def setUpClass(cls): ds = DataSet.getDataSet('pyseg') cls.ds = ds cls.preSegStar = join(ds.getPath(), 'preseg.star') setupTestProject(cls) cls.ds = DataSet.getDataSet('pyseg') cls.preSegStar = join(cls.ds.getPath(), 'preseg.star')
def setUpClass(cls): cls.dataset = DataSet.getDataSet('xmipp_tutorial') cls.moviewset = DataSet.getDataSet('jmbFalconMovies') cls.mic1 = cls.dataset.getFile('mic1') cls.particlesStk = os.path.join(cls.dataset.getPath(), 'particles', 'BPV_1386.stk') cls.movieFn = cls.moviewset.getFile("movie1")
def setUpClass(cls): setupTestProject(cls) cls.dsXmipp = DataSet.getDataSet('xmipp_tutorial') cls.dsGrigorieff = DataSet.getDataSet('grigorieff') # First, import a set of micrographs that will be used # from all ctf test cases cls.protImport = cls.newProtocol(ProtImportMicrographs, filesPath=cls.dsXmipp.getFile('allMics'), samplingRate=1.237, voltage=300) cls.launchProtocol(cls.protImport)
def setUpClass(cls): """Prepare the data that we will use later on.""" print "\n", greenStr(" Set Up - Collect data ".center(75, '-')) setupTestProject(cls) # defined in BaseTest, creates cls.proj cls.dataset_xmipp = DataSet.getDataSet('xmipp_tutorial') cls.dataset_mda = DataSet.getDataSet('mda') cls.dataset_ribo = DataSet.getDataSet('ribo_movies') # # Imports # new = cls.proj.newProtocol # short notation launch = cls.proj.launchProtocol # Micrographs print magentaStr("\n==> Importing data - micrographs") p_imp_micros = new(ProtImportMicrographs, filesPath=cls.dataset_xmipp.getFile('allMics'), samplingRate=1.237, voltage=300) launch(p_imp_micros, wait=True) cls.micros = p_imp_micros.outputMicrographs # Volumes print magentaStr("\n==> Importing data - volumes") p_imp_volumes = new(ProtImportVolumes, filesPath=cls.dataset_xmipp.getFile('volumes'), samplingRate=9.896) launch(p_imp_volumes, wait=True) cls.vols = p_imp_volumes.outputVolumes # Movies print magentaStr("\n==> Importing data - movies") p_imp_movies = new(ProtImportMovies, filesPath=cls.dataset_ribo.getFile('movies'), samplingRate=2.37, magnification=59000, voltage=300, sphericalAberration=2.0) launch(p_imp_movies, wait=True) cls.movies = p_imp_movies.outputMovies # Particles print magentaStr("\n==> Importing data - particles") p_imp_particles = new(ProtImportParticles, filesPath=cls.dataset_mda.getFile('particles'), samplingRate=3.5) launch(p_imp_particles, wait=True) cls.particles = p_imp_particles.outputParticles
def _runTomoSubtomogramInitialModelWithVolume(self): protTomoExtraction = self._runPreviousProtocols() particles = protTomoExtraction.outputSetOfSubtomogram self.dataset = DataSet.getDataSet('eman') self.vol = self.dataset.getFile('volume') self.protImportVol = self.runImportVolumes(self.vol, 3.5) self.assertIsNotNone(self.protImportVol.outputVolume, "There was a problem with SetOfSubtomogram output") protInitialModel = self.newProtocol(EmanProtTomoInitialModel, particles=particles, reference=self.protImportVol.outputVolume, symmetry="c1", gaussFilter=-1.5, filterto=0.03, fourier=False, batchSize=20, learningRate=1, numberOfIterations=2, numberOfBatches=1, shrink=4, applySim=False) self.launchProtocol(protInitialModel) self.assertIsNotNone(protInitialModel.averageSubTomogram, "There was a problem with subTomograms output") self.assertIsNotNone(protInitialModel.outputParticles, "There was a problem with particles output") return protInitialModel
