def main():
usage = '''
Usage:
------------------------------------------------
parallelized cross-validation. Prints
misclassification rate and standard deviation
python %s [OPTIONS] infile trainshapefile
Options:
-h this help
-a <int> algorithm 1=MaxLike(def
fault)
2=Gausskernel
3=NNet(backprop)
4=NNet(congrad)
5=NNet(Kalman)
6=Dnn(tensorflow)
7=SVM
-p <list> band positions (default all)
e.g. -p [1,2,3]
-L <list> hidden neurons (default [10])
e.g. [10,10]
-e <int> epochs (default 100)
-------------------------------------------------''' % sys.argv[0]
options, args = getopt.getopt(sys.argv[1:], 'hp:a:e:L:')
pos = None
L = [10]
trainalg = 1
epochs = 100
for option, value in options:
if option == '-h':
print usage
return
elif option == '-p':
pos = eval(value)
elif option == '-e':
epochs = eval(value)
elif option == '-a':
trainalg = eval(value)
elif option == '-L':
L = eval(value)
if len(args) != 2:
print 'Incorrect number of arguments'
print usage
sys.exit(1)
infile = args[0]
trnfile = args[1]
gdal.AllRegister()
inDataset = gdal.Open(infile, GA_ReadOnly)
bands = inDataset.RasterCount
if pos is None:
pos = range(1, bands + 1)
N = len(pos)
if trainalg == 1:
algorithm = 'MaxLike'
elif trainalg == 2:
algorithm = 'Gausskernel'
elif trainalg == 3:
algorithm = 'NNet(Backprop)'
elif trainalg == 4:
algorithm = 'NNet(Congrad)'
elif trainalg == 5:
algorithm = 'NNet(Kalman)'
elif trainalg == 6:
algorithm = 'Dnn(Tensorflow)'
else:
algorithm = 'SVM'
print 'Algorithm: %s' % algorithm
# get the training data
Gs, ls, K, _ = rs.readshp(trnfile, inDataset, pos)
m = ls.shape[0]
print str(m) + ' training pixel vectors were read in'
# stretch the pixel vectors to [-1,1] (for ffn)
maxx = np.max(Gs, 0)
minx = np.min(Gs, 0)
for j in range(N):
Gs[:,j]=2*(Gs[:,j]-minx[j])/(maxx[j]-minx[j]) \
- 1.0
# random permutation of training data
idx = np.random.permutation(m)
Gs = Gs[idx, :]
ls = ls[idx, :]
# cross-validation
start = time.time()
traintest = []
for i in range(10):
sl = slice(i * m // 10, (i + 1) * m // 10)
traintest.append(
(np.delete(Gs,sl,0),np.delete(ls,sl,0), \
Gs[sl,:],ls[sl,:],L,epochs,trainalg) )
try:
print 'attempting parallel calculation ...'
c = Client()
print 'available engines %s' % str(c.ids)
v = c[:]
result = v.map_sync(crossvalidate, traintest)
except Exception as e:
print '%s \nfailed, running sequentially ...' % e
result = map(crossvalidate, traintest)
print 'execution time: %s' % str(time.time() - start)
print 'misclassification rate: %f' % np.mean(result)
print 'standard deviation: %f' % np.std(result)
def main():
usage = '''
Usage:
--------------------------------------
Supervised classification of multispectral images
python %s [OPTIONS] filename shapefile
Options:
-h this help
-p <list> RGB band positions to be included
(default all) e.g. -p [1,2,3]
-a <int> algorithm 1=MaxLike
2=Gausskernel
3=NNet(backprop)
4=NNet(congrad)
5=NNet(Kalman)
6=Dnn(tensorflow)
7=SVM
-e <int> number of epochs (default 100)
-t <float> fraction for training (default 0.67)
-v use validation (reserve half of training
data for validation)
-P generate class probability image (not
available for MaxLike)
-n suppress graphical output
-L <list> list of hidden neurons in each
hidden layer (default [10])
If the input file is named
