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utils.py
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utils.py
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import numpy as np
import numpy.matlib
import scipy.io as sio
from natsort import natsorted
from PIL import Image
from random import shuffle,seed
from os import listdir,mkdir
from os.path import join,isdir,isfile
import matplotlib.pyplot as plt
from keras.metrics import top_k_categorical_accuracy
import copy
from sklearn.model_selection import train_test_split
import scipy.io as sio
def rgb2gray(np_imgs):
"""
convert a 3D image or a 4D numpy array (channel last) to grayscale
return a grayscale 4D numpy array
"""
gray_imgs = np.dot(np_imgs,[0.299, 0.587, 0.114])
if len(gray_imgs.shape) < 4:
gray_imgs = gray_imgs[...,np.newaxis]
return gray_imgs
def load_imgs(folder):
imgs_list = []
lists = listdir(folder)
lists = natsorted(lists)
for f in lists:
fname = join(folder,f)
if isdir(fname):
continue
img = Image.open(fname)
imgarray = np.array(img,dtype=np.uint16)
imgs_list.append(imgarray)
np_imgs = np.array(imgs_list)
if len(np_imgs.shape) < 4:
np_imgs = np_imgs[...,np.newaxis]
return np_imgs
def load_soap_imgs(folder):
"""
load soap imgs from the folder and return dictionary
dict's keys: sub folder name
dict's values: [imgs labels]
"""
lists = listdir(folder)
dict = {}
for f in lists:
l_split = f.split('_')
f_type = l_split[0]
print('key: {0}'.format(f_type))
if f_type=='above':
label=1
elif f_type=='below':
label=0
subf = join(folder,f)
imgs = load_imgs(subf)
labels = np.ones((imgs.shape[0],)) * label
keys = dict.keys()
if f_type not in keys:
dict[f_type] = [imgs,labels]
else:
dict[f_type][0] = np.append(dict[f_type][0],imgs,axis=0)
dict[f_type][1] = np.append(dict[f_type][1],labels,axis=0)
return dict
def load_beans_imgs_split_by_precent(folder,percent,is_orig=False):
"""
load beans imgs from the folder
and split the train and test by percentage
"""
test_imgs = None
test_labels = None
lists = listdir(folder)
dict = {} # for training
for i,f in enumerate(lists):
l_split = f.split('-')
bean_type = l_split[0]
label_pattern = l_split[-1]
l_str = label_pattern.split('l')[-1]
label = int(l_str)
subf = join(folder,f)
imgs = load_imgs(subf)
labels = np.ones((imgs.shape[0],)) * label
#split data by percentage
num_train = imgs.shape[0] * percent
assert(np.floor(num_train) == np.array(num_train))
num_train = int(num_train)
if i == 0:
print('num of train: {0}'.format(num_train))
if test_imgs is None:
test_imgs = imgs[num_train:]
test_labels = labels[num_train:]
else:
test_imgs = np.append(test_imgs,imgs[num_train:],axis=0)
test_labels = np.append(test_labels,labels[num_train:],axis=0)
keys = dict.keys()
if bean_type not in keys:
dict[bean_type] = [imgs[0:num_train],labels[0:num_train]]
else:
dict[bean_type][0] = np.append(dict[bean_type][0],imgs[0:num_train],axis=0)
dict[bean_type][1] = np.append(dict[bean_type][1],labels[0:num_train],axis=0)
if is_orig:
test_data = [test_imgs,test_labels]
else:
test_data = None
return dict,test_data
def load_beans_imgs(folder):
"""
load beans imgs from the folder and return dictionary
dict's keys: bean types
dict's values: [imgs labels]
"""
