def binImageCalibration(config, mask, dark, flat_struct): """ Bin the calibration images. """ # Bin the mask if mask is not None: mask.img = Image.binImage(mask.img, config.detection_binning_factor, 'avg') # Bin the dark if dark is not None: dark = Image.binImage(dark, config.detection_binning_factor, 'avg') # Bin the flat if flat_struct is not None: flat_struct.binFlat(config.detection_binning_factor, 'avg') return mask, dark, flat_struct
def plotStars(ff, x2, y2): """ Plots detected stars on the input image. """ # Plot image with adjusted levels to better see stars plt.imshow(Image.adjustLevels(ff.avepixel, 0, 1.3, 255), cmap='gray') # Plot stars for star in zip(list(y2), list(x2)): y, x = star c = plt.Circle((x, y), 5, fill=False, color='r') plt.gca().add_patch(c) plt.show() plt.clf() plt.close()
def plotStars(ff, x2, y2): """ Plots detected stars on the input image. """ # Plot image with adjusted levels to better see stars plt.imshow(Image.adjustLevels(ff.avepixel, 0, 1.3, 255), cmap='gray') # Plot stars for star in zip(list(y2), list(x2)): y, x = star c = plt.Circle((x, y), 5, fill=False, color='r') plt.gca().add_patch(c) plt.show() plt.clf() plt.close()
def loadImageCalibration(dir_path, config, dtype=None, byteswap=False): """ Load the mask, dark and flat. Arguments: dir_path: [str] Path to the directory with calibration. config: [ConfigStruct] Keyword arguments: dtype: [object] Numpy array dtype for the image. None by default, if which case it will be determined from the input image. byteswap: [bool] If the dark and flat should be byteswapped. False by default, and should be True for UWO PNGs. Return: mask, dark, flat_struct: [tuple of ndarrays] """ mask_path = None mask = None # Try loading the mask if os.path.exists(os.path.join(dir_path, config.mask_file)): mask_path = os.path.join(dir_path, config.mask_file) # Try loading the default mask elif os.path.exists(config.mask_file): mask_path = os.path.abspath(config.mask_file) # Load the mask if given if mask_path: mask = MaskImage.loadMask(mask_path) if mask is not None: print('Loaded mask:', mask_path) log.info('Loaded mask: {:s}'.format(mask_path)) # Try loading the dark frame dark = None if config.use_dark: dark_path = None # Check if dark is in the data directory if os.path.exists(os.path.join(dir_path, config.dark_file)): dark_path = os.path.join(dir_path, config.dark_file) # Try loading the default dark elif os.path.exists(config.dark_file): dark_path = os.path.abspath(config.dark_file) if dark_path is not None: # Load the dark dark = Image.loadDark(*os.path.split(dark_path), dtype=dtype, byteswap=byteswap) if dark is not None: print('Loaded dark:', dark_path) log.info('Loaded dark: {:s}'.format(dark_path)) # Try loading a flat field image flat_struct = None if config.use_flat: flat_path = None # Check if there is flat in the data directory if os.path.exists(os.path.join(dir_path, config.flat_file)): flat_path = os.path.join(dir_path, config.flat_file) # Try loading the default flat elif os.path.exists(config.flat_file): flat_path = os.path.abspath(config.flat_file) if flat_path is not None: # Load the flat flat_struct = Image.loadFlat(*os.path.split(flat_path), dtype=dtype, byteswap=byteswap) if flat_struct is not None: print('Loaded flat:', flat_path) log.info('Loaded flat: {:s}'.format(flat_path)) return mask, dark, flat_struct
def getThresholdedStripe3DPoints(config, img_handle, frame_min, frame_max, rho, theta, mask, flat_struct, \ dark, stripe_width_factor=1.0, centroiding=False, point1=None, point2=None, debug=False): """ Threshold the image and get a list of pixel positions and frames of threshold passers. This function handles all input types of data. Arguments; config: [config object] configuration object (loaded from the .config file). img_handle: [FrameInterface instance] Object which has a common interface to various input files. frame_min: [int] First frame to process. frame_max: [int] Last frame to process. rho: [float] Line distance from the center in HT space (pixels). theta: [float] Angle in degrees in HT space. mask: [ndarray] Image mask. flat_struct: [Flat struct] Structure containing the flat field. None by default. dark: [ndarray] Dark frame. Keyword arguments: stripe_width_factor: [float] Multipler by which the default stripe width will be multiplied. Default is 1.0 centroiding: [bool] If True, the indices will be returned in the centroiding mode, which means that point1 and point2 arguments must be given. point1: [list] (x, y, frame) Of the first reference point of the detection. point2: [list] (x, y, frame) Of the second reference point of the detection. debug: [bool] If True, extra debug messages and plots will be shown. Return: xs, ys, zs: [tuple of lists] Indices of (x, y, frame) of threshold passers for every frame. """ # Get indices of stripe pixels around the line of the meteor img_h, img_w = img_handle.ff.maxpixel.shape stripe_indices = getStripeIndices(rho, theta, stripe_width_factor*config.stripe_width, img_h, img_w) # If centroiding should be done, prepare everything for cutting out parts of the image for photometry if centroiding: # Compute the unit vector which describes the motion of the meteor in the image domain point1 = np.array(point1) point2 = np.array(point2) motion_vect = point2[:2] - point1[:2] motion_vect_unit = vectNorm(motion_vect) # Get coordinates of 2 points that describe the line x1, y1, z1 = point1 x2, y2, z2 = point2 # Compute the average angular velocity in px per frame ang_vel = np.sqrt((x2 - x1)**2 + (y2 - y1)**2)/(z2 - z1) # Compute the vector describing the length and direction of the meteor per frame motion_vect = ang_vel*motion_vect_unit # If the FF files is given, extract the points from FF after threshold if img_handle.input_type == 'ff': # Threshold the FF file img_thres = Image.thresholdFF(img_handle.ff, config.k1_det, config.j1_det, mask=mask, \ mask_ave_bright=False) # Extract the thresholded image by min and max frames from FF file img = selectFFFrames(np.copy(img_thres), img_handle.ff, frame_min, frame_max) # Remove lonely pixels img = morph.clean(img) # Extract the stripe from the thresholded image stripe = np.zeros(img.shape, img.dtype) stripe[stripe_indices] = img[stripe_indices] # Show stripe # show2("stripe", stripe*255) # Show 3D could # show3DCloud(ff, stripe) # Get stripe positions (x, y, frame) stripe_positions = stripe.nonzero() xs = stripe_positions[1] ys = stripe_positions[0] zs = img_handle.ff.maxframe[stripe_positions] return xs, ys, zs # If video frames are available, extract indices on all frames in the given range else: xs_array = [] ys_array = [] zs_array = [] # Go through all frames in the frame range for fr in range(frame_min, frame_max + 1): # Break the loop if outside frame size if fr == (img_handle.total_frames - 1): break # Set the frame number img_handle.setFrame(fr) # Load the frame fr_img = img_handle.loadFrame() # Apply the dark frame if dark is not None: fr_img = Image.applyDark(fr_img, dark) # Apply the flat to frame if flat_struct is not None: fr_img = Image.applyFlat(fr_img, flat_struct) # Mask the image fr_img = MaskImage.applyMask(fr_img, mask) # Threshold the frame img_thres = Image.thresholdImg(fr_img, img_handle.ff.avepixel, img_handle.ff.stdpixel, \ config.k1_det, config.j1_det, mask=mask, mask_ave_bright=False) # Remove lonely pixels img_thres = morph.clean(img_thres) # Extract the stripe from the thresholded image stripe = np.zeros(img_thres.shape, img_thres.dtype) stripe[stripe_indices] = img_thres[stripe_indices] # Include more pixels for centroiding and photometry and mask out per frame pixels if centroiding: # Dilate the pixels in the stripe twice, to include more pixels for photometry stripe = morph.dilate(stripe) stripe = morph.dilate(stripe) # Get indices of the stripe that is perpendicular to the meteor, and whose thickness is the # length of the meteor on this particular frame - this is called stripe_indices_motion # Compute the previous, current, and the next linear model position of the meteor on the # image model_pos_prev = point1[:2] + (fr - 1 - z1)*motion_vect model_pos = point1[:2] + (fr - z1)*motion_vect model_pos_next = point1[:2] + (fr + 1 - z1)*motion_vect # Get the rho, theta of the line perpendicular to the meteor line x_inters, y_inters = model_pos # Check if the previous, current or the next centroids are outside bounds, and if so, skip the # frame if (not checkCentroidBounds(model_pos_prev, img_w, img_h)) or \ (not checkCentroidBounds(model_pos, img_w, img_h)) or \ (not checkCentroidBounds(model_pos_next, img_w, img_h)): continue # Get parameters of the perpendicular line to the meteor line rho2, theta2 = htLinePerpendicular(rho, theta, x_inters, y_inters, img_h, img_w) # Compute the image indices of this position which will be the intersection with the stripe # The width of the line will be 2x the angular velocity stripe_length = 6*ang_vel if stripe_length < stripe_width_factor*config.stripe_width: stripe_length = stripe_width_factor*config.stripe_width stripe_indices_motion = getStripeIndices(rho2, theta2, stripe_length, img_h, img_w) # Mark only those parts which overlap both lines, which effectively creates a mask for # photometry an centroiding, excluding other influences stripe_new = np.zeros_like(stripe) stripe_new[stripe_indices_motion] = stripe[stripe_indices_motion] stripe = stripe_new if debug: # Show the extracted stripe img_stripe = np.zeros_like(stripe) img_stripe[stripe_indices] = 1 final_stripe = np.zeros_like(stripe) final_stripe[stripe_indices_motion] = img_stripe[stripe_indices_motion] plt.imshow(final_stripe) plt.show() if debug and centroiding: print(fr) print('mean stdpixel3:', np.mean(img_handle.ff.stdpixel)) print('mean avepixel3:', np.mean(img_handle.ff.avepixel)) print('mean frame:', np.mean(fr_img)) fig, (ax1, ax2) = plt.subplots(nrows=2, sharex=True, sharey=True) fr_img_noavg = Image.applyDark(fr_img, img_handle.ff.avepixel) #fr_img_noavg = fr_img # Auto levels min_lvl = np.percentile(fr_img_noavg[2:, :], 1) max_lvl = np.percentile(fr_img_noavg[2:, :], 99.0) # Adjust levels fr_img_autolevel = Image.adjustLevels(fr_img_noavg, min_lvl, 1.0, max_lvl) ax1.imshow(stripe, cmap='gray') ax2.imshow(fr_img_autolevel, cmap='gray') plt.show() pass # Get stripe positions (x, y, frame) stripe_positions = stripe.nonzero() xs = stripe_positions[1] ys = stripe_positions[0] zs = np.zeros_like(xs) + fr # Add the points to the list xs_array.append(xs) ys_array.append(ys) zs_array.append(zs) if debug: print('---') print(stripe.nonzero()) print(xs, ys, zs) if len(xs_array) > 0: # Flatten the arrays xs_array = np.concatenate(xs_array) ys_array = np.concatenate(ys_array) zs_array = np.concatenate(zs_array) else: xs_array = np.array(xs_array) ys_array = np.array(ys_array) zs_array = np.array(zs_array) return xs_array, ys_array, zs_array
def loadImageCalibration(dir_path, config, dtype=None, byteswap=False): """ Load the mask, dark and flat. Arguments: dir_path: [str] Path to the directory with calibration. config: [ConfigStruct] Keyword arguments: dtype: [object] Numpy array dtype for the image. None by default, if which case it will be determined from the input image. byteswap: [bool] If the dark and flat should be byteswapped. False by default, and should be True for UWO PNGs. Return: mask, dark, flat_struct: [tuple of ndarrays] """ mask_path = None mask = None # Try loading the mask if os.path.exists(os.path.join(dir_path, config.mask_file)): mask_path = os.path.join(dir_path, config.mask_file) # Try loading the default mask elif os.path.exists(config.mask_file): mask_path = os.path.abspath(config.mask_file) # Load the mask if given if mask_path: mask = MaskImage.loadMask(mask_path) if mask is not None: print('Loaded mask:', mask_path) log.info('Loaded mask: {:s}'.format(mask_path)) # Try loading the dark frame dark = None if config.use_dark: dark_path = None # Check if dark is in the data directory if os.path.exists(os.path.join(dir_path, config.dark_file)): dark_path = os.path.join(dir_path, config.dark_file) # Try loading the default dark elif os.path.exists(config.dark_file): dark_path = os.path.abspath(config.dark_file) if dark_path is not None: # Load the dark dark = Image.loadDark(*os.path.split(dark_path), dtype=dtype, byteswap=byteswap) if dark is not None: print('Loaded dark:', dark_path) log.info('Loaded dark: {:s}'.format(dark_path)) # Try loading a flat field image flat_struct = None if config.use_flat: flat_path = None # Check if there is flat in the data directory if os.path.exists(os.path.join(dir_path, config.flat_file)): flat_path = os.path.join(dir_path, config.flat_file) # Try loading the default flat elif os.path.exists(config.flat_file): flat_path = os.path.abspath(config.flat_file) if flat_path is not None: # Load the flat flat_struct = Image.loadFlat(*os.path.split(flat_path), dtype=dtype, byteswap=byteswap) if flat_struct is not None: print('Loaded flat:', flat_path) log.info('Loaded flat: {:s}'.format(flat_path)) return mask, dark, flat_struct
