def main(): # analyse command line arguments file_name, interactive = lib_args.get_args() pixels = None pixels, header = lib_fits.read_first_image(file_name) background, dispersion, mx, hist_sum = lib_background.compute_background( pixels, interactive) test_gaussian = lib_background.modelling_function( np.arange(-10.0, 10.0, 1.0), 1.0, 1.0, 1.0).sum() print('RESULT: test_gaussian = {:3f}'.format(test_gaussian)) signature_hist = 'RESULT: histogram = {:5d}'.format(hist_sum) print(signature_hist) print('RESULT: background = {:d}'.format(int(background))) print('RESULT: dispersion = {:d}'.format(int(dispersion))) # graphic output if interactive: # ... pass # end return 0
def main(): file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) background, dispersion, _ = lib_background.compute_background(pixels) # search for clusters time0 = time.time() clustering = ParallelClustering() clusters = clustering(pixels, background, dispersion) time1 = time.time() max_cluster = clusters[0] # console output print( 'number of clusters: {:2d}, greatest integral: {:7d}, x: {:4.1f}, y: {:4.1f}' .format(len(clusters), max_cluster.integral, max_cluster.column, max_cluster.row)) print('clustering execution time: {:.3f} seconds'.format(time1 - time0)) # graphic output if interactive: _, axis = plt.subplots() axis.imshow(lib_cluster.add_crosses(pixels, clusters)) plt.show() return 0
def main(): file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) background, dispersion, max_x = lib_background.compute_background(pixels) # console output print('background: {:d}, dispersion: {:d}'.format(int(background),int(dispersion))) # graphic output if interactive: fig, axis = plt.subplots() imgplot = axis.imshow(pixels) ax_thresh = plt.axes([0.25, 0.92, 0.65, 0.03]) s_thresh = widgets.Slider(ax_thresh, 'Threshold', 0.0, max_x, valinit=background) update_slider = UpdateSlider(pixels,imgplot,fig) s_thresh.on_changed(update_slider) update_slider(background) plt.show() return 0
def main(): file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) background, dispersion, max_x = lib_background.compute_background(pixels) clustering = lib_cluster.Clustering() clusters = clustering(pixels, background, dispersion) # console output if not interactive: print('{} clusters'.format(len(clusters))) else: # graphic output fig, axis = plt.subplots() imgplot = axis.imshow(pixels) axcolor = 'lightgoldenrodyellow' ax_thresh = plt.axes([0.25, 0.92, 0.65, 0.03], axisbg=axcolor) threshold = 6.0 slider = widgets.Slider(ax_thresh, 'Threshold', 0.0, 5*threshold, valinit=threshold) update_slider = UpdateSlider(pixels, background, dispersion, imgplot, fig) slider.on_changed(update_slider) update_slider(threshold) plt.show() return 0
def main(): file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) background, dispersion, _ = lib_background.compute_background(pixels) clustering = lib_cluster.Clustering() clusters = clustering(pixels, background, dispersion) max_cluster = clusters[0] # coordinates ra dec wcs = lib_wcs.get_wcs(header) for i, c in enumerate(clusters): show_cluster(wcs, i, c) # graphic output if interactive: import matplotlib.pyplot as plt import lib_graphics fig, axis = plt.subplots() axis.imshow(pixels, interpolation='none') fig.canvas.mpl_connect('motion_notify_event', lib_graphics.ShowClusterProperties(fig,clusters,ShowCelestialObjects(wcs))) plt.show() return 0
def main(): # analyse command line arguments file_name, interactive = lib_args.get_args() pixels = None pixels, header = lib_fits.read_first_image(file_name) signature_fmt_1 = 'RESULT: cd1_1 = {:.10f}'.format(header["CD1_1"]) signature_fmt_2 = 'RESULT: cd1_2 = {:.10f}'.format(header["CD1_2"]) signature_fmt_3 = 'RESULT: cd2_1 = {:.10f}'.format(header["CD2_1"]) signature_fmt_4 = 'RESULT: cd2_2 = {:.10f}'.format(header["CD2_2"]) print(signature_fmt_1) print(signature_fmt_2) print(signature_fmt_3) print(signature_fmt_4) if interactive: fig, main_axes = plt.subplots() main_axes.imshow(pixels) plt.show() return 0
