from collections import OrderedDict import unicodedata from typing import Optional import math import numpy as np from tinygrad.nn import state from tinygrad.tensor import Tensor, dtypes from tinygrad.helpers import getenv # # checkpointing utils # def invert_dict(d): return {v: k for k, v in reversed(d.items())} def dedup_dict(d): return invert_dict(invert_dict(d)) # store each tensor into the first key it appears in def get_training_state(model, optimizer, scheduler): # hack: let get_state_dict walk the tree starting with model, so that the checkpoint keys are # readable and can be loaded as a model for eval train_state = {'model': model, 'optimizer': optimizer, 'scheduler': scheduler} return dedup_dict(state.get_state_dict(train_state)) def load_training_state(model, optimizer, scheduler, state_dict): # use fresh model to restore duplicate keys train_state = {'model': model, 'optimizer': optimizer, 'scheduler': scheduler} big_dict = state.get_state_dict(train_state) # hack: put back the dupes dupe_names = {} for k, v in big_dict.items(): if v not in dupe_names: dupe_names[v] = k assert k in state_dict state_dict[k] = state_dict[dupe_names[v]] # scheduler contains optimizer and all params, load each weight only once scheduler_state = {'scheduler': scheduler} state.load_state_dict(scheduler_state, state_dict) def gaussian_kernel(n, std): from scipy import signal gaussian_1d = signal.windows.gaussian(n, std) gaussian_2d = np.outer(gaussian_1d, gaussian_1d) gaussian_3d = np.outer(gaussian_2d, gaussian_1d) gaussian_3d = gaussian_3d.reshape(n, n, n) gaussian_3d = np.cbrt(gaussian_3d) gaussian_3d /= gaussian_3d.max() return gaussian_3d def prepare_arrays(image, roi_shape=(128, 128, 128)): assert len(roi_shape) == 3 and any(roi_shape) image_shape = list(image.shape[2:]) result = np.zeros((1, 3, *image_shape), dtype=image.dtype) norm_map = np.zeros_like(result) norm_patch = gaussian_kernel(roi_shape[0], 0.125 * roi_shape[0]).astype(norm_map.dtype) return result, norm_map, norm_patch def get_slice(image, roi_shape=(128, 128, 128), overlap_factor=0.5): assert len(roi_shape) == 3 and any(roi_shape) assert 0 < overlap_factor < 1 image_shape, dim = list(image.shape[2:]), len(image.shape[2:]) strides = [int(roi_shape[i] * (1 - overlap_factor)) for i in range(dim)] size = [(image_shape[i] - roi_shape[i]) // strides[i] + 1 for i in range(dim)] for i in range(0, strides[0] * size[0], strides[0]): for j in range(0, strides[1] * size[1], strides[1]): for k in range(0, strides[2] * size[2], strides[2]): yield i, j, k def _get_best_indices(logits, n_best_size): index_and_score = sorted(enumerate(logits), key=lambda x: x[1], reverse=True) return list(map(lambda x: x[0], index_and_score))[:n_best_size] def _is_punctuation(char): if (cp := ord(char)) in range(33, 48) or cp in range(58, 65) or cp in range(91, 97) or cp in range(123, 127): return True return unicodedata.category(char).startswith("P") def _is_whitespace(char): if char == " " or char == "\t" or char == "\n" or char == "\r": return True return unicodedata.category(char) == "Zs" def _is_control(char): if char == "\t" or char == "\n" or char == "\r": return False return unicodedata.category(char).startswith("C") def _run_split_on_punc(text): if text in ("[UNK]", "[SEP]", "[PAD]", "[CLS]", "[MASK]"): return [text] start_new_word = True output = [] for i in range(len(text)): if _is_punctuation(char := text[i]): output.append([char]) start_new_word = True else: if start_new_word: output.append([]) start_new_word = False output[-1].append(char) return ["".join(x) for x in output] def _run_strip_accents(text): output = [] for char in unicodedata.normalize("NFD", text): if unicodedata.category(char) != "Mn": output.append(char) return "".join(output) def _clean_text(text): output = [] for char in text: if not ((cp := ord(char)) == 0 or cp == 0xfffd or _is_control(char)): output.append(" " if _is_whitespace(char) else char) return "".join(output) def _get_final_text(pred_text, orig_text): def _strip_spaces(text): ns_text = "" ns_to_s_map = OrderedDict() for i, c in enumerate(text): if c == " ": continue ns_to_s_map[len(ns_text)] = i ns_text += c return ns_text, ns_to_s_map orig_tokens = _clean_text(orig_text).strip().split() split_tokens = [] for token in orig_tokens: if token not in ("[UNK]", "[SEP]", "[PAD]", "[CLS]", "[MASK]"): token = token.lower() token = _run_strip_accents(token) split_tokens.extend(_run_split_on_punc(token)) tok_text = " ".join(" ".join(split_tokens).strip().split()) start_position = tok_text.find(pred_text) if start_position == -1: return orig_text end_position = start_position + len(pred_text) - 1 orig_ns_text, orig_ns_to_s_map = _strip_spaces(orig_text) tok_ns_text, tok_ns_to_s_map = _strip_spaces(tok_text) if len(orig_ns_text) != len(tok_ns_text): return orig_text tok_s_to_ns_map = {v: k for k, v in tok_ns_to_s_map.items()} orig_start_position = None if start_position in tok_s_to_ns_map: if (ns_start_position := tok_s_to_ns_map[start_position]) in orig_ns_to_s_map: orig_start_position = orig_ns_to_s_map[ns_start_position] if orig_start_position is None: return orig_text orig_end_position = None if end_position in tok_s_to_ns_map: if (ns_end_position := tok_s_to_ns_map[end_position]) in orig_ns_to_s_map: orig_end_position = orig_ns_to_s_map[ns_end_position] if orig_end_position is None: return orig_text output_text = orig_text[orig_start_position:(orig_end_position + 1)] return output_text def get_bert_qa_prediction(features, example, start_end_logits): prelim_predictions = [] for i, feature in enumerate(features): for start_index in _get_best_indices(start_end_logits[i][0], 20): for end_index in _get_best_indices(start_end_logits[i][1], 20): if start_index >= len(feature["tokens"]) or end_index >= len(feature["tokens"]): continue if start_index not in feature["token_to_orig_map"] or end_index not in feature["token_to_orig_map"]: continue if not feature["token_is_max_context"].get(start_index, False): continue if end_index < start_index or end_index - start_index + 1 > 30: continue prelim_predictions.append({ "feature_index": i, "start_index": start_index, "end_index": end_index, "start_logit": start_end_logits[i][0, start_index], "end_logit": start_end_logits[i][1, end_index] }) predictions = sorted(prelim_predictions, key=lambda x: (x["start_logit"] + x["end_logit"]), reverse=True) if len(predictions) > 0: feature = features[predictions[0]["feature_index"]] tok_tokens = feature["tokens"][predictions[0]["start_index"]:(predictions[0]["end_index"] + 1)] orig_doc_start = feature["token_to_orig_map"][predictions[0]["start_index"]] orig_doc_end = feature["token_to_orig_map"][predictions[0]["end_index"]] orig_tokens = example["context"][orig_doc_start:(orig_doc_end + 1)] tok_text = " ".join(tok_tokens).replace(" ##", "").replace("##", "") tok_text = " ".join(tok_text.strip().split()) orig_text = " ".join(orig_tokens) return _get_final_text(tok_text, orig_text) return "empty" def get_mlperf_bert_config(): """benchmark is BERT-large""" ret = {"attention_probs_dropout_prob": 0.1, "hidden_dropout_prob": 0.1, "vocab_size": 30522, "type_vocab_size": 2, "max_position_embeddings": 512} match (bert_size:=getenv("BERT_SIZE", "large")): case "large": ret.update({"hidden_size": 1024, "intermediate_size": 4096, "num_attention_heads": 16, "num_hidden_layers": 24}) case "tiny": ret.update({"hidden_size": 128, "intermediate_size": 512, "num_attention_heads": 2, "num_hidden_layers": 2}) case _: raise RuntimeError(f"unhandled {bert_size=}") if (bert_layers:=getenv("BERT_LAYERS")): ret["num_hidden_layers"] = bert_layers return ret def get_mlperf_bert_model(): from extra.models import bert from examples.mlperf.initializers import LinearBert, EmbeddingBert, LayerNormBert bert.Linear = LinearBert bert.Embedding = EmbeddingBert bert.LayerNorm = LayerNormBert from extra.models.bert import BertForPretraining config = get_mlperf_bert_config() if getenv("DISABLE_DROPOUT", 0): config["hidden_dropout_prob"] = config["attention_probs_dropout_prob"] = 0.0 return BertForPretraining(**config) def get_fake_data_bert(BS:int): return { "input_ids": Tensor.empty((BS, 512), dtype=dtypes.int32, device="CPU"), "input_mask": Tensor.empty((BS, 512), dtype=dtypes.int32, device="CPU"), "segment_ids": Tensor.empty((BS, 512), dtype=dtypes.int32, device="CPU"), "masked_lm_positions": Tensor.empty((BS, 76), dtype=dtypes.int32, device="CPU"), "masked_lm_ids": Tensor.empty((BS, 76), dtype=dtypes.int32, device="CPU"), "masked_lm_weights": Tensor.empty((BS, 76), dtype=dtypes.float32, device="CPU"), "next_sentence_labels": Tensor.empty((BS, 1), dtype=dtypes.int32, device="CPU"), } def find_matches(match_quality_matrix:np.ndarray, high_threshold:float=0.5, low_threshold:float=0.4, allow_low_quality_matches:bool=False) -> np.ndarray: BELOW_LOW_THRESHOLD, BETWEEN_THRESHOLDS = -1, -2 def _set_low_quality_matches_(matches:np.ndarray, all_matches:np.ndarray, match_quality_matrix:np.ndarray): highest_quality_foreach_gt = np.max(match_quality_matrix, axis=1) pred_inds_to_update = np.nonzero(match_quality_matrix == highest_quality_foreach_gt[:, None])[1] matches[pred_inds_to_update] = all_matches[pred_inds_to_update] assert low_threshold <= high_threshold matched_vals, matches = match_quality_matrix.max(axis=0), match_quality_matrix.argmax(axis=0) all_matches = np.copy(matches) if allow_low_quality_matches else None below_low_threshold = matched_vals < low_threshold between_thresholds = (matched_vals >= low_threshold) & (matched_vals < high_threshold) matches[below_low_threshold] = BELOW_LOW_THRESHOLD matches[between_thresholds] = BETWEEN_THRESHOLDS if allow_low_quality_matches: assert all_matches is not None _set_low_quality_matches_(matches, all_matches, match_quality_matrix) return matches def box_iou(boxes1:np.ndarray, boxes2:np.ndarray) -> np.ndarray: def _box_area(boxes:np.ndarray) -> np.ndarray: return (boxes[:, 2] - boxes[:, 0]) * (boxes[:, 3] - boxes[:, 1]) def _box_inter_union(boxes1:np.ndarray, boxes2:np.ndarray) -> tuple[np.ndarray, np.ndarray]: area1, area2 = _box_area(boxes1), _box_area(boxes2) lt, rb = np.maximum(boxes1[:, None, :2], boxes2[:, :2]), np.minimum(boxes1[:, None, 2:], boxes2[:, 2:]) wh = np.clip(rb - lt, a_min=0, a_max=None) inter = wh[:, :, 0] * wh[:, :, 1] union = area1[:, None] + area2 - inter return inter, union inter, union = _box_inter_union(boxes1, boxes2) return inter / union def generate_anchors(input_size:tuple[int, int], scales:Optional[tuple[Tensor, ...]]=None, aspect_ratios:Optional[tuple[Tensor, ...]]=None) -> list[np.ndarray]: def _compute_grid_sizes(input_size:tuple[int, int]) -> np.ndarray: return np.ceil(np.array(input_size)[None, :] / 2 ** np.arange(3, 8)[:, None]) scales = tuple((i, int(i * 2 ** (1/3)), int(i * 2 ** (2/3))) for i in 2 ** np.arange(5, 10)) if scales is None else scales aspect_ratios = ((0.5, 1.0, 2.0),) * len(scales) if aspect_ratios is None else aspect_ratios aspect_ratios = tuple(ar for ar in aspect_ratios) grid_sizes = _compute_grid_sizes(input_size) assert len(scales) == len(aspect_ratios) == len(grid_sizes), "scales, aspect_ratios, and grid_sizes must have the same length" anchors = [] for s, ar, gs in zip(scales, aspect_ratios, grid_sizes): s, ar = np.array(s), np.array(ar) h_ratios = np.sqrt(ar) w_ratios = 1 / h_ratios ws = (w_ratios[:, None] * s[None, :]).reshape(-1) hs = (h_ratios[:, None] * s[None, :]).reshape(-1) base_anchors = (np.stack([-ws, -hs, ws, hs], axis=1) / 2).round() stride_h, stride_w = input_size[0] // gs[0], input_size[1] // gs[1] shifts_x, shifts_y = np.meshgrid(np.arange(gs[1]) * stride_w, np.arange(gs[0]) * stride_h) shifts_x, shifts_y = shifts_x.reshape(-1), shifts_y.reshape(-1) shifts = np.stack([shifts_x, shifts_y, shifts_x, shifts_y], axis=1, dtype=np.float32) anchors.append((shifts[:, None] + base_anchors[None, :]).reshape(-1, 4)) return anchors