def addMoleculesWithXYZCat(self, x, y, z, cat): i3data = i3dtype.createDefaultI3Data(x.size) i3dtype.posSet(i3data, 'x', x) i3dtype.posSet(i3data, 'y', y) i3dtype.posSet(i3data, 'z', z) i3dtype.setI3Field(i3data, 'c', cat) self.addMolecules(i3data)
def addDAOSTORMMolecules(self, frame, xc, yc, br, be, msky, niter, sharp, chi, err): """ This is for localizations identified by the original DAOSTORM algorithm, not the 3D-DAOSTORM algorithm. DAOSTORM -> Insight3 format mapping. xc - xcenter yc - ycenter br - brightness -> peak height be - brightness error (?) -> peak area msky - background -> peak background niter - fit iterations sharp - sharpness (?) -> peak angle chi - fit quality -> peak width err - error flag -> link """ i3data = i3dtype.createDefaultI3Data(xc.size) i3dtype.posSet(i3data, 'x', xc) i3dtype.posSet(i3data, 'y', yc) i3dtype.setI3Field(i3data, 'h', br) i3dtype.setI3Field(i3data, 'a', be) i3dtype.setI3Field(i3data, 'bg', msky) i3dtype.setI3Field(i3data, 'fi', niter) i3dtype.setI3Field(i3data, 'phi', sharp) i3dtype.setI3Field(i3data, 'w', chi) i3dtype.setI3Field(i3data, 'lk', err) self.addMolecules(i3data)
def addDAOSTORMMolecules(self, frame, xc, yc, br, be, msky, niter, sharp, chi, err): # # DAOSTORM -> Insight3 format mapping. # # xc - xcenter # yc - ycenter # br - brightness -> peak height # be - brightness error (?) -> peak area # msky - background -> peak background # niter - fit iterations # sharp - sharpness (?) -> peak angle # chi - fit quality -> peak width # err - error flag -> link # i3data = i3dtype.createDefaultI3Data(xc.size) i3dtype.posSet(i3data, 'x', xc) i3dtype.posSet(i3data, 'y', yc) i3dtype.setI3Field(i3data, 'h', br) i3dtype.setI3Field(i3data, 'a', be) i3dtype.setI3Field(i3data, 'bg', msky) i3dtype.setI3Field(i3data, 'fi', niter) i3dtype.setI3Field(i3data, 'phi', sharp) i3dtype.setI3Field(i3data, 'w', chi) i3dtype.setI3Field(i3data, 'lk', err) self.addMolecules(i3data)
def addMoleculesWithXYAFrame(self, x, y, pa, frame): i3data = i3dtype.createDefaultI3Data(x.size) i3dtype.posSet(i3data, 'x', x) i3dtype.posSet(i3data, 'y', y) i3dtype.setI3Field(i3data, 'a', pa) i3dtype.setI3Field(i3data, 'fr', frame) self.addMolecules(i3data)
def addMoleculesWithXYCatF(self, x, y, cat,f): i3data = i3dtype.createDefaultI3Data(x.size) i3dtype.posSet(i3data, 'x', x) i3dtype.posSet(i3data, 'y', y) i3dtype.setI3Field(i3data, 'c', cat) i3dtype.setI3Field(i3data, 'fr', f) self.addMolecules(i3data)
def addMoleculesWithXYIWFrame(self, x, y, pi, width, frame): i3data = i3dtype.createDefaultI3Data(x.size) i3dtype.posSet(i3data, 'x', x) i3dtype.posSet(i3data, 'y', y) i3dtype.setI3Field(i3data, 'i', pi) i3dtype.setI3Field(i3data, 'w', width) i3dtype.setI3Field(i3data, 'fr', frame) self.addMolecules(i3data)
def addMoleculesWithXYZIFrame(self, x, y, z, pi, f): i3data = i3dtype.createDefaultI3Data(x.size) i3dtype.posSet(i3data, 'x', x) i3dtype.posSet(i3data, 'y', y) i3dtype.posSet(i3data, 'z', z) i3dtype.setI3Field(i3data, 'i', pi) i3dtype.setI3Field(i3data, 'fr', f) self.addMolecules(i3data)
def test_i3dtype_2(): """ Test creation and setting position with an array. """ i3_locs = i3dtype.createDefaultI3Data(10) i3dtype.posSet(i3_locs, 'x', numpy.arange(10)) for i in range(10): assert(abs(i3_locs["x"][i] - i) < 1.0e-6) assert(abs(i3_locs["xc"][i] - i) < 1.0e-6)