lists = listdir(folder)
dict = {}
for f in lists:
l_split = f.split('-')
bean_type = l_split[0]
label_pattern = l_split[-1]
l_str = label_pattern.split('l')[-1]
label = int(l_str)
subf = join(folder,f)
imgs = load_imgs(subf)
labels = np.ones((imgs.shape[0],)) * label
keys = dict.keys()
if bean_type not in keys:
dict[bean_type] = [imgs,labels]
else:
dict[bean_type][0] = np.append(dict[bean_type][0],imgs,axis=0)
dict[bean_type][1] = np.append(dict[bean_type][1],labels,axis=0)
return dict
def generate_beans_transfer_data(dict_orig,dict_aug, train_tuple, test_tuple):
ks = dict_aug.keys()
y_train = None
X_train = None
X_test = None
for k in ks:
data_aug = dict_aug[k]
data_orig = dict_orig[k]
# scale data
rgb_imgs_aug = data_aug[0]
rgb_imgs_orig = data_orig[0]
labels_aug = data_aug[1]
labels_orig = data_orig[1]
if k in train_tuple:
print('train: {0}'.format(k))
# cat as 4th channel
if X_train is None:
X_train = rgb_imgs_aug
y_train = labels_aug
else:
X_train = np.append(X_train, rgb_imgs_aug,axis = 0)
y_train = np.append(y_train,labels_aug, axis = 0)
print('test: {0}'.format(k))
if X_test is None:
X_test = rgb_imgs_orig
y_test = labels_orig
else:
X_test = np.append(X_test,rgb_imgs_orig,axis=0)
y_test = np.append(y_test,labels_orig,axis=0)
elif k in test_tuple:
print('test: {0}'.format(k))
if X_test is None:
X_test = rgb_imgs_orig
y_test = labels_orig
else:
X_test = np.append(X_test,rgb_imgs_orig,axis=0)
y_test = np.append(y_test,labels_orig,axis=0)
print()
return X_train,y_train,X_test,y_test
def generate_beans_leave_one_data_all(dict_orig,dict_aug,key):
'''generate leave one data with orig and augmentation
return 4D data, first three as rgb
'''
ks = dict_aug.keys()
rgb_cat = None
y_train = None
for k in ks:
data_aug = dict_aug[k]
data_orig = dict_orig[k]
# scale data
rgb_imgs_aug = data_aug[0]
rgb_imgs_orig = data_orig[0]
labels_aug = data_aug[1]
labels_orig = data_orig[1]
if k == key:
print('test: {0}'.format(k))
# cat as 4th channel
X_test = rgb_imgs_orig
y_test = labels_orig
else:
print('train: {0}'.format(k))
if rgb_cat is None:
rgb_cat = rgb_imgs_aug
rgb_cat = np.append(rgb_cat,rgb_imgs_orig,axis=0)
y_train = labels_aug
y_train = np.append(y_train,labels_orig,axis=0)
else:
rgb_cat = np.append(rgb_cat,rgb_imgs_aug,axis=0)
rgb_cat = np.append(rgb_cat,rgb_imgs_orig,axis=0)
y_train = np.append(y_train,labels_aug,axis=0)
y_train = np.append(y_train,labels_orig,axis=0)
X_train = rgb_cat
print()
return X_train,y_train,X_test,y_test
def generate_beans_train_one_data_all(dict_orig,dict_aug,key):
'''generate leave one data with orig and augmentation
return 4D data, first three as rgb
'''
ks = dict_aug.keys()
rgb_cat = None
y_train = None
for k in ks:
data_aug = dict_aug[k]
data_orig = dict_orig[k]
# scale data
rgb_imgs_aug = data_aug[0]
rgb_imgs_orig = data_orig[0]
labels_aug = data_aug[1]
labels_orig = data_orig[1]
if k == key:
print('train: {0}'.format(k))
# cat as 4th channel
X_train = rgb_imgs_orig
y_train = labels_orig
X_train = np.append(X_train, rgb_imgs_aug,axis = 0)
y_train = np.append(y_train,labels_aug, axis = 0)
else:
print('test: {0}'.format(k))
if rgb_cat is None:
rgb_cat = rgb_imgs_orig
y_test = labels_orig
else:
rgb_cat = np.append(rgb_cat,rgb_imgs_orig,axis=0)
