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)