def test_i3dtype_3(): """ Test creation and setting with a scalar. """ i3_locs = i3dtype.createDefaultI3Data(10) i3dtype.posSet(i3_locs, 'x', 10.0) for i in range(10): assert(abs(i3_locs["x"][i] - 10.0) < 1.0e-6) assert(abs(i3_locs["xc"][i] - 10.0) < 1.0e-6)
def test_good_i3(): mlist_name = storm_analysis.getPathOutputTest("test_i3_io_mlist.bin") # Create data. locs = i3dtype.createDefaultI3Data(100) # Save the data. with writeinsight3.I3Writer(mlist_name) as i3w: i3w.addMolecules(locs) # Read the data. locs = readinsight3.loadI3File(mlist_name) assert(locs.shape[0] == 100)
def test_bad_i3(): mlist_name = storm_analysis.getPathOutputTest("test_i3_io_mlist.bin") # Create data. locs = i3dtype.createDefaultI3Data(100) # Save the data. i3w = writeinsight3.I3Writer(mlist_name) i3w.addMolecules(locs) i3w.fp.close() # Read the data. locs = readinsight3.loadI3File(mlist_name) assert(locs is None)
def test_write_read_1(): """ Test writing and reading. """ bin_name = storm_analysis.getPathOutputTest("test_insight3io.bin") i3_locs = i3dtype.createDefaultI3Data(10) i3dtype.posSet(i3_locs, 'x', 10.0) with writeinsight3.I3Writer(bin_name) as i3: i3.addMolecules(i3_locs) i3_in = readinsight3.loadI3File(bin_name, verbose = False) assert(numpy.allclose(i3_locs['x'], i3_in['x']))
def test_write_read_3(): """ Test I3Reader on an empty file. """ bin_name = storm_analysis.getPathOutputTest("test_insight3io.bin") i3_locs = i3dtype.createDefaultI3Data(10) i3dtype.posSet(i3_locs, 'x', 10.0) with writeinsight3.I3Writer(bin_name) as i3: pass i3_reader = readinsight3.I3Reader(bin_name) # Read localizations. i3_in = i3_reader.nextBlock() assert(i3_in is False)
def test_good_i3_metadata(): mlist_name = storm_analysis.getPathOutputTest("test_i3_io_mlist.bin") # Create data. locs = i3dtype.createDefaultI3Data(100) # Save data and metadata. i3w = writeinsight3.I3Writer(mlist_name) i3w.addMolecules(locs) etree = ElementTree.Element("xml") test = ElementTree.SubElement(etree, "test") test.text = "test" i3w.closeWithMetadata(ElementTree.tostring(etree, 'ISO-8859-1')) # Read the data. locs = readinsight3.loadI3File(mlist_name) assert(locs.shape[0] == 100) # Read the metadata. metadata = readinsight3.loadI3Metadata(mlist_name) assert(metadata.find("test").text == "test")
def test_write_read_2(): """ Test I3Reader. """ bin_name = storm_analysis.getPathOutputTest("test_insight3io.bin") i3_locs = i3dtype.createDefaultI3Data(10) i3dtype.posSet(i3_locs, 'x', 10.0) with writeinsight3.I3Writer(bin_name) as i3: i3.addMolecules(i3_locs) i3_reader = readinsight3.I3Reader(bin_name) # Read localizations. i3_in = i3_reader.nextBlock() assert(numpy.allclose(i3_locs['x'], i3_in['x'])) assert(i3_in is not False) # This should return False because there are no more localizations. i3_in = i3_reader.nextBlock() assert(i3_in is False)