def detectMeteors(ff_directory, ff_name, config, flat_struct=None): """ Detect meteors on the given FF bin image. Here are the steps in the detection: - input image (FF bin format file) is thresholded (converted to black and white) - several morphological operations are applied to clean the image - image is then broken into several image "windows" (these "windows" are reconstructed from the input FF file, given an input frame range (e.g. 64-128) which helps reduce the noise further) - on each "window" the Kernel-based Hough transform is performed to find any lines on the image - similar lines are joined - stripe around the lines is extracted - 3D line finding (third dimension is time) is applied to check if the line propagates in time - centroiding is performed, which calculates the position and intensity of meteor on each frame Arguments: ff_directory: [string] an absolute path to the input FF bin file ff_name: [string] file name of the FF bin file on which to run the detection on config: [config object] configuration object (loaded from the .config file) Keyword arguments: flat_struct: [Flat struct] Structure containing the flat field. None by default. Return: meteor_detections: [list] a list of detected meteors, with these elements: - rho: [float] meteor line distance from image center (polar coordinates, in pixels) - theta: [float] meteor line angle from image center (polar coordinates, in degrees) - centroids: [list] [frame, X, Y, level] list of meteor points """ t1 = time() t_all = time() # Load the FF bin file ff = FFfile.read(ff_directory, ff_name) # Load the mask file mask = MaskImage.loadMask(config.mask_file) # Mask the FF file ff = MaskImage.applyMask(ff, mask, ff_flag=True) # Apply the flat to maxpixel and avepixel if flat_struct is not None: ff.maxpixel = Image.applyFlat(ff.maxpixel, flat_struct) ff.avepixel = Image.applyFlat(ff.avepixel, flat_struct) # At the end, a check that the detection has a surface brightness above the background will be performed. # The assumption here is that the peak of the meteor should have the intensity which is at least # that of a patch of 4x4 pixels that are of the mean background brightness min_patch_intensity = 4 * 4 * (np.mean(ff.maxpixel - ff.avepixel) + config.k1_det * np.mean(ff.stdpixel) + config.j1) # # Show the maxpixel image # show2(ff_name+' maxpixel', ff.maxpixel) # Get lines on the image line_list = getLines(ff, config.k1_det, config.j1_det, config.time_slide, config.time_window_size, config.max_lines_det, config.max_white_ratio, config.kht_lib_path) logDebug('List of lines:', line_list) # Init meteor list meteor_detections = [] # Only if there are some lines in the image if len(line_list): # Join similar lines line_list = mergeLines(line_list, config.line_min_dist, ff.ncols, ff.nrows) logDebug('Time for finding lines:', time() - t1) logDebug('Number of KHT lines: ', len(line_list)) logDebug(line_list) # Plot lines # plotLines(ff, line_list) # Threshold the image img_thres = thresholdImg(ff, config.k1_det, config.j1_det) filtered_lines = [] # Analyze stripes of each line for line in line_list: rho, theta, frame_min, frame_max = line logDebug('rho, theta, frame_min, frame_max') logDebug(rho, theta, frame_min, frame_max) # Bounded the thresholded image by min and max frames img = selectFrames(np.copy(img_thres), ff, frame_min, frame_max) # Remove lonely pixels img = morph.clean(img) # Get indices of stripe pixels around the line stripe_indices = getStripeIndices(rho, theta, config.stripe_width, img.shape[0], img.shape[1]) # Extract the stripe from the thresholded image stripe = np.zeros((ff.nrows, ff.ncols), np.uint8) stripe[stripe_indices] = img[stripe_indices] # Show stripe #COMMENTED # show2("stripe", stripe*255) # Show 3D could # show3DCloud(ff, stripe) # Get stripe positions stripe_positions = stripe.nonzero() xs = stripe_positions[1] ys = stripe_positions[0] zs = ff.maxframe[stripe_positions] # Limit the number of points to search if too large if len(zs) > config.max_points_det: # Extract weights of each point maxpix_elements = ff.maxpixel[ys, xs].astype(np.float64) weights = maxpix_elements / np.sum(maxpix_elements) # Random sample the point, sampling is weighted by pixel intensity indices = np.random.choice(len(zs), config.max_points_det, replace=False, p=weights) ys = ys[indices] xs = xs[indices] zs = zs[indices] # Make an array to feed into the gropuing algorithm stripe_points = np.vstack((xs, ys, zs)) stripe_points = np.swapaxes(stripe_points, 0, 1) # Sort stripe points by frame stripe_points = stripe_points[stripe_points[:, 2].argsort()] t1 = time() logDebug('finding lines...') # Find a single line in the point cloud detected_line = find3DLines(stripe_points, time(), config, fireball_detection=False) logDebug('time for GROUPING: ', time() - t1) # Extract the first and only line if any if detected_line: detected_line = detected_line[0] # logDebug(detected_line) # Show 3D cloud # show3DCloud(ff, stripe, detected_line, stripe_points, config) # Add the line to the results list filtered_lines.append(detected_line) # Merge similar lines in 3D filtered_lines = merge3DLines(filtered_lines, config.vect_angle_thresh) logDebug('after filtering:') logDebug(filtered_lines) for detected_line in filtered_lines: # Get frame range frame_min = detected_line[4] frame_max = detected_line[5] # Check if the line covers a minimum frame range if (abs(frame_max - frame_min) + 1 < config.line_minimum_frame_range_det): continue # Extand the frame range for several frames, just to be sure to catch all parts of a meteor frame_min -= config.frame_extension frame_max += config.frame_extension # Cap values to 0-255 frame_min = max(frame_min, 0) frame_max = min(frame_max, 255) logDebug(detected_line) # Get coordinates of 2 points that describe the line x1, y1, z1 = detected_line[0] x2, y2, z2 = detected_line[1] # Convert Cartesian line coordinates to polar rho, theta = getPolarLine(x1, y1, x2, y2, ff.nrows, ff.ncols) # Convert Cartesian line coordinate to CAMS compatible polar coordinates (flipped Y axis) rho_cams, theta_cams = getPolarLine(x1, ff.nrows - y1, x2, ff.nrows - y2, ff.nrows, ff.ncols) logDebug('converted rho, theta') logDebug(rho, theta) # Bounded the thresholded image by min and max frames img = selectFrames(np.copy(img_thres), ff, frame_min, frame_max) # Remove lonely pixels img = morph.clean(img) # Get indices of stripe pixels around the line stripe_indices = getStripeIndices(rho, theta, int(config.stripe_width * 1.5), img.shape[0], img.shape[1]) # Extract the stripe from the thresholded image stripe = np.zeros((ff.nrows, ff.ncols), np.uint8) stripe[stripe_indices] = img[stripe_indices] # Show detected line # show('detected line: '+str(frame_min)+'-'+str(frame_max), stripe) # Get stripe positions stripe_positions = stripe.nonzero() xs = stripe_positions[1] ys = stripe_positions[0] zs = ff.maxframe[stripe_positions] # Make an array to feed into the centroiding algorithm stripe_points = np.vstack((xs, ys, zs)) stripe_points = np.swapaxes(stripe_points, 0, 1) # Sort stripe points by frame stripe_points = stripe_points[stripe_points[:, 2].argsort()] # Show 3D cloud # show3DCloud(ff, stripe, detected_line, stripe_points, config) # Get points of the given line line_points = getAllPoints(stripe_points, x1, y1, z1, x2, y2, z2, config, fireball_detection=False) # Skip if no points were returned if not line_points.any(): continue # Skip if the points cover too small a frame range if abs(np.max(line_points[:, 2]) - np.min(line_points[:, 2]) ) + 1 < config.line_minimum_frame_range_det: continue # Calculate centroids centroids = [] for i in range(frame_min, frame_max + 1): # Select pixel indicies belonging to a given frame frame_pixels_inds = np.where(line_points[:, 2] == i) # Get pixel positions in a given frame (pixels belonging to a found line) frame_pixels = line_points[frame_pixels_inds].astype(np.int64) # Get pixel positions in a given frame (pixels belonging to the whole stripe) frame_pixels_stripe = stripe_points[np.where( stripe_points[:, 2] == i)].astype(np.int64) # Skip if there are no pixels in the frame if not len(frame_pixels): continue # Calculate weights for centroiding max_avg_corrected = ff.maxpixel - ff.avepixel flattened_weights = (max_avg_corrected).astype( np.float32) / ff.stdpixel # Calculate centroids by half-frame for half_frame in range(2): # Apply deinterlacing if it is present in the video if config.deinterlace_order >= 0: # Deinterlace by fields (line lixels) half_frame_pixels = frame_pixels[ frame_pixels[:, 1] % 2 == (config.deinterlace_order + half_frame) % 2] # Deinterlace by fields (stripe pixels) half_frame_pixels_stripe = frame_pixels_stripe[ frame_pixels_stripe[:, 1] % 2 == (config.deinterlace_order + half_frame) % 2] # Skip if there are no pixels in the half-frame if not len(half_frame_pixels): continue # Calculate half-frame value frame_no = i + half_frame * 0.5 # No deinterlacing else: # Skip the second half frame if half_frame == 1: continue half_frame_pixels = frame_pixels half_frame_pixels_stripe = frame_pixels_stripe frame_no = i # Get maxpixel-avepixel values of given pixel indices (this will be used as weights) max_weights = flattened_weights[half_frame_pixels[:, 1], half_frame_pixels[:, 0]] # Calculate weighted centroids x_weighted = half_frame_pixels[:, 0] * np.transpose( max_weights) x_centroid = np.sum(x_weighted) / float( np.sum(max_weights)) y_weighted = half_frame_pixels[:, 1] * np.transpose( max_weights) y_centroid = np.sum(y_weighted) / float( np.sum(max_weights)) # Calculate intensity as the sum of threshold passer pixels on the stripe #intensity_values = max_avg_corrected[half_frame_pixels[:,1], half_frame_pixels[:,0]] intensity_values = max_avg_corrected[ half_frame_pixels_stripe[:, 1], half_frame_pixels_stripe[:, 0]] intensity = np.sum(intensity_values) logDebug("centroid: ", frame_no, x_centroid, y_centroid, intensity) centroids.append( [frame_no, x_centroid, y_centroid, intensity]) # Filter centroids centroids = filterCentroids(centroids, config.centroids_max_deviation, config.centroids_max_distance) # Convert to numpy array for easy slicing centroids = np.array(centroids) # Reject the solution if there are too few centroids if len(centroids) < config.line_minimum_frame_range_det: continue # Check that the detection has a surface brightness above the background # The assumption here is that the peak of the meteor should have the intensity which is at least # that of a patch of 4x4 pixels that are of the mean background brightness if np.max(centroids[:, 3]) < min_patch_intensity: continue # Check the detection if it has the proper angular velocity if not checkAngularVelocity(centroids, config): continue # Append the result to the meteor detections meteor_detections.append([rho_cams, theta_cams, centroids]) logDebug('time for processing:', time() - t_all) # # Plot centroids to image # fig, (ax1, ax2) = plt.subplots(nrows=2) # ax1.imshow(ff.maxpixel - ff.avepixel, cmap='gray') # ax1.scatter(centroids[:,1], centroids[:,2], s=5, c='r', edgecolors='none') # # Plot lightcurve # ax2.plot(centroids[:,0], centroids[:,3]) # # # Plot relative angular velocity # # ang_vels = [] # # fr_prev, x_prev, y_prev, _ = centroids[0] # # for fr, x, y, _ in centroids[1:]: # # dx = x - x_prev # # dy = y - y_prev # # dfr = fr - fr_prev # # ddist = np.sqrt(dx**2 + dy**2) # # dt = dfr/config.fps # # ang_vels.append(ddist/dt) # # x_prev = x # # y_prev = y # # fr_prev = fr # # ax2.plot(ang_vels) # plt.show() return meteor_detections
