import datetime import numpy as np from matplotlib.backends.backend_pdf import PdfPages import matplotlib.pyplot as plt import math import cv2 import os STANDARD_FIG_SIZE = (16, 9) OUT_PDF_FILE_NAME = 'tmp/fisheye_pdf.pdf' os.makedirs('tmp', exist_ok=True) def make_pdf(i, state, result, dataset, table_headers): fish_info = result["fish_info"][i] fish_table = result["fish_table"][i] json_result = result['json_result'][i] dataset = result['datasets'][i] metadata = json_result['metadata'] with PdfPages(OUT_PDF_FILE_NAME) as pdf: plt.rcParams['text.usetex'] = False generate_title_page(pdf, metadata, state) generate_global_result(pdf, fish_info) generate_fish_list(pdf, table_headers, fish_table) for i, fish in enumerate(json_result['fish']): calculate_fish_paths(json_result, dataset, i) draw_combined_fish_graphs(pdf, json_result) for i, fish in enumerate(json_result['fish']): draw_fish_tracks(pdf, json_result, dataset, i) # We can also set the file's metadata via the PdfPages object: d = pdf.infodict() d['Title'] = 'Multipage PDF Example' d['Author'] = 'Oskar Åström' d['Subject'] = 'How to create a multipage pdf file and set its metadata' d['Keywords'] = '' d['CreationDate'] = datetime.datetime.today() d['ModDate'] = datetime.datetime.today() def generate_title_page(pdf, metadata, state): # set up figure that will be used to display the opening banner fig = plt.figure(figsize=STANDARD_FIG_SIZE) plt.axis('off') title_font_size = 40 minor_font_size = 20 # stuff to be printed out on the first page of the report plt.text(0.5,-0.5,f'{metadata["FILE_NAME"].split("/")[-1]}',fontsize=title_font_size, horizontalalignment='center') plt.text(0,1,f'Duration: {metadata["TOTAL_TIME"]}',fontsize=minor_font_size) plt.text(0,1.5,f'Frames: {metadata["TOTAL_FRAMES"]}',fontsize=minor_font_size) plt.text(0,2,f'Frame Rate: {metadata["FRAME_RATE"]}',fontsize=minor_font_size) plt.text(0.5,1,f'Time of filming: {metadata["DATE"]} ({metadata["START"]} - {metadata["END"]})',fontsize=minor_font_size) plt.text(0.5,1.5,f'Web app version: {state["version"]}',fontsize=minor_font_size) plt.text(1.1,4.5,f'PDF generated on {datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")}',fontsize=minor_font_size, horizontalalignment='right') plt.ylim([-1, 4]) plt.xlim([0, 1]) plt.gca().invert_yaxis() pdf.savefig(fig) plt.close(fig) def generate_global_result(pdf, fish_info): # set up figure that will be used to display the opening banner fig = plt.figure(figsize=STANDARD_FIG_SIZE) plt.axis('off') # stuff to be printed out on the first page of the report minor_font_size = 18 headers = ["Result", "Camera Info", "Hyperparameters"] info_col_1 = [] info_col_2 = [] info_col = info_col_1 row_state = -1 for row in fish_info: if row_state >= 0: info_col.append([row[0].replace("**","").replace("_", " ").lower(), row[1], 'normal']) if (row[0] == "****"): row_state += 1 if row_state == 2: info_col = info_col_2 info_col.append([headers[row_state], "", 'bold']) for row_i, row in enumerate(info_col_1): h = -1 + 5*row_i/len(info_col_1) plt.text(0, h, row[0], fontsize=minor_font_size, weight=row[2]) plt.text(0.25, h, row[1], fontsize=minor_font_size, weight=row[2]) for row_i, row in enumerate(info_col_2): h = -1 + 5*row_i/len(info_col_2) plt.text(0.5, h, row[0], fontsize=minor_font_size, weight=row[2]) plt.text(0.75, h, row[1], fontsize=minor_font_size, weight=row[2]) plt.ylim([-1, 4]) plt.xlim([0, 1]) plt.gca().invert_yaxis() pdf.savefig(fig) plt.close(fig) def generate_fish_list(pdf, table_headers, fish_table): # set up figure that will be used to display the