def _runTomoSubtomogramRefinementWithVolume(self, niter=2, mass=500.0, threads=1, pkeep=1, goldstandard=-1, goldcontinue=False, sym="c1", localfilter=False, maxtilt=90.0): protTomoExtraction = self._runPreviousProtocols() particles = protTomoExtraction.outputSetOfSubtomogram self.dataset = DataSet.getDataSet('eman') self.vol = self.dataset.getFile('volume') self.protImportVol = self.runImportVolumes(self.vol, 3.5) self.assertIsNotNone(self.protImportVol.outputVolume, "There was a problem with SetOfSubtomogram output") protTomoRefinement = self.newProtocol(EmanProtTomoRefinement, inputSetOfSubTomogram=particles, inputRef=self.protImportVol.outputVolume, niter=niter, mass=mass, threads=threads, pkeep=pkeep, goldstandard=goldstandard, goldcontinue=goldcontinue, sym=sym, localfilter=localfilter, maxtilt=maxtilt) self.launchProtocol(protTomoRefinement) self.assertIsNotNone(protTomoRefinement.averageSubTomogram, "There was a problem with subTomograms output") self.assertIsNotNone(protTomoRefinement.outputParticles, "There was a problem with particles output") return protTomoRefinement
def setUpClass(cls): setupTestProject(cls) cls.ds = DataSet.getDataSet('movies') cls.importThread = threading.Thread(target=cls._createInputLinks) cls.importThread.start() # Wait until the first link is created time.sleep(5)
def setUpClass(cls): setupTestProject(cls) cls.dsRct = DataSet.getDataSet('rct') cls.micsFn = cls.dsRct.getFile('positions/input_micrographs.xmd') cls.patternU1 = cls.dsRct.getFile('positions/F_rct_u_*.pos') cls.patternT1 = cls.dsRct.getFile('positions/F_rct_t_*.pos') cls.micsUFn1 = cls.dsRct.getFile('untilted') cls.micsTFn1 = cls.dsRct.getFile('tilted') cls.dsEman = DataSet.getDataSet('eman') cls.micsUFn2 = cls.dsEman.getFile('micU') cls.micsTFn2 = cls.dsEman.getFile('micT') cls.patternU2 = cls.dsEman.getFile( "coords/ip3r10252011-0005_0-2_info.json") cls.patternT2 = cls.dsEman.getFile( "coords/ip3r10252011-0005_10_info.json")
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('relion_tutorial') cls.partFn = cls.dataset.getFile( 'import/refine3d_case2/relion_data.star') cls.protImport = cls.runImportParticlesStar(cls.partFn, 50000, 3.54) cls.protPreprocess = cls.runPreprocess(cls.protImport.outputParticles)
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('relion_tutorial') cls.particlesFn = cls.dataset.getFile('import/case2/particles.sqlite') print(magentaStr("\n==> Importing data - particles:")) cls.protImport = cls.runImportParticlesSqlite(cls.particlesFn, sampling=3.5)
def setUpClass(cls): """Prepare the data that we will use later on.""" setupTestProject(cls) # defined in BaseTest, creates cls.proj cls.jjsoftDataTest = DataSet.getDataSet('tomo-em') cls.getFile = cls.jjsoftDataTest.getFile('etomo') cls.setOfTs = cls._runImportTiltSeries() cls.setOfXcorrTs = cls._runXcorrPrealignment() cls.setOfFiducials, cls.setOfFiducialTs = cls._runFiducialModel()
def setData(cls, projectData='tomo-em'): from tomo.tests import DataSet cls.dataset = DataSet.getDataSet(projectData) cls.tomogram = cls.dataset.getFile('tomo1') cls.coords3D = cls.dataset.getFile('overview_wbp.txt') cls.coords3D_Large = cls.dataset.getFile('overview_wbp_large.txt') cls.inputSetOfSubTomogram = cls.dataset.getFile('subtomo') cls.smallTomogram = cls.dataset.getFile('coremask_normcorona.mrc')