def fitPSF(ff, avepixel_mean, x2, y2, config): """ Fit a 2D Gaussian to the star candidate cutout to check if it's a star. Arguments: ff: [ff bin struct] FF bin file loaded in the FF bin structure avepixel_mean: [float] mean of the avepixel image x2: [list] a list of estimated star position (X axis) xy: [list] a list of estimated star position (Y axis) config: [config object] configuration object (loaded from the .config file) """ # Load parameters form config if present if config is not None: # segment_radius: [int] radius (in pixels) of image segment around the detected star on which to # perform the fit # roundness_threshold: [float] minimum ratio of 2D Gaussian sigma X and sigma Y to be taken as a stars # (hot pixels are narrow, while stars are round) # max_feature_ratio: [float] maximum ratio between 2 sigma of the star and the image segment area segment_radius = config.segment_radius roundness_threshold = config.roundness_threshold max_feature_ratio = config.max_feature_ratio x_fitted = [] y_fitted = [] amplitude_fitted = [] intensity_fitted = [] sigma_y_fitted = [] sigma_x_fitted = [] # Set the initial guess initial_guess = (30.0, segment_radius, segment_radius, 1.0, 1.0, 0.0, avepixel_mean) # Go through all stars for star in zip(list(y2), list(x2)): y, x = star y_min = y - segment_radius y_max = y + segment_radius x_min = x - segment_radius x_max = x + segment_radius if y_min < 0: y_min = 0 if y_max > ff.nrows: y_max = ff.nrows if x_min < 0: x_min = 0 if x_max > ff.ncols: x_max = ff.ncols x_min = int(x_min) x_max = int(x_max) y_min = int(y_min) y_max = int(y_max) # Extract an image segment around each star star_seg = ff.avepixel[y_min:y_max, x_min:x_max] # Create x and y indices y_ind, x_ind = np.indices(star_seg.shape) # Estimate saturation level from image type saturation = 2**(8*star_seg.itemsize) - 1 # Fit a PSF to the star try: # Fit the 2D Gaussian with the limited number of iterations - this reduces the processing time # and most of the bad star candidates take more iterations to fit popt, pcov = opt.curve_fit(twoDGaussian, (y_ind, x_ind, saturation), star_seg.ravel(), \ p0=initial_guess, maxfev=200) # print(popt) except RuntimeError: # print('Fitting failed!') # Skip stars that can't be fitted in 200 iterations continue # Unpack fitted gaussian parameters amplitude, yo, xo, sigma_y, sigma_x, theta, offset = popt # Filter hot pixels by looking at the ratio between x and y sigmas (HPs are very narrow) if min(sigma_y/sigma_x, sigma_x/sigma_y) < roundness_threshold: # Skip if it is a hot pixel continue # Reject the star candidate if it is too large if (4*sigma_x*sigma_y / segment_radius**2 > max_feature_ratio): continue ### If the fitting was successfull, compute the star intensity # Crop the star segment to take 3 sigma portion around the star crop_y_min = int(yo - 3*sigma_y) + 1 if crop_y_min < 0: crop_y_min = 0 crop_y_max = int(yo + 3*sigma_y) + 1 if crop_y_max >= star_seg.shape[0]: crop_y_max = star_seg.shape[0] - 1 crop_x_min = int(xo - 3*sigma_x) + 1 if crop_x_min < 0: crop_x_min = 0 crop_x_max = int(xo + 3*sigma_x) + 1 if crop_x_max >= star_seg.shape[1]: crop_x_max = star_seg.shape[1] - 1 # If the segment is too small, set a fixed size if (y_max - y_min) < 3: crop_y_min = int(yo - 2) crop_y_max = int(yo + 2) if (x_max - x_min) < 3: crop_x_min = int(xo - 2) crop_x_max = int(xo + 2) star_seg_crop = star_seg[crop_y_min:crop_y_max, crop_x_min:crop_x_max] # Skip the star if the shape is too small if (star_seg_crop.shape[0] == 0) or (star_seg_crop.shape[1] == 0): continue # Gamma correct the star segment star_seg_crop = Image.gammaCorrection(star_seg_crop.astype(np.float32), config.gamma) # Correct the background for gamma bg_corrected = Image.gammaCorrection(offset, config.gamma) # Subtract the background from the star segment and compute the total intensity intensity = np.sum(star_seg_crop - bg_corrected) # Skip stars with zero intensity if intensity <= 0: continue # print(intensity) # plt.imshow(star_seg_crop - bg_corrected, cmap='gray', vmin=0, vmax=255) # plt.show() ### # Calculate the intensity (as a volume under the 2D Gaussian) (OLD, before gamma correction) # intensity = 2*np.pi*amplitude*sigma_x*sigma_y # # Skip if the star intensity is below background level # if intensity < offset: # continue # Add stars to the final list x_fitted.append(x_min + xo) y_fitted.append(y_min + yo) amplitude_fitted.append(amplitude) intensity_fitted.append(intensity) sigma_y_fitted.append(sigma_y) sigma_x_fitted.append(sigma_x) # # Plot fitted stars # data_fitted = twoDGaussian((y_ind, x_ind), *popt) - offset # fig, ax = plt.subplots(1, 1) # ax.hold(True) # plt.title('Center Y: '+str(y_min[0])+', X:'+str(x_min[0])) # ax.imshow(star_seg.reshape(segment_radius*2, segment_radius*2), cmap=plt.cm.inferno, origin='bottom', # extent=(x_ind.min(), x_ind.max(), y_ind.min(), y_ind.max())) # # ax.imshow(data_fitted.reshape(segment_radius*2, segment_radius*2), cmap=plt.cm.jet, origin='bottom') # ax.contour(x_ind, y_ind, data_fitted.reshape(segment_radius*2, segment_radius*2), 8, colors='w') # plt.show() # plt.clf() # plt.close() return x_fitted, y_fitted, amplitude_fitted, intensity_fitted, sigma_y_fitted, sigma_x_fitted
def runCapture(config, duration=None, video_file=None, nodetect=False, detect_end=False, upload_manager=None): """ Run capture and compression for the given time.given Arguments: config: [config object] Configuration read from the .config file Keyword arguments: duration: [float] Time in seconds to capture. None by default. video_file: [str] Path to the video file, if it was given as the video source. None by default. nodetect: [bool] If True, detection will not be performed. False by defualt. detect_end: [bool] If True, detection will be performed at the end of the night, when capture finishes. False by default. upload_manager: [UploadManager object] A handle to the UploadManager, which handles uploading files to the central server. None by default. """ global STOP_CAPTURE # Create a directory for captured files night_data_dir_name = str( config.stationID) + '_' + datetime.datetime.utcnow().strftime( '%Y%m%d_%H%M%S_%f') # Full path to the data directory night_data_dir = os.path.join(os.path.abspath(config.data_dir), config.captured_dir, night_data_dir_name) # Make a directory for the night mkdirP(night_data_dir) log.info('Data directory: ' + night_data_dir) # Load the default flat field image if it is available flat_struct = None if config.use_flat: # Check if the flat exists if os.path.exists(os.path.join(os.getcwd(), config.flat_file)): flat_struct = Image.loadFlat(os.getcwd(), config.flat_file) log.info('Loaded flat field image: ' + os.path.join(os.getcwd(), config.flat_file)) # Get the platepar file platepar, platepar_path, platepar_fmt = getPlatepar(config) log.info('Initializing frame buffers...') ### For some reason, the RPi 3 does not like memory chunks which size is the multipier of its L2 ### cache size (512 kB). When such a memory chunk is provided, the compression becomes 10x slower ### then usual. We are applying a dirty fix here where we just add an extra image row and column ### if such a memory chunk will be created. The compression is performed, and the image is cropped ### back to its original dimensions. array_pad = 0 # Check if the image dimensions are divisible by RPi3 L2 cache size and add padding if (256 * config.width * config.height) % (512 * 1024) == 0: array_pad = 1 # Init arrays for parallel compression on 2 cores sharedArrayBase = multiprocessing.Array( ctypes.c_uint8, 256 * (config.width + array_pad) * (config.height + array_pad)) sharedArray = np.ctypeslib.as_array(sharedArrayBase.get_obj()) sharedArray = sharedArray.reshape(256, (config.height + array_pad), (config.width + array_pad)) startTime = multiprocessing.Value('d', 0.0) sharedArrayBase2 = multiprocessing.Array( ctypes.c_uint8, 256 * (config.width + array_pad) * (config.height + array_pad)) sharedArray2 = np.ctypeslib.as_array(sharedArrayBase2.get_obj()) sharedArray2 = sharedArray2.reshape(256, (config.height + array_pad), (config.width + array_pad)) startTime2 = multiprocessing.Value('d', 0.0) log.info('Initializing frame buffers done!') # Check if the detection should be performed or not if nodetect: detector = None else: if detect_end: # Delay detection until the end of the night delay_detection = duration else: # Delay the detection for 2 minutes after capture start delay_detection = 120 # Initialize the detector detector = QueuedPool(detectStarsAndMeteors, cores=1, log=log, delay_start=delay_detection) detector.startPool() # Initialize buffered capture bc = BufferedCapture(sharedArray, startTime, sharedArray2, startTime2, config, video_file=video_file) # Initialize the live image viewer live_view = LiveViewer(window_name='Maxpixel') # Initialize compression compressor = Compressor(night_data_dir, sharedArray, startTime, sharedArray2, startTime2, config, detector=detector, live_view=live_view, flat_struct=flat_struct) # Start buffered capture bc.startCapture() # Start the compression compressor.start() # Capture until Ctrl+C is pressed wait(duration) # If capture was manually stopped, end capture if STOP_CAPTURE: log.info('Ending capture...') # Stop the capture log.debug('Stopping capture...') bc.stopCapture() log.debug('Capture stopped') dropped_frames = bc.dropped_frames log.info('Total number of dropped frames: ' + str(dropped_frames)) # Stop the compressor log.debug('Stopping compression...') detector, live_view = compressor.stop() log.debug('Compression stopped') # Stop the live viewer log.debug('Stopping live viewer...') live_view.stop() del live_view log.debug('Live view stopped') # Init data lists star_list = [] meteor_list = [] ff_detected = [] # If detection should be performed if not nodetect: log.info('Finishing up the detection, ' + str(detector.input_queue.qsize()) + ' files to process...') # Reset the Ctrl+C to KeyboardInterrupt resetSIGINT() try: # If there are some more files to process, process them on more cores if detector.input_queue.qsize() > 0: # Let the detector use all cores, but leave 1 free available_cores = multiprocessing.cpu_count() - 1 if available_cores > 1: log.info('Running the detection on {:d} cores...'.format( available_cores)) # Start the detector detector.updateCoreNumber(cores=available_cores) log.info('Waiting for the detection to finish...') # Wait for the detector to finish and close it detector.closePool() log.info('Detection finished!') except KeyboardInterrupt: log.info('Ctrl + C pressed, exiting...') if upload_manager is not None: # Stop the upload manager if upload_manager.is_alive(): log.debug('Closing upload manager...') upload_manager.stop() del upload_manager # Terminate the detector if detector is not None: del detector sys.exit() # Set the Ctrl+C back to 'soft' program kill setSIGINT() ### SAVE DETECTIONS TO FILE log.info('Collecting results...') # Get the detection results from the queue detection_results = detector.getResults() # Remove all 'None' results, which were errors detection_results = [ res for res in detection_results if res is not None ] # Count the number of detected meteors meteors_num = 0 for _, _, meteor_data in detection_results: for meteor in meteor_data: meteors_num += 1 log.info('TOTAL: ' + str(meteors_num) + ' detected meteors.') # Save the detections to a file for ff_name, star_data, meteor_data in detection_results: x2, y2, background, intensity = star_data # Skip if no stars were found if not x2: continue # Construct the table of the star parameters star_data = zip(x2, y2, background, intensity) # Add star info to the star list star_list.append([ff_name, star_data]) # Handle the detected meteors meteor_No = 1 for meteor in meteor_data: rho, theta, centroids = meteor # Append to the results list meteor_list.append([ff_name, meteor_No, rho, theta, centroids]) meteor_No += 1 # Add the FF file to the archive list if a meteor was detected on it if meteor_data: ff_detected.append(ff_name) # Generate the name for the CALSTARS file calstars_name = 'CALSTARS_' + "{:s}".format(str(config.stationID)) + '_' \ + os.path.basename(night_data_dir) + '.txt' # Write detected stars to the CALSTARS file CALSTARS.writeCALSTARS(star_list, night_data_dir, calstars_name, config.stationID, config.height, \ config.width) # Generate FTPdetectinfo file name ftpdetectinfo_name = 'FTPdetectinfo_' + os.path.basename( night_data_dir) + '.txt' # Write FTPdetectinfo file FTPdetectinfo.writeFTPdetectinfo(meteor_list, night_data_dir, ftpdetectinfo_name, night_data_dir, \ config.stationID, config.fps) # Get the platepar file platepar, platepar_path, platepar_fmt = getPlatepar(config) # Run calibration check and auto astrometry refinement if platepar is not None: # Read in the CALSTARS file calstars_list = CALSTARS.readCALSTARS(night_data_dir, calstars_name) # Run astrometry check and refinement platepar, fit_status = autoCheckFit(config, platepar, calstars_list) # If the fit was sucessful, apply the astrometry to detected meteors if