opening banner fig = plt.figure(figsize=STANDARD_FIG_SIZE) plt.axis('off') # stuff to be printed out on the first page of the report title_font_size = 40 header_font_size = 12 body_font_size = 20 # Title plt.text(0.5,-1.3,f'{"Identified Fish"}',fontsize=title_font_size, horizontalalignment='center', weight='bold') # Identified fish row_h = 0.25 col_start = 0 row_l = 1 dropout_i = None for col_i, col in enumerate(table_headers): x = col_start + row_l*(col_i+0.5)/len(table_headers) if col == "TOTAL": col = "ID" if col == "DETECTION_DROPOUT": col = "frame drop rate" dropout_i = col_i col = col.lower().replace("_", " ") plt.text(x, -1, col, fontsize=header_font_size, horizontalalignment='center', weight="bold") plt.plot([col_start*2, -col_start*2 + row_l], [-1 + 0.05, -1 + 0.05], color='black') for row_i, row in enumerate(fish_table): y = -1 + (row_i+1)*row_h plt.plot([col_start*2, -col_start*2 + row_l], [y+0.05, y+0.05], color='black') for col_i, col in enumerate(row): x = col_start + row_l*(col_i+0.5)/len(row) if (col_i == dropout_i and type(col) is not str): col = str(int(col*100)) + "%" elif type(col) == float: col = "{:.4f}".format(col) plt.text(x, y, col, fontsize=body_font_size, horizontalalignment='center') plt.ylim([-1, 4]) plt.xlim([0, 1]) plt.gca().invert_yaxis() pdf.savefig(fig) plt.close(fig) def calculate_fish_paths(result, dataset, id): fish = result['metadata']['FISH'][id] start_frame = fish['START_FRAME'] end_frame = fish['END_FRAME'] fps = result['metadata']['FRAME_RATE'] # Extract base frame (first frame for that fish) w, h = 1, 2 img = None if (dataset is not None): images = dataset.didson.load_frames(start_frame=start_frame, end_frame=start_frame+1) img = images[0] w, h = img.shape frame_height = 2 scale_factor = frame_height / h h = frame_height w = int(scale_factor*w) fish['base_frame'] = img fish['scaled_frame_size'] = (h, w) # Find frames for this fish bboxes = [] for frame in result['frames'][start_frame:end_frame+1]: bbox = None for ann in frame['fish']: if ann['fish_id'] == id+1: bbox = ann bboxes.append(bbox) # Calculate tracks through frames missed = 0 X = [] Y = [] V = [] certainty = [] for bbox in bboxes: if bbox is not None: # Find fish centers x = (bbox['bbox'][0] + bbox['bbox'][2])/2 y = (bbox['bbox'][1] + bbox['bbox'][3])/2 # Calculate velocity v = None if len(X) > 0: last_x = X[-1] last_y = Y[-1] dx = result['image_meter_width']*(last_x - x)/(missed+1) dy = result['image_meter_height']*(last_y - y)/(missed+1) v = math.sqrt(dx*dx + dy*dy) * fps # Interpolate over missing frames if missed > 0: for i in range(missed): p = (i+1)/(missed+1) X.append(last_x*(1-p) + p*x) Y.append(last_y*(1-p) + p*y) V.append(v) certainty.append(False) # Append new track frame X.append(x) Y.append(y) if v is not None: V.append(v) certainty.append(True) missed = 0 else: missed += 1 fish['path'] = { 'X': X, 'Y': Y, 'certainty': certainty, 'V': V } def draw_combined_fish_graphs(pdf, result): vel = [] log_vel = [] eps = 0.00000000001 for fish in result['metadata']['FISH']: for v in fish['path']['V']: vel += [v] if v > 0: log_vel += [math.log(v)] fig, axs = plt.subplots(2, 2, sharex=False, sharey=False, figsize=STANDARD_FIG_SIZE) # Title fig.suptitle('Fish velocities', fontsize=40, horizontalalignment='center', weight='bold') axs[0,0].hist(log_vel, bins=20) axs[0,0].set_title('Fish Log-Velocities between frames') axs[0,0].set_xlabel("Log-Velocity (log(m/s))") axs[0,1].hist(vel, bins=20) axs[0,1].set_title('Fish Velocities between frames') axs[0,1].set_xlabel("Velocity (m/s)") for fish in