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crfcnn_combine.py
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crfcnn_combine.py
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import tensorflow as tf
import scipy
import numpy as np
import scipy.io as sio
import os
import scipy.misc
#import matplotlib.pyplot as plt
import utils_combine
from utils_combine import fetchdatalabel, calfilter, init, initcomb, model, crfatmodel, cnnatmodel, meanstd, cnnmodel, dice
rng = np.random.RandomState(1234)
tf.set_random_seed(1)
lrbig = 0.01 #0.01
lrmid = 0.003 #5
lr = 0.003 #2#5 #2 #3 #4 #3#5
lrsmall = 0.002
l2factor = 0.5 #0.01 # 0.01
totalepoch = 5000 #7000 #7000 #300 #200 #120
atepsilon = 1e-1 #5e-1 #0 #-1
modelname = 'cnn' #'crfcomb'
debug = False #False
savename = str(lr)+str(totalepoch)+str(atepsilon)+'2lrfsave'+str(5)+modelname+'norm' + 'valpara335'
fusion=None #'late' #None #'late'
saveperepoch = False #True #False #True #True # True
savefreq = 10
print(savename)
boxheight = 40
boxwidth = 40
batchsize = 29
#thresh = 0.885
postfix='roienhance.mat' # 'roienhance.mat' 'roienhance.jpeg'
traindatapath = '../trainroi1dilbig/'
trainlabelpath = '../trainroi1dilbig/'
testdatapath = '../testroi1dilbig/'
testlabelpath = '../testroi1dilbig/'
if __name__ == '__main__':
assert(modelname!='crf' or modelname!='cnn' or modelname!='cnnat' or modelname!='crfat'
or modelname!='cnncomb' or modelname!='crfcomb' or modelname!='cnncombat' or modelname!='crfcombat')
traindata, trainlabel, trainfname = fetchdatalabel(path=traindatapath, postfix=postfix, flag='train')
testdata, testlabel, testfname = fetchdatalabel(path=testdatapath, postfix=postfix, flag='test')
if savename[-4:] == 'norm':
print('norm')
meandata = traindata.mean(axis=0)
stddata = traindata.std(axis=0)
traindata = meanstd(traindata, meandata, stddata)
testdata = meanstd(testdata, meandata, stddata)
traink1, traink2 = calfilter(traindata)
testk1, testk2 = calfilter(testdata)
X = tf.placeholder(tf.float32, [None, boxheight, boxwidth])
Y = tf.placeholder(tf.float32, [None, boxheight, boxwidth])
k1 = tf.placeholder(tf.float32, [None, boxheight*boxwidth, boxheight*boxwidth])
k2 = tf.placeholder(tf.float32, [None, boxheight*boxwidth, boxheight*boxwidth])
print(modelname[3:7])
if modelname[3:7] == 'comb':
paras = initcomb(nhid221=37, nhid222=12, nhid223=355, lrf221=2, lrf222=2, lrf223=9,
nhid331=16, nhid332=13, nhid333=415, lrf331=3, lrf332=3, lrf333=8,
nhid441=9, nhid442=12, nhid443=588, lrf441=4, lrf442=4, lrf443=7,
nhid551=6, nhid552=12, nhid553=588, lrf551=5, lrf552=5, lrf553=7, fusion=fusion)
else:
paras = init(nhid1=44, nhid2=16, nhid3=335, lrf1=2, lrf2=2, lrf3=9) # nhid441=9, nhid442=12, nhid443=588, lrf441=4, lrf442=4, lrf443=7,
if modelname == 'cnn':
trainenergy, accuracy, di, testenergy, qtest = cnnmodel(X, Y, paras)
elif modelname == 'cnnat':
trainenergy, accuracy, di, testenergy, qtest, advloss = cnnatmodel(X, Y, paras, atepsilon)
elif modelname == 'crfat':
trainenergy, accuracy, di, testenergy, qtest, advloss= crfatmodel(X, Y, k1, k2, paras, atepsilon)
elif modelname == 'crf':
trainenergy, accuracy, di, testenergy, qtest = model(X, Y, k1, k2, paras)
elif modelname == 'cnncomb':
trainenergy, accuracy, di, testenergy, qtest = cnnmodel(X, Y, paras, flag='combine')
elif modelname == 'cnncombat':
trainenergy, accuracy, di, testenergy, qtest, advloss = cnnatmodel(X, Y, paras, atepsilon, flag='combine')
elif modelname == 'crfcomb':