path/filenbasename.ext then
The output classification file is named
path/filebasename_class.ext
the class probabilities output file is named
path/filebasename_classprobs.ext
and the test results file is named
path/filebasename_<classifier>.tst
-------------------------------------'''%sys.argv[0]
outbuffer = 100
options, args = getopt.getopt(sys.argv[1:],'hnvPp:t:e:a:L:')
pos = None
probs = False
L = [10]
trainalg = 1
epochs = 100
graphics = True
validation = False
trainfrac = 0.67
for option, value in options:
if option == '-h':
print usage
return
elif option == '-p':
pos = eval(value)
elif option == '-n':
graphics = False
elif option == '-v':
validation = True
elif option == '-t':
trainfrac = eval(value)
elif option == '-e':
epochs = eval(value)
elif option == '-a':
trainalg = eval(value)
elif option == '-L':
L = eval(value)
elif option == '-P':
probs = True
if len(args) != 2:
print 'Incorrect number of arguments'
print usage
sys.exit(1)
if trainalg == 1:
algorithm = 'MaxLike'
elif trainalg == 2:
algorithm = 'Gausskernel'
elif trainalg == 3:
algorithm = 'NNet(Backprop)'
elif trainalg == 4:
algorithm = 'NNet(Congrad)'
elif trainalg == 5:
algorithm = 'NNet(Kalman)'
elif trainalg == 6:
algorithm = 'Dnn(tensorflow)'
else:
algorithm = 'SVM'
print 'Training with %s'%algorithm
infile = args[0]
trnfile = args[1]
gdal.AllRegister()
if infile:
inDataset = gdal.Open(infile,GA_ReadOnly)
cols = inDataset.RasterXSize
rows = inDataset.RasterYSize
bands = inDataset.RasterCount
geotransform = inDataset.GetGeoTransform()
else:
return
if pos is None:
pos = range(1,bands+1)
N = len(pos)
rasterBands = []
for b in pos:
rasterBands.append(inDataset.GetRasterBand(b))
# output files
path = os.path.dirname(infile)
basename = os.path.basename(infile)
root, ext = os.path.splitext(basename)
outfile = '%s/%s_class%s'%(path,root,ext)
tstfile = '%s/%s_%s.tst'%(path,root,algorithm)
if (trainalg in (2,3,4,5,6)) and probs:
# class probabilities file
probfile = '%s/%s_classprobs%s'%(path,root,ext)
else:
probfile = None
# get the training data
Xs,Ls,K,classnames = rs.readshp(trnfile,inDataset,pos)
m = Ls.shape[0]
# stretch the pixel vectors to [-1,1] for ffn, dnn
maxx = np.max(Xs,0)
minx = np.min(Xs,0)
for j in range(len(pos)):
Xs[:,j] = 2*(Xs[:,j]-minx[j])/(maxx[j]-minx[j]) - 1.0
# random permutation of training data
idx = np.random.permutation(m)
Xs = Xs[idx,:]
Ls = Ls[idx,:]
# train on trainfrac of training examples, rest for testing
Xstrn = Xs[:int(trainfrac*m),:]
Lstrn = Ls[:int(trainfrac*m),:]
Xstst = Xs[int(trainfrac*m):,:]
Lstst = Ls[int(trainfrac*m):,:]
# setup output datasets
driver = inDataset.GetDriver()
outDataset = driver.Create(outfile,cols,rows,1,GDT_Byte)
projection = inDataset.GetProjection()
if geotransform is not None:
outDataset.SetGeoTransform(geotransform)
if projection is not None:
outDataset.SetProjection(projection)
outBand = outDataset.GetRasterBand(1)
if probfile:
probDataset = driver.Create(probfile,cols,rows,K,GDT_Byte)
if geotransform is not None:
probDataset.SetGeoTransform(geotransform)
if projection is not None:
probDataset.SetProjection(projection)
probBands = []
for k in range(K):
probBands.append(probDataset.GetRasterBand(k+1))
# initialize classifier
if trainalg == 1:
classifier = sc.Maxlike(Xstrn,Lstrn)
elif trainalg == 2:
classifier = sc.Gausskernel(Xstrn,Lstrn)
elif trainalg == 3:
classifier = sc.Ffnbp(Xstrn,Lstrn,L,epochs,validation)
elif trainalg == 4:
classifier = sc.Ffncg(Xstrn,Lstrn,L,epochs,validation)
elif trainalg == 5:
classifier = sc.Ffnekf(Xstrn,Lstrn,L,epochs,validation)
elif trainalg == 6:
# classifier = sc.Dnn_learn(Xstrn,Lstrn,L,epochs)
# classifier = sc.Dnn_core(Xstrn,Lstrn,L,epochs)
classifier = sc.Dnn_keras(Xstrn,Lstrn,L,epochs)
elif trainalg == 7:
classifier = sc.Svm(Xstrn,Lstrn)
# train it
print 'training on %i pixel vectors...' % np.max(classifier._Gs.shape)
print 'classes: %s'%str(classnames)
start = time.time()
result = classifier.train()
print 'elapsed time %s' %str(time.time()-start)
if result is not None:
if (trainalg in [3,4,5]) and graphics:
# the cost arrays are returned in result
cost = np.log(result[0])
costv = np.log(result[1])
ymax = np.max(cost)
#ymin = np.min(cost)-1
ymin = 5.0
xmax = len(cost)
plt.plot(range(xmax),costv,'r',range(xmax),cost,'b')
plt.axis([0,xmax,ymin,ymax])
plt.title('Log(Cross entropy)')
plt.xlabel('Epoch')
# classify the image
print 'classifying...'
start = time.time()
tile = np.zeros((outbuffer*cols,N),dtype=np.float32)
for row in range(rows/outbuffer):
print 'row: %i'%(row*outbuffer)
for j in range(N):
tile[:,j] = rasterBands[j].ReadAsArray(0,row*outbuffer,cols,outbuffer).ravel()
tile[:,j] = 2*(tile[:,j]-minx[j])/(maxx[j]-minx[j]) - 1.0
cls, Ms = classifier.classify(tile)
outBand.WriteArray(np.reshape(cls,(outbuffer,cols)),0,row*outbuffer)
if probfile and Ms is not None:
Ms = np.byte(Ms*255)
for k in range(K):
probBands[k].WriteArray(np.reshape(Ms[:,k],(outbuffer,cols)),0,row*outbuffer)
outBand.FlushCache()
print 'elapsed time %s' %str(time.time()-start)
outDataset = None
inDataset = None
if probfile:
for probBand in probBands:
probBand.FlushCache()
probDataset = None
print 'class probabilities written to: %s'%probfile
print 'thematic map written to: %s'%outfile
if (trainalg in [3,4,5]) and graphics:
plt.show()
if tstfile:
with open(tstfile,'w') as f:
print >>f, algorithm +'test results for %s'%infile
print >>f, time.asctime()
print >>f, 'Classification image: %s'%outfile
print >>f, 'Class probabilities image: %s'%probfile
print >>f, Lstst.shape[0],Lstst.shape[1]
classes, _ = classifier.classify(Xstst)
labels = np.argmax(Lstst,axis=1)+1
for i in range(len(classes)):
print >>f, classes[i], labels[i]
f.close()
print 'test results written to: %s'%tstfile
print 'done'
else:
print 'an error occured'
return
def main():
usage = '''
Usage:
---------------------------------------------------------
python %s [-a algorithm] [-p bands] [-L hidden neurons] [-e epochs] infile trainShapefile
bandPositions is a list, e.g., -p [1,2,4]
algorithm 1=MaxLike
2=Gausskernel
3=NNet(backprop)
4=NNet(congrad)
5=NNet(Kalman)
6=Dnn(tensorflow)
7=SVM
prints misclassification rate and standard deviation
--------------------------------------------------------''' %sys.argv[0]
options, args = getopt.getopt(sys.argv[1:],'hp:a:e:L:')
pos = None
L = [10]
trainalg = 1
epochs = 100
for option, value in options:
if option == '-h':
print usage
return
elif option == '-p':
pos = eval(value)
elif option == '-e':
epochs = eval(value)