def main(): file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) background, dispersion, _ = lib_background.compute_background(pixels) # search for clusters clustering = RecursiveClustering() clusters = clustering(pixels, background, dispersion) max_cluster = clusters[0] wcs = lib_wcs.get_wcs(header) pxy = lib_wcs.PixelXY(max_cluster.column, max_cluster.row) radec = lib_wcs.xy_to_radec(wcs, pxy) cobjects, _, _ = lib_stars.get_celestial_objects(radec) # console output print( 'number of clusters: {:2d}, greatest integral: {:7d}, x: {:4.1f}, y: {:4.1f}' .format(len(clusters), max_cluster.integral, max_cluster.column, max_cluster.row)) for cobj in cobjects.keys(): print('celestial object: {}'.format(cobj)) # graphic output if interactive: _, axis = plt.subplots() axis.imshow(lib_cluster.add_crosses(pixels, clusters)) plt.show() return 0
def main(): # analyse command line arguments file_name, interactive = lib_args.get_args() data = None data, header = lib_fits.read_first_image(file_name) data = data[400:600, 300:500] done = np.zeros(data.shape) background, dispersion, mx, hist_sum = lib_background.compute_background( data, False) threshold = 2 * background + 6. * dispersion #threshold=11000 cluster_pix_list = [] for i in range(data.shape[0]): for j in range(data.shape[1]): if not done[i][j]: done[i][j] = 1 if data[i][j] > threshold: cluster_pixels = lib_pixels_set.PixelsSet() cluster_pixels.add(i, j, data[i][j]) recursive_search(i, j, data, done, cluster_pixels, threshold) if cluster_pixels.get_len() > 1: cluster_pix_list.append(cluster_pixels) print([str(cluster) for cluster in cluster_pix_list]) if interactive: fig, main_axes = plt.subplots() main_axes.imshow(data) for cluster in cluster_pix_list: peak = cluster.get_peak() plt.scatter([peak[1]], [peak[0]]) fig, main_axes = plt.subplots() main_axes.imshow(data) for cluster in cluster_pix_list: for pixel in cluster.pixels: plt.plot(pixel[1], pixel[0], 'rs', alpha=0.05) fig, main_axes = plt.subplots() main_axes.imshow(data) matrix = np.zeros(data.shape) for cluster in cluster_pix_list: for pixel in cluster.pixels: matrix[pixel[0], pixel[1]] = 1 plt.contour(matrix) plt.show() return 0
def main(): # analyse command line arguments file_name, interactive = lib_args.get_args() logging.info('----------------') logging.info('name of file: {}'.format(file_name)) # read fits file header, pixels = lib_fits.read_first_image(file_name) logging.info('cd1_1: {CD1_1:.10f}'.format(**header)) logging.info('cd1_2: {CD1_2:.10f}'.format(**header)) logging.info('cd2_1: {CD2_1:.10f}'.format(**header)) logging.info('cd2_2: {CD2_2:.10f}'.format(**header)) # compute background background, dispersion, _ = lib_background.compute_background(pixels) logging.info('background: {:d}'.format(int(background))) logging.info('dispersion: {:d}'.format(int(dispersion))) # clustering clustering = lib_cluster.Clustering() clusters = clustering(pixels, background, dispersion) for icl, cl in enumerate(clusters): logging.info('----------------') logging.info('cluster {:d}: {}'.format(icl, cl)) # radec coordinates of the greatest cluster wcs = lib_wcs.get_wcs(header) pxy = lib_wcs.PixelXY(cl.column, cl.row) radec = lib_wcs.xy_to_radec(wcs, pxy) logging.info('right ascension: {:.3f}'.format(radec.ra)) logging.info('declination: {:.3f}'.format(radec.dec)) # celestial objects for the biggest cluster cobjects, _, _ = get_celestial_objects(wcs, cl) for icobj, cobj in enumerate(cobjects.keys()): logging.info('celestial object {}: {}'.format(icobj, cobj)) # graphic output if interactive: fig, axis = plt.subplots() axis.imshow(pixels, interpolation='none') fig.canvas.mpl_connect( 'motion_notify_event', lib_graphics.ShowClusterProperties(fig, clusters, ShowCelestialObjects(wcs))) plt.show() logging.info('----------------') return 0
def main(): file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) background, dispersion, _ = lib_background.compute_background(pixels) clustering = lib_cluster.Clustering() clusters = clustering(pixels, background, dispersion) max_cluster = clusters[0] # coordinates ra dec wcs = lib_wcs.get_wcs(header) for i, c in enumerate(clusters): show_cluster(wcs, i, c) break return 0