trainenergy, accuracy, di, testenergy, qtest = model(X, Y, k1, k2, paras, flag='combine', fusion=fusion)
elif modelname == 'crfcombat':
trainenergy, accuracy, di, testenergy, qtest, advloss= crfatmodel(X, Y, k1, k2, paras, atepsilon,
flag='combine', fusion=fusion)
learningrate = tf.Variable(lr, trainable=False)
opt = tf.train.AdamOptimizer(learning_rate=learningrate)
params = tf.trainable_variables()
if modelname[:3] == 'crf':
if fusion=='late':
l2loss = tf.nn.l2_loss(paras['wsmooth22']) + tf.nn.l2_loss(paras['wcontra22'])
l2loss = l2loss + tf.nn.l2_loss(paras['wsmooth33']) + tf.nn.l2_loss(paras['wcontra33'])
l2loss = l2loss + tf.nn.l2_loss(paras['wsmooth44']) + tf.nn.l2_loss(paras['wcontra44'])
l2loss = l2loss + tf.nn.l2_loss(paras['wsmooth55']) + tf.nn.l2_loss(paras['wcontra55'])
else:
l2loss = tf.nn.l2_loss(paras['wsmooth']) + tf.nn.l2_loss(paras['wcontra'])
l2loss = l2loss * l2factor
trainenergy = trainenergy + l2loss
grads = tf.gradients(trainenergy, params, aggregation_method=2)
optimizer = opt.apply_gradients(zip(grads, params))
#optimizer = tf.train.AdamOptimizer(learning_rate=learningrate).minimize(trainenergy)
init = tf.initialize_all_variables()
saver = tf.train.Saver()
gpu_options = tf.GPUOptions(per_process_gpu_memory_fraction=0.25)
with tf.Session(config=tf.ConfigProto(gpu_options=gpu_options)) as sess:
#with tf.Session() as sess:
sess.run(init)
tf.set_random_seed(1)
trenerls, traccls, trdils, teenerls, teaccls, tedils = [], [], [], [], [], []
besttrener, tolstep, besttedi, besttrdi = 1e6, 0, 0, 0
predmat = {}
for epoch in range(0,totalepoch):
randindex = np.random.permutation(batchsize*8)
trainloss, trainacc, traindi, trainl2 = 0, 0, 0, 0
for iindex in range(8):
#print(epoch)
randindexii = randindex[iindex*batchsize : (iindex+1)*batchsize]
traindataii = traindata[randindexii, :, :]
trainlabelii = trainlabel[randindexii, :, :]
#print(len(randindexii))
if modelname[:3] == 'cnn':
if not debug:
energy, acc, dival, _ = sess.run([trainenergy, accuracy, di, optimizer], feed_dict={X: traindataii,
Y: trainlabelii, learningrate: lr})
if debug and modelname[-2:] == 'at':
energy, acc, dival, adv, _ = sess.run([trainenergy, accuracy, di, advloss, optimizer], feed_dict={X: traindataii,
Y: trainlabelii, learningrate: lr})
print(adv)
else:
traink1ii = traink1[randindexii, :, :]
traink2ii = traink2[randindexii, :, :]
if not debug:
energy, acc, dival, l2val, _ = sess.run([trainenergy, accuracy, di, l2loss, optimizer], feed_dict={X: traindataii,
Y: trainlabelii, learningrate: lrbig, k1: traink1ii, k2: traink2ii})
if debug and modelname[-2:] == 'at':
energy, acc, dival, l2val, adv,_ = sess.run([trainenergy, accuracy, di, l2loss, advloss, optimizer], feed_dict={X: traindataii,
Y: trainlabelii, learningrate: lrbig, k1: traink1ii, k2: traink2ii})
print(adv)
trainl2 += l2val
traindi += dival
trainloss += energy
trainacc += acc
print('epoch'+str(epoch)+', '+str(trainloss/8)+' '+str(trainl2/84)+' '+str(trainacc/8)+' '+str(traindi/8))
#if trainloss/4 < besttrainloss:
# besttrainloss = trainloss/4
# tolstep = 0
#else: tolstep += 1
#if tolstep == 8: lr *= .99
for iindex in range(2):
testdataii = testdata[iindex*batchsize:(iindex+1)*batchsize, :, :]
testlabelii = testlabel[iindex*batchsize:(iindex+1)*batchsize, :, :]
if modelname[:3] == 'cnn':
#print(testlabelii.shape, type(testlabelii))
energy, acc, dival, qtestval = sess.run([testenergy, accuracy, di, qtest], feed_dict={X: testdataii,
Y: testlabelii, learningrate: 0})
else:
testk1ii = testk1[iindex*batchsize:(iindex+1)*batchsize, :, :]