elif option == '-a':
trainalg = eval(value)
elif option == '-L':
L = eval(value)
if len(args) != 2:
print 'Incorrect number of arguments'
print usage
sys.exit(1)
infile = args[0]
trnfile = args[1]
gdal.AllRegister()
inDataset = gdal.Open(infile,GA_ReadOnly)
bands = inDataset.RasterCount
if pos is None:
pos = range(1,bands+1)
N = len(pos)
if trainalg == 1:
algorithm = 'MaxLike'
elif trainalg == 2:
algorithm = 'Gausskernel'
elif trainalg == 3:
algorithm = 'NNet(Backprop)'
elif trainalg == 4:
algorithm = 'NNet(Congrad)'
elif trainalg == 5:
algorithm = 'NNet(Kalman)'
elif trainalg == 6:
algorithm = 'Dnn(Tensorflow)'
else:
algorithm = 'SVM'
print 'Algorithm: %s'%algorithm
# get the training data
Gs,ls,K,classnames = rs.readshp(trnfile,inDataset,pos)
m = ls.shape[0]
print str(m) + ' training pixel vectors were read in'
# stretch the pixel vectors to [-1,1] (for ffn)
maxx = np.max(Gs,0)
minx = np.min(Gs,0)
for j in range(N):
Gs[:,j] = 2*(Gs[:,j]-minx[j])/(maxx[j]-minx[j]) - 1.0
# random permutation of training data
idx = np.random.permutation(m)
Gs = Gs[idx,:]
ls = ls[idx,:]
# cross-validation
start = time.time()
rc = ipyparallel.Client()
print 'running %i IPython engines'%len(rc)
traintest = []
for i in range(10):
sl = slice(i*m//10,(i+1)*m//10)
traintest.append(
(np.delete(Gs,sl,0),np.delete(ls,sl,0), \
Gs[sl,:],ls[sl,:],L,epochs,trainalg) )
v = rc[:]
v.execute('import auxil.supervisedclass as sc')
result = v.map(crossvalidate,traintest).get()
print 'execution time: %s' %str(time.time()-start)
print 'misclassification rate: %f' %np.mean(result)
print 'standard deviation: %f' %np.std(result)
def main():
usage = '''
Usage:
------------------------------------------------
supervised classification of multispectral images with ADABOOST.M1
python %s [OPTIONS] filename trainShapefile
Options:
-h this help
-p <list> band positions e.g. -p [1,2,3,4]
-L <int> number of hidden neurons (default 10)
-n <int> number of nnet instances (default 50)
-e <int> epochs for ekf training (default 3)
If the input file is named
path/filenbasename.ext then
The output classification file is named
path/filebasename_class.ext
------------------------------------------------''' % sys.argv[0]
outbuffer = 100
options, args = getopt.getopt(sys.argv[1:], 'hp:n:e:L:')
pos = None
L = [10]
epochs = 3
instances = 50
for option, value in options:
if option == '-h':
print usage
return
elif option == '-p':
pos = eval(value)
elif option == '-e':
epochs = eval(value)
elif option == '-n':
instances = eval(value)
elif option == '-L':
L = [eval(value)]
if len(args) != 2:
print 'Incorrect number of arguments'
print usage
sys.exit(1)
print 'Training with ADABOOST.M1 and %i epochs per ffn' % epochs
infile = args[0]
trnfile = args[1]
gdal.AllRegister()
if infile:
inDataset = gdal.Open(infile, GA_ReadOnly)
cols = inDataset.RasterXSize
rows = inDataset.RasterYSize
bands = inDataset.RasterCount
geotransform = inDataset.GetGeoTransform()
else:
return
if pos is None:
pos = range(1, bands + 1)
N = len(pos)
rasterBands = []
for b in pos:
rasterBands.append(inDataset.GetRasterBand(b))
# output file
path = os.path.dirname(infile)
basename = os.path.basename(infile)
root, ext = os.path.splitext(basename)
outfile = '%s/%s_class%s' % (path, root, ext)
