utils.py

# --------------------------------------------------------
# Swin Transformer
# Copyright (c) 2021 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ze Liu
# --------------------------------------------------------

import os
import copy
from tabnanny import check
import numpy as np
import pandas as pd
import torch
import torch.distributed as dist
import torch.nn.functional as F

from PIL import Image
import matplotlib.cm as mpl_color_map

from sklearn.metrics import roc_auc_score

try:
    # noinspection PyUnresolvedReferences
    from apex import amp
except ImportError:
    amp = None


def load_checkpoint(config, model, optimizer, lr_scheduler, logger,
                    scaler=None, scaler_flag=None):
    logger.info(f"==============> Resuming form {config.MODEL.RESUME}....................")
    if config.MODEL.RESUME.startswith('https'):
        checkpoint = torch.hub.load_state_dict_from_url(
            config.MODEL.RESUME, map_location='cpu', check_hash=True)
    else:
        checkpoint = torch.load(config.MODEL.RESUME, map_location='cpu')
    msg = model.load_state_dict(checkpoint['model'], strict=False)
    logger.info(msg)
    max_accuracy = 0.0
    if not config.EVAL_MODE and 'optimizer' in checkpoint and 'lr_scheduler' in checkpoint and 'epoch' in checkpoint:
        optimizer.load_state_dict(checkpoint['optimizer'])
        lr_scheduler.load_state_dict(checkpoint['lr_scheduler'])
        config.defrost()
        config.TRAIN.START_EPOCH = checkpoint['epoch'] + 1
        config.freeze()
        if 'amp' in checkpoint and config.AMP_OPT_LEVEL != "O0" and checkpoint['config'].AMP_OPT_LEVEL != "O0":
            if scaler_flag:
                scaler.load_state_dict(checkpoint['amp'])
            else:
                amp.load_state_dict(checkpoint['amp'])
        logger.info(f"=> loaded successfully '{config.MODEL.RESUME}' (epoch {checkpoint['epoch']})")
        if 'max_accuracy' in checkpoint:
            max_accuracy = checkpoint['max_accuracy']

    del checkpoint
    torch.cuda.empty_cache()
    return max_accuracy


def load_pretrained(config, model, logger):
    logger.info(f"==============> Loading weight {config.MODEL.PRETRAINED} for fine-tuning......")
    checkpoint = torch.load(config.MODEL.PRETRAINED, map_location='cpu')
    state_dict = checkpoint['model']

    # delete relative_position_index since we always re-init it
    relative_position_index_keys = [k for k in state_dict.keys() if "relative_position_index" in k]
    for k in relative_position_index_keys:
        del state_dict[k]

    # delete relative_coords_table since we always re-init it
    relative_position_index_keys = [k for k in state_dict.keys() if "relative_coords_table" in k]
    for k in relative_position_index_keys:
        del state_dict[k]

    # delete attn_mask since we always re-init it
    attn_mask_keys = [k for k in state_dict.keys() if "attn_mask" in k]
    for k in attn_mask_keys:
        del state_dict[k]

    # bicubic interpolate relative_position_bias_table if not match
    relative_position_bias_table_keys = [k for k in state_dict.keys() if "relative_position_bias_table" in k]
    for k in relative_position_bias_table_keys:
        relative_position_bias_table_pretrained = state_dict[k]
        relative_position_bias_table_current = model.state_dict()[k]
        L1, nH1 = relative_position_bias_table_pretrained.size()
        L2, nH2 = relative_position_bias_table_current.size()
        if nH1 != nH2:
            logger.warning(f"Error in loading {k}, passing......")
        else:
            if L1 != L2:
                # bicubic interpolate relative_position_bias_table if not match
                S1 = int(L1 ** 0.5)
                S2 = int(L2 ** 0.5)
                relative_position_bias_table_pretrained_resized = torch.nn.functional.interpolate(
                    relative_position_bias_table_pretrained.permute(1, 0).view(1, nH1, S1, S1), size=(S2, S2),
                    mode='bicubic')
                state_dict[k] = relative_position_bias_table_pretrained_resized.view(nH2, L2).permute(1, 0)