def setUpClass(cls): setupTestProject(cls) cls.ds = DataSet.getDataSet('relion_tutorial') cls.importThread = threading.Thread(name="createInputLinksR", target=cls._createInputLinks) cls.importThread.start() # Wait until the first link is created time.sleep(5)
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('groel') cls.averages = cls.dataset.getFile('averages') cls.symmetry = 'd7' cls.numberOfIterations = 20 cls.numberOfModels = 2 print(magentaStr("\n==> Importing data - class averages:")) cls.protImportAvg = cls.runImportAverages(cls.averages, 2.1)
def setUpClass(cls): setupTestProject(cls) cls.ds = DataSet.getDataSet('relion_tutorial') cls.ds2 = DataSet.getDataSet('mda') cls.micsFn = cls.ds.getFile('micrographs/*mrc') cls.avgsFn = cls.ds2.getFile('averages/averages.stk') print(magentaStr("\n==> Importing data - micrographs:")) cls.protImportMics = cls.newProtocol(ProtImportMicrographs, filesPath=cls.micsFn, samplingRate=7.08) cls.launchProtocol(cls.protImportMics) print(magentaStr("\n==> Importing data - averages:")) cls.protImportAvgs = cls.newProtocol(ProtImportAverages, filesPath=cls.avgsFn, samplingRate=5.04, checkStack=True) cls.launchProtocol(cls.protImportAvgs)
def setUpClass(cls): setupTestProject(cls) # Data cls.dataset = DataSet.getDataSet('10010') cls.initialVolume = cls.dataset.getFile('initialVolume') cls.particles = cls.dataset.getFile('particles') cls.protImportVol = cls.runImportVolume(cls.initialVolume, 4.95) cls.protImportParts = cls.runImportParticles()
def setData(cls): cls.dataset = DataSet(name='test_zernike3d', folder='test_zernike3d', files={ 'particles': 'particles/images_1720_norm.xmd', 'volumes': 'volumes/*.vol', '1720': 'volumes/EMD-1720_norm.vol', '1723': 'volumes/EMD-1723_norm.vol' }) cls.dataset = DataSet.getDataSet('test_zernike3d') cls.particles = cls.dataset.getFile('particles') cls.volumes = cls.dataset.getFile('volumes') cls.volume_1720 = cls.dataset.getFile('1720') cls.volume_1723 = cls.dataset.getFile('1723') cls.clnm_pd_cpu_gold = cls.dataset.getFile( 'gold_standard_pd/CPU/Volumes_clnm.txt') cls.clnm_pd_gpu_gold = cls.dataset.getFile( 'gold_standard_pd/GPU/Volumes_clnm.txt')
def setUpClass(cls): setupTestProject(cls) cls.ds = DataSet.getDataSet('relion_tutorial') pathFns = 'import/refine3d/extra' cls.volFn = cls.ds.getFile(os.path.join(pathFns, 'relion_class001.mrc')) cls.half1Fn = cls.ds.getFile( os.path.join(pathFns, 'relion_it025_half1_class001.mrc')) cls.half2Fn = cls.ds.getFile( os.path.join(pathFns, 'relion_it025_half2_class001.mrc'))
def setUpClass(cls): setupTestProject(cls) cls.dsRelion = DataSet.getDataSet('relion_tutorial') cls.protImport1 = cls.newProtocol(ProtImportVolumes, filesPath=cls.dsRelion.getFile('volumes/reference_rotated_masked.vol'), samplingRate=1.0) cls.launchProtocol(cls.protImport1) cls.protImport2 = cls.newProtocol(ProtImportVolumes, filesPath=cls.dsRelion.getFile('volumes/reference_masked.vol'), samplingRate=1.0) cls.launchProtocol(cls.protImport2)
def setUpClass(cls): setupTestProject(cls) cls.dsRelion = DataSet.getDataSet('relion_tutorial') cls.protImport1 = cls.newProtocol(ProtImportVolumes, filesPath=cls.dsRelion.getFile('volumes/reference_rotated.vol'), samplingRate=1.0) cls.launchProtocol(cls.protImport1) cls.protImport2 = cls.newProtocol(ProtImportVolumes, filesPath=cls.dsRelion.getFile('volumes/reference.mrc'), samplingRate=1.0) cls.launchProtocol(cls.protImport2)