result['metadata']['FISH']: data = [] for v in fish['path']['V']: if v > 0: data += [math.log(v)] n, bin_c = make_hist(data) axs[1,0].plot(bin_c, n) axs[1,0].set_title('Fish Log-Velocities between frames (per fish)') axs[1,0].set_xlabel("Log-Velocity (log(m/s))") for fish in result['metadata']['FISH']: data = fish['path']['V'] n, bin_c = make_hist(data) axs[1,1].plot(bin_c, n) axs[1,1].set_title('Fish Velocities between frames (per fish)') axs[1,1].set_xlabel("Velocity (m/s)") pdf.savefig(fig) plt.close(fig) def make_hist(data): '''histogram and return vectors for plotting''' # figure out the bins min_bin = np.min(data) max_bin = np.max(data) PTS_PER_BIN = 6 #np.sqrt(len(data)) #300 bin_sz = (max_bin-min_bin)/(len(data)/PTS_PER_BIN) bins = np.arange(min_bin-bin_sz,max_bin+2*bin_sz,bin_sz) bin_centers = (bins[0:-1]+bins[1:])/2 # bin centers # compute the histogram n,b = np.histogram(data,bins=bins,density=False) return n,bin_centers def draw_fish_tracks(pdf, result, dataset, id): fish = result['metadata']['FISH'][id] start_frame = fish['START_FRAME'] end_frame = fish['END_FRAME'] print(fish) fig, ax = plt.subplots(figsize=STANDARD_FIG_SIZE) plt.axis('off') w, h = fish['scaled_frame_size'] if (fish['base_frame'] is not None): img = fish['base_frame'] img = cv2.rotate(img, cv2.ROTATE_90_CLOCKWISE) plt.imshow(img, extent=(0, h, 0, w), cmap=plt.colormaps['Greys']) # Title plt.text(h/2,2,f'Fish {id+1} (frames {start_frame}-{end_frame})',fontsize=40, color="black", horizontalalignment='center', zorder=5) X = fish['path']['X'] Y = fish['path']['Y'] certainty = fish['path']['certainty'] plt.text(h*(1-Y[0]), w*(1-X[0]), "Start", fontsize=15, weight="bold") plt.text(h*(1-Y[-1]), w*(1-X[-1]), "End", fontsize=15, weight="bold") colors = [""] for i in range(1, len(X)): certain = certainty[i] fully_certain = certain half_certain = certain if i > 0: fully_certain &= certainty[i-1] half_certain |= certainty[i-1] #color = 'yellow' if certain else 'orangered' #plt.plot(h*(1-y), w*(1-x), marker='o', markersize=3, color=color, zorder=3) col = 'yellow' if fully_certain else ('darkorange' if half_certain else 'orangered') colors.append(col) ax.plot([h*(1-Y[i-1]), h*(1-Y[i])], [w*(1-X[i-1]), w*(1-X[i])], color=col, linewidth=1) for i in range(1, len(X)): ax.plot(h*(1-Y[i]), w*(1-X[i]), color=colors[i], marker='o', markersize=3) plt.ylim([0, w]) plt.xlim([0, h]) pdf.savefig(fig) plt.close(fig) if (dataset is not None): indices = [start_frame, int(2/3*start_frame + end_frame/3), int(1/3*start_frame + 2/3*end_frame), end_frame] fig, axs = plt.subplots(2, len(indices), sharex=False, sharey=False, figsize=STANDARD_FIG_SIZE) print("id", id) print('indices', indices) for i, frame_index in enumerate(indices): img = dataset.didson.load_frames(start_frame=frame_index, end_frame=frame_index+1)[0] box = None for fi in range(frame_index, min(frame_index+10, len(result['frames']))): for ann in result['frames'][fi]['fish']: if ann['fish_id'] == id+1: box = ann['bbox'] frame_index = fi break print("box", i, box) if box is not None: h, w = img.shape print(w, h) x1, x2, y1, y2 = int(box[0]*w), int(box[2]*w), int(box[1]*h), int(box[3]*h) cx, cy = int((x2 + x1)/2), int((y2 + y1)/2) s = min(int(max(x2 - x1, y2 - y1)*5/2), cx, cy, w-cx, h-cy) print(x1, x2, y1, y2) print(cx, cy, s) cropped_img = img[cy-s:cy+s, cx-s:cx+s] axs[0, i].imshow(cropped_img, extent=(cx-s, cx+s, cy-s, cy+s), cmap=plt.colormaps['Greys_r']) axs[0, i].plot([x1, x1, x2, x2, x1], [y1, y2, y2, y1, y1], color="red") axs[0, i].set_title('Frame ' + str(frame_index)) pdf.savefig(fig) plt.close(fig)