    # bicubic interpolate absolute_pos_embed if not match
    absolute_pos_embed_keys = [k for k in state_dict.keys() if "absolute_pos_embed" in k]
    for k in absolute_pos_embed_keys:
        # dpe
        absolute_pos_embed_pretrained = state_dict[k]
        absolute_pos_embed_current = model.state_dict()[k]
        _, L1, C1 = absolute_pos_embed_pretrained.size()
        _, L2, C2 = absolute_pos_embed_current.size()
        if C1 != C1:
            logger.warning(f"Error in loading {k}, passing......")
        else:
            if L1 != L2:
                S1 = int(L1 ** 0.5)
                S2 = int(L2 ** 0.5)
                absolute_pos_embed_pretrained = absolute_pos_embed_pretrained.reshape(-1, S1, S1, C1)
                absolute_pos_embed_pretrained = absolute_pos_embed_pretrained.permute(0, 3, 1, 2)
                absolute_pos_embed_pretrained_resized = torch.nn.functional.interpolate(
                    absolute_pos_embed_pretrained, size=(S2, S2), mode='bicubic')
                absolute_pos_embed_pretrained_resized = absolute_pos_embed_pretrained_resized.permute(0, 2, 3, 1)
                absolute_pos_embed_pretrained_resized = absolute_pos_embed_pretrained_resized.flatten(1, 2)
                state_dict[k] = absolute_pos_embed_pretrained_resized

    # check classifier, if not match, then re-init classifier to zero
    head_bias_pretrained = state_dict['head.bias']
    Nc1 = head_bias_pretrained.shape[0]
    Nc2 = model.head.bias.shape[0]
    if (Nc1 != Nc2):
        if Nc1 == 21841 and Nc2 == 1000:
            logger.info("loading ImageNet-22K weight to ImageNet-1K ......")
            map22kto1k_path = f'data/map22kto1k.txt'
            with open(map22kto1k_path) as f:
                map22kto1k = f.readlines()
            map22kto1k = [int(id22k.strip()) for id22k in map22kto1k]
            state_dict['head.weight'] = state_dict['head.weight'][map22kto1k, :]
            state_dict['head.bias'] = state_dict['head.bias'][map22kto1k]
        else:
            torch.nn.init.constant_(model.head.bias, 0.)
            torch.nn.init.constant_(model.head.weight, 0.)
            del state_dict['head.weight']
            del state_dict['head.bias']
            logger.warning(f"Error in loading classifier head, re-init classifier head to 0")

    msg = model.load_state_dict(state_dict, strict=False)
    logger.warning(msg)

    logger.info(f"=> loaded successfully '{config.MODEL.PRETRAINED}'")

    del checkpoint
    torch.cuda.empty_cache()


def save_checkpoint(config, epoch, model, max_accuracy, optimizer, lr_scheduler, logger,
                    scaler=None, scaler_flag=None):
    save_state = {'model': model.state_dict(),
                  'optimizer': optimizer.state_dict(),
                  'lr_scheduler': lr_scheduler.state_dict(),
                  'max_accuracy': max_accuracy,
                  'epoch': epoch,
                  'config': config}
    if config.AMP_OPT_LEVEL != "O0":
        if scaler_flag:
            save_state['amp'] = scaler.state_dict()
        else:
            save_state['amp'] = amp.state_dict()


    save_path = os.path.join(config.OUTPUT, f'ckpt_epoch_{epoch}.pth')
    logger.info(f"{save_path} saving......")
    torch.save(save_state, save_path)
    logger.info(f"{save_path} saved !!!")


def get_grad_norm(parameters, norm_type=2):
    if isinstance(parameters, torch.Tensor):
        parameters = [parameters]
    parameters = list(filter(lambda p: p.grad is not None, parameters))
    norm_type = float(norm_type)
    total_norm = 0
    for p in parameters:
        param_norm = p.grad.data.norm(norm_type)
        total_norm += param_norm.item() ** norm_type
    total_norm = total_norm ** (1. / norm_type)
    return total_norm


def auto_resume_helper(output_dir):
    checkpoints = os.listdir(output_dir)
    checkpoints = [ckpt for ckpt in checkpoints if ckpt.endswith('pth')]
    print(f"All checkpoints founded in {output_dir}: {checkpoints}")
    if len(checkpoints) > 0:
        latest_checkpoint = max([os.path.join(output_dir, d) for d in checkpoints], key=os.path.getmtime)
        print(f"The latest checkpoint founded: {latest_checkpoint}")
        resume_file = latest_checkpoint
    else:
        resume_file = None
    return resume_file


def list_all_checkpoints(output_dir):
    checkpoints = os.listdir(output_dir)
    checkpoints = [ckpt for ckpt in checkpoints if ckpt.endswith('pth')]
    checkpoints = [os.path.join(output_dir, ckpt) for ckpt in checkpoints]
    checkpoints = list(sorted(checkpoints, key=os.path.getmtime))
    print(f"All checkpoints founded in {output_dir}: {checkpoints}")
    return checkpoints


def find_best_checkpoint(output_dir, criterion='auc_val'):
    checkpoints = os.listdir(output_dir)
    checkpoints = [ckpt for ckpt in checkpoints if ckpt.endswith('pth')]
    checkpoints = [os.path.join(output_dir, ckpt) for ckpt in checkpoints]
    checkpoints = list(sorted(checkpoints, key=os.path.getmtime))

    stats_file = os.path.join(output_dir, 'summary_test.csv')
    df = pd.read_csv(stats_file)

    idx = (df[criterion].idxmax())
    print(idx)
    entry_id = str(int(df.loc[idx]['epoch']))
    print(entry_id)
    for checkpoint in checkpoints:
        if entry_id in checkpoint.split('/')[-1]:
            return [checkpoint]



    
def reduce_tensor(tensor):
    rt = tensor.clone()
    dist.all_reduce(rt, op=dist.ReduceOp.SUM)
    rt /= dist.get_world_size()
    return rt


def calculate_roc_auc(output, target):

    logit, pred = torch.max(output, 1)
    probs = F.softmax(output, dim=1).cpu().numpy()

    auc = roc_auc_score(target.cpu().numpy(), probs[:, 1])

    return auc


def apply_colormap_on_image(org_im, activation, colormap_name):
    """
        Apply heatmap on image
    Args:
        org_img (PIL img): Original image
        activation_map (numpy arr): Activation map (grayscale) 0-255
        colormap_name (str): Name of the colormap
    """
    # Get colormap
    color_map = mpl_color_map.get_cmap(colormap_name)
    no_trans_heatmap = color_map(activation)
    # Change alpha channel in colormap to make sure original image is displayed
    heatmap = copy.copy(no_trans_heatmap)
    heatmap[:, :, 3] = 0.4
    heatmap = Image.fromarray((heatmap*255).astype(np.uint8))
    no_trans_heatmap = Image.fromarray((no_trans_heatmap*255).astype(np.uint8))

    # Apply heatmap on iamge
    heatmap_on_image = Image.new("RGBA", org_im.size)
    heatmap_on_image = Image.alpha_composite(heatmap_on_image, org_im.convert('RGBA'))
    heatmap_on_image = Image.alpha_composite(heatmap_on_image, heatmap)
    return no_trans_heatmap, heatmap_on_image


def format_np_output(np_arr):
    """
        This is a (kind of) bandaid fix to streamline saving procedure.
        It converts all the outputs to the same format which is 3xWxH
        with using sucecssive if clauses.
    Args:
        im_as_arr (Numpy array): Matrix of shape 1xWxH or WxH or 3xWxH
    """
    # Phase/Case 1: The np arr only has 2 dimensions
    # Result: Add a dimension at the beginning
    if len(np_arr.shape) == 2:
        np_arr = np.expand_dims(np_arr, axis=0)
    # Phase/Case 2: Np arr has only 1 channel (assuming first dim is channel)
    # Result: Repeat first channel and convert 1xWxH to 3xWxH
    if np_arr.shape[0] == 1:
        np_arr = np.repeat(np_arr, 3, axis=0)
    # Phase/Case 3: Np arr is of shape 3xWxH
    # Result: Convert it to WxHx3 in order to make it saveable by PIL
    if np_arr.shape[0] == 3:
        np_arr = np_arr.transpose(1, 2, 0)
    # Phase/Case 4: NP arr is normalized between 0-1
    # Result: Multiply with 255 and change type to make it saveable by PIL
    if np.max(np_arr) <= 1:
        np_arr = (np_arr*255).astype(np.uint8)
    return np_arr


def save_image(im, path):
    """
        Saves a numpy matrix or PIL image as an image
    Args:
        im_as_arr (Numpy array): Matrix of shape DxWxH
        path (str): Path to the image
    """
    if isinstance(im, (np.ndarray, np.generic)):
        im = format_np_output(im)
        im = Image.fromarray(im)
    im.save(path)