Download count	718
SerialEM version ≥	3.6

MacroName TimeK2
Require arrays

testGPU = 1          # Set to 1 to test with GPU
testSaving = 1     # Set to 1 to test with file saving using current parameters

# These two entries determine how many frames and how many different numbers of frames are tested
# If you do enough frames to trigger smoothing (15 by default), then you should turn off smoothing for a
# test that is not redundant with the the test with multiple filters.
frameTime = 0.2
exposures = {1.6 2.8}

# Binnings for counting and super-resolution mode alignment
faBinnings = {4 8}

# Filter radii for multiple-filter case
radii = { 0.06 0.08 0.1 }

# This saves your parameters for restoration at the end
# But you can use the names of these variables to know how to change these settings below 
# for the two tests or add your own test
ReportFrameAliParams saveBin saveKeep saveStrategy saveAVA saveRefine saveGroup
ReportFrameAli2 saveGPU saveTrunc saveHybrid saveRad1 saveRad2 saveRad3

OnStopCallFunc RestoreAliChanges

SuppressReports

numOuter = $testSaving + 1
Loop $numOuter outerInd
   ifSave = $outerInd - 1
   SetBinning R 1
   RestoreCameraSet R
   SetDoseFracParams R 1 $ifSave 1 1
   SetBinning R 1
   numTimes = 3
   if $ifSave == 0
      SetProcessing R 2
      numTimes = 4
   endif
   
   echo **********************************************
   echo Pairwise 8, one filter, no refine, saving $ifSave
   SetFrameAliParams 4 $saveKeep 0 8 0 0
   SetFrameAli2 0 0 0 $radii[1] 0. 0.
   CallFunction TimingLoop 4
   
   echo **********************************************
   echo All pairs, 3 filters, refine 5, saving $ifSave
   SetFrameAliParams 4 $saveKeep 0 8 0 0
   SetFrameAli2 0 0 0 $radii[1] $radii[2] $radii[3]
   CallFunction TimingLoop 4
EndLoop

# TimingLoop runs mode/exposure/GPU loops
#
Function TimingLoop 0 0 
   
   numTest = $testGPU + 1
   proc = { CPU GPU }
   modeText = { Counting Super-res }
   
   Loop $numTest indTest
      Loop 2 K2mode
         SetK2ReadMode R $K2mode
         SetFrameAliParams $faBinnings[$K2mode] $saveKeep
         Loop $#exposures indExp
            thisExp = $exposures[$indExp]
            SetFrameTime R $frameTime
            SetExposure R $thisExp
            numFrames = NEARINT ($thisExp / $frameTime)
            ifGPU = $indTest - 1
            SetFrameAli2 $ifGPU
            meanSum = 0
            Loop $numTimes indTime
               ResetClock
               R
               ReportClock thisTime
               if $indTime == 1
                  timeArr = $thisTime
                else
                  timeArr = { $timeArr $thisTime }
               endif
               #echo Time = $thisTime
               meanSum = ROUND ( $meanSum + ($thisTime / $numTimes)  2)
            EndLoop 
            echo Times: $timeArr
            echo Mean $modeText[$K2mode] mode, $numFrames frames, $proc[$indTest]  time = $meanSum
         EndLoop 
      EndLoop 
   EndLoop 
EndFunction

### RestoreAliChanges
###
Function RestoreAliChanges
   SetFrameAliParams $saveBin $saveKeep $saveStrategy $saveAVA $saveRefine $saveGroup
   SetFrameAli2 $saveGPU $saveTrunc $saveHybrid $saveRad1 $saveRad2 $saveRad3
EndFunction

License

This code can be shared and adapted under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License (https://creativecommons.org/licenses/by-nc-sa/4.0/)