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): setupTestProject(cls) TestBase.setData() print(magentaStr("\n==> Importing data - micrographs:")) cls.protImport = cls.runImportMicrographBPV(cls.micFn) print(magentaStr("\n==> Running cistem - ctffind:")) cls.protCtfRun = cls.runCtffind(cls.protImport.outputMicrographs)
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('tomo-em') cls.tomogram = cls.dataset.getFile('tomo1') cls.coords3D = cls.dataset.getFile('overview_wbp.txt') cls.table = cls.dataset.getFile('initial.tbl') cls.path = cls.dataset.getPath()
def setUpClass(cls): # Prepare test project setupTestProject(cls) # Prepare the test data cls.setData() # Run needed protocols cls.runImportMicrograph()
def setUpClass(cls): pwtests.setupTestProject(cls) cls.dsXmipp = pwtests.DataSet.getDataSet('xmipp_tutorial') cls.dsRelion = pwtests.DataSet.getDataSet('relion_tutorial') cls.dsEmx = pwtests.DataSet.getDataSet('emx') cls.dsMda = pwtests.DataSet.getDataSet('mda') cls.dsModBuild = pwtests.DataSet.getDataSet('model_building_tutorial')
def setUpClass(cls): pwtests.setupTestProject(cls, writeLocalConfig=True) cls.dataPath = os.environ.get("SCIPION_ED_TESTDATA") if not os.path.exists(cls.dataPath): raise Exception("Can not run DIALS tests, missing file:\n %s" % cls.dataPath)
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): 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): setupTestProject(cls) TestMonoResBase.setData() cls.protImportVol = cls.runImportVolumes(cls.map3D, 3.54) cls.protImportHalf1 = cls.runImportVolumes(cls.half1, 3.54) cls.protImportHalf2 = cls.runImportVolumes(cls.half2, 3.54) cls.protCreateMask = cls.runCreateMask(cls.protImportVol.outputVolume, 0.02)
def setUpClass(cls): def generate(suffix="feat"): (fd, filename) = mkstemp(suffix=suffix) f = os.fdopen(fd, "w") fileContent = """# XMIPP_STAR_1 * # Type of feature (sph, blo, gau, Cyl, dcy, cub, ell, con)(Required) # The operation after adding the feature to the phantom (+/=) (Required) # The feature density (Required) # The feature center (Required) # The vector for special parameters of each vector (Required) # Sphere: [radius] Blob : [radius alpha m] Gaussian : [sigma] # Cylinder : [xradius yradius height rot tilt psi] # DCylinder : [radius height separation rot tilt psi] # Cube : [xdim ydim zdim rot tilt psi] # Ellipsoid : [xradius yradius zradius rot tilt psi] # Cone : [radius height rot tilt psi] data_block1 _dimensions3D '100 100 100' _phantomBGDensity 0. _scale 1. data_block2 loop_ _featureType _featureOperation _featureDensity _featureCenter _featureSpecificVector blo = 1 '0 0 0' '50 10.4 2' """ f.write(fileContent) f.close() return filename cls.inFileName = generate() pwtests.setupTestProject(cls)
def setUpClass(cls): pwtests.setupTestOutput(cls) # Set the application domain Config.setDomain("pyworkflowtests") pwtests.setupTestProject(cls)
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) TestResMapBase.setData() cls.protImportVol = cls.runImportVolumes(cls.map3D, 3.54) cls.protImportHalf1 = cls.runImportVolumes(cls.half1, 3.54) cls.protImportHalf2 = cls.runImportVolumes(cls.half2, 3.54) cls.protImportMask = cls.runImportMask(cls.mask, 3.54)
def setUpClass(cls): pwtest.setupTestProject(cls) cls.setData() cls.protImportHalf1 = cls.runImportVolumes(cls.half1, 3.54, 'import half1') cls.protImportHalf2 = cls.runImportVolumes(cls.half2, 3.54, 'import half2')
def setUpClass(cls): setupTestProject(cls) TestEmanBase.setData('mda') print(magentaStr("\n==> Importing data - particles:")) cls.protImport = cls.runImportParticles(cls.particlesFn, 3.5) print(magentaStr("\n==> Importing data - volume:")) cls.protImportVol = cls.runImportVolumes(cls.vol, 3.5)
def setUpClass(cls): pwtests.setupTestProject(cls) cls.dataset = pwtests.DataSet.getDataSet('rct') cls.allCrdsDir = cls.dataset.getFile('positions') cls.micsUFn = cls.dataset.getFile('untilted') cls.micsTFn = cls.dataset.getFile('tilted') cls.classesSqlite = cls.dataset.getFile('classes')
def setUpClass(cls): setupTestProject(cls) cls.setData() print(magentaStr("\n==> Importing data - movies:")) cls.protImport1 = cls.runImportMovies( cls.ds.getFile('qbeta/qbeta.mrc'), magnification=50000) cls.protImport2 = cls.runImportMovies(cls.ds.getFile('cct/cct_1.em'), magnification=61000)
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 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): pwtests.setupTestProject(cls, writeLocalConfig=True) cls.dataPath = os.path.join(pwed.Config.SCIPION_ED_TESTDATA, '190503') if not os.path.exists(cls.dataPath): raise Exception("Can not run XDS tests, missing file:\n %s" % cls.dataPath)
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('tomo-em') cls.parentDir = cls.dataset.getFile('tsMParentFolder') cls.ts10Dir = cls.dataset.getFile('tsM10Dir') cls.ts31Dir = cls.dataset.getFile('tsM31Dir') cls.path = cls.dataset.getPath() cls.pattern = '*/stack*.mdoc' cls.sRate = 1.716