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('eman') cls.vol = cls.dataset.getFile('volume') cls.micsUFn = cls.dataset.getFile('micU') cls.micsTFn = cls.dataset.getFile('micT') cls.patternU = cls.dataset.getFile( "coords/ip3r10252011-0005_0-2_info.json") cls.patternT = cls.dataset.getFile( "coords/ip3r10252011-0005_10_info.json") cls.protImportVol = cls.runImportVolumes(cls.vol, 3.6)
def setUpClass(cls): setupTestProject(cls) cls.inputDataSet = DataSet.getDataSet('tutorialDataImodCTF') cls.inputSoTS = cls.inputDataSet.getFile('tsCtf1') print(magentaStr("\n==> Importing data - tilt series:")) cls.protImportTS = cls.runImportTiltSeries( filesPath=os.path.dirname(cls.inputSoTS), filesPattern="WTI042413_1series4.mdoc", voltage=300, sphericalAberration=2.7, amplitudeContrast=0.07, anglesFrom=2)
def setUpClass(cls): setupTestProject(cls) cls.ds = DataSet.getDataSet('relion_tutorial') inputStar = cls.ds.getFile('import/classify3d/extra/' 'relion_it015_data.star') cls.protImport = cls.newProtocol( ProtImportParticles, objLabel='particles from relion (auto-refine 3d)', importFrom=ProtImportParticles.IMPORT_FROM_RELION, starFile=inputStar, magnification=10000, samplingRate=7.08, haveDataBeenPhaseFlipped=True) cls.launchProtocol(cls.protImport)
def setUpClass(cls): setupTestProject(cls) cls.dataSet = DataSet.getDataSet('xmipp_tutorial') # # Imports # print magentaStr("\n==> Importing data - Input data") new = cls.proj.newProtocol # short notation launch = cls.proj.launchProtocol # Volumes print magentaStr("\nImporting Volumes:") pImpVolume = new(ProtImportVolumes, samplingRate=1, filesPath=cls.dataSet.getFile('vol2')) launch(pImpVolume, wait=True) # volume.vol cls.inputVol = pImpVolume.outputVolume pImpVolume2 = new(ProtImportVolumes, samplingRate=1, filesPath=cls.dataSet.getFile('vol1')) launch(pImpVolume2, wait=True) cls.inputVol2 = pImpVolume2.outputVolume # References print magentaStr("\nImporting References:") pImpRef = new(ProtImportVolumes, samplingRate=1, filesPath=cls.dataSet.getFile('vol3')) launch(pImpRef, wait=True) # reference.vol cls.inputRef = pImpRef.outputVolume pImpRef2 = new(ProtImportVolumes, samplingRate=1, filesPath=cls.dataSet.getFile('vol1')) launch(pImpRef2, wait=True) cls.inputRef2 = pImpRef2.outputVolume # Masks print magentaStr("\nImporting Mask:") pImpMask = new(ProtImportMask, maskPath=cls.dataSet.getFile('mask3d'), samplingRate=1) launch(pImpMask, wait=True) cls.mask = pImpMask.outputMask
def _runTomoTempMatch(self): protImportTomogramBig = self.newProtocol(tomo.protocols.ProtImportTomograms, filesPath=self.tomogram, samplingRate=5) protImportTomogramSmall = self.newProtocol(tomo.protocols.ProtImportTomograms, filesPath=self.smallTomogram, samplingRate=5) self.launchProtocol(protImportTomogramBig) self.launchProtocol(protImportTomogramSmall) self.assertSetSize(protImportTomogramBig.outputTomograms, size=1, msg="There was a problem with tomogram output") self.assertSetSize(protImportTomogramSmall.outputTomograms, size=1, msg="There was a problem with tomogram " "output") self.dataset = DataSet.getDataSet('eman') self.vol = self.dataset.getFile('volume') self.protImportVol = self.runImportVolumes(self.vol, 3.5) self.assertIsNotNone(self.protImportVol.outputVolume, "There was a problem with SetOfSubtomogram output") protTomoTempMatchBig = self.newProtocol(EmanProtTomoTempMatch, inputSet=protImportTomogramBig.outputTomograms, ref=self.protImportVol.outputVolume, boxSize=128, sym="c1") protTomoTempMatchSmall = self.newProtocol(EmanProtTomoTempMatch, inputSet=protImportTomogramSmall.outputTomograms, ref=self.protImportVol.outputVolume, boxSize=128, sym="d1") self.launchProtocol(protTomoTempMatchBig) self.launchProtocol(protTomoTempMatchSmall) return protTomoTempMatchBig, protTomoTempMatchSmall