def main(): ''' Main function of the program ''' global reg # process command-line options file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) logging.debug('cd1_1: %s, cd1_2: %s, cd2_1: %s, cd2_2: %s', header['CD1_1'], header['CD1_2'], header['CD2_1'], header['CD2_2']) logging.debug('height: %s, width: %s', pixels.shape[0], pixels.shape[1]) # compute background background, dispersion, _ = lib_background.compute_background(pixels) logging.debug('background: %s, dispersion: %s', int(background), int(dispersion)) print('---------------------') # search for clusters in a sub-region of the image threshold = 6.0 # graphic output if interactive: image = pixels reg = lib_cluster_thr.RegionThr(image, background + threshold * dispersion) reg.run_threaded() max_integral = reg.clusters[0].integral logging.info( 'number of clusters: %2d, greatest integral: %7d, centroid x: %4.1f, centroid y: %4.1f', len(reg.clusters), max_integral, reg.clusters[0].centroid[1], reg.clusters[0].centroid[0]) plt.show() return 0
def main(): # analyse command line arguments file_name, interactive = lib_args.get_args() # main tasks # ... # example of console output # ... print('RESULT: file = {}'.format(file_name)) print('RESULT: interactive = {}'.format(interactive)) # graphic output if interactive: # ... pass # end return 0
def main(): file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) # console output print('RESULT: cd1_1 = {CD1_1:.10f}'.format(**header)) print('RESULT: cd1_2 = {CD1_2:.10f}'.format(**header)) print('RESULT: cd2_1 = {CD2_1:.10f}'.format(**header)) print('RESULT: cd2_2 = {CD2_2:.10f}'.format(**header)) # graphic output if interactive: import matplotlib.pyplot as plt _, axis = plt.subplots() plt.text(0, -10, file_name, fontsize=14, color='white') axis.imshow(pixels) plt.show() return 0
def main(): file_name, interactive = lib_args.get_args() # importing image pixels = None pixels, header = lib_fits.read_first_image(file_name) my_wcs = lib_wcs.get_wcs(header) clusters = ex3_clusters.find_clusters(pixels, False) for j in range(len(clusters)): peak_pixel = lib_wcs.PixelXY(clusters[j].y, clusters[j].x) cel_coord = lib_wcs.xy_to_radec(my_wcs, peak_pixel) acc_radius = 0.001 celestial_objects, out, req = lib_stars.get_celestial_objects( cel_coord, acc_radius) signature_fmt_1 = 'RESULT: right_ascension_{:d} = {:.3f}'.format( j, cel_coord[0]) signature_fmt_2 = 'RESULT: declination_{:d} = {:.3f}'.format( j, cel_coord[1]) print(signature_fmt_1) print(signature_fmt_2) for i, key in enumerate(celestial_objects.keys()): signature_fmt_3 = 'RESULT: celestial_object_{:d}_{:d} = {}'.format( j, i, key) print(signature_fmt_3) # graphic output if interactive: fig, main_axes = plt.subplots() handler = Handler(fig, main_axes, my_wcs) main_axes.imshow(pixels) #fig.canvas.mpl_connect('motion_notify_event', handler.move) fig.canvas.mpl_connect('button_press_event', handler.on_click) plt.show() # end return 0
def main(): # analyse command line arguments file_name, interactive = lib_args.get_args() # importing image pixels = None pixels, header = lib_fits.read_first_image(file_name) my_wcs = lib_wcs.get_wcs(header) sorted_clusters = ex3_clusters.find_clusters(pixels, False) peak_pixel = lib_wcs.PixelXY(sorted_clusters[0].y, sorted_clusters[0].x) cel_coord = lib_wcs.xy_to_radec(my_wcs, peak_pixel) acc_radius = 0.001 celestial_objects, out, req = lib_stars.get_celestial_objects( cel_coord, acc_radius) signature_fmt_1 = 'RESULT: right_ascension = {:.3f}'.format(cel_coord[0]) signature_fmt_2 = 'RESULT: declination = {:.3f}'.format(cel_coord[1]) print(signature_fmt_1) print(signature_fmt_2) i = 0 for key in celestial_objects.keys(): signature_fmt_3 = 'RESULT: celestial_object_{:d} = {}'.format(i, key) print(signature_fmt_3) i += 1 # graphic output if interactive: # ... pass # end return 0
def main(): dirpath, interactive = lib_args.get_args() filepaths = scan_dir(dirpath) # batch console output if not interactive: for filepath in filepaths: print(filepath) # graphic interaction else: fig, img_axis = plt.subplots(figsize=(10, 5)) plt.subplots_adjust(left=0.05, right=0.45, bottom=0.1, top=0.9) buttons_axis = plt.axes([0.55, 0.1, 0.4, 0.8]) buttons = widgets.RadioButtons(buttons_axis, filepaths) callback = UpdateFile(img_axis, fig) buttons.on_clicked(callback) callback(filepaths[0]) plt.show() return 0