y_test = np.append(y_test,labels_orig,axis=0)
X_test = rgb_cat
print()
return X_train,y_train,X_test,y_test
def generate_beans_train_two_data_all(dict_orig,dict_aug,keys):
'''generate leave one data with orig and augmentation
return 4D data, first three as rgb
'''
ks = dict_aug.keys()
rgb_cat = None
y_train = None
X_train = None
for k in ks:
data_aug = dict_aug[k]
data_orig = dict_orig[k]
# scale data
rgb_imgs_aug = data_aug[0]
rgb_imgs_orig = data_orig[0]
labels_aug = data_aug[1]
labels_orig = data_orig[1]
if k in keys:
print('train: {0}'.format(k))
# cat as 4th channel
if X_train is None:
X_train = rgb_imgs_orig
y_train = labels_orig
else:
X_train = np.append(X_train, rgb_imgs_orig,axis = 0)
y_train = np.append(y_train,labels_orig, axis = 0)
X_train = np.append(X_train, rgb_imgs_aug,axis = 0)
y_train = np.append(y_train,labels_aug, axis = 0)
else:
print('test: {0}'.format(k))
if rgb_cat is None:
rgb_cat = rgb_imgs_orig
y_test = labels_orig
else:
rgb_cat = np.append(rgb_cat,rgb_imgs_orig,axis=0)
y_test = np.append(y_test,labels_orig,axis=0)
X_test = rgb_cat
print()
return X_train,y_train,X_test,y_test
def generate_labels(len,num_class):
assert(len % num_class == 0)
labels = None
target_num = int(len / num_class)
for c in range(num_class):
tmp = np.ones((target_num,)) * c
if labels is None:
labels = tmp
else:
labels = np.append(labels,tmp,axis=0)
return labels
def generate_regression_labels(len):
labels = []
for i in range(len):
labels.append(i + 1)
labels = np.array(labels)
labels = labels / len
return labels
def load_imgs_labels(folder):
rgb_folder = join(folder,'rgb')
rgb_imgs = load_imgs(rgb_folder)
flir_folder = join(folder,'flir')
flir_imgs = load_imgs(flir_folder)
# load labels
labels = np.loadtxt(join(folder,'labels.txt'))
# load avg Ts
file = join(folder,'avg_Ts.txt')
ts = None
if isfile(file):
ts = np.loadtxt(file)
assert(labels.shape[0] == flir_imgs.shape[0])
return flir_imgs,rgb_imgs,labels,ts
def load_imgs_from_folders(folder,load_aug,issubtract,isregression=False):
'''load imgs from BOTH original and augment folder or JUST original folder
'''
lists = listdir(folder)
lists = natsorted(lists)
dict_aug = None
if load_aug:
dict_aug = {}
dict_orig = {}
for f in lists:
# use capture num and t-setting as key
idx = f.find('-')
idx2 = f.rfind('-')
capture_num = f[0:idx2]
print('folder name: {0}'.format(f))
print('key: {0}'.format(capture_num))
subf = join(folder,f)
flir_imgs2,rgb_imgs2,labels2,ts2 = load_imgs_labels(subf)
if isregression:
labels2 = generate_regression_labels(labels2.shape[0])
if issubtract:
# truncate to same length
ts2 = ts2[0:flir_imgs2.shape[0]]
for i in range(len(flir_imgs2.shape) - 1):
ts2 = ts2[...,np.newaxis]
ts2 = np.tile(ts2,(1,flir_imgs2.shape[1],flir_imgs2.shape[2],flir_imgs2.shape[3]))
flir_imgs2 = np.absolute(ts2 - flir_imgs2)
dict_orig[capture_num] = (flir_imgs2,rgb_imgs2,labels2)
if load_aug:
subf = join(folder,f,'train')
flir_imgs,rgb_imgs,labels,ts = load_imgs_labels(subf)
assert(labels.shape[0] % labels2.shape[0] == 0)
aug_size = int(labels.shape[0] / labels2.shape[0])
if isregression:
labels = np.repeat(labels2,aug_size,axis=0)
if issubtract:
ts_aug = np.repeat(ts2,aug_size,axis=0)
