import readmagick
import pymorph
import mahotas
dna = readmagick.readimg('dna-0.xcf[0]').max(2)
dna2 = readmagick.readimg('dna-1.xcf[0]').max(2)
borders = readmagick.readimg('dna-0.xcf[1]')
borders = borders[:,:,0] > borders[:,:,1]
for i in xrange(2): borders = mahotas.dilate(borders, np.ones((3,3)))
readmagick.writeimg(pymorph.overlay(dna, borders), 'dna.png')
readmagick.writeimg(pymorph.overlay(dna2, borders), 'dna2.png')
def write_readback(C,fname):
C = C.copy()
writeimg(C,fname)
C2 = readimg(fname)
return C, C2
def test_one(C,fname,correct):
writeimg(C,fname)
C,C2 = write_readback(C,fname)
if correct: C2 //= 257
assert C.shape == C2.shape
assert numpy.all(C == C2)
print "showing..."
# pylab.imshow(imlabel)
# pylab.show()
# Particles is a list of images
Particles = extractParticles(im1, imlabel)
li = 1
ColNum = 10 # ten columns and len(Particles)/ColNum lines
il = 0
iw = 0
for i in range(0, len(Particles)):
# first convert and save particle as 8bits png image
file = "part" + str(i) + ".png"
saveim = gray12_to8(Particles[i])
pathtoparticles = os.path.join(workdir, "particules", file)
savedfile = saveim.astype(np.uint8)
readmagick.writeimg(savedfile, pathtoparticles)
print "saving:" + file
# loading a 8bits png
# (next thing to do:building a mosaic directly from Particles list)
#
# print pathtoparticles
# impng=readmagick.readimg(pathtoparticles)
# col=i%ColNum+1
# print "im shape:",impng.shape," i:",i," li:",li," col:",col
# there should be len(Particles)+1 subplots
# pylab.subplot(1,i+1,i+1)
# pylab.imshow(impng)
# if col == 1 :
# li=li+1
# pylab.show()
def savejet(img, name):
img = (img - img.min()) / float(img.ptp()) * 255
img = img.astype(np.uint8)
readmagick.writeimg((cm.jet(img)[:, :, :3] * 255).astype(np.uint8),
name)
def savejet(img):
readmagick.writeimg((cm.jet(dnaf)[:,:,:3]*255).astype(np.uint8), name)
imlabel,npart=nd.label(LowResSegmentation(dapi))
print "showing..."
#pylab.imshow(imlabel)
#pylab.show()
#Particles is a list of images
Particles=extractParticles(im1,imlabel)
li=1
ColNum=10#ten columns and len(Particles)/ColNum lines
il=0
iw=0
for i in range(0,len(Particles)):
#first convert and save particle as 8bits png image
file='part'+str(i)+'.png'
saveim=gray12_to8(Particles[i])
pathtoparticles=os.path.join(workdir,"particules",file)
savedfile=saveim.astype(np.uint8)
readmagick.writeimg(savedfile, pathtoparticles)
print "saving:"+file
#loading a 8bits png
#(next thing to do:building a mosaic directly from Particles list)
#
#print pathtoparticles
#impng=readmagick.readimg(pathtoparticles)
#col=i%ColNum+1
#print "im shape:",impng.shape," i:",i," li:",li," col:",col
#there should be len(Particles)+1 subplots
#pylab.subplot(1,i+1,i+1)
#pylab.imshow(impng)
#if col == 1 :
# li=li+1
#pylab.show()
def savejet(img):
readmagick.writeimg((cm.jet(dnaf)[:, :, :3] * 255).astype(np.uint8),
name)
def savejet(img, name):
img = (img - img.min())/float(img.ptp())*255
img = img.astype(np.uint8)
readmagick.writeimg((cm.jet(img)[:,:,:3]*255).astype(np.uint8), name)
def write(img, name):
transformed = (img - img.min()).astype(float)/img.ptp()
transformed = (transformed * 255).astype(np.uint8)
readmagick.writeimg(transformed, name)
