def test_nlm3_thresh():
from imgtools import test_images, calcPSNR, read3dTiff
dev = OCLDevice(useDevice=1)
# data = test_images.blobs64()
data = read3dTiff("/Users/mweigert/Data/synthetics/blobs64.tif")
np.random.seed(0)
data = 100.*data/np.amax(data)
y = np.maximum(0,data + np.random.normal(0,20,data.shape))
y = y.astype(np.float32)
y = y.astype(np.uint16)
t = time()
out = nlm3_thresh(dev,y,2,3,30,60)
print time()-t
print calcPSNR(data,out)
# sigs = np.linspace(3,70,30)
# bests = []
# for s0 in np.linspace(2,20,10):
# y = data + np.random.normal(0,s0,data.shape)
# y = y.astype(np.float32)
# sigs = s0*np.linspace(.1,5 ,20)
# ind=np.argmax([calcPSNR(data,nlm3_fast(dev,y,2,3,s)) for s in sigs])
# print s0,sigs[ind]
# bests.append([s0,sigs[ind]])
return out
def test_nlm3_thresh():
from imgtools import test_images, calcPSNR, read3dTiff
dev = OCLDevice(useDevice=1)
# data = test_images.blobs64()
data = read3dTiff("/Users/mweigert/Data/synthetics/blobs64.tif")
np.random.seed(0)
data = 100.*data/np.amax(data)
y = np.maximum(0,data + np.random.normal(0,20,data.shape))
y = y.astype(np.float32)
y = y.astype(np.uint16)
t = time()
out = nlm3_thresh(dev,y,2,3,30,60)
print time()-t
print calcPSNR(data,out)
# sigs = np.linspace(3,70,30)
# bests = []
# for s0 in np.linspace(2,20,10):
# y = data + np.random.normal(0,s0,data.shape)
# y = y.astype(np.float32)
# sigs = s0*np.linspace(.1,5 ,20)
# ind=np.argmax([calcPSNR(data,nlm3_fast(dev,y,2,3,s)) for s in sigs])
# print s0,sigs[ind]
# bests.append([s0,sigs[ind]])
return out
def bm4d(data,sigma):
tmpName = utils.absPath("0123456789_TMP.tiff")
tmpName2 = utils.absPath("0123456789_OUT_TMP.tiff")
imgtools.write3dTiff(data,tmpName)
subprocess.call([utils.absPath("cxx_code/bm4d/bm4d.sh"),tmpName,tmpName2,str(sigma)], stdout=subprocess.PIPE)
out = imgtools.read3dTiff(tmpName2)
# os.remove(tmpName)
# os.remove(tmpName2)
return out
def bm4d(data,sigma):
tmpName = utils.absPath("0123456789_TMP.tiff")
tmpName2 = utils.absPath("0123456789_OUT_TMP.tiff")
imgtools.write3dTiff(data,tmpName)
subprocess.call([utils.absPath("cxx_code/bm4d/bm4d.sh"),tmpName,tmpName2,str(sigma)], stdout=subprocess.PIPE)
out = imgtools.read3dTiff(tmpName2)
# os.remove(tmpName)
# os.remove(tmpName2)
return out
def test_bm4d():
from imgtools import test_images, calcPSNR, read3dTiff
dev = OCLDevice()
data = test_images.blobs64()
data = read3dTiff("/Users/mweigert/Data/synthetics/filaments64.tif")
data = 100.*data/np.amax(data)
y = data + np.random.normal(0,20,data.shape)
y = y.astype(np.float32)
out = bm4d(y,20)
print calcPSNR(data,out)
sigs = np.linspace(3,70,30)
return data,out
def test_tv3_gpu():
from imgtools import test_images, calcPSNR, read3dTiff
dev = OCLDevice(useDevice=1)
data = read3dTiff("/Users/mweigert/Data/synthetics/blobs64.tif")
np.random.seed(0)
data = 100.*data/np.amax(data)
y = np.maximum(0,data + np.random.normal(0,0.2*np.amax(data),data.shape))
y = y.astype(np.float32)
t = time()
out = tv3_gpu(dev,y,.4*np.amax(data))
print "time:", time()-t
print "PSNR: ",utils.calcPSNR(data,out)
return data,y,out
def test_bm4d():
from imgtools import test_images, calcPSNR, read3dTiff
dev = OCLDevice()
data = test_images.blobs64()
data = read3dTiff("/Users/mweigert/Data/synthetics/filaments64.tif")
data = 100.*data/np.amax(data)
y = data + np.random.normal(0,20,data.shape)
y = y.astype(np.float32)
out = bm4d(y,20)
print calcPSNR(data,out)
sigs = np.linspace(3,70,30)
return data,out
def test_tv3_gpu():
from imgtools import test_images, calcPSNR, read3dTiff
dev = OCLDevice(useDevice=1)
data = read3dTiff("/Users/mweigert/Data/synthetics/blobs64.tif")
np.random.seed(0)
data = 100.*data/np.amax(data)
y = np.maximum(0,data + np.random.normal(0,0.2*np.amax(data),data.shape))
y = y.astype(np.float32)
t = time()
out = tv3_gpu(dev,y,.4*np.amax(data))
print "time:", time()-t
print "PSNR: ",utils.calcPSNR(data,out)
return data,y,out
def test_real():
import imgtools
import time
d = imgtools.read3dTiff("/Users/mweigert/Data/sqeazy_corpus/Norden_GFP-LAP_4-1.tif")
rend = VolumeRenderer((600,600))
rend.set_modelView(mat4_rotation(.5,0,1.,0))
# rend.set_box_boundaries(.3*np.array([-1,1,-1,1,-1,1]))
t1 = time.time()
rend.set_data(d, autoConvert = True)
rend.set_units([1.,1.,6.])
t2 = time.time()
out = rend.render(maxVal = 200.)
print "time to set data :\t %.2f ms"%(1000*(t2-t1))
print "time to render:\t %.2f ms"%(1000*(time.time()-t2))
return d, rend, out