def test_i3dtype_1(): """ Test conversion to and from the fitter format. """ x_size = 100 y_size = 100 frame = 10 nm_per_pixel = 100.0 data_in = i3dtype.createDefaultI3Data(10) i3dtype.posSet(data_in, 'x', numpy.arange(10)) i3dtype.posSet(data_in, 'y', numpy.arange(10) + 30.0) i3dtype.posSet(data_in, 'z', numpy.arange(10) + 60.0) i3dtype.setI3Field(data_in, 'fr', frame) peaks = i3dtype.convertToMultiFit(data_in, frame, nm_per_pixel) data_out = i3dtype.createFromMultiFit(peaks, frame, nm_per_pixel) fields = ['x', 'ax', 'w'] for i in range(10): for field in fields: assert(abs(data_in[field][i] - data_out[field][i]) < 1.0e-6)
random.seed(0) nx = args.nx ny = args.ny spacing = args.spacing z_range = args.zrange if (nx * ny > 1): curz = -z_range z_inc = 2.0 * z_range / (nx * ny - 1) else: curz = 0.0 z_inc = 0.0 i3data = i3dtype.createDefaultI3Data(nx * ny) curx = spacing for i in range(nx): cury = spacing for j in range(ny): k = i * ny + j i3data['x'][k] = curx + random.random() - 0.5 i3data['y'][k] = cury + random.random() - 0.5 i3data['z'][k] = curz i3data['xc'][k] = i3data['x'][k] i3data['yc'][k] = i3data['y'][k] i3data['zc'][k] = i3data['z'][k] # Record emitter id in the 'i' field.
def addMoleculesWithXY(self, x, y): i3data = i3dtype.createDefaultI3Data(x.size) i3dtype.posSet(i3data, 'x', x) i3dtype.posSet(i3data, 'y', y) self.addMolecules(i3data)
def addMoleculesWithXYFrame(self, x, y, frame): i3data = i3dtype.createDefaultI3Data(x.size) i3dtype.posSet(i3data, 'x', x) i3dtype.posSet(i3data, 'y', y) i3dtype.setI3Field(i3data, 'fr', frame) self.addMolecules(i3data)
def addMoleculesWithXYI(self, x, y, pi): i3data = i3dtype.createDefaultI3Data(x.size) i3dtype.posSet(i3data, 'x', x) i3dtype.posSet(i3data, 'y', y) i3dtype.setI3Field(i3data, 'i', pi) self.addMolecules(i3data)
def addMoleculesWithXYZ(self, x, y, z): i3data = i3dtype.createDefaultI3Data(x.size) i3dtype.posSet(i3data, 'x', x) i3dtype.posSet(i3data, 'y', y) i3dtype.posSet(i3data, 'z', z) self.addMolecules(i3data)
def addMoleculesWithXYI(self, x, y, pi): i3data = i3dtype.createDefaultI3Data(x.size) i3dtype.posSet(i3data, 'x', x) i3dtype.posSet(i3data, 'y', y) i3dtype.setI3Field(i3data, 'i', pi) self.addMolecules(i3data)
random.seed(0) nx = args.nx ny = args.ny spacing = args.spacing z_range = args.zrange if (nx*ny > 1): curz = -z_range z_inc = 2.0 * z_range/(nx*ny - 1) else: curz = 0.0 z_inc = 0.0 i3data = i3dtype.createDefaultI3Data(nx * ny) curx = spacing for i in range(nx): cury = spacing for j in range(ny): k = i*ny+j i3data['x'][k] = curx + random.random() - 0.5 i3data['y'][k] = cury + random.random() - 0.5 i3data['z'][k] = curz i3data['xc'][k] = i3data['x'][k] i3data['yc'][k] = i3data['y'][k] i3data['zc'][k] = i3data['z'][k] # Record emitter id in the 'i' field.
help="Stopping value for z position, default is 500nm.") args = parser.parse_args() # Create line segments. lines = [] for i in range(args.nlines): lines.append( Line(x_pos=random.uniform(0.0, args.sx), y_pos=random.uniform(0.0, args.sy), z_pos=random.uniform(args.z_start, args.z_stop), angle=random.uniform(args.start_a, args.stop_a), length=random.uniform(args.minl, args.maxl))) # Generate emitter locations. i3data = i3dtype.createDefaultI3Data(args.nemitters) i = 0 printed = False while (i < args.nemitters): if ((i % 1000) == 0): if not printed: print("Adding point", i) printed = True else: printed = False # Get a random line. line = random.choice(lines) # Get a random point on the line.