def main(): file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) z = lib_model.gaussian_model(np.arange(-10.0, 10.0, 1.0), 1.0, 1.0, 1.0) print('RESULT: test_gaussian = {:3f}'.format(np.sum(z))) y, x = lib_background.build_pixel_histogram(pixels, 200) print('RESULT: histogram = {:5d}'.format(np.sum(y))) background, dispersion, mx, y, x = lib_background.compute_background_from_histogram((y, x)) # console output print('RESULT: background = {:d}'.format(int(background))) print('RESULT: dispersion = {:d}'.format(int(dispersion))) # graphic output if interactive: import matplotlib.pyplot as plt _, axis = plt.subplots() # axis.imshow(pixels) z = lib_model.gaussian_model(x, 1.0, background/mx, dispersion/mx) plt.plot(x, y, 'b+:', label='data') plt.plot(x, z, 'r.:', label='fit') plt.legend() plt.title('Flux distribution') plt.xlabel('Amplitude') plt.ylabel('Frequence') plt.show() return 0
def main(): ''' Main function of the program ''' global reg global strategy global in_cluster global in_scanning # process command-line options file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) logging.debug('cd1_1: %s, cd1_2: %s, cd2_1: %s, cd2_2: %s', header['CD1_1'], header['CD1_2'], header['CD2_1'], header['CD2_2']) logging.debug('height: %s, width: %s', pixels.shape[0], pixels.shape[1]) # compute background background, dispersion, _ = lib_background.compute_background(pixels) logging.debug('background: %s, dispersion: %s', int(background), int(dispersion)) print('---------------------') # search for clusters in a sub-region of the image threshold = 6.0 # graphic output if interactive: # cluster central image = pixels[45:70, 40:65] reg = lib_cluster.Region(image, background + threshold * dispersion) strategy = '4centers' in_cluster = 1.0 in_scanning = 0.1 def select_strategy(value): global strategy print(('select strategy=', value)) strategy = value def select_in_cluster(value): global in_cluster in_cluster = value def select_in_scanning(value): global in_scanning in_scanning = value def start_animate(value): print(('animate with strategy=', strategy)) reg.animate(in_cluster=in_cluster, in_scanning=in_scanning, strategy=strategy) strategies = ['random', 'all', 'center', '4centers'] axis_strategy = plt.axes([0.2, 0.8, 0.15, 0.15]) axis_strategy.set_title('Scanning strategy') strategy_widget = RadioButtons(axis_strategy, strategies) strategy_widget.set_active(strategies.index(strategy)) strategy_widget.on_clicked(select_strategy) axis_in_cluster = plt.axes([0.2, 0.7, 0.65, 0.03]) in_cluster_widget = Slider(axis_in_cluster, 'wait in clusters', 0.0, 5.0, valinit=in_cluster) in_cluster_widget.on_changed(select_in_cluster) axis_in_scanning = plt.axes([0.2, 0.6, 0.65, 0.03]) in_scanning_widget = Slider(axis_in_scanning, 'wait in scanning', 0.0, 1.0, valinit=in_scanning) in_scanning_widget.on_changed(select_in_scanning) axis_animate = plt.axes([0.2, 0.5, 0.1, 0.03]) in_animate = Button(axis_animate, 'Animate') in_animate.on_clicked(start_animate) plt.show() return 0
def main(): # analyse command line arguments file_name, interactive = lib_args.get_args() # importing image pixels = None pixels, header = lib_fits.read_first_image(file_name) pattern = lib_cluster.build_pattern(interactive) background, dispersion, mx, hist_sum = lib_background.compute_background( pixels, interactive) threshold = background + 6. * dispersion extended_image = lib_cluster.extend(pixels, interactive, 0, 4) convolved_image = lib_cluster.convolve(extended_image, pattern) extended_convolved_image = lib_cluster.extend(convolved_image, interactive, 0, 1) max_mask = lib_cluster.has_peak(convolved_image, interactive, threshold) peak_list = lib_cluster.get_peaks_from_mask(max_mask) clusters = lib_cluster.get_clusters(peak_list, pixels, threshold) sorted_clusters = sorted(clusters, key=lambda cluster: -cluster.int_lumi) print('RESULT: pattern_sum = {:5.0f}'.format(pattern.sum().sum())) print('RESULT: extended_image_width = {:2d}'.format( extended_image.shape[0])) print('RESULT: extended_image_height = {:2d}'.format( extended_image.shape[1])) print('RESULT: extended_image_sum = {:5.0f}'.format( extended_image.sum().sum())) print('RESULT: convolution_image_width = {:2d}'.format( convolved_image.shape[0])) print('RESULT: convolution_image_height = {:2d}'.format( convolved_image.shape[1])) print('RESULT: convolution_image_sum = {:5.0f}'.format( convolved_image.sum().sum())) print('RESULT: extended_convolution_image_width = {:2d}'.format( extended_convolved_image.shape[0])) print('RESULT: extended_convolution_image_height = {:2d}'.format( extended_convolved_image.shape[1])) print('RESULT: extended_convolution_image_sum = {:5.0f}'.format( extended_convolved_image.sum().sum())) print('RESULT: peaks_number={:2d}'.format(max_mask.sum().sum())) print('RESULT: clusters_number={:2d}'.format(len(sorted_clusters))) print('RESULT: cluster_max_top={:5d}'.format( int(sorted_clusters[0].peak_lumi))) print('RESULT: cluster_max_integral={:5d}'.format( int(sorted_clusters[0].int_lumi))) print('RESULT: cluster_max_column={:5d}'.format(int(sorted_clusters[0].y))) print('RESULT: cluster_max_row={:5d}'.format(int(sorted_clusters[0].x))) # graphic output if interactive: fig, main_axes = plt.subplots() main_axes.imshow(convolved_image) #plt.show() # end return 0
def main(): file_name, interactive = lib_args.get_args() #print(file_name) header, pixels = lib_fits.read_first_image(file_name) background, dispersion, _ = lib_background.compute_background(pixels) # search for clusters clustering = lib_cluster.Clustering() # clusters = clustering(pixels, background, dispersion) pattern = clustering.step_build_pattern() print('RESULT: pattern_sum = {:5.0f}'.format(np.sum(pattern))) ext_image = clustering.step_extend_image(pixels) print('RESULT: extended_image_width = {:2d}'.format(ext_image.shape[1])) print('RESULT: extended_image_height = {:2d}'.format(ext_image.shape[0])) print('RESULT: extended_image_sum = {:5.0f}'.format(np.sum(ext_image))) cp_image = clustering.step_build_convolution_image(ext_image) print('RESULT: convolution_image_width = {:2d}'.format(cp_image.shape[1])) print('RESULT: convolution_image_height = {:2d}'.format(cp_image.shape[0])) print('RESULT: convolution_image_sum = {:5.0f}'.format(np.sum(cp_image))) ext_cp_image = clustering.step_extend_convolution_image(cp_image) print('RESULT: extended_convolution_image_width = {:2d}'.format(ext_cp_image.shape[1])) print('RESULT: extended_convolution_image_height = {:2d}'.format(ext_cp_image.shape[0])) print('RESULT: extended_convolution_image_sum = {:5.0f}'.format(np.sum(ext_cp_image))) peaks = clustering.step_detect_peaks(pixels, cp_image, ext_cp_image, background, dispersion) print('RESULT: peaks_number = {:2d}'.format(len(peaks))) #for npeak, peak in enumerate(peaks): # print('peak[{}]: {}'.format(npeak, peak)) clusters = clustering.step_build_clusters(pixels, peaks, background, dispersion) print('RESULT: clusters_number = {:2d}'.format(len(clusters))) clusters, max_top = clustering.step_sort_clusters(clusters) print('RESULT: cluster_max_top = {:5d}'.format(max_top)) max_cluster = clusters[0] # console output print('RESULT: cluster_max_integral = {:5d}'.format(max_cluster.integral)) print('RESULT: cluster_max_column = {:5d}'.format(max_cluster.column)) print('RESULT: cluster_max_row = {:5d}'.format(max_cluster.row)) # graphic output if interactive: import matplotlib.pyplot as plt _, axes = plt.subplots(2) _ = axes[0].imshow(clustering._build_pattern()) _ = axes[1].imshow(lib_cluster.add_crosses(pixels,clusters)) plt.show() return 0
# -*- coding: utf-8 -*- import sys sys.path.append('../skeletons') sys.path.append('../solutions') import lib_args import lib_fits import lib_background import lib_cluster import lib_wcs import lib_stars # prepare clusters file_name, interactive = lib_args.get_args() header, pixels = lib_fits.read_first_image(file_name) print('image shape is {}'.format(pixels.shape)) background, dispersion, _ = lib_background.compute_background(pixels) pattern_radius = 4 clustering = lib_cluster.Clustering(pattern_radius) clusters = clustering(pixels, background, dispersion) nb_patho = 0 nb_symptom = 0 # print clusters details for icl, cl in enumerate(clusters): print('cluster {:d}: {}'.format(icl, cl)) # check no cluster if len(clusters) == 0: