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global_analysis.py
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import torch
import torch.utils.data
import torchvision.transforms as transforms
import torchvision.datasets as datasets
from dataHelper import DatasetFolder
import numpy as np
import cv2
import matplotlib.pyplot as plt
import re
from settings import prototype_activation_function_in_numpy
import os
from helpers import makedir
import model
import find_nearest
import last_layer
import train_and_test as tnt
from preprocess import preprocess_input_function
from highlighting_precision import hp
import argparse
# Usage: python3 global_analysis.py -modeldir='./saved_models/' -model=''
parser = argparse.ArgumentParser()
parser.add_argument('-gpuid', nargs=1, type=str, default='0')
parser.add_argument('-modeldir', nargs=1, type=str)
parser.add_argument('-model', nargs=1, type=str)
parser.add_argument('-test_dir', nargs=1, type=str)
parser.add_argument('-push_dir', nargs=1, type=str)
#parser.add_argument('-dataset', nargs=1, type=str, default='cub200')
args = parser.parse_args()
os.environ['CUDA_VISIBLE_DEVICES'] = args.gpuid[0]
load_model_dir = args.modeldir[0]
load_model_name = args.model[0]
load_model_path = os.path.join(load_model_dir, load_model_name)
epoch_number_str = re.search(r'\d+', load_model_name).group(0)
start_epoch_number = int(epoch_number_str)
# load the model
print('load model from ' + load_model_path)
ppnet = torch.load(load_model_path)
# print('convert to maxpool logic')
# ppnet.set_topk_k(1)
ppnet = ppnet.cuda()
ppnet_multi = torch.nn.DataParallel(ppnet)
img_size = ppnet_multi.module.img_size
# load the data
# must use unaugmented (original) dataset
train_dir = args.push_dir[0]
test_dir = args.test_dir[0]
batch_size = 100
# train set: do not normalize
train_dataset = DatasetFolder(
train_dir,
augmentation=False,
loader=np.load,
extensions=("npy",),
transform = transforms.Compose([
torch.from_numpy,
]))
train_loader = torch.utils.data.DataLoader(
train_dataset, batch_size=batch_size, shuffle=True,
num_workers=4, pin_memory=False)
# test set
test_dataset =DatasetFolder(
test_dir,
loader=np.load,
extensions=("npy",),
transform = transforms.Compose([
torch.from_numpy,
]))
test_loader = torch.utils.data.DataLoader(
test_dataset, batch_size=batch_size, shuffle=False,
num_workers=4, pin_memory=False)
root_dir_for_saving_train_images = os.path.join(load_model_dir,
load_model_name.split('.pth')[0] + '_nearest_train')
root_dir_for_saving_test_images = os.path.join(load_model_dir,
load_model_name.split('.pth')[0] + '_nearest_test')
makedir(root_dir_for_saving_train_images)
makedir(root_dir_for_saving_test_images)
# save prototypes in original images
load_img_dir = os.path.join(load_model_dir, 'img')
prototype_info = np.load(os.path.join(load_img_dir, 'epoch-'+str(start_epoch_number), 'bb'+str(start_epoch_number)+'.npy'))
def save_prototype_original_img_with_bbox(fname, epoch, index,
bbox_height_start, bbox_height_end,
bbox_width_start, bbox_width_end, color=(0, 255, 255)):
p_img_bgr = cv2.imread(os.path.join(load_img_dir, 'epoch-'+str(epoch), 'prototype-img-original'+str(index)+'.png'))
cv2.rectangle(p_img_bgr, (bbox_width_start, bbox_height_start), (bbox_width_end-1, bbox_height_end-1),
color, thickness=2)
p_img_rgb = p_img_bgr[...,::-1]
p_img_rgb = np.float32(p_img_rgb) / 255
#plt.imshow(p_img_rgb)
#plt.axis('off')
plt.imsave(fname, p_img_rgb)
for j in range(ppnet.num_prototypes):
makedir(os.path.join(root_dir_for_saving_train_images, str(j)))
makedir(os.path.join(root_dir_for_saving_test_images, str(j)))
save_prototype_original_img_with_bbox(fname=os.path.join(root_dir_for_saving_train_images, str(j),
'prototype_in_original_pimg.png'),
epoch=start_epoch_number,
index=j,
bbox_height_start=prototype_info[j][1],
bbox_height_end=prototype_info[j][2],
bbox_width_start=prototype_info[j][3],
bbox_width_end=prototype_info[j][4],
color=(0, 255, 255))
save_prototype_original_img_with_bbox(fname=os.path.join(root_dir_for_saving_test_images, str(j),
'prototype_in_original_pimg.png'),
epoch=start_epoch_number,
index=j,
bbox_height_start=prototype_info[j][1],
bbox_height_end=prototype_info[j][2],
bbox_width_start=prototype_info[j][3],
bbox_width_end=prototype_info[j][4],
color=(0, 255, 255))
k = 5
print(find_nearest.find_k_nearest_patches_to_prototypes(
dataloader=train_loader, # pytorch dataloader (must be unnormalized in [0,1])
prototype_network_parallel=ppnet_multi, # pytorch network with prototype_vectors
k=k+1,
preprocess_input_function=preprocess_input_function, # normalize if needed
full_save=True,
root_dir_for_saving_images=root_dir_for_saving_train_images,
prototype_activation_function_in_numpy=prototype_activation_function_in_numpy,
log=print))
print(find_nearest.find_k_nearest_patches_to_prototypes(
dataloader=test_loader, # pytorch dataloader (must be unnormalized in [0,1])
prototype_network_parallel=ppnet_multi, # pytorch network with prototype_vectors
k=k,
preprocess_input_function=preprocess_input_function, # normalize if needed
full_save=True,
root_dir_for_saving_images=root_dir_for_saving_test_images,
prototype_activation_function_in_numpy=prototype_activation_function_in_numpy,
log=print))
#activation precisions by proto
per_proto_lhp = np.asarray(hp(test_dir, load_model_path, per_proto=True))
per_proto_fhp = np.asarray(hp('/usr/xtmp/mammo/Lo1136i_finer/by_margin/test/', load_model_path, per_proto=True))
print("Avg lesion activation precision: ", per_proto_lhp)
print("Avg fine activation precision: ", per_proto_fhp)
#class connection weights
print("last layer trasnpose: \n", last_layer.show_last_layer_connections_T(ppnet))
#activation precision averages
avg_lhp = hp(test_dir, load_model_path)
avg_fhp = hp('/usr/xtmp/mammo/Lo1136i_finer/by_margin/test/', load_model_path)
pm_lhp = 1.96 * per_proto_lhp.std(axis=0)[1] / np.sqrt(per_proto_lhp.shape[0])
pm_fhp = 1.96 * per_proto_fhp.std(axis=0)[1] / np.sqrt(per_proto_fhp.shape[0])
print("Avg lesion activation precision: ", avg_lhp,\
" pm ", pm_lhp, ". \n", avg_lhp-pm_lhp, " to ", avg_lhp+pm_lhp)
print("Avg fine activation precision: ", avg_fhp,\
" pm ", pm_fhp, ". \n", avg_fhp-pm_fhp, " to ", avg_fhp+pm_fhp)
print("see analysis in ", root_dir_for_saving_train_images)
print("see analysis in ", root_dir_for_saving_test_images)