flir_imgs = np.absolute(flir_imgs - ts_aug)
dict_aug[capture_num] = (flir_imgs,rgb_imgs,labels)
return dict_orig,dict_aug
def generate_n_fold_data(n,dict_orig,dict_aug):
keys = list(dict_orig.keys())
assert(len(keys) % n == 0)
if dict_aug is None:
load_aug = False
else:
load_aug = True
target_num = len(keys) / n
SEED = 7
seed(SEED)
shuffle(keys)
print('\nrandom shuffle...\n')
print('\n'.join(keys))
print('')
dict_nfold_aug = None
if load_aug:
dict_nfold_aug = {}
dict_nfold_orig = {}
flir_cat = None
rgb_cat = None
y_cat = None
flir_orig_cat = None
rgb_orig_cat = None
y_orig_cat = None
for i,k in enumerate(keys,1):
print('cat {0}'.format(k))
if load_aug:
data = dict_aug[k]
flir_imgs = data[0]
rgb_imgs = data[1]
labels = data[2]
data_orig = dict_orig[k]
flir_imgs_orig = data_orig[0]
rgb_imgs_orig = data_orig[1]
labels_orig = data_orig[2]
# concat data
if flir_orig_cat is None:
if load_aug:
flir_cat = flir_imgs
rgb_cat = rgb_imgs
y_cat = labels
flir_orig_cat = flir_imgs_orig
rgb_orig_cat = rgb_imgs_orig
y_orig_cat = labels_orig
else:
if load_aug:
flir_cat = np.append(flir_cat,flir_imgs,axis=0)
rgb_cat = np.append(rgb_cat,rgb_imgs,axis=0)
y_cat = np.append(y_cat,labels,axis=0)
flir_orig_cat = np.append(flir_orig_cat,flir_imgs_orig,axis=0)
rgb_orig_cat = np.append(rgb_orig_cat,rgb_imgs_orig,axis=0)
y_orig_cat = np.append(y_orig_cat,labels_orig,axis=0)
if i % target_num == 0:
print('split here\n')
newk = int(i / target_num)
if load_aug:
dict_nfold_aug[newk] = (flir_cat,rgb_cat,y_cat)
dict_nfold_orig[newk] = (flir_orig_cat,rgb_orig_cat,y_orig_cat)
flir_cat = None
rgb_cat = None
y_cat = None
flir_orig_cat = None
rgb_orig_cat = None
y_orig_cat = None
return dict_nfold_orig,dict_nfold_aug
def generate_leave_one_data_all(dict_orig,dict_aug,key):
'''generate leave one data with orig and augmentation
return 4D data, first three as rgb, last one as flir
'''
ks = dict_aug.keys()
flir_cat = None
rgb_cat = None
y_train = None
for k in ks:
data = dict_aug[k]
data_orig = dict_orig[k]
# scale data
flir_imgs = data[0]
flir_imgs_orig = data_orig[0]
rgb_imgs = data[1]
rgb_imgs_orig = data_orig[1]
labels = data[2]
labels_orig = data_orig[2]
if k == key:
print('test: {0}'.format(k))
# cat as 4th channel
X_test = np.append(rgb_imgs_orig,flir_imgs_orig,axis=-1)
y_test = labels_orig
else:
print('train: {0}'.format(k))
if flir_cat is None:
flir_cat = flir_imgs
flir_cat = np.append(flir_cat,flir_imgs_orig,axis=0)
y_train = labels
y_train = np.append(y_train,labels_orig,axis=0)
rgb_cat = rgb_imgs
rgb_cat = np.append(rgb_cat,rgb_imgs_orig,axis=0)
else:
flir_cat = np.append(flir_cat,flir_imgs,axis=0)
flir_cat = np.append(flir_cat,flir_imgs_orig,axis=0)
y_train = np.append(y_train,labels,axis=0)
y_train = np.append(y_train,labels_orig,axis=0)
rgb_cat = np.append(rgb_cat,rgb_imgs,axis=0)
rgb_cat = np.append(rgb_cat,rgb_imgs_orig,axis=0)
# cat as 4th channel
X_train = np.append(rgb_cat,flir_cat,axis=-1)
return X_train,y_train,X_test,y_test
def generate_leave_one_data_orig(dict,key):
'''generate leave one data with ONLY original data
return 4D data, first three as rgb, last one as flir
'''
ks = dict.keys()
flir_cat = None
rgb_cat = None
y_train = None
for k in ks:
data = dict[k]