testk2ii = testk2[iindex*batchsize:(iindex+1)*batchsize, :, :]
energy, acc, dival, qtestval = sess.run([testenergy, accuracy, di, qtest], feed_dict={X: testdataii,
Y: testlabelii, learningrate: 0, k1: testk1ii, k2: testk2ii})
if iindex == 0:
testenergyval, testacc, testpred = energy, acc, qtestval
else:
testenergyval += energy
testacc += acc
testpred = np.concatenate((testpred, qtestval), axis=0)
testdi = dice(testlabel[:], (testpred.argmax(3))[:])
if saveperepoch and (epoch%savefreq==0): #(totalepoch<200 or testdi>thresh): # because of model size, save the result and tune further
for iindex in range(8):
traindataii = traindata[iindex*batchsize:(iindex+1)*batchsize, :, :]
trainlabelii = trainlabel[iindex*batchsize:(iindex+1)*batchsize, :, :]
if modelname[:3] == 'cnn':
qtestval = sess.run(qtest, feed_dict={X: traindataii,
Y: trainlabelii, learningrate: 0})
else:
traink1ii = traink1[iindex*batchsize:(iindex+1)*batchsize, :, :]
traink2ii = traink2[iindex*batchsize:(iindex+1)*batchsize, :, :]
qtestval = sess.run(qtest, feed_dict={X: traindataii,
Y: trainlabelii, learningrate: 0, k1: traink1ii, k2: traink2ii})
if iindex == 0:
trainpred = qtestval
else:
trainpred = np.concatenate((trainpred, qtestval), axis=0)
savemat={}
savemat['testpred'] = testpred
#savemat['testlabel'] = testlabel
savemat['trainpred'] = trainpred
#savemat['trainlabel'] = trainlabel
sio.savemat(savename+str(epoch)+'.mat', savemat)
print('epoch'+str(epoch)+', '+str(testenergyval/2)+' '+str(testacc/2)+' '+str(testdi))
if testdi > besttedi:
saver.save(sess, savename+'.ckpt')
besttedi = testdi
besttrdi = traindi/8
predmat['test'] = testpred
# lrbig = lrmid
#if traindi/12 > 0.885:
if testdi > 0.88:
lrbig = lr
if testdi > 0.89:
lrbig = lrsmall
trenerls.append(trainloss/8)
traccls.append(trainacc/8)
trdils.append(traindi/8)
teenerls.append(testenergyval/8)
teaccls.append(testacc/8)
tedils.append(testdi)
print(str(besttedi)+' '+str(max(trdils)))
saver.restore(sess, savename+'.ckpt')
#argpred, dival = sess.run([predarg, di], feed_dict={X: testdata,
# Y: testlabel, learningrate: 0})#, k1: testk1, k2: testk2})
#assert(dival==besttedi)
predmat['trainloss'] = trenerls
predmat['trainacc'] = traccls
predmat['traindi'] = trdils
predmat['testfname'] = testfname
predmat['testloss'] = teenerls
predmat['testacc'] = teaccls
predmat['testdi'] = tedils
predmat['testlabel'] = testlabel
predmat['trainlabel'] = trainlabel
predmat['traindata'] = traindata
predmat['trainfname'] = trainfname
predmat['testdata'] = testdata
for iindex in range(8):
traindataii = traindata[iindex*batchsize:(iindex+1)*batchsize, :, :]
trainlabelii = trainlabel[iindex*batchsize:(iindex+1)*batchsize, :, :]
if modelname[:3] == 'cnn':
qtestval = sess.run(qtest, feed_dict={X: traindataii,
Y: trainlabelii, learningrate: 0})
else:
traink1ii = traink1[iindex*batchsize:(iindex+1)*batchsize, :, :]
traink2ii = traink2[iindex*batchsize:(iindex+1)*batchsize, :, :]
qtestval = sess.run(qtest, feed_dict={X: traindataii,
Y: trainlabelii, learningrate: 0, k1: traink1ii, k2: traink2ii})
if iindex == 0:
trainpred = qtestval
else:
trainpred = np.concatenate((trainpred, qtestval), axis=0)
predmat['trainpred'] = trainpred
print(savename+'.mat', str(max(tedils)))
sio.savemat(savename+'.mat', predmat)
plt.figure(1)
t = np.arange(0, totalepoch, 1)
plt.subplot(311)
plt.plot(t, trenerls, 'r', t, teenerls, 'b')
plt.subplot(312)
plt.plot(t, traccls, 'r', t, teaccls, 'b')
plt.subplot(313)
plt.plot(t, trdils, 'r', t, tedils, 'b')
plt.savefig(savename+'.png')