def test_ctf2(self):
"""
This test requires:
Download a file with one parametric CTF in EMX exchange format.
Download a file with two test images in CCP4 format (these images are zero valued except in a single pixel). Their sampling rate is 2A/px
Convert them to your package format.
Apply the CTF to the corresponding image.
Create a 2D CCP4 stack file with the two images resulting from applying the CTF to the test image
The sampling of the resulting stack should be the same 2 Angstrom/pixel
Upload the stack file.
Three galleries of images will be displayed: the gold standard, the one just uploaded and the differences between them. The test has been successful if the gold standard and the images updated are identical.
As extra check, the Web Site will make a pixel by pixel comparison between images belonging to both galleries. A green tick will appear if both images are identical and a red cross if any pair of pixels differ more than 10-2.
Note: both CTFs as well as the test image have different sampling rate . The sampling rate of the output image should be 2 A/px.
"""
#download data
self.url = "CTF/Test2/"
deltaPArticle = self.downloadFile("data.mrc")
emxFn = self.downloadFile("ctf2.emx")
deltaParticleCTF = self.downloadFile("ctf.mrcs")
#import ctf
protEmxImport = self.newProtocol(
ProtImportParticles,
objLabel='from emx (ctfTest2)',
importFrom=ProtImportParticles.IMPORT_FROM_EMX,
emxFile=emxFn,
alignType=3, #none?
voltage=100,
magnification=10000,
samplingRate=2.)
self.launchProtocol(protEmxImport)
outputMics = getattr(protEmxImport, 'outputMicrographs', None)
outputCTFs = getattr(protEmxImport, 'outputCTF', None)
outputParts = getattr(protEmxImport, 'outputParticles', None)
self.assertIsNotNone(outputMics)
self.assertIsNotNone(outputCTFs)
self.assertIsNotNone(outputParts)
#split input particles
protSplit = self.newProtocol(
ProtSplitSet,
numberOfSets=2,
)
protSplit.inputSet.set(outputParts)
protSplit.randomize.set(False)
self.proj.launchProtocol(protSplit, wait=True)
outputParts01 = getattr(protSplit, 'outputParticles01', None)
outputParts02 = getattr(protSplit, 'outputParticles02', None)
#filter with CTF1
protFilter1 = self.newProtocol(XmippProtFilterParticles)
protFilter1.inputParticles.set(outputParts01)
#protFilter1.inputCTF.set(outputCTFs)
#protFilter1.inputCTF.setExtended(1)
protFilter1.filterSpace.set(0) #fourier space
protFilter1.filterModeFourier.set(3) #ctf
self.launchProtocol(protFilter1)
#filter with CTF2
protFilter2 = self.newProtocol(XmippProtFilterParticles)
protFilter2.inputParticles.set(outputParts02)
#protFilter2.inputCTF.set(outputCTFs)
#ssprotFilter2.inputCTF.setExtended(2)
protFilter2.filterSpace.set(0) #fourier space
protFilter2.filterModeFourier.set(3) #ctf
self.launchProtocol(protFilter2)
#create a single set of particles
protUnion = self.newProtocol(ProtUnionSet)
protUnion.inputSets.append(protFilter1.outputParticles)
protUnion.inputSets.append(protFilter2.outputParticles)
self.launchProtocol(protUnion)
#export as emx
protEmxExport = self.newProtocol(ProtEmxExport)
protEmxExport.inputSet.set(protUnion.outputSet)
self.launchProtocol(protEmxExport)
#TODO: upload result to emx web site. Now it is down
stackFn = os.path.join(protEmxExport._getPath('emxData'), "data.mrc")
self.assertTrue(ImageHandler().compareData(deltaParticleCTF,
stackFn,
tolerance=0.01))
def runVolumeConvertStep(self, reconstructedFilteredVolume, maskedFileName):
from pyworkflow.em.convert import ImageHandler
img = ImageHandler()
img.convert(reconstructedFilteredVolume, maskedFileName)