flir_imgs = data[0]
rgb_imgs = data[1]
labels = data[2]
if k == key:
print('test: {0}'.format(k))
# cat as 4th channel
X_test = np.append(rgb_imgs,flir_imgs,axis=-1)
y_test = labels
else:
print('train: {0}'.format(k))
if flir_cat is None:
flir_cat = flir_imgs
rgb_cat = rgb_imgs
y_train = labels
else:
flir_cat = np.append(flir_cat,flir_imgs,axis=0)
rgb_cat = np.append(rgb_cat,rgb_imgs,axis=0)
y_train = np.append(y_train,labels,axis=0)
# cat as 4th channel
X_train = np.append(rgb_cat,flir_cat,axis=-1)
return X_train,y_train,X_test,y_test
def rollback(data_4d):
'''4D data roll back to rgb and flir
'''
rgb = data_4d[:,:,:,0:3]
flir = data_4d[:,:,:,3]
flir = flir[...,np.newaxis]
return rgb,flir
def scale_imarray(array,nbits=8):
scaled_array = array / (2 ** nbits - 1)
return scaled_array
def save_imarray(array,folder,labels,predicts,precision=2,map='jet'):
assert(len(array.shape) == 4)
is_flir = False
if array.shape[-1] == 1:
is_flir = True
newarr = np.squeeze(array,axis=-1)
elif array.shape[-1] > 3:
newarr = array[:,:,:,:3]
else:
newarr = array
fig, ax = plt.subplots()
ax.set_axis_off()
if is_flir:
im = ax.imshow(newarr[0],cmap=map)
else:
im = ax.imshow(newarr[0])
for i in range(array.shape[0]):
im.set_data(newarr[i])
fname = join(folder,str(i) + '.tiff')
l1 = labels[i].astype(float)
p1 = predicts[i].astype(float)
ax.set_title('label: {0}\n predict: {1}'.format(np.around(l1,precision), np.around(p1,precision)))
fig.savefig(fname)
def top_2_accuracy(y_true,y_pred):
return top_k_categorical_accuracy(y_true,y_pred,2)
def calculate_top_k_acc(labels,predicts,top_k):
'''calculate adjacent top k accuracy
'''
assert(len(labels.shape) == 1)
assert(len(predicts.shape) == 2)
predicts = np.argpartition(predicts,-top_k)[:,-top_k:]
count = 0
for i in range(predicts.shape[0]):
if labels[i] in predicts[i]:
sorted_predicts = np.sort(predicts[i])
l2 = np.array(range(0,top_k)) + sorted_predicts[0]
tmp = sum(sorted_predicts == l2)
if tmp == predicts[i].shape[0]:
count +=1
acc = count / predicts.shape[0]
return acc
'''
labels=labels[...,np.newaxis]
labels=np.repeat(labels,top_k,axis=-1)
log=predicts==labels
top_k_acc=np.zeros(log[:,0].shape)
for i in range(log.shape[-1]-1):
tmp = np.logical_or(log[:,i],log[:,i+1])
top_k_acc = np.logical_or(top_k_acc,tmp)
return np.mean(top_k_acc)'''
def get_cv_LSTM(X_train, Y_train, video_length, total_videos, part):
SEED = 7
seed(SEED)
field = list(range(0,total_videos-part))
shuffle(field)
indx = field[0:part]
dX_train = None
dY_train = None
X_cv = np.copy(X_train[indx[0]*video_length:(indx[0]+1)*video_length])
Y_cv = np.copy(Y_train[indx[0]*video_length:(indx[0]+1)*video_length])
cv_list = list(range(indx[0]*video_length,(indx[0]+1)*video_length))
for i in range(1,part):
X_cv = np.append(X_cv, np.copy(X_train[indx[i]*video_length:(indx[i]+1)*video_length]), axis = 0)
Y_cv = np.append(Y_cv, np.copy(Y_train[indx[i]*video_length:(indx[i]+1)*video_length]), axis = 0)
cv_list += list(range(indx[i]*video_length,(indx[i]+1)*video_length))
for i in range(0, X_train.shape[0]):
if i in cv_list:
pass
else:
if dX_train is None:
dX_train = np.copy(X_train[i])
else:
dX_train = np.append(dX_train, X_train[i], axis = 0)
img_shape = X_train[0].shape
