def produceAlignedImagesStep(self, volumeIsCTFCorrected, fn, images): from numpy import array, dot fnOut = 'classes_aligned@' + fn MDin = MetaData(images) MDout = MetaData() n = 1 hasCTF = MDin.containsLabel(xmipp.MDL_CTF_MODEL) for i in MDin: fnImg = MDin.getValue(xmipp.MDL_IMAGE, i) fnImgRef = MDin.getValue(xmipp.MDL_IMAGE_REF, i) maxCC = MDin.getValue(xmipp.MDL_MAXCC, i) rot = MDin.getValue(xmipp.MDL_ANGLE_ROT, i) tilt = MDin.getValue(xmipp.MDL_ANGLE_TILT, i) psi = -1. * MDin.getValue(xmipp.MDL_ANGLE_PSI, i) flip = MDin.getValue(xmipp.MDL_FLIP, i) if flip: psi = -psi eulerMatrix = Euler_angles2matrix(0., 0., psi) x = MDin.getValue(xmipp.MDL_SHIFT_X, i) y = MDin.getValue(xmipp.MDL_SHIFT_Y, i) shift = array([x, y, 0]) shiftOut = dot(eulerMatrix, shift) [x, y, z] = shiftOut if flip: x = -x id = MDout.addObject() MDout.setValue(xmipp.MDL_IMAGE, fnImg, id) MDout.setValue(xmipp.MDL_IMAGE_REF, fnImgRef, id) MDout.setValue(xmipp.MDL_IMAGE1, "%05d@%s" % (n, self._getExtraPath("diff.stk")), id) if hasCTF: fnCTF = MDin.getValue(xmipp.MDL_CTF_MODEL, i) MDout.setValue(xmipp.MDL_CTF_MODEL, fnCTF, id) MDout.setValue(xmipp.MDL_MAXCC, maxCC, id) MDout.setValue(xmipp.MDL_ANGLE_ROT, rot, id) MDout.setValue(xmipp.MDL_ANGLE_TILT, tilt, id) MDout.setValue(xmipp.MDL_ANGLE_PSI, psi, id) MDout.setValue(xmipp.MDL_SHIFT_X, x, id) MDout.setValue(xmipp.MDL_SHIFT_Y, y, id) MDout.setValue(xmipp.MDL_FLIP, flip, id) MDout.setValue(xmipp.MDL_ENABLED, 1, id) n += 1 MDout.write(fnOut, xmipp.MD_APPEND) # Actually create the differences img = Image() imgRef = Image() if hasCTF and volumeIsCTFCorrected: Ts = MDin.getValue(xmipp.MDL_SAMPLINGRATE, MDin.firstObject()) for i in MDout: img.readApplyGeo(MDout, i) imgRef.read(MDout.getValue(xmipp.MDL_IMAGE_REF, i)) if hasCTF and volumeIsCTFCorrected: fnCTF = MDout.getValue(xmipp.MDL_CTF_MODEL, i) imgRef.applyCTF(fnCTF, Ts) img.convert2DataType(DT_DOUBLE) imgDiff = img - imgRef imgDiff.write(MDout.getValue(xmipp.MDL_IMAGE1, i))
def checkResult(self, testfiles, outDir, random): error = "" try: from xmipp import FileName, Image, compareTwoFiles, compareTwoMetadataFiles for file in testfiles: file = join(outDir, file) fileGoldStd = file.replace(self.fnDir, 'goldStandard') result = True if not exists(file): error += file + " was NOT produced\n" else: if (random): self.warning += file + " was created using a random seed, check skipped\n" self.warningFlag = True else: fnGoldStd = FileName(fileGoldStd) if fnGoldStd.isImage(): im1 = Image(fileGoldStd) im2 = Image(file) result = im1.equal(im2, 0.001) elif fnGoldStd.isMetaData(): result = compareTwoMetadataFiles(file, fileGoldStd) else: result = compareTwoFiles(file, fileGoldStd, 0) if not result: error += " file '%s' and '%s' are NOT identical\n" % ( file, fileGoldStd) except KeyboardInterrupt: raise except Exception, ex: error += " Error checking results: '%s'\n" % str(ex)