def setUpClass(cls): setupTestOutput(cls) cls.ds = DataSet.getDataSet('xmipp_tutorial') cls.dsEmx = DataSet.getDataSet('emx')
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('ribo_movies') cls.movies = cls.dataset.getFile('movies') cls.crdsDir = cls.dataset.getFile('posAllDir')
def setData(cls, dataProject='resmap'): cls.dataset = DataSet.getDataSet(dataProject) cls.map3D = cls.dataset.getFile('betagal') cls.setVols = cls.dataset.getFile('*.mrc') cls.dsParticles = DataSet.getDataSet('xmipp_tutorial')
def setUpClass(cls): setupTestProject(cls) cls.dsXmipp = DataSet.getDataSet("xmipp_tutorial") cls.dsEmx = DataSet.getDataSet("emx") cls.dsMda = DataSet.getDataSet("mda") cls.dsRelion = DataSet.getDataSet("relion_tutorial")
def setData(cls, dataProject='resmap'): cls.dataset = DataSet.getDataSet(dataProject) cls.map3D = cls.dataset.getFile('betagal') cls.half1 = cls.dataset.getFile('betagal_half1') cls.half2 = cls.dataset.getFile('betagal_half2') cls.mask = cls.dataset.getFile('betagal_mask')
def setUpClass(cls): setupTestOutput(cls) cls.ds = DataSet.getDataSet('relion31_tutorial_precalculated')
def setUpClass(cls): setupTestProject(cls) cls.dsXmipp = DataSet.getDataSet('xmipp_tutorial') #cls.dsRelion = DataSet.getDataSet('relion_tutorial') cls.dsGroel = DataSet.getDataSet('groel')
def setUpClass(cls): setupTestProject(cls) cls.dsXmipp = DataSet.getDataSet('xmipp_tutorial') cls.dsEmx = DataSet.getDataSet('emx') cls.dsMda = DataSet.getDataSet('mda') cls.dsRelion = DataSet.getDataSet('relion_tutorial')
def setUpClass(cls): # Create a new project setupTestProject(cls) cls.dataset = DataSet.getDataSet('mda') cls.particlesFn = cls.dataset.getFile('particles/xmipp_particles.xmd')
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('xmipp_tutorial') cls.crdsDir = cls.dataset.getFile('boxingDir') cls.micsFn = cls.dataset.getFile('allMics') cls.vol1 = cls.dataset.getFile('vol1')
def setUpClass(cls): setupTestProject(cls) cls.dsXmipp = DataSet.getDataSet('xmipp_tutorial') cls.dsGrigorieff = DataSet.getDataSet('grigorieff')
def setUpClass(cls): setupTestOutput(cls) cls.dataset = DataSet.getDataSet('relion_tutorial') cls.getFile = cls.dataset.getFile cls.ds = DataSet.getDataSet('relion_tutorial')
def setUpClass(cls): setupTestProject(cls) cls.ds = DataSet.getDataSet('relion_tutorial')
def setUpClass(cls): setupTestOutput(cls) cls.dataset = DataSet.getDataSet('emx')
def setUpClass(cls): # Create a new project setupTestProject(cls) cls.dataset = DataSet.getDataSet('mda') cls.particlesFn = cls.dataset.getFile('particles')
def setUpClass(cls): setupTestOutput(cls) cls.ds = DataSet.getDataSet('relion_tutorial')
def setUpClass(cls): setupTestProject(cls) cls.dsMovies = DataSet.getDataSet('movies')
def setUpClass(cls): # Create a new project setupTestProject(cls) cls.ds = DataSet.getDataSet("nma")
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('groel') cls.averages = cls.dataset.getFile('averages')
def setUpClass(cls): setupTestProject(cls) cls.dsRelion = DataSet.getDataSet("relion_tutorial") # Import only once for all tests cls.protImport = cls.runImportFromScipion()