fit_status: log.info('Astrometric calibration SUCCESSFUL!') # Save the refined platepar to the night directory and as default platepar.write(os.path.join(night_data_dir, config.platepar_name), fmt=platepar_fmt) platepar.write(platepar_path, fmt=platepar_fmt) else: log.info( 'Astrometric calibration FAILED!, Using old platepar for calibration...' ) # Calculate astrometry for meteor detections applyAstrometryFTPdetectinfo(night_data_dir, ftpdetectinfo_name, platepar_path) log.info('Plotting field sums...') # Plot field sums to a graph plotFieldsums(night_data_dir, config) # Archive all fieldsums to one archive archiveFieldsums(night_data_dir) # List for any extra files which will be copied to the night archive directory. Full paths have to be # given extra_files = [] log.info('Making a flat...') # Make a new flat field flat_img = makeFlat(night_data_dir, config) # If making flat was sucessfull, save it if flat_img is not None: # Save the flat in the root directory, to keep the operational flat updated scipy.misc.imsave(config.flat_file, flat_img) flat_path = os.path.join(os.getcwd(), config.flat_file) log.info('Flat saved to: ' + flat_path) # Copy the flat to the night's directory as well extra_files.append(flat_path) else: log.info('Making flat image FAILED!') ### Add extra files to archive # Add the platepar to the archive if it exists if os.path.exists(platepar_path): extra_files.append(platepar_path) # Add the config file to the archive too extra_files.append(os.path.join(os.getcwd(), '.config')) ### ### night_archive_dir = os.path.join(os.path.abspath(config.data_dir), config.archived_dir, night_data_dir_name) log.info('Archiving detections to ' + night_archive_dir) # Archive the detections archive_name = archiveDetections(night_data_dir, night_archive_dir, ff_detected, config, \ extra_files=extra_files) # Put the archive up for upload if upload_manager is not None: log.info('Adding file on upload list: ' + archive_name) upload_manager.addFiles([archive_name]) # If capture was manually stopped, end program if STOP_CAPTURE: log.info('Ending program') # Stop the upload manager if upload_manager is not None: if upload_manager.is_alive(): upload_manager.stop() log.info('Closing upload manager...') sys.exit()
def extractStars(ff_dir, ff_name, config=None, max_global_intensity=150, border=10, neighborhood_size=10, intensity_threshold=5, flat_struct=None, dark=None, mask=None): """ Extracts stars on a given FF bin by searching for local maxima and applying PSF fit for star confirmation. Source of one part of the code: http://stackoverflow.com/questions/9111711/get-coordinates-of-local-maxima-in-2d-array-above-certain-value Arguments: ff_dir: [str] Path to directory where FF files are. ff_name: [str] Name of the FF file. config: [config object] configuration object (loaded from the .config file) max_global_intensity: [int] maximum mean intensity of an image before it is discared as too bright border: [int] apply a mask on the detections by removing all that are too close to the given image border (in pixels) neighborhood_size: [int] size of the neighbourhood for the maximum search (in pixels) intensity_threshold: [float] a threshold for cutting the detections which are too faint (0-255) flat_struct: [Flat struct] Structure containing the flat field. None by default. dark: [ndarray] Dark frame. None by default. mask: [ndarray] Mask image. None by default. Return: x2, y2, background, intensity, fwhm: [list of ndarrays] - x2: X axis coordinates of the star - y2: Y axis coordinates of the star - background: background intensity - intensity: intensity of the star - Gaussian Full width at half maximum (FWHM) of fitted stars """ # This will be returned if there was an error error_return = [[], [], [], [], [], []] # Load parameters from config if given if config: max_global_intensity = config.max_global_intensity border = config.border neighborhood_size = config.neighborhood_size intensity_threshold = config.intensity_threshold # Load the FF bin file ff = FFfile.read(ff_dir, ff_name) # If the FF file could not be read, skip star extraction if ff is None: return error_return # Apply the dark frame if dark is not None: ff.avepixel = Image.applyDark(ff.avepixel, dark) # Apply the flat if flat_struct is not None: ff.avepixel = Image.applyFlat(ff.avepixel, flat_struct) # Mask the FF file if mask is not None: ff = MaskImage.applyMask(ff, mask, ff_flag=True) # Calculate image mean and stddev global_mean = np.mean(ff.avepixel) # Check if the image is too bright and skip the image if global_mean > max_global_intensity: return error_return data = ff.avepixel.astype(np.float32) # Apply a mean filter to the image to reduce noise data = ndimage.filters.convolve(data, weights=np.full((2, 2), 1.0 / 4)) # Locate local maxima on the image data_max = filters.maximum_filter(data, neighborhood_size) maxima = (data == data_max) data_min = filters.minimum_filter(data, neighborhood_size) diff = ((data_max - data_min) > intensity_threshold) maxima[diff == 0] = 0 # Apply a border mask border_mask = np.ones_like(maxima) * 255 border_mask[:border, :] = 0 border_mask[-border:, :] = 0 border_mask[:, :border] = 0 border_mask[:, -border:] = 0 maxima = MaskImage.applyMask(maxima, border_mask, image=True) # Remove all detections close to the mask image if mask is not None: erosion_kernel = np.ones((5, 5), mask.img.dtype) mask_eroded = cv2.erode(mask.img, erosion_kernel, iterations=1) maxima = MaskImage.applyMask(maxima, mask_eroded, image=True) # Find and label the maxima labeled, num_objects = ndimage.label(maxima) # Skip the image if there are too many maxima to process if num_objects > config.max_stars: print('Too many candidate stars to process! {:d}/{:d}'.format( num_objects, config.max_stars)) return error_return # Find centres of mass of each labeled objects xy = np.array( ndimage.center_of_mass(data, labeled, range(1, num_objects + 1))) # Remove all detection on the border #xy = xy[np.where((xy[:, 1] > border) & (xy[:,1] < ff.ncols - border) & (xy[:,0] > border) & (xy[:,0] < ff.nrows - border))] # Unpack star coordinates y, x = np.hsplit(xy, 2) # # Plot stars before the PSF fit # plotStars(ff, x, y) # Fit a PSF to each star x2, y2, amplitude, intensity, sigma_y_fitted, sigma_x_fitted = fitPSF( ff, global_mean, x, y, config) # x2, y2, amplitude, intensity = list(x), list(y), [], [] # Skip PSF fit # # Plot stars after PSF fit filtering # plotStars(ff, x2, y2) # Compute FWHM from one dimensional sigma sigma_x_fitted = np.array(sigma_x_fitted) sigma_y_fitted = np.array(sigma_y_fitted) sigma_fitted = np.sqrt(sigma_x_fitted**2 + sigma_y_fitted**2) fwhm = 2.355 * sigma_fitted return ff_name, x2, y2, amplitude, intensity, fwhm
def fitPSF(ff, avepixel_mean, x2, y2, config): """ Fit a 2D Gaussian to the star candidate cutout to check if it's a star. Arguments: ff: [ff bin struct] FF bin file loaded in the FF bin structure avepixel_mean: [float] mean of the avepixel image x2: [list] a list of estimated star position (X axis) xy: [list] a list of estimated star position (Y axis) config: [config object] configuration object (loaded from the .config file) """ # Load parameters form config if present if config is not None: # segment_radius: [int] radius (in pixels) of image segment around the detected star on which to # perform the fit # roundness_threshold: [float] minimum ratio of 2D Gaussian sigma X and sigma Y to be taken as a stars # (hot pixels are narrow, while stars are round) # max_feature_ratio: [float] maximum ratio between 2 sigma of the star and the image segment area segment_radius = config.segment_radius roundness_threshold = config.roundness_threshold max_feature_ratio = config.max_feature_ratio x_fitted = [] y_fitted = [] amplitude_fitted = [] intensity_fitted = [] sigma_y_fitted = [] sigma_x_fitted = [] # Set the initial guess initial_guess = (30.0, segment_radius, segment_radius, 1.0, 1.0, 0.0, avepixel_mean) # Go through all stars for star in zip(list(y2), list(x2)): y, x = star y_min = y - segment_radius y_max = y + segment_radius x_min = x - segment_radius x_max = x + segment_radius if y_min < 0: y_min = np.array([0]) if y_max > ff.nrows: y_max = np.array([ff.nrows]) if x_min < 0: x_min = np.array([0]) if x_max > ff.ncols: x_max = np.array([ff.ncols]) # Check if any of these values is NaN and skip the star if np.any(np.isnan([x_min, x_max, y_min, y_max])): continue x_min = int(x_min) x_max = int(x_max) y_min = int(y_min) y_max = int(y_max) # Extract an image segment around each star star_seg = ff.avepixel[y_min:y_max, x_min:x_max] # Create x and y indices y_ind, x_ind = np.indices(star_seg.shape) # Estimate saturation level from image type saturation = (2**(8 * star_seg.itemsize) - 1) * np.ones_like(y_ind) # Fit a PSF to the star try: # Fit the 2D Gaussian with the limited number of iterations - this reduces the processing time # and most of the bad star candidates take more iterations to fit popt, pcov = opt.curve_fit(twoDGaussian, (y_ind, x_ind, saturation), star_seg.ravel(), \ p0=initial_guess, maxfev=200) # print(popt) except RuntimeError: # print('Fitting failed!') # Skip stars that can't be fitted in 200 iterations continue # Unpack fitted gaussian parameters amplitude, yo, xo, sigma_y, sigma_x, theta, offset = popt # Filter hot pixels by looking at the ratio between x and y sigmas (HPs are very narrow) if min(sigma_y / sigma_x, sigma_x / sigma_y) < roundness_threshold: # Skip if it is a hot pixel continue # Reject the star candidate if it is too large if (4 * sigma_x * sigma_y / segment_radius**2 > max_feature_ratio): continue ### If the fitting was successfull, compute the star intensity # Crop the star segment to take 3 sigma portion around the star crop_y_min = int(yo - 3 * sigma_y) + 1 if crop_y_min < 0: crop_y_min = 0 crop_y_max = int(yo + 3 * sigma_y) + 1 if crop_y_max >= star_seg.shape[0]: crop_y_max = star_seg.shape[0] - 1 crop_x_min = int(xo - 3 * sigma_x) + 1 if crop_x_min < 0: crop_x_min = 0 crop_x_max = int(xo + 3 * sigma_x) + 1 if crop_x_max >= star_seg.shape[1]: crop_x_max = star_seg.shape[1] - 1 # If the segment is too small, set a fixed size if (y_max - y_min) < 3: crop_y_min = int(yo - 2) crop_y_max = int(yo + 2) if (x_max - x_min) < 3: crop_x_min = int(xo - 2) crop_x_max = int(xo + 2) star_seg_crop = star_seg[crop_y_min:crop_y_max, crop_x_min:crop_x_max] # Skip the star if the shape is too small if (star_seg_crop.shape[0] == 0) or (star_seg_crop.shape[1] == 0): continue # Gamma correct the star segment star_seg_crop = Image.gammaCorrection(star_seg_crop.astype(np.float32), config.gamma) # Correct the background for gamma bg_corrected = Image.gammaCorrection(offset, config.gamma) # Subtract the background from the star segment and compute the total intensity intensity = np.sum(star_seg_crop - bg_corrected) # Skip stars with zero intensity if intensity <= 0: continue # print(intensity) # plt.imshow(star_seg_crop - bg_corrected, cmap='gray', vmin=0, vmax=255) # plt.show() ### # Calculate the intensity (as a volume under the 2D Gaussian) (OLD, before gamma correction) # intensity = 2*np.pi*amplitude*sigma_x*sigma_y # # Skip if the star intensity is below background level # if intensity < offset: # continue # Add stars to the final list x_fitted.append(x_min + xo) y_fitted.append(y_min + yo) amplitude_fitted.append(amplitude) intensity_fitted.append(intensity) sigma_y_fitted.append(sigma_y) sigma_x_fitted.append(sigma_x) # # Plot fitted stars # data_fitted = twoDGaussian((y_ind, x_ind), *popt) - offset # fig, ax = plt.subplots(1, 1) # ax.hold(True) # plt.title('Center Y: '+str(y_min[0])+', X:'+str(x_min[0])) # ax.imshow(star_seg.reshape(segment_radius*2, segment_radius*2), cmap=plt.cm.inferno, origin='bottom', # extent=(x_ind.min(), x_ind.max(), y_ind.min(), y_ind.max())) # # ax.imshow(data_fitted.reshape(segment_radius*2, segment_radius*2), cmap=plt.cm.jet, origin='bottom') # ax.contour(x_ind, y_ind, data_fitted.reshape(segment_radius*2, segment_radius*2), 8, colors='w') # plt.show() # plt.clf() # plt.close() return x_fitted, y_fitted, amplitude_fitted, intensity_fitted, sigma_y_fitted, sigma_x_fitted