# Save the image. dax_data.addFrame(image) # Save the molecule locations. a_vals = PSF.PSFIntegral(z_vals, h_vals) ax = numpy.ones(num_objects) ww = 2.0 * 160.0 * numpy.ones(num_objects) if (PSF.psf_type == "astigmatic"): sx_vals = objects[:,3] sy_vals = objects[:,4] ax = sy_vals/sx_vals ww = 2.0*160.0*numpy.sqrt(sx_vals*sy_vals) mols = i3dtype.createDefaultI3Data(num_objects) i3dtype.posSet(mols, 'x', x_vals + 1.0) i3dtype.posSet(mols, 'y', y_vals + 1.0) i3dtype.posSet(mols, 'z', z_vals) i3dtype.setI3Field(mols, 'a', a_vals) i3dtype.setI3Field(mols, 'h', h_vals) i3dtype.setI3Field(mols, 'w', ww) i3dtype.setI3Field(mols, 'ax', ax) i3dtype.setI3Field(mols, 'fr', i+1) i3_data.addMolecules(mols) dax_data.close() i3_data.close() #
import storm_analysis.sa_library.writeinsight3 as writeinsight3 parser = argparse.ArgumentParser(description = 'Generate test data for Micrometry') parser.add_argument('--total', dest='total', type=int, required=True, help = "The total number of localizations.") parser.add_argument('--match', dest='match', type=float, required=True, help = "The fraction of localizations that match.") args = parser.parse_args() im_size = 512 # Create matching points. total_match = int(args.total * args.match) m_data = i3dtype.createDefaultI3Data(total_match) i3dtype.posSet(m_data, "x", numpy.random.uniform(high = im_size, size = total_match)) i3dtype.posSet(m_data, "y", numpy.random.uniform(high = im_size, size = total_match)) # Create noise 1. total_noise = args.total - total_match n1_data = i3dtype.createDefaultI3Data(total_noise) i3dtype.posSet(n1_data, "x", numpy.random.uniform(high = im_size, size = total_noise)) i3dtype.posSet(n1_data, "y", numpy.random.uniform(high = im_size, size = total_noise)) # Create noise 2. n2_data = i3dtype.createDefaultI3Data(total_noise) i3dtype.posSet(n2_data, "x", numpy.random.uniform(high = im_size, size = total_noise))
zp = None for clc in cl_centers: if xp is None: xp = numpy.random.normal(scale=args.dev, size=args.nlocs) + clc[0] yp = numpy.random.normal(scale=args.dev, size=args.nlocs) + clc[1] # Z is in nm, we'll assume a 100nm pixel size. zp = numpy.random.normal(scale=args.dev * 100.0, size=args.nlocs) + clc[2] else: xp = numpy.append( xp, numpy.random.normal(scale=args.dev, size=args.nlocs) + clc[0]) yp = numpy.append( yp, numpy.random.normal(scale=args.dev, size=args.nlocs) + clc[1]) zp = numpy.append( zp, numpy.random.normal(scale=args.dev * 100.0, size=args.nlocs) + clc[2]) # Create a molecule list structure & save it. i3data = i3dtype.createDefaultI3Data(args.ncl * args.nlocs) i3dtype.posSet(i3data, "x", xp) i3dtype.posSet(i3data, "y", yp) i3dtype.posSet(i3data, "z", zp) with writeinsight3.I3Writer(args.i3bin) as i3w: i3w.addMolecules(i3data)