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): if SKIP_BASE_TESTS: cls.skipTest(cls, "Skipping base tests") pwtests.setupTestProject(cls, writeLocalConfig=True) cls.dataPath = pwed.Config.SCIPION_ED_TESTDATA if not os.path.exists(cls.dataPath): raise Exception( f"Can not run ED tests, missing file:\n {cls.dataPath}")
def setUpClass(cls): setupTestProject(cls) TestLocalDeblurBase.setData() cls.protImportVol = cls.runImportVolumes(cls.map3D, 3.54) cls.protCreateMask = cls.runCreateMask(cls.protImportVol.outputVolume, 0.02) cls.protImportVol2 = cls.runImportVolumes2('3488') cls.protCreateMask2 = cls.runCreateMask2( cls.protImportVol2.outputVolume, 0.167)
def setUpClass(cls): setupTestProject(cls) TestZernike3DBase.setData() cls.protImportPart = cls.runImportParticles(cls.particles) cls.protImportVols = cls.runImportVolumes(cls.volumes) cls.protImportVol_1720 = cls.runImportVolume(cls.volume_1720, '1720') cls.protImportVol_1723 = cls.runImportVolume(cls.volume_1723, '1723') cls.CORR_FILE = 'CoordinateMatrixCorr3.txt' cls.EXPECTED_CORR_MAP = 'Unexpected correlation structure mapping'
def setUpClass(cls): setupTestProject(cls) TestMultipleFSCsBase.setData() cls.protImportVol = cls.runImportVolumes(cls.map3D, 3.54, 'import vol') cls.protImportHalf1 = cls.runImportVolumes(cls.half1, 3.54, 'import half1') cls.protImportHalf2 = cls.runImportVolumes(cls.half2, 3.54, 'import half2') cls.protImportMask = cls.runImportMask(cls.mask, 3.54, 'import mask')
def setUpClass(cls): # Prepare test project setupTestProject(cls) # Prepare the test data cls.setData() # Execute the protocols required to generate the inputs for the janni protocol, which will be the preprocessed # images (downsampled) in the xmipp tutorial. Thus, the micrographs must be loaded and preprocessed before # executing the test cls.runImportMicrograph() cls.runMicPreprocessing()
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 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): pwtests.setupTestProject(cls) ds = pwtests.DataSet.getDataSet('tomosegmemtv') cls.ds = ds cls.samplingRate = 1 # Because only one tomogram is provided in the tutorial, 2 links will be created pointing to the same file, so # they can be interpreted as a set of two tomograms, making the test complexity closer to the real usage cls.virtualTomos = ['vTomo1', 'vTomo2'] virtualTomos = [join(ds.getPath(), fpath + '.mrc') for fpath in cls.virtualTomos] [symlink(ds.getFile('tomogram'), virtualTomo) for virtualTomo in virtualTomos if not exists(virtualTomo)]
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): 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): """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 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 setUpClass(cls): setupTestProject(cls) TestAddNoiseBase.setData() cls.protImportVol = cls.runImportVolumes(cls.map3D, 3.54) cls.protImportVols = cls.runImportVolumes(cls.setVols, 3.54) cls.protImportParts = cls.runImportParticles()
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('groel') cls.averages = cls.dataset.getFile('averages')
def setUpClass(cls): tests.setupTestProject(cls) cls.dataset = tests.DataSet.getDataSet('emx') cls.dsRelion = tests.DataSet.getDataSet('relion_tutorial')
def setUpClass(cls): # Create a new project setupTestProject(cls) cls.ds = DataSet.getDataSet("nma")
def setUpClass(cls): setupTestProject(cls)
def setUpClass(cls): tests.setupTestProject(cls) cls.dataset = tests.DataSet.getDataSet('emx')
def setUpClass(cls): # Create a new project tests.setupTestProject(cls) cls.ds = tests.DataSet.getDataSet('initial_volume')
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): tests.setupTestProject(cls) cls.baseUrl = "http://i2pc.cnb.csic.es/emx/resourcesEmx/Tests/"
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.dsXmipp = DataSet.getDataSet('xmipp_tutorial') #cls.dsRelion = DataSet.getDataSet('relion_tutorial') cls.dsGroel = DataSet.getDataSet('groel')
def setUpClass(cls): setupTestProject(cls) cls.dataset = DataSet.getDataSet('ribo_movies') cls.movies = cls.dataset.getFile('movies') cls.crdsDir = cls.dataset.getFile('posAllDir')
def setUpClass(cls): setupTestProject(cls) cls.dsXmipp = DataSet.getDataSet('xmipp_tutorial') cls.dsGrigorieff = DataSet.getDataSet('grigorieff')
def setUpClass(cls): tests.setupTestProject(cls) cls.dataset = tests.DataSet.getDataSet('CTFDiscrepancy')
def setUpClass(cls): setupTestProject(cls) cls.dsMovies = DataSet.getDataSet('movies')
def setUpClass(cls): setupTestProject(cls) cls.dsRelion = DataSet.getDataSet("relion_tutorial") # Import only once for all tests cls.protImport = cls.runImportFromScipion()
def setUpClass(cls): tests.setupTestProject(cls)
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.ds = DataSet.getDataSet('relion_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")