dX_train = dX_train.reshape(dX_train.shape[0]//img_shape[0],img_shape[0], img_shape[1], img_shape[2])
for i in range(0, X_train.shape[0]):
if i in cv_list:
pass
else:
if dY_train is None:
dY_train = [Y_train[i]]
else:
dY_train.append(Y_train[i])
dY_train = np.array(dY_train)
return dX_train, dY_train, X_cv, Y_cv
def regroup_train_LSTM(train_data, samples):
shape = train_data.shape
new_train = []
for j in range(0, samples):
for i in range(0, shape[0]//samples):
new_train.append(train_data[i*samples+j])
new_train = np.array(new_train)
return new_train
def split_train_cv_LSTM(X_train_index, Y_train_index, video_length, part, validation_ratio = 0.2):
SEED = 7
seed(SEED)
X_index, Xcv_index,Y_index, Y_cv_index = train_test_split(X_train_index, Y_train_index, test_size = 0.2)
return X_index, Xcv_index,Y_index, Y_cv_index
def load_KLT_data(folder):
files = listdir(folder)
files = natsorted(files)
data = []
for f in files:
datafile = join(folder, f)
img = sio.loadmat(datafile)
#img = Image.open(datafile)
#imgarray = np.array(img,dtype=np.uint16)
img_np = np.array(img['KLTload'], dtype=np.float)
data.append(img_np)
data = np.array(data)
return data
def load_KLT_from_folders(folder):
dict_KLT_orig = {}
lists = listdir(folder)
lists = natsorted(lists)
for f in lists:
KLTfile = join(folder, f, 'KLTtrackingtrainkltmat')
indx = f.find('-')
indx2 = f.rfind('-')
capnum = f[0:indx2]
mat_data = load_KLT_data(KLTfile)
dict_KLT_orig[capnum] = mat_data
return dict_KLT_orig
def generate_n_folder_KLT(n, dict_KLT_orig):
keys = list(dict_KLT_orig.keys())
dict_orig = {}
assert(len(keys) % n == 0)
target_num = len(keys) / n
SEED = 7
seed(SEED)
shuffle(keys)
datamat = []
for i, k in enumerate(keys, 1):
datamat.append(dict_KLT_orig[k])
if i%target_num == 0:
newkey = int(i/target_num)
dict_orig[newkey] = np.array(datamat)
datamat = []
return dict_orig
def generate_leave_one_KLTdata_orig(dict,key):
ks = list(dict.keys())
X_train = None
for k in ks:
if k==key:
X_test = dict[k]
shape = X_test.shape
X_real_test = None
for i in range(0, shape[0]):
if X_real_test is None:
X_real_test = X_test[0]
else:
X_real_test = np.append(X_real_test, X_test[i], axis = 0)
y_tmp = list(range(1, shape[1]+1))*shape[0]
Y_test = np.array(y_tmp)/shape[1]
else:
if X_train is None:
X_train = dict[k]
else:
X_train = np.append(X_train, dict[k], axis = 0)
X_real_train = None
for i in range(0, X_train.shape[0]):
if X_real_train is None:
X_real_train = X_train[i]
else:
X_real_train = np.append(X_real_train, X_train[i], axis = 0)
video_len = dict[ks[0]].shape[1]
repeat = X_train.shape[0]
y_tmp = list(range(1, video_len+1))*repeat
Y_train = np.array(y_tmp)/video_len
return X_real_train, Y_train, X_real_test, Y_test
def generate_combined_data(X_train, Y_train, X_KLT_train, Y_KLT_train, X_test, Y_test, X_KLT_test, Y_KLT_test):
X_combined_train = []
Y_combined_train = []
X_combined_test = []
Y_combined_test = []
for i in range(0, X_train.shape[0]):
X_combined_train.append([X_train[i], X_KLT_train[i]])
for i in range(0, X_test.shape[0]):
X_combined_test.append([X_test[i], X_KLT_test[i]])
Y_combined_train = Y_train
Y_combined_test = Y_test
return X_combined_train, Y_combined_train, X_combined_test, Y_combined_test