| | |
| | |
| |
|
| | import numpy as np |
| | import torch |
| | from .helpers import ( |
| | local_maxima, |
| | peak_picking, |
| | |
| | ) |
| | from dataset.label2id import LABEL_TO_ID, ID_TO_LABEL |
| | from dataset.custom_types import MsaInfo |
| |
|
| |
|
| | def event_frames_to_time(frame_rates, boundary: np.array): |
| | boundary = np.array(boundary) |
| | boundary_times = boundary / frame_rates |
| | return boundary_times |
| |
|
| |
|
| | def postprocess_functional_structure( |
| | logits, |
| | config, |
| | ): |
| | |
| | boundary_logits = logits["boundary_logits"] |
| | function_logits = logits["function_logits"] |
| |
|
| | assert boundary_logits.shape[0] == 1 and function_logits.shape[0] == 1, ( |
| | "Only batch size 1 is supported" |
| | ) |
| | raw_prob_sections = torch.sigmoid(boundary_logits[0]) |
| | raw_prob_functions = torch.softmax(function_logits[0].transpose(0, 1), dim=0) |
| |
|
| | |
| | prob_sections, _ = local_maxima( |
| | raw_prob_sections, filter_size=config.local_maxima_filter_size |
| | ) |
| | prob_sections = prob_sections.cpu().numpy() |
| |
|
| | prob_functions = raw_prob_functions.cpu().numpy() |
| |
|
| | boundary_candidates = peak_picking( |
| | boundary_activation=prob_sections, |
| | window_past=int(12 * config.frame_rates), |
| | window_future=int(12 * config.frame_rates), |
| | ) |
| | boundary = boundary_candidates > 0.0 |
| |
|
| | duration = len(prob_sections) / config.frame_rates |
| | pred_boundary_times = event_frames_to_time( |
| | frame_rates=config.frame_rates, boundary=np.flatnonzero(boundary) |
| | ) |
| | if pred_boundary_times[0] != 0: |
| | pred_boundary_times = np.insert(pred_boundary_times, 0, 0) |
| | if pred_boundary_times[-1] != duration: |
| | pred_boundary_times = np.append(pred_boundary_times, duration) |
| | pred_boundaries = np.stack([pred_boundary_times[:-1], pred_boundary_times[1:]]).T |
| |
|
| | pred_boundary_indices = np.flatnonzero(boundary) |
| | pred_boundary_indices = pred_boundary_indices[pred_boundary_indices > 0] |
| | prob_segment_function = np.split(prob_functions, pred_boundary_indices, axis=1) |
| | pred_labels = [p.mean(axis=1).argmax().item() for p in prob_segment_function] |
| |
|
| | segments: MsaInfo = [] |
| | for (start, end), label in zip(pred_boundaries, pred_labels): |
| | segment = (float(start), str(ID_TO_LABEL[label])) |
| | segments.append(segment) |
| |
|
| | segments.append((float(pred_boundary_times[-1]), "end")) |
| | return segments |
| |
|