def generateCalibrationReport(config, night_dir_path, match_radius=2.0, platepar=None, show_graphs=False): """ Given the folder of the night, find the Calstars file, check the star fit and generate a report with the quality of the calibration. The report contains information about both the astrometry and the photometry calibration. Graphs will be saved in the given directory of the night. Arguments: config: [Config instance] night_dir_path: [str] Full path to the directory of the night. Keyword arguments: match_radius: [float] Match radius for star matching between image and catalog stars (px). platepar: [Platepar instance] Use this platepar instead of finding one in the folder. show_graphs: [bool] Show the graphs on the screen. False by default. Return: None """ # Find the CALSTARS file in the given folder calstars_file = None for calstars_file in os.listdir(night_dir_path): if ('CALSTARS' in calstars_file) and ('.txt' in calstars_file): break if calstars_file is None: print('CALSTARS file could not be found in the given directory!') return None # Load the calstars file star_list = readCALSTARS(night_dir_path, calstars_file) ### Load recalibrated platepars, if they exist ### # Find recalibrated platepars file per FF file platepars_recalibrated_file = None for file_name in os.listdir(night_dir_path): if file_name == config.platepars_recalibrated_name: platepars_recalibrated_file = file_name break # Load all recalibrated platepars if the file is available recalibrated_platepars = None if platepars_recalibrated_file: with open(os.path.join(night_dir_path, platepars_recalibrated_file)) as f: recalibrated_platepars = json.load(f) print('Loaded recalibrated platepars JSON file for the calibration report...') ### ### ### Load the platepar file ### # Find the platepar file in the given directory if it was not given if platepar is None: # Find the platepar file platepar_file = None for file_name in os.listdir(night_dir_path): if file_name == config.platepar_name: platepar_file = file_name break if platepar_file is None: print('The platepar cannot be found in the night directory!') return None # Load the platepar file platepar = Platepar() platepar.read(os.path.join(night_dir_path, platepar_file)) ### ### night_name = os.path.split(night_dir_path.strip(os.sep))[1] # Go one mag deeper than in the config lim_mag = config.catalog_mag_limit + 1 # Load catalog stars (load one magnitude deeper) catalog_stars, mag_band_str, config.star_catalog_band_ratios = StarCatalog.readStarCatalog(\ config.star_catalog_path, config.star_catalog_file, lim_mag=lim_mag, \ mag_band_ratios=config.star_catalog_band_ratios) ### Take only those CALSTARS entires for which FF files exist in the folder ### # Get a list of FF files in the folder\ ff_list = [] for file_name in os.listdir(night_dir_path): if validFFName(file_name): ff_list.append(file_name) # Filter out calstars entries, generate a star dictionary where the keys are JDs of FFs star_dict = {} ff_dict = {} for entry in star_list: ff_name, star_data = entry # Check if the FF from CALSTARS exists in the folder if ff_name not in ff_list: continue dt = getMiddleTimeFF(ff_name, config.fps, ret_milliseconds=True) jd = date2JD(*dt) # Add the time and the stars to the dict star_dict[jd] = star_data ff_dict[jd] = ff_name ### ### # If there are no FF files in the directory, don't generate a report if len(star_dict) == 0: print('No FF files from the CALSTARS file in the directory!') return None # If the recalibrated platepars file exists, take the one with the most stars max_jd = 0 if recalibrated_platepars is not None: max_stars = 0 for ff_name_temp in recalibrated_platepars: # Compute the Julian date of the FF middle dt = getMiddleTimeFF(ff_name_temp, config.fps, ret_milliseconds=True) jd = date2JD(*dt) # Check that this file exists in CALSTARS and the list of FF files if (jd not in star_dict) or (jd not in ff_dict): continue # Check if the number of stars on this FF file is larger than the before if len(star_dict[jd]) > max_stars: max_jd = jd max_stars = len(star_dict[jd]) # Set a flag to indicate if using recalibrated platepars has failed if max_jd == 0: using_recalib_platepars = False else: print('Using recalibrated platepars, file:', ff_dict[max_jd]) using_recalib_platepars = True # Select the platepar where the FF file has the most stars platepar_dict = recalibrated_platepars[ff_dict[max_jd]] platepar = Platepar() platepar.loadFromDict(platepar_dict) filtered_star_dict = {max_jd: star_dict[max_jd]} # Match stars on the image with the stars in the catalog n_matched, avg_dist, cost, matched_stars = matchStarsResiduals(config, platepar, catalog_stars, \ filtered_star_dict, match_radius, ret_nmatch=True, lim_mag=lim_mag) max_matched_stars = n_matched # Otherwise take the optimal FF file for evaluation if (recalibrated_platepars is None) or (not using_recalib_platepars): # If there are more than a set number of FF files to evaluate, choose only the ones with most stars on # the image if len(star_dict) > config.calstars_files_N: # Find JDs of FF files with most stars on them top_nstars_indices = np.argsort([len(x) for x in star_dict.values()])[::-1][:config.calstars_files_N \ - 1] filtered_star_dict = {} for i in top_nstars_indices: filtered_star_dict[list(star_dict.keys())[i]] = list(star_dict.values())[i] star_dict = filtered_star_dict # Match stars on the image with the stars in the catalog n_matched, avg_dist, cost, matched_stars = matchStarsResiduals(config, platepar, catalog_stars, \ star_dict, match_radius, ret_nmatch=True, lim_mag=lim_mag) # If no recalibrated platepars where found, find the image with the largest number of matched stars if (not using_recalib_platepars) or (max_jd == 0): max_jd = 0 max_matched_stars = 0 for jd in matched_stars: _, _, distances = matched_stars[jd] if len(distances) > max_matched_stars: max_jd = jd max_matched_stars = len(distances) # If there are no matched stars, use the image with the largest number of detected stars if max_matched_stars <= 2: max_jd = max(star_dict, key=lambda x: len(star_dict[x])) distances = [np.inf] # Take the FF file with the largest number of matched stars ff_name = ff_dict[max_jd] # Load the FF file ff = readFF(night_dir_path, ff_name) img_h, img_w = ff.avepixel.shape dpi = 200 plt.figure(figsize=(ff.avepixel.shape[1]/dpi, ff.avepixel.shape[0]/dpi), dpi=dpi) # Take the average pixel img = ff.avepixel # Slightly adjust the levels img = Image.adjustLevels(img, np.percentile(img, 1.0), 1.2, np.percentile(img, 99.99)) plt.imshow(img, cmap='gray', interpolation='nearest') legend_handles = [] # Plot detected stars for img_star in star_dict[max_jd]: y, x, _, _ = img_star rect_side = 5*match_radius square_patch = plt.Rectangle((x - rect_side/2, y - rect_side/2), rect_side, rect_side, color='g', \ fill=False, label='Image stars') plt.gca().add_artist(square_patch) legend_handles.append(square_patch) # If there are matched stars, plot them if max_matched_stars > 2: # Take the solution with the largest number of matched stars image_stars, matched_catalog_stars, distances = matched_stars[max_jd] # Plot matched stars for img_star in image_stars: x, y, _, _ = img_star circle_patch = plt.Circle((y, x), radius=3*match_radius, color='y', fill=False, \ label='Matched stars') plt.gca().add_artist(circle_patch) legend_handles.append(circle_patch) ### Plot match residuals ### # Compute preducted positions of matched image stars from the catalog x_predicted, y_predicted = raDecToXYPP(matched_catalog_stars[:, 0], \ matched_catalog_stars[:, 1], max_jd, platepar) img_y, img_x, _, _ = image_stars.T delta_x = x_predicted - img_x delta_y = y_predicted - img_y # Compute image residual and angle of the error res_angle = np.arctan2(delta_y, delta_x) res_distance = np.sqrt(delta_x**2 + delta_y**2) # Calculate coordinates of the beginning of the residual line res_x_beg = img_x + 3*match_radius*np.cos(res_angle) res_y_beg = img_y + 3*match_radius*np.sin(res_angle) # Calculate coordinates of the end of the residual line res_x_end = img_x + 100*np.cos(res_angle)*res_distance res_y_end = img_y + 100*np.sin(res_angle)*res_distance # Plot the 100x residuals for i in range(len(x_predicted)): res_plot = plt.plot([res_x_beg[i], res_x_end[i]], [res_y_beg[i], res_y_end[i]], color='orange', \ lw=0.5, label='100x residuals') legend_handles.append(res_plot[0]) ### ### else: distances = [np.inf] # If there are no matched stars, plot large text in the middle of the screen plt.text(img_w/2, img_h/2, "NO MATCHED STARS!", color='r', alpha=0.5, fontsize=20, ha='center', va='center') ### Plot positions of catalog stars to the limiting magnitude of the faintest matched star + 1 mag ### # Find the faintest magnitude among matched stars if max_matched_stars > 2: faintest_mag = np.max(matched_catalog_stars[:, 2]) + 1 else: # If there are no matched stars, use the limiting magnitude from config faintest_mag = config.catalog_mag_limit + 1 # Estimate RA,dec of the centre of the FOV _, RA_c, dec_c, _ = xyToRaDecPP([jd2Date(max_jd)], [platepar.X_res/2], [platepar.Y_res/2], [1], platepar) RA_c = RA_c[0] dec_c = dec_c[0] fov_radius = np.hypot(*computeFOVSize(platepar)) # Get stars from the catalog around the defined center in a given radius _, extracted_catalog = subsetCatalog(catalog_stars, RA_c, dec_c, fov_radius, faintest_mag) ra_catalog, dec_catalog, mag_catalog = extracted_catalog.T # Compute image positions of all catalog stars that should be on the image x_catalog, y_catalog = raDecToXYPP(ra_catalog, dec_catalog, max_jd, platepar) # Filter all catalog stars outside the image temp_arr = np.c_[x_catalog, y_catalog, mag_catalog] temp_arr = temp_arr[temp_arr[:, 0] >= 0] temp_arr = temp_arr[temp_arr[:, 0] <= ff.avepixel.shape[1]] temp_arr = temp_arr[temp_arr[:, 1] >= 0] temp_arr = temp_arr[temp_arr[:, 1] <= ff.avepixel.shape[0]] x_catalog, y_catalog, mag_catalog = temp_arr.T # Plot catalog stars on the image cat_stars_handle = plt.scatter(x_catalog, y_catalog, c='none', marker='D', lw=1.0, alpha=0.4, \ s=((4.0 + (faintest_mag - mag_catalog))/3.0)**(2*2.512), edgecolor='r', label='Catalog stars') legend_handles.append(cat_stars_handle) ### ### # Add info text info_text = ff_dict[max_jd] + '\n' \ + "Matched stars: {:d}/{:d}\n".format(max_matched_stars, len(star_dict[max_jd])) \ + "Median distance: {:.2f} px\n".format(np.median(distances)) \ + "Catalog limiting magnitude: {:.1f}".format(lim_mag) plt.text(10, 10, info_text, bbox=dict(facecolor='black', alpha=0.5), va='top', ha='left', fontsize=4, \ color='w') legend = plt.legend(handles=legend_handles, prop={'size': 4}, loc='upper right') legend.get_frame().set_facecolor('k') legend.get_frame().set_edgecolor('k') for txt in legend.get_texts(): txt.set_color('w') plt.axis('off') plt.gca().get_xaxis().set_visible(False) plt.gca().get_yaxis().set_visible(False) plt.xlim([0, ff.avepixel.shape[1]]) plt.ylim([ff.avepixel.shape[0], 0]) # Remove the margins plt.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0) plt.savefig(os.path.join(night_dir_path, night_name + '_calib_report_astrometry.jpg'), \ bbox_inches='tight', pad_inches=0, dpi=dpi) if show_graphs: plt.show() else: plt.clf() plt.close() if max_matched_stars > 2: ### Plot the photometry ### plt.figure(dpi=dpi) # Take only those stars which are inside the 3/4 of the shorter image axis from the center photom_selection_radius = np.min([img_h, img_w])/3 filter_indices = ((image_stars[:, 0] - img_h/2)**2 + (image_stars[:, 1] \ - img_w/2)**2) <= photom_selection_radius**2 star_intensities = image_stars[filter_indices, 2] catalog_mags = matched_catalog_stars[filter_indices, 2] # Plot intensities of image stars #star_intensities = image_stars[:, 2] plt.scatter(-2.5*np.log10(star_intensities), catalog_mags, s=5, c='r') # Fit the photometry on automated star intensities photom_offset, fit_stddev, _ = photometryFit(np.log10(star_intensities), catalog_mags) # Plot photometric offset from the platepar x_min, x_max = plt.gca().get_xlim() y_min, y_max = plt.gca().get_ylim() x_min_w = x_min - 3 x_max_w = x_max + 3 y_min_w = y_min - 3 y_max_w = y_max + 3 photometry_info = 'Platepar: {:+.2f}LSP {:+.2f} +/- {:.2f} \nGamma = {:.2f}'.format(platepar.mag_0, \ platepar.mag_lev, platepar.mag_lev_stddev, platepar.gamma) # Plot the photometry calibration from the platepar logsum_arr = np.linspace(x_min_w, x_max_w, 10) plt.plot(logsum_arr, logsum_arr + platepar.mag_lev, label=photometry_info, linestyle='--', \ color='k', alpha=0.5) # Plot the fitted photometry calibration fit_info = "Fit: {:+.2f}LSP {:+.2f} +/- {:.2f}".format(-2.5, photom_offset, fit_stddev) plt.plot(logsum_arr, logsum_arr + photom_offset, label=fit_info, linestyle='--', color='red', alpha=0.5) plt.legend() plt.ylabel("Catalog magnitude ({:s})".format(mag_band_str)) plt.xlabel("Uncalibrated magnitude") # Set wider axis limits plt.xlim(x_min_w, x_max_w) plt.ylim(y_min_w, y_max_w) plt.gca().invert_yaxis() plt.gca().invert_xaxis() plt.grid() plt.savefig(os.path.join(night_dir_path, night_name + '_calib_report_photometry.png'), dpi=150) if show_graphs: plt.show() else: plt.clf() plt.close()