# setup output class image dataset
driver = inDataset.GetDriver()
outDataset = driver.Create(outfile, cols, rows, 1, GDT_Byte)
projection = inDataset.GetProjection()
if geotransform is not None:
outDataset.SetGeoTransform(geotransform)
if projection is not None:
outDataset.SetProjection(projection)
outBand = outDataset.GetRasterBand(1)
# get the training data
Xs, Ls, K, _ = rs.readshp(trnfile, inDataset, pos)
m = Ls.shape[0]
# stretch the pixel vectors to [-1,1]
maxx = np.max(Xs, 0)
minx = np.min(Xs, 0)
for j in range(len(pos)):
Xs[:, j] = 2 * (Xs[:, j] - minx[j]) / (maxx[j] - minx[j]) - 1.0
# random permutation of training data
idx = np.random.permutation(m)
Xs = Xs[idx, :]
Ls = Ls[idx, :]
# train on 2/3 of training examples, rest for testing
mtrn = int(0.67 * m)
mtst = m - mtrn
Xstrn = Xs[:mtrn, :]
Lstrn = Ls[:mtrn, :]
Xstst = Xs[mtrn:, :]
Lstst = Ls[mtrn:, :]
labels_train = np.argmax(Lstrn, 1)
labels_test = np.argmax(Lstst, 1)
# list of network instances, weights and errors
ffns = []
alphas = []
errtrn = []
errtst = []
# initial probability distribution
p = np.ones(mtrn) / mtrn
# loop through the network instance
start = time.time()
instance = 1
while instance < instances:
trial = 1
while trial < 6:
print 'running instance: %i trial: %i' \
%(instance,trial)
# instantiate a ffn and train it
ffn = Ffnekfab(Xstrn, Lstrn, p, L, epochs)
ffn.train()
# determine beta
labels, _ = ffn.classify(Xstrn)
labels -= 1
idxi = np.where(labels != labels_train)[0]
idxc = np.where(labels == labels_train)[0]
epsilon = np.sum(p[idxi])
beta = epsilon / (1 - epsilon)
if beta < 1.0:
# continue
ffns.append(ffn)
alphas.append(np.log(1.0 / beta))
# update distribution
p[idxc] = p[idxc] * beta
p = p / np.sum(p)
# train error
labels, _ = seq_class(ffns, Xstrn, alphas, K)
tmp = np.where(labels != labels_train, 1, 0)
errtrn.append(np.sum(tmp) / float(mtrn))
# test error
labels, _ = seq_class(ffns, Xstst, alphas, K)
tmp = np.where(labels != labels_test, 1, 0)
errtst.append(np.sum(tmp) / float(mtst))
print 'train error: %f test error: %f'\
%(errtrn[-1],errtst[-1])
# this instance is done
trial = 6
instance += 1
else:
trial += 1
# break off training
if trial == 6:
instance = instances
print 'elapsed time %s' % str(time.time() - start)
# plot errors
n = len(errtrn)
errtrn = np.array(errtrn)
errtst = np.array(errtst)
x = np.arange(1, n + 1, 1)
ax = plt.subplot(111)
ax.semilogx(x, errtrn, label='train')
ax.semilogx(x, errtst, label='test')
ax.legend()
ax.set_xlabel('number of networks')
ax.set_ylabel('classification error')
plt.savefig('/home/mort/LaTeX/new projects/CRC4/Chapter7/fig7_3.eps',
bbox_inches='tight')
plt.show()
# classify the image
print 'classifying...'
start = time.time()
tile = np.zeros((outbuffer * cols, N), dtype=np.float32)
for row in range(rows / outbuffer):
print 'row: %i' % (row * outbuffer)
for j in range(N):
tile[:, j] = rasterBands[j].ReadAsArray(0, row * outbuffer, cols,
outbuffer).ravel()
tile[:, j] = 2 * (tile[:, j] - minx[j]) / (maxx[j] - minx[j]) - 1.0
cls, _ = seq_class(ffns, tile, alphas, K)
outBand.WriteArray(np.reshape(cls, (outbuffer, cols)), 0,
row * outbuffer)
outBand.FlushCache()
print 'thematic map written to: %s' % outfile
print 'elapsed time %s' % str(time.time() - start)