import torch import random import numpy as np import copy import librosa import torch.nn.functional as F import torchaudio import os import sys sys.path.append(os.path.join('..', '..')) import bat_detect.utils.audio_utils as au def generate_gt_heatmaps(spec_op_shape, sampling_rate, ann, params): # spec may be resized on input into the network num_classes = len(params['class_names']) op_height = spec_op_shape[0] op_width = spec_op_shape[1] freq_per_bin = (params['max_freq'] - params['min_freq']) / op_height # start and end times x_pos_start = au.time_to_x_coords(ann['start_times'], sampling_rate, params['fft_win_length'], params['fft_overlap']) x_pos_start = (params['resize_factor']*x_pos_start).astype(np.int) x_pos_end = au.time_to_x_coords(ann['end_times'], sampling_rate, params['fft_win_length'], params['fft_overlap']) x_pos_end = (params['resize_factor']*x_pos_end).astype(np.int) # location on y axis i.e. frequency y_pos_low = (ann['low_freqs'] - params['min_freq']) / freq_per_bin y_pos_low = (op_height - y_pos_low).astype(np.int) y_pos_high = (ann['high_freqs'] - params['min_freq']) / freq_per_bin y_pos_high = (op_height - y_pos_high).astype(np.int) bb_widths = x_pos_end - x_pos_start bb_heights = (y_pos_low - y_pos_high) valid_inds = np.where((x_pos_start >= 0) & (x_pos_start < op_width) & (y_pos_low >= 0) & (y_pos_low < (op_height-1)))[0] ann_aug = {} ann_aug['x_inds'] = x_pos_start[valid_inds] ann_aug['y_inds'] = y_pos_low[valid_inds] keys = ['start_times', 'end_times', 'high_freqs', 'low_freqs', 'class_ids', 'individual_ids'] for kk in keys: ann_aug[kk] = ann[kk][valid_inds] # if the number of calls is only 1, then it is unique # TODO would be better if we found these unique calls at the merging stage if len(ann_aug['individual_ids']) == 1: ann_aug['individual_ids'][0] = 0 y_2d_det = np.zeros((1, op_height, op_width), dtype=np.float32) y_2d_size = np.zeros((2, op_height, op_width), dtype=np.float32) # num classes and "background" class y_2d_classes = np.zeros((num_classes+1, op_height, op_width), dtype=np.float32) # create 2D ground truth heatmaps for ii in valid_inds: draw_gaussian(y_2d_det[0,:], (x_pos_start[ii], y_pos_low[ii]), params['target_sigma']) #draw_gaussian(y_2d_det[0,:], (x_pos_start[ii], y_pos_low[ii]), params['target_sigma'], params['target_sigma']*2) y_2d_size[0, y_pos_low[ii], x_pos_start[ii]] = bb_widths[ii] y_2d_size[1, y_pos_low[ii], x_pos_start[ii]] = bb_heights[ii] cls_id = ann['class_ids'][ii] if cls_id > -1: draw_gaussian(y_2d_classes[cls_id, :], (x_pos_start[ii], y_pos_low[ii]), params['target_sigma']) #draw_gaussian(y_2d_classes[cls_id, :], (x_pos_start[ii], y_pos_low[ii]), params['target_sigma'], params['target_sigma']*2) # be careful as this will have a 1.0 places where we have event but dont know gt class # this will be masked in training anyway y_2d_classes[num_classes, :] = 1.0 - y_2d_classes.sum(0) y_2d_classes = y_2d_classes / y_2d_classes.sum(0)[np.newaxis, ...] y_2d_classes[np.isnan(y_2d_classes)] = 0.0 return y_2d_det, y_2d_size, y_2d_classes, ann_aug def draw_gaussian(heatmap, center, sigmax, sigmay=None): # center is (x, y) # this edits the heatmap inplace if sigmay is None: sigmay = sigmax tmp_size = np.maximum(sigmax, sigmay) * 3 mu_x = int(center[0] + 0.5) mu_y = int(center[1] + 0.5) w, h = heatmap.shape[0], heatmap.shape[1] ul = [int(mu_x - tmp_size), int(mu_y - tmp_size)] br = [int(mu_x + tmp_size + 1), int(mu_y + tmp_size + 1)] if ul[0] >= h or ul[1] >= w or br[0] < 0 or br[1] < 0: return False size = 2 * tmp_size + 1 x = np.arange(0, size, 1, np.float32) y = x[:, np.newaxis] x0 = y0 = size // 2 #g = np.exp(- ((x - x0) ** 2 + (y - y0) ** 2) / (2 * sigma ** 2)) g = np.exp(- ((x - x0) ** 2)/(2 * sigmax ** 2) - ((y - y0) ** 2)/(2 * sigmay ** 2)) g_x = max(0, -ul[0]), min(br[0], h) - ul[0] g_y = max(0, -ul[1]), min(br[1], w) - ul[1] img_x = max(0, ul[0]), min(br[0], h) img_y = max(0, ul[1]), min(br[1], w) heatmap[img_y[0]:img_y[1], img_x[0]:img_x[1]] = np.maximum( heatmap[img_y[0]:img_y[1], img_x[0]:img_x[1]], g[g_y[0]:g_y[1], g_x[0]:g_x[1]]) return True def pad_aray(ip_array, pad_size): return np.hstack((ip_array, np.ones(pad_size, dtype=np.int)*-1)) def warp_spec_aug(spec, ann, return_spec_for_viz, params): # This is messy # Augment spectrogram by randomly stretch and squeezing # NOTE this also changes the start and stop time in place # not taking care of spec for viz if return_spec_for_viz: assert False delta = params['stretch_squeeze_delta'] op_size = (spec.shape[1], spec.shape[2]) resize_fract_r = np.random.rand()*delta*2 - delta + 1.0 resize_amt = int(spec.shape[2]*resize_fract_r) if resize_amt >= spec.shape[2]: spec_r = torch.cat((spec, torch.zeros((1, spec.shape[1], resize_amt-spec.shape[2]), dtype=spec.dtype)), 2) else: spec_r = spec[:, :, :resize_amt] spec = F.interpolate(spec_r.unsqueeze(0), size=op_size, mode='bilinear', align_corners=False).squeeze(0) ann['start_times'] *= (1.0/resize_fract_r) ann['end_times'] *= (1.0/resize_fract_r) return spec def mask_time_aug(spec, params): # Mask out a random block of time - repeat up to 3 times # SpecAugment: A Simple Data Augmentation Methodfor Automatic Speech Recognition fm = torchaudio.transforms.TimeMasking(int(spec.shape[1]*params['mask_max_time_perc'])) for ii in range(np.random.randint(1, 4)): spec = fm(spec) return spec def mask_freq_aug(spec, params): # Mask out a random frequncy range - repeat up to 3 times # SpecAugment: A Simple Data Augmentation Method for Automatic Speech Recognition fm = torchaudio.transforms.FrequencyMasking(int(spec.shape[1]*params['mask_max_freq_perc'])) for ii in range(np.random.randint(1, 4)): spec = fm(spec) return spec def scale_vol_aug(spec, params): return spec * np.random.random()*params['spec_amp_scaling'] def echo_aug(audio, sampling_rate, params): sample_offset = int(params['echo_max_delay']*np.random.random()*sampling_rate) + 1 audio[:-sample_offset] += np.random.random()*audio[sample_offset:] return audio def resample_aug(audio, sampling_rate, params): sampling_rate_old = sampling_rate sampling_rate = np.random.choice(params['aug_sampling_rates']) audio = librosa.resample(audio, sampling_rate_old, sampling_rate, res_type='polyphase') audio = au.pad_audio(audio, sampling_rate, params['fft_win_length'], params['fft_overlap'], params['resize_factor'], params['spec_divide_factor'], params['spec_train_width']) duration = audio.shape[0] / float(sampling_rate) return audio, sampling_rate, duration def resample_audio(num_samples, sampling_rate, audio2, sampling_rate2): if sampling_rate != sampling_rate2: audio2 = librosa.resample(audio2, sampling_rate2, sampling_rate, res_type='polyphase') sampling_rate2 = sampling_rate if audio2.shape[0] < num_samples: audio2 = np.hstack((audio2, np.zeros((num_samples-audio2.shape[0]), dtype=audio2.dtype))) elif audio2.shape[0] > num_samples: audio2 = audio2[:num_samples] return audio2, sampling_rate2 def combine_audio_aug(audio, sampling_rate, ann, audio2, sampling_rate2, ann2): # resample so they are the same audio2, sampling_rate2 = resample_audio(audio.shape[0], sampling_rate, audio2, sampling_rate2) # # set mean and std to be the same # audio2 = (audio2 - audio2.mean()) # audio2 = (audio2/audio2.std())*audio.std() # audio2 = audio2 + audio.mean() if ann['annotated'] and (ann2['annotated']) and \ (sampling_rate2 == sampling_rate) and (audio.shape[0] == audio2.shape[0]): comb_weight = 0.3 + np.random.random()*0.4 audio = comb_weight*audio + (1-comb_weight)*audio2 inds = np.argsort(np.hstack((ann['start_times'], ann2['start_times']))) for kk in ann.keys(): # when combining calls from different files, assume they come from different individuals if kk == 'individual_ids': if (ann[kk]>-1).sum() > 0: ann2[kk][ann2[kk]>-1] += np.max(ann[kk][ann[kk]>-1]) + 1 if (kk != 'class_id_file') and (kk != 'annotated'): ann[kk] = np.hstack((ann[kk], ann2[kk]))[inds] return audio, ann class AudioLoader(torch.utils.data.Dataset): def __init__(self, data_anns_ip, params, dataset_name=None, is_train=False): self.data_anns = [] self.is_train = is_train self.params = params self.return_spec_for_viz = False for ii in range(len(data_anns_ip)): dd = copy.deepcopy(data_anns_ip[ii]) # filter out unused annotation here filtered_annotations = [] for ii, aa in enumerate(dd['annotation']): if 'individual' in aa.keys(): aa['individual'] = int(aa['individual']) # if only one call labeled it has to be from the same individual if len(dd['annotation']) == 1: aa['individual'] = 0 # convert class name into class label if aa['class'] in self.params['class_names']: aa['class_id'] = self.params['class_names'].index(aa['class']) else: aa['class_id'] = -1 if aa['class'] not in self.params['classes_to_ignore']: filtered_annotations.append(aa) dd['annotation'] = filtered_annotations dd['start_times'] = np.array([aa['start_time'] for aa in dd['annotation']]) dd['end_times'] = np.array([aa['end_time'] for aa in dd['annotation']]) dd['high_freqs'] = np.array([float(aa['high_freq']) for aa in dd['annotation']]) dd['low_freqs'] = np.array([float(aa['low_freq']) for aa in dd['annotation']]) dd['class_ids'] = np.array([aa['class_id'] for aa in dd['annotation']]).astype(np.int) dd['individual_ids'] = np.array([aa['individual'] for aa in dd['annotation']]).astype(np.int) # file level class name dd['class_id_file'] = -1 if 'class_name' in dd.keys(): if dd['class_name'] in self.params['class_names']: dd['class_id_file'] = self.params['class_names'].index(dd['class_name']) self.data_anns.append(dd) ann_cnt = [len(aa['annotation']) for aa in self.data_anns] self.max_num_anns = 2*np.max(ann_cnt) # x2 because we may be combining files during training print('\n') if dataset_name is not None: print('Dataset : ' + dataset_name) if self.is_train: print('Split type : train') else: print('Split type : test') print('Num files : ' + str(len(self.data_anns))) print('Num calls : ' + str(np.sum(ann_cnt))) def get_file_and_anns(self, index=None): # if no file specified, choose random one if index == None: index = np.random.randint(0, len(self.data_anns)) audio_file = self.data_anns[index]['file_path'] sampling_rate, audio_raw = au.load_audio_file(audio_file, self.data_anns[index]['time_exp'], self.params['target_samp_rate'], self.params['scale_raw_audio']) # copy annotation ann = {} ann['annotated'] = self.data_anns[index]['annotated'] ann['class_id_file'] = self.data_anns[index]['class_id_file'] keys = ['start_times', 'end_times', 'high_freqs', 'low_freqs', 'class_ids', 'individual_ids'] for kk in keys: ann[kk] = self.data_anns[index][kk].copy() # if train then grab a random crop if self.is_train: nfft = int(self.params['fft_win_length']*sampling_rate) noverlap = int(self.params['fft_overlap']*nfft) length_samples = self.params['spec_train_width']*(nfft - noverlap) + noverlap if audio_raw.shape[0] - length_samples > 0: sample_crop = np.random.randint(audio_raw.shape[0] - length_samples) else: sample_crop = 0 audio_raw = audio_raw[sample_crop:sample_crop+length_samples] ann['start_times'] = ann['start_times'] - sample_crop/float(sampling_rate) ann['end_times'] = ann['end_times'] - sample_crop/float(sampling_rate) # pad audio if self.is_train: op_spec_target_size = self.params['spec_train_width'] else: op_spec_target_size = None audio_raw = au.pad_audio(audio_raw, sampling_rate, self.params['fft_win_length'], self.params['fft_overlap'], self.params['resize_factor'], self.params['spec_divide_factor'], op_spec_target_size) duration = audio_raw.shape[0] / float(sampling_rate) # sort based on time inds = np.argsort(ann['start_times']) for kk in ann.keys(): if (kk != 'class_id_file') and (kk != 'annotated'): ann[kk] = ann[kk][inds] return audio_raw, sampling_rate, duration, ann def __getitem__(self, index): # load audio file audio, sampling_rate, duration, ann = self.get_file_and_anns(index) # augment on raw audio if self.is_train and self.params['augment_at_train']: # augment - combine with random audio file if self.params['augment_at_train_combine'] and np.random.random() < self.params['aug_prob']: audio2, sampling_rate2, duration2, ann2 = self.get_file_and_anns() audio, ann = combine_audio_aug(audio, sampling_rate, ann, audio2, sampling_rate2, ann2) # simulate echo by adding delayed copy of the file if np.random.random() < self.params['aug_prob']: audio = echo_aug(audio, sampling_rate, self.params) # resample the audio #if np.random.random() < self.params['aug_prob']: # audio, sampling_rate, duration = resample_aug(audio, sampling_rate, self.params) # create spectrogram spec, spec_for_viz = au.generate_spectrogram(audio, sampling_rate, self.params, self.return_spec_for_viz) rsf = self.params['resize_factor'] spec_op_shape = (int(self.params['spec_height']*rsf), int(spec.shape[1]*rsf)) # resize the spec spec = torch.from_numpy(spec).unsqueeze(0).unsqueeze(0) spec = F.interpolate(spec, size=spec_op_shape, mode='bilinear', align_corners=False).squeeze(0) # augment spectrogram if self.is_train and self.params['augment_at_train']: if np.random.random() < self.params['aug_prob']: spec = scale_vol_aug(spec, self.params) if np.random.random() < self.params['aug_prob']: spec = warp_spec_aug(spec, ann, self.return_spec_for_viz, self.params) if np.random.random() < self.params['aug_prob']: spec = mask_time_aug(spec, self.params) if np.random.random() < self.params['aug_prob']: spec = mask_freq_aug(spec, self.params) outputs = {} outputs['spec'] = spec if self.return_spec_for_viz: outputs['spec_for_viz'] = torch.from_numpy(spec_for_viz).unsqueeze(0) # create ground truth heatmaps outputs['y_2d_det'], outputs['y_2d_size'], outputs['y_2d_classes'], ann_aug =\ generate_gt_heatmaps(spec_op_shape, sampling_rate, ann, self.params) # hack to get around requirement that all vectors are the same length in # the output batch pad_size = self.max_num_anns-len(ann_aug['individual_ids']) outputs['is_valid'] = pad_aray(np.ones(len(ann_aug['individual_ids'])), pad_size) keys = ['class_ids', 'individual_ids', 'x_inds', 'y_inds', 'start_times', 'end_times', 'low_freqs', 'high_freqs'] for kk in keys: outputs[kk] = pad_aray(ann_aug[kk], pad_size) # convert to pytorch for kk in outputs.keys(): if type(outputs[kk]) != torch.Tensor: outputs[kk] = torch.from_numpy(outputs[kk]) # scalars outputs['class_id_file'] = ann['class_id_file'] outputs['annotated'] = ann['annotated'] outputs['duration'] = duration outputs['sampling_rate'] = sampling_rate outputs['file_id'] = index return outputs def __len__(self): return len(self.data_anns)