def updateImage(self): """ Updates the current plot. """ # Reset circle patches self.circle_aperature = None self.circle_aperature_outer = None # Reset centroid patch self.centroid_handle = None # Reset photometry coloring self.photometry_coloring_handle = None # Save the previous zoom if self.current_image is not None: self.prev_xlim = plt.gca().get_xlim() self.prev_ylim = plt.gca().get_ylim() plt.clf() # PNG mode if self.png_mode: # Get path to current PNG image self.png_img_path = os.path.join( self.png_dir, self.png_list[int(self.current_frame)]) # Read the image img = scipy.misc.imread(self.png_img_path) # FF mode else: # If FF is given, reconstruct frames if self.ff is not None: # Take the current frame from FF file img = np.copy(self.ff.avepixel) frame_mask = np.where( self.ff.maxframe == int(self.current_frame)) img[frame_mask] = self.ff.maxpixel[frame_mask] # Otherwise, create a blank background with the size enough to fit the FR bin else: # Get the maximum extent of the meteor frames y_size = max(max(np.array(self.fr.yc[i]) + np.array(self.fr.size[i])//2) for i in \ range(self.fr.lines)) x_size = max(max(np.array(self.fr.xc[i]) + np.array(self.fr.size[i])//2) for i in \ range(self.fr.lines)) # Make the image square img_size = max(y_size, x_size) img = np.zeros((img_size, img_size), np.uint8) # If FR is given, paste the raw frame onto the image if self.fr is not None: # Compute the index of the frame in the FR bin structure frame_indx = int( self.current_frame) - self.fr.t[self.current_line][0] # Reconstruct the frame if it is within the bounds if (frame_indx < self.fr.frameNum[self.current_line]) and ( frame_indx >= 0): # Get the center position of the detection on the current frame yc = self.fr.yc[self.current_line][frame_indx] xc = self.fr.xc[self.current_line][frame_indx] # # Get the frame number # t = self.fr.t[self.current_line][frame_indx] # Get the size of the window size = self.fr.size[self.current_line][frame_indx] # Paste the frames onto the big image y_img = np.arange(yc - size // 2, yc + size // 2) x_img = np.arange(xc - size // 2, xc + size // 2) Y_img, X_img = np.meshgrid(y_img, x_img) y_frame = np.arange(len(y_img)) x_frame = np.arange(len(x_img)) Y_frame, X_frame = np.meshgrid(y_frame, x_frame) img[Y_img, X_img] = self.fr.frames[ self.current_line][frame_indx][Y_frame, X_frame] # Save the limits of the FR self.fr_xmin = np.min(x_img) self.fr_xmax = np.max(x_img) self.fr_ymin = np.max(y_img) self.fr_ymax = np.min(y_img) # Draw a red rectangle around the pasted frame rect_x = np.min(x_img) rect_y = np.max(y_img) rect_w = np.max(x_img) - rect_x rect_h = np.min(y_img) - rect_y plt.gca().add_patch(mpatches.Rectangle((rect_x, rect_y), rect_w, rect_h, fill=None, \ edgecolor='red', alpha=0.5)) # Apply the deinterlace if self.deinterlace_mode > -1: # Set the deinterlace index to handle proper deinterlacing order if self.deinterlace_mode == 0: deinter_indx = 0 else: deinter_indx = 1 # Deinterlace the image using the appropriate method if (self.current_frame + deinter_indx * 0.5) % 1 == 0: img = Image.deinterlaceOdd(img) else: img = Image.deinterlaceEven(img) # Current image without adjustments self.current_image = np.copy(img) ### Adjust image levels # Guess the bit depth from the array type bit_depth = 8 * img.itemsize img = Image.adjustLevels(img, 0, self.img_gamma, (2**bit_depth - 1), bit_depth) ### plt.imshow(img, cmap='gray', vmin=0, vmax=255) if (self.prev_xlim is not None) and (self.prev_ylim is not None): # Restore previous zoom plt.xlim(self.prev_xlim) plt.ylim(self.prev_ylim) self.drawText() # Don't draw the picks in the photometry coloring more if not self.photometry_coloring_mode: # Plot image pick self.drawPicks(update_plot=False) # Plot the photometry coloring self.drawPhotometryColoring(update_plot=False) plt.gcf().canvas.draw()
def extractStars(ff_dir, ff_name, config=None, max_global_intensity=150, border=10, neighborhood_size=10, intensity_threshold=5, flat_struct=None, dark=None, mask=None): """ Extracts stars on a given FF bin by searching for local maxima and applying PSF fit for star confirmation. Source of one part of the code: http://stackoverflow.com/questions/9111711/get-coordinates-of-local-maxima-in-2d-array-above-certain-value Arguments: ff: [ff bin struct] FF bin file loaded in the FF bin structure config: [config object] configuration object (loaded from the .config file) max_global_intensity: [int] maximum mean intensity of an image before it is discared as too bright border: [int] apply a mask on the detections by removing all that are too close to the given image border (in pixels) neighborhood_size: [int] size of the neighbourhood for the maximum search (in pixels) intensity_threshold: [float] a threshold for cutting the detections which are too faint (0-255) flat_struct: [Flat struct] Structure containing the flat field. None by default. dark: [ndarray] Dark frame. None by default. mask: [ndarray] Mask image. None by default. Return: x2, y2, background, intensity, sigma_fitted: [list of ndarrays] - x2: X axis coordinates of the star - y2: Y axis coordinates of the star - background: background intensity - intensity: intensity of the star - Gaussian stddev of fitted stars """ # This will be returned if there was an error error_return = [[], [], [], []] # Load parameters from config if given if config: max_global_intensity = config.max_global_intensity border = config.border neighborhood_size = config.neighborhood_size intensity_threshold = config.intensity_threshold # Load the FF bin file ff = FFfile.read(ff_dir, ff_name) # If the FF file could not be read, skip star extraction if ff is None: return error_return # Apply the dark frame if dark is not None: ff.avepixel = Image.applyDark(ff.avepixel, dark) # Apply the flat if flat_struct is not None: ff.avepixel = Image.applyFlat(ff.avepixel, flat_struct) # Mask the FF file if mask is not None: ff = MaskImage.applyMask(ff, mask, ff_flag=True) # Calculate image mean and stddev global_mean = np.mean(ff.avepixel) # Check if the image is too bright and skip the image if global_mean > max_global_intensity: return error_return data = ff.avepixel.astype(np.float32) # Apply a mean filter to the image to reduce noise data = ndimage.filters.convolve(data, weights=np.full((2, 2), 1.0/4)) # Locate local maxima on the image data_max = filters.maximum_filter(data, neighborhood_size) maxima = (data == data_max) data_min = filters.minimum_filter(data, neighborhood_size) diff = ((data_max - data_min) > intensity_threshold) maxima[diff == 0] = 0 # Apply a border mask border_mask = np.ones_like(maxima)*255 border_mask[:border,:] = 0 border_mask[-border:,:] = 0 border_mask[:,:border] = 0 border_mask[:,-border:] = 0 maxima = MaskImage.applyMask(maxima, border_mask, image=True) # Find and label the maxima labeled, num_objects = ndimage.label(maxima) # Skip the image if there are too many maxima to process if num_objects > config.max_stars: print('Too many candidate stars to process! {:d}/{:d}'.format(num_objects, config.max_stars)) return error_return # Find centres of mass of each labeled objects xy = np.array(ndimage.center_of_mass(data, labeled, range(1, num_objects+1))) # Remove all detection on the border #xy = xy[np.where((xy[:, 1] > border) & (xy[:,1] < ff.ncols - border) & (xy[:,0] > border) & (xy[:,0] < ff.nrows - border))] # Unpack star coordinates y, x = np.hsplit(xy, 2) # # Plot stars before the PSF fit # plotStars(ff, x, y) # Fit a PSF to each star x2, y2, amplitude, intensity, sigma_y_fitted, sigma_x_fitted = fitPSF(ff, global_mean, x, y, config) # x2, y2, amplitude, intensity = list(x), list(y), [], [] # Skip PSF fit # # Plot stars after PSF fit filtering # plotStars(ff, x2, y2) # Compute one dimensional sigma sigma_x_fitted = np.array(sigma_x_fitted) sigma_y_fitted = np.array(sigma_y_fitted) sigma_fitted = np.sqrt(sigma_x_fitted**2 + sigma_y_fitted**2) return ff_name, x2, y2, amplitude, intensity, sigma_fitted
def getThresholdedStripe3DPoints(config, img_handle, frame_min, frame_max, rho, theta, mask, flat_struct, \ dark, stripe_width_factor=1.0, centroiding=False, point1=None, point2=None, debug=False): """ Threshold the image and get a list of pixel positions and frames of threshold passers. This function handles all input types of data. Arguments; config: [config object] configuration object (loaded from the .config file). img_handle: [FrameInterface instance] Object which has a common interface to various input files. frame_min: [int] First frame to process. frame_max: [int] Last frame to process. rho: [float] Line distance from the center in HT space (pixels). theta: [float] Angle in degrees in HT space. mask: [ndarray] Image mask. flat_struct: [Flat struct] Structure containing the flat field. None by default. dark: [ndarray] Dark frame. Keyword arguments: stripe_width_factor: [float] Multipler by which the default stripe width will be multiplied. Default is 1.0 centroiding: [bool] If True, the indices will be returned in the centroiding mode, which means that point1 and point2 arguments must be given. point1: [list] (x, y, frame) Of the first reference point of the detection. point2: [list] (x, y, frame) Of the second reference point of the detection. debug: [bool] If True, extra debug messages and plots will be shown. Return: xs, ys, zs: [tuple of lists] Indices of (x, y, frame) of threshold passers for every frame. """ # Get indices of stripe pixels around the line of the meteor img_h, img_w = img_handle.ff.maxpixel.shape stripe_indices = getStripeIndices( rho, theta, stripe_width_factor * config.stripe_width, img_h, img_w) # If centroiding should be done, prepare everything for cutting out parts of the image for photometry if centroiding: # Compute the unit vector which describes the motion of the meteor in the image domain point1 = np.array(point1) point2 = np.array(point2) motion_vect = point2[:2] - point1[:2] motion_vect_unit = vectNorm(motion_vect) # Get coordinates of 2 points that describe the line x1, y1, z1 = point1 x2, y2, z2 = point2 # Compute the average angular velocity in px per frame ang_vel = np.sqrt((x2 - x1)**2 + (y2 - y1)**2) / (z2 - z1) # Compute the vector describing the length and direction of the meteor per frame motion_vect = ang_vel * motion_vect_unit # If the FF files is given, extract the points from FF after threshold if img_handle.input_type == 'ff': # Threshold the FF file img_thres = Image.thresholdFF(img_handle.ff, config.k1_det, config.j1_det, mask=mask, \ mask_ave_bright=False) # Extract the thresholded image by min and max frames from FF file img = selectFFFrames(np.copy(img_thres), img_handle.ff, frame_min, frame_max) # Remove lonely pixels img = morph.clean(img) # Extract the stripe from the thresholded image stripe = np.zeros(img.shape, img.dtype) stripe[stripe_indices] = img[stripe_indices] # Show stripe # show2("stripe", stripe*255) # Show 3D could # show3DCloud(ff, stripe) # Get stripe positions (x, y, frame) stripe_positions = stripe.nonzero() xs = stripe_positions[1] ys = stripe_positions[0] zs = img_handle.ff.maxframe[stripe_positions] return xs, ys, zs # If video frames are available, extract indices on all frames in the given range else: xs_array = [] ys_array = [] zs_array = [] # Go through all frames in the frame range for fr in range(frame_min, frame_max + 1): # Break the loop if outside frame size if fr == (img_handle.total_frames - 1): break # Set the frame number img_handle.setFrame(fr) # Load the frame fr_img = img_handle.loadFrame() # Apply the dark frame if dark is not None: fr_img = Image.applyDark(fr_img, dark) # Apply the flat to frame if flat_struct is not None: fr_img = Image.applyFlat(fr_img, flat_struct) # Mask the image fr_img = MaskImage.applyMask(fr_img, mask) # Threshold the frame img_thres = Image.thresholdImg(fr_img, img_handle.ff.avepixel, img_handle.ff.stdpixel, \ config.k1_det, config.j1_det, mask=mask, mask_ave_bright=False) # Remove lonely pixels img_thres = morph.clean(img_thres) # Extract the stripe from the thresholded image stripe = np.zeros(img_thres.shape, img_thres.dtype) stripe[stripe_indices] = img_thres[stripe_indices] # Include more pixels for centroiding and photometry and mask out per frame pixels if centroiding: # Dilate the pixels in the stripe twice, to include more pixels for photometry stripe = morph.dilate(stripe) stripe = morph.dilate(stripe) # Get indices of the stripe that is perpendicular to the meteor, and whose thickness is the # length of the meteor on this particular frame - this is called stripe_indices_motion # Compute the previous, current, and the next linear model position of the meteor on the # image model_pos_prev = point1[:2] + (fr - 1 - z1) * motion_vect model_pos = point1[:2] + (fr - z1) * motion_vect model_pos_next = point1[:2] + (fr + 1 - z1) * motion_vect # Get the rho, theta of the line perpendicular to the meteor line x_inters, y_inters = model_pos # Check if the previous, current or the next centroids are outside bounds, and if so, skip the # frame if (not checkCentroidBounds(model_pos_prev, img_w, img_h)) or \ (not checkCentroidBounds(model_pos, img_w, img_h)) or \ (not checkCentroidBounds(model_pos_next, img_w, img_h)): continue # Get parameters of the perpendicular line to the meteor line rho2, theta2 = htLinePerpendicular(rho, theta, x_inters, y_inters, img_h, img_w) # Compute the image indices of this position which will be the intersection with the stripe # The width of the line will be 2x the angular velocity stripe_length = 6 * ang_vel if stripe_length < stripe_width_factor * config.stripe_width: stripe_length = stripe_width_factor * config.stripe_width stripe_indices_motion = getStripeIndices( rho2, theta2, stripe_length, img_h, img_w) # Mark only those parts which overlap both lines, which effectively creates a mask for # photometry an centroiding, excluding other influences stripe_new = np.zeros_like(stripe) stripe_new[stripe_indices_motion] = stripe[ stripe_indices_motion] stripe = stripe_new if debug: # Show the extracted stripe img_stripe = np.zeros_like(stripe) img_stripe[stripe_indices] = 1 final_stripe = np.zeros_like(stripe) final_stripe[stripe_indices_motion] = img_stripe[ stripe_indices_motion] plt.imshow(final_stripe) plt.show() if debug and centroiding: print(fr) print('mean stdpixel3:', np.mean(img_handle.ff.stdpixel)) print('mean avepixel3:', np.mean(img_handle.ff.avepixel)) print('mean frame:', np.mean(fr_img)) fig, (ax1, ax2) = plt.subplots(nrows=2, sharex=True, sharey=True) fr_img_noavg = Image.applyDark(fr_img, img_handle.ff.avepixel) #fr_img_noavg = fr_img # Auto levels min_lvl = np.percentile(fr_img_noavg[2:, :], 1) max_lvl = np.percentile(fr_img_noavg[2:, :], 99.0) # Adjust levels fr_img_autolevel = Image.adjustLevels(fr_img_noavg, min_lvl, 1.0, max_lvl) ax1.imshow(stripe, cmap='gray') ax2.imshow(fr_img_autolevel, cmap='gray') plt.show() pass # Get stripe positions (x, y, frame) stripe_positions = stripe.nonzero() xs = stripe_positions[1] ys = stripe_positions[0] zs = np.zeros_like(xs) + fr # Add the points to the list xs_array.append(xs) ys_array.append(ys) zs_array.append(zs) if debug: print('---') print(stripe.nonzero()) print(xs, ys, zs) if len(xs_array) > 0: # Flatten the arrays xs_array = np.concatenate(xs_array) ys_array = np.concatenate(ys_array) zs_array = np.concatenate(zs_array) else: xs_array = np.array(xs_array) ys_array = np.array(ys_array) zs_array = np.array(zs_array) return xs_array, ys_array, zs_array
def extractStars(ff_dir, ff_name, config=None, max_global_intensity=150, border=10, neighborhood_size=10, intensity_threshold=5, flat_struct=None): """ Extracts stars on a given FF bin by searching for local maxima and applying PSF fit for star confirmation. Source of one part of the code: http://stackoverflow.com/questions/9111711/get-coordinates-of-local-maxima-in-2d-array-above-certain-value Arguments: ff: [ff bin struct] FF bin file loaded in the FF bin structure config: [config object] configuration object (loaded from the .config file) max_global_intensity: [int] maximum mean intensity of an image before it is discared as too bright border: [int] apply a mask on the detections by removing all that are too close to the given image border (in pixels) neighborhood_size: [int] size of the neighbourhood for the maximum search (in pixels) intensity_threshold: [float] a threshold for cutting the detections which are too faint (0-255) flat_struct: [Flat struct] Structure containing the flat field. None by default. Return: x2, y2, background, intensity: [list of ndarrays] - x2: X axis coordinates of the star - y2: Y axis coordinates of the star - background: background intensity - intensity: intensity of the star """ # Load parameters from config if given if config: max_global_intensity = config.max_global_intensity border = config.border neighborhood_size = config.neighborhood_size intensity_threshold = config.intensity_threshold # Load the FF bin file ff = FFfile.read(ff_dir, ff_name) # Load the mask file mask = MaskImage.loadMask(config.mask_file) # Mask the FF file ff = MaskImage.applyMask(ff, mask, ff_flag=True) # Apply the flat to maxpixel and avepixel if flat_struct is not None: ff.maxpixel = Image.applyFlat(ff.maxpixel, flat_struct) ff.avepixel = Image.applyFlat(ff.avepixel, flat_struct) # Calculate image mean and stddev global_mean = np.mean(ff.avepixel) # Check if the image is too bright and skip the image if global_mean > max_global_intensity: return [[], [], [], []] data = ff.avepixel.astype(np.float32) # Apply a mean filter to the image to reduce noise data = ndimage.filters.convolve(data, weights=np.full((2, 2), 1.0 / 4)) # Locate local maxima on the image data_max = filters.maximum_filter(data, neighborhood_size) maxima = (data == data_max) data_min = filters.minimum_filter(data, neighborhood_size) diff = ((data_max - data_min) > intensity_threshold) maxima[diff == 0] = 0 # Apply a border mask border_mask = np.ones_like(maxima) * 255 border_mask[:border, :] = 0 border_mask[-border:, :] = 0 border_mask[:, :border] = 0 border_mask[:, -border:] = 0 maxima = MaskImage.applyMask(maxima, (True, border_mask)) # Find and label the maxima labeled, num_objects = ndimage.label(maxima) # Skip the image if there are too many maxima to process if num_objects > config.max_stars: print('Too many candidate stars to process! {:d}/{:d}'.format( num_objects, config.max_stars)) return [[], [], [], []] # Find centres of mass of each labeled objects xy = np.array( ndimage.center_of_mass(data, labeled, range(1, num_objects + 1))) # Remove all detection on the border #xy = xy[np.where((xy[:, 1] > border) & (xy[:,1] < ff.ncols - border) & (xy[:,0] > border) & (xy[:,0] < ff.nrows - border))] # Unpack star coordinates y, x = np.hsplit(xy, 2) # # Plot stars before the PSF fit # plotStars(ff, x, y) # Fit a PSF to each star x2, y2, amplitude, intensity = fitPSF(ff, global_mean, x, y, config=config) # x2, y2, amplitude, intensity = list(x), list(y), [], [] # Skip PSF fit # # Plot stars after PSF fit filtering # plotStars(ff, x2, y2) return x2, y2, amplitude, intensity
# Check if there are any file in the directory if(len(ff_list) == None): print("No files found!") sys.exit() # Try loading a flat field image flat_struct = None if config.use_flat: # Check if there is flat in the data directory if os.path.exists(os.path.join(ff_dir, config.flat_file)): flat_struct = Image.loadFlat(ff_dir, config.flat_file) # Try loading the default flat elif os.path.exists(config.flat_file): flat_struct = Image.loadFlat(os.getcwd(), config.flat_file) # Initialize the detector detector = QueuedPool(detectStarsAndMeteors, cores=-1, log=log) # Give detector jobs for ff_name in ff_list: detector.addJob([ff_dir, ff_name, config, flat_struct]) # Start the detection
# Get paths to every FF bin file in a directory ff_list = [ff for ff in os.listdir(dir_path) if FFfile.validFFName(ff)] # Check if there are any file in the directory if (len(ff_list) == None): print("No files found!") sys.exit() # Try loading a flat field image flat_struct = None if config.use_flat: # Check if there is flat in the data directory if os.path.exists(os.path.join(dir_path, config.flat_file)): flat_struct = Image.loadFlat(dir_path, config.flat_file) # Try loading the default flat elif os.path.exists(config.flat_file): flat_struct = Image.loadFlat(os.getcwd(), config.flat_file) # Init results list results_list = [] # Open a file for results results_path = os.path.abspath(dir_path) + os.sep results_name = results_path.split(os.sep)[-2] results_file = open(results_path + results_name + '_results.txt', 'w') total_meteors = 0
def generateCalibrationReport(config, night_dir_path, match_radius=2.0, platepar=None, show_graphs=False): """ Given the folder of the night, find the Calstars file, check the star fit and generate a report with the quality of the calibration. The report contains information about both the astrometry and the photometry calibration. Graphs will be saved in the given directory of the night. Arguments: config: [Config instance] night_dir_path: [str] Full path to the directory of the night. Keyword arguments: match_radius: [float] Match radius for star matching between image and catalog stars (px). platepar: [Platepar instance] Use this platepar instead of finding one in the folder. show_graphs: [bool] Show the graphs on the screen. False by default. Return: None """ # Find the CALSTARS file in the given folder calstars_file = None for calstars_file in os.listdir(night_dir_path): if ('CALSTARS' in calstars_file) and ('.txt' in calstars_file): break if calstars_file is None: print('CALSTARS file could not be found in the given directory!') return None # Load the calstars file star_list = readCALSTARS(night_dir_path, calstars_file) ### Load recalibrated platepars, if they exist ### # Find recalibrated platepars file per FF file platepars_recalibrated_file = None for file_name in os.listdir(night_dir_path): if file_name == config.platepars_recalibrated_name: platepars_recalibrated_file = file_name break # Load all recalibrated platepars if the file is available recalibrated_platepars = None if platepars_recalibrated_file: with open(os.path.join(night_dir_path, platepars_recalibrated_file)) as f: recalibrated_platepars = json.load(f) print( 'Loaded recalibrated platepars JSON file for the calibration report...' ) ### ### ### Load the platepar file ### # Find the platepar file in the given directory if it was not given if platepar is None: # Find the platepar file platepar_file = None for file_name in os.listdir(night_dir_path): if file_name == config.platepar_name: platepar_file = file_name break if platepar_file is None: print('The platepar cannot be found in the night directory!') return None # Load the platepar file platepar = Platepar() platepar.read(os.path.join(night_dir_path, platepar_file), use_flat=config.use_flat) ### ### night_name = os.path.split(night_dir_path.strip(os.sep))[1] # Go one mag deeper than in the config lim_mag = config.catalog_mag_limit + 1 # Load catalog stars (load one magnitude deeper) catalog_stars, mag_band_str, config.star_catalog_band_ratios = StarCatalog.readStarCatalog(\ config.star_catalog_path, config.star_catalog_file, lim_mag=lim_mag, \ mag_band_ratios=config.star_catalog_band_ratios) ### Take only those CALSTARS entires for which FF files exist in the folder ### # Get a list of FF files in the folder ff_list = [] for file_name in os.listdir(night_dir_path): if validFFName(file_name): ff_list.append(file_name) # Filter out calstars entries, generate a star dictionary where the keys are JDs of FFs star_dict = {} ff_dict = {} for entry in star_list: ff_name, star_data = entry # Check if the FF from CALSTARS exists in the folder if ff_name not in ff_list: continue dt = getMiddleTimeFF(ff_name, config.fps, ret_milliseconds=True) jd = date2JD(*dt) # Add the time and the stars to the dict star_dict[jd] = star_data ff_dict[jd] = ff_name ### ### # If there are no FF files in the directory, don't generate a report if len(star_dict) == 0: print('No FF files from the CALSTARS file in the directory!') return None # If the recalibrated platepars file exists, take the one with the most stars max_jd = 0 using_recalib_platepars = False if recalibrated_platepars is not None: max_stars = 0 for ff_name_temp in recalibrated_platepars: # Compute the Julian date of the FF middle dt = getMiddleTimeFF(ff_name_temp, config.fps, ret_milliseconds=True) jd = date2JD(*dt) # Check that this file exists in CALSTARS and the list of FF files if (jd not in star_dict) or (jd not in ff_dict): continue # Check if the number of stars on this FF file is larger than the before if len(star_dict[jd]) > max_stars: max_jd = jd max_stars = len(star_dict[jd]) # Set a flag to indicate if using recalibrated platepars has failed if max_jd == 0: using_recalib_platepars = False else: print('Using recalibrated