import sa_library.datareader as datareader import sa_library.parameters as parameters import setup_A_matrix if (len(sys.argv) != 3): print("usage <dax> <xml>") exit() dax_file = datareader.DaxReader(sys.argv[1]) params = parameters.Parameters(sys.argv[2]) a_mat_file = params.a_matrix print("Using A matrix file:", a_mat_file) a_mat = setup_A_matrix.loadAMatrix(a_mat_file) image = dax_file.loadAFrame(30) htia = HomotopyIA(a_mat, params.epsilon, image.shape) hres_image = htia.analyzeImage(image) [cs_x, cs_y, cs_a, cs_i] = htia.getPeaks(hres_image) print("Number peaks:", cs_x.size) htia.printProfilingData() # # See the accompanying license.txt file. # # Copyright (c) 2013 Zhuang Lab, Harvard University #
import homotopy_c import sa_library.datareader as datareader import sa_library.daxwriter as daxwriter import setup_A_matrix # Setup. src_directory = os.path.dirname(__file__) if (len(sys.argv) != 3): print("usage: homotopy_vs_fista <input_dax_file> <a_matrix>") exit() in_dax_file = datareader.DaxReader(sys.argv[1]) a_mat = setup_A_matrix.loadAMatrix(sys.argv[2]) x_start = 20 y_start = 20 aoi_size = 7 keep_size = 5 scale = 8 blocks = 3 low_res = numpy.zeros((blocks * keep_size, blocks * keep_size)) ht_hres = numpy.zeros((blocks * keep_size * scale, blocks * keep_size * scale)) fista_hres = numpy.zeros((ht_hres.shape)) # Initialize solvers print("Initializing solvers")
# # FIXME: # # This should also start at the same frame as hres in the event of a restart. # i3_file = writeinsight3.I3Writer(sys.argv[4]) params = parameters.Parameters(sys.argv[2]) # # Load the a matrix and setup the homotopy image analysis class. # a_mat_file = params.a_matrix print "Using A matrix file:", a_mat_file a_mat = setup_A_matrix.loadAMatrix(a_mat_file) image = dax_file.loadAFrame(0) htia = homotopy_imagea_c.HomotopyIA(a_mat, params.epsilon, image.shape) # # This opens the file. If it already exists, then it sets the file pointer # to the end of the file & returns the number of the last frame analyzed. # curf = htia.openHRDataFile(sys.argv[3]) # # Figure out which frame to start & stop at. #
import sa_library.datareader as datareader import sa_library.daxwriter as daxwriter import setup_A_matrix # Setup. src_directory = os.path.dirname(__file__) if len(sys.argv) != 3: print("usage: homotopy_vs_fista <input_dax_file> <a_matrix>") exit() in_dax_file = datareader.DaxReader(sys.argv[1]) a_mat = setup_A_matrix.loadAMatrix(sys.argv[2]) x_start = 20 y_start = 20 aoi_size = 7 keep_size = 5 scale = 8 blocks = 3 low_res = numpy.zeros((blocks * keep_size, blocks * keep_size)) ht_hres = numpy.zeros((blocks * keep_size * scale, blocks * keep_size * scale)) fista_hres = numpy.zeros((ht_hres.shape)) # Initialize solvers