platepars, file:', ff_dict[max_jd]) using_recalib_platepars = True # Select the platepar where the FF file has the most stars platepar_dict = recalibrated_platepars[ff_dict[max_jd]] platepar = Platepar() platepar.loadFromDict(platepar_dict, use_flat=config.use_flat) filtered_star_dict = {max_jd: star_dict[max_jd]} # Match stars on the image with the stars in the catalog n_matched, avg_dist, cost, matched_stars = matchStarsResiduals(config, platepar, catalog_stars, \ filtered_star_dict, match_radius, ret_nmatch=True, lim_mag=lim_mag) max_matched_stars = n_matched # Otherwise take the optimal FF file for evaluation if (recalibrated_platepars is None) or (not using_recalib_platepars): # If there are more than a set number of FF files to evaluate, choose only the ones with most stars on # the image if len(star_dict) > config.calstars_files_N: # Find JDs of FF files with most stars on them top_nstars_indices = np.argsort([len(x) for x in star_dict.values()])[::-1][:config.calstars_files_N \ - 1] filtered_star_dict = {} for i in top_nstars_indices: filtered_star_dict[list(star_dict.keys())[i]] = list( star_dict.values())[i] star_dict = filtered_star_dict # Match stars on the image with the stars in the catalog n_matched, avg_dist, cost, matched_stars = matchStarsResiduals(config, platepar, catalog_stars, \ star_dict, match_radius, ret_nmatch=True, lim_mag=lim_mag) # If no recalibrated platepars where found, find the image with the largest number of matched stars if (not using_recalib_platepars) or (max_jd == 0): max_jd = 0 max_matched_stars = 0 for jd in matched_stars: _, _, distances = matched_stars[jd] if len(distances) > max_matched_stars: max_jd = jd max_matched_stars = len(distances) # If there are no matched stars, use the image with the largest number of detected stars if max_matched_stars <= 2: max_jd = max(star_dict, key=lambda x: len(star_dict[x])) distances = [np.inf] # Take the FF file with the largest number of matched stars ff_name = ff_dict[max_jd] # Load the FF file ff = readFF(night_dir_path, ff_name) img_h, img_w = ff.avepixel.shape dpi = 200 plt.figure(figsize=(ff.avepixel.shape[1] / dpi, ff.avepixel.shape[0] / dpi), dpi=dpi) # Take the average pixel img = ff.avepixel # Slightly adjust the levels img = Image.adjustLevels(img, np.percentile(img, 1.0), 1.3, np.percentile(img, 99.99)) plt.imshow(img, cmap='gray', interpolation='nearest') legend_handles = [] # Plot detected stars for img_star in star_dict[max_jd]: y, x, _, _ = img_star rect_side = 5 * match_radius square_patch = plt.Rectangle((x - rect_side/2, y - rect_side/2), rect_side, rect_side, color='g', \ fill=False, label='Image stars') plt.gca().add_artist(square_patch) legend_handles.append(square_patch) # If there are matched stars, plot them if max_matched_stars > 2: # Take the solution with the largest number of matched stars image_stars, matched_catalog_stars, distances = matched_stars[max_jd] # Plot matched stars for img_star in image_stars: x, y, _, _ = img_star circle_patch = plt.Circle((y, x), radius=3*match_radius, color='y', fill=False, \ label='Matched stars') plt.gca().add_artist(circle_patch) legend_handles.append(circle_patch) ### Plot match residuals ### # Compute preducted positions of matched image stars from the catalog x_predicted, y_predicted = raDecToXYPP(matched_catalog_stars[:, 0], \ matched_catalog_stars[:, 1], max_jd, platepar) img_y, img_x, _, _ = image_stars.T delta_x = x_predicted - img_x delta_y = y_predicted - img_y # Compute image residual and angle of the error res_angle = np.arctan2(delta_y, delta_x) res_distance = np.sqrt(delta_x**2 + delta_y**2) # Calculate coordinates of the beginning of the residual line res_x_beg = img_x + 3 * match_radius * np.cos(res_angle) res_y_beg = img_y + 3 * match_radius * np.sin(res_angle) # Calculate coordinates of the end of the residual line res_x_end = img_x + 100 * np.cos(res_angle) * res_distance res_y_end = img_y + 100 * np.sin(res_angle) * res_distance # Plot the 100x residuals for i in range(len(x_predicted)): res_plot = plt.plot([res_x_beg[i], res_x_end[i]], [res_y_beg[i], res_y_end[i]], color='orange', \ lw=0.5, label='100x residuals') legend_handles.append(res_plot[0]) ### ### else: distances = [np.inf] # If there are no matched stars, plot large text in the middle of the screen plt.text(img_w / 2, img_h / 2, "NO MATCHED STARS!", color='r', alpha=0.5, fontsize=20, ha='center', va='center') ### Plot positions of catalog stars to the limiting magnitude of the faintest matched star + 1 mag ### # Find the faintest magnitude among matched stars if max_matched_stars > 2: faintest_mag = np.max(matched_catalog_stars[:, 2]) + 1 else: # If there are no matched stars, use the limiting magnitude from config faintest_mag = config.catalog_mag_limit + 1 # Estimate RA,dec of the centre of the FOV _, RA_c, dec_c, _ = xyToRaDecPP([jd2Date(max_jd)], [platepar.X_res / 2], [platepar.Y_res / 2], [1], platepar) RA_c = RA_c[0] dec_c = dec_c[0] fov_radius = np.hypot(*computeFOVSize(platepar)) # Get stars from the catalog around the defined center in a given radius _, extracted_catalog = subsetCatalog(catalog_stars, RA_c, dec_c, fov_radius, faintest_mag) ra_catalog, dec_catalog, mag_catalog = extracted_catalog.T # Compute image positions of all catalog stars that should be on the image x_catalog, y_catalog = raDecToXYPP(ra_catalog, dec_catalog, max_jd, platepar) # Filter all catalog stars outside the image temp_arr = np.c_[x_catalog, y_catalog, mag_catalog] temp_arr = temp_arr[temp_arr[:, 0] >= 0] temp_arr = temp_arr[temp_arr[:, 0] <= ff.avepixel.shape[1]] temp_arr = temp_arr[temp_arr[:, 1] >= 0] temp_arr = temp_arr[temp_arr[:, 1] <= ff.avepixel.shape[0]] x_catalog, y_catalog, mag_catalog = temp_arr.T # Plot catalog stars on the image cat_stars_handle = plt.scatter(x_catalog, y_catalog, c='none', marker='D', lw=1.0, alpha=0.4, \ s=((4.0 + (faintest_mag - mag_catalog))/3.0)**(2*2.512), edgecolor='r', label='Catalog stars') legend_handles.append(cat_stars_handle) ### ### # Add info text in the corner info_text = ff_dict[max_jd] + '\n' \ + "Matched stars within {:.1f} px radius: {:d}/{:d} \n".format(match_radius, max_matched_stars, \ len(star_dict[max_jd])) \ + "Median distance = {:.2f} px\n".format(np.median(distances)) \ + "Catalog lim mag = {:.1f}".format(lim_mag) plt.text(10, 10, info_text, bbox=dict(facecolor='black', alpha=0.5), va='top', ha='left', fontsize=4, \ color='w', family='monospace') legend = plt.legend(handles=legend_handles, prop={'size': 4}, loc='upper right') legend.get_frame().set_facecolor('k') legend.get_frame().set_edgecolor('k') for txt in legend.get_texts(): txt.set_color('w') ### Add FOV info (centre, size) ### # Mark FOV centre plt.scatter(platepar.X_res / 2, platepar.Y_res / 2, marker='+', s=20, c='r', zorder=4) # Compute FOV centre alt/az azim_centre, alt_centre = raDec2AltAz(max_jd, platepar.lon, platepar.lat, RA_c, dec_c) # Compute FOV size fov_h, fov_v = computeFOVSize(platepar) # Compute the rotation wrt. horizon rot_horizon = rotationWrtHorizon(platepar) fov_centre_text = "Azim = {:6.2f}$\\degree$\n".format(azim_centre) \ + "Alt = {:6.2f}$\\degree$\n".format(alt_centre) \ + "Rot h = {:6.2f}$\\degree$\n".format(rot_horizon) \ + "FOV h = {:6.2f}$\\degree$\n".format(fov_h) \ + "FOV v = {:6.2f}$\\degree$".format(fov_v) \ plt.text(10, platepar.Y_res - 10, fov_centre_text, bbox=dict(facecolor='black', alpha=0.5), \ va='bottom', ha='left', fontsize=4, color='w', family='monospace') ### ### # Plot RA/Dec gridlines # addEquatorialGrid(plt, platepar, max_jd) plt.axis('off') plt.gca().get_xaxis().set_visible(False) plt.gca().get_yaxis().set_visible(False) plt.xlim([0, ff.avepixel.shape[1]]) plt.ylim([ff.avepixel.shape[0], 0]) # Remove the margins plt.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=0, hspace=0) plt.savefig(os.path.join(night_dir_path, night_name + '_calib_report_astrometry.jpg'), \ bbox_inches='tight', pad_inches=0, dpi=dpi) if show_graphs: plt.show() else: plt.clf() plt.close() if max_matched_stars > 2: ### PHOTOMETRY FIT ### # If a flat is used, set the vignetting coeff to 0 if config.use_flat: platepar.vignetting_coeff = 0.0 # Extact intensities and mangitudes star_intensities = image_stars[:, 2] catalog_mags = matched_catalog_stars[:, 2] # Compute radius of every star from image centre radius_arr = np.hypot(image_stars[:, 0] - img_h / 2, image_stars[:, 1] - img_w / 2) # Fit the photometry on automated star intensities (use the fixed vignetting coeff, use robust fit) photom_params, fit_stddev, fit_resid, star_intensities, radius_arr, catalog_mags = \ photometryFitRobust(star_intensities, radius_arr, catalog_mags, \ fixed_vignetting=platepar.vignetting_coeff) photom_offset, _ = photom_params ### ### ### PLOT PHOTOMETRY ### # Note: An almost identical code exists in RMS.Astrometry.SkyFit in the PlateTool.photometry function dpi = 130 fig_p, (ax_p, ax_r) = plt.subplots(nrows=2, facecolor=None, figsize=(6.0, 7.0), dpi=dpi, \ gridspec_kw={'height_ratios':[2, 1]}) # Plot raw star intensities ax_p.scatter(-2.5 * np.log10(star_intensities), catalog_mags, s=5, c='r', alpha=0.5, label="Raw") # If a flat is used, disregard the vignetting if not config.use_flat: # Plot intensities of image stars corrected for vignetting lsp_corr_arr = np.log10(correctVignetting(star_intensities, radius_arr, \ platepar.vignetting_coeff)) ax_p.scatter(-2.5*lsp_corr_arr, catalog_mags, s=5, c='b', alpha=0.5, \ label="Corrected for vignetting") # Plot photometric offset from the platepar x_min, x_max = ax_p.get_xlim() y_min, y_max = ax_p.get_ylim() x_min_w = x_min - 3 x_max_w = x_max + 3 y_min_w = y_min - 3 y_max_w = y_max + 3 photometry_info = "Platepar: {:+.1f}*LSP + {:.2f} +/- {:.2f}".format(platepar.mag_0, \ platepar.mag_lev, platepar.mag_lev_stddev) \ + "\nVignetting coeff = {:.5f}".format(platepar.vignetting_coeff) \ + "\nGamma = {:.2f}".format(platepar.gamma) # Plot the photometry calibration from the platepar logsum_arr = np.linspace(x_min_w, x_max_w, 10) ax_p.plot(logsum_arr, logsum_arr + platepar.mag_lev, label=photometry_info, linestyle='--', \ color='k', alpha=0.5) # Plot the fitted photometry calibration fit_info = "Fit: {:+.1f}*LSP + {:.2f} +/- {:.2f}".format( -2.5, photom_offset, fit_stddev) ax_p.plot(logsum_arr, logsum_arr + photom_offset, label=fit_info, linestyle='--', color='b', alpha=0.75) ax_p.legend() ax_p.set_ylabel("Catalog magnitude ({:s})".format(mag_band_str)) ax_p.set_xlabel("Uncalibrated magnitude") # Set wider axis limits ax_p.set_xlim(x_min_w, x_max_w) ax_p.set_ylim(y_min_w, y_max_w) ax_p.invert_yaxis() ax_p.invert_xaxis() ax_p.grid() ### Plot photometry vs radius ### img_diagonal = np.hypot(img_h / 2, img_w / 2) # Plot photometry residuals (including vignetting) ax_r.scatter(radius_arr, fit_resid, c='b', alpha=0.75, s=5, zorder=3) # Plot a zero line ax_r.plot(np.linspace(0, img_diagonal, 10), np.zeros(10), linestyle='dashed', alpha=0.5, \ color='k') # Plot only when no flat is used if not config.use_flat: # Plot radius from centre vs. fit residual fit_resids_novignetting = catalog_mags - photomLine((np.array(star_intensities), \ np.array(radius_arr)), photom_offset, 0.0) ax_r.scatter(radius_arr, fit_resids_novignetting, s=5, c='r', alpha=0.5, zorder=3) px_sum_tmp = 1000 radius_arr_tmp = np.linspace(0, img_diagonal, 50) # Plot vignetting loss curve vignetting_loss = 2.5*np.log10(px_sum_tmp) \ - 2.5*np.log10(correctVignetting(px_sum_tmp, radius_arr_tmp, \ platepar.vignetting_coeff)) ax_r.plot(radius_arr_tmp, vignetting_loss, linestyle='dotted', alpha=0.5, color='k') ax_r.grid() ax_r.set_ylabel("Fit residuals (mag)") ax_r.set_xlabel("Radius from centre (px)") ax_r.set_xlim(0, img_diagonal) ### ### plt.tight_layout() plt.savefig(os.path.join(night_dir_path, night_name + '_calib_report_photometry.png'), dpi=150) if show_graphs: plt.show() else: plt.clf() plt.close()
# Check if there are any file in the directory if(len(ff_list) == None): print("No files found!") sys.exit() # Try loading a flat field image flat_struct = None if config.use_flat: # Check if there is flat in the data directory if os.path.exists(os.path.join(ff_dir, config.flat_file)): flat_struct = Image.loadFlat(ff_dir, config.flat_file) # Try loading the default flat elif os.path.exists(config.flat_file): flat_struct = Image.loadFlat(os.getcwd(), config.flat_file) extraction_list = [] # Go through all files in the directory and add them to the detection list for ff_name in sorted(ff_list): # Check if the given file is a valid FF file if not FFfile.validFFName(ff_name):