def processImage(self):
log.debug("IMAGE: " + self.image.z + ',' + self.image.t + ',' + self.image.ch)
print 'In process image'
if int(self.image.z) == 1 and int(self.image.t) == 1 and (int(self.image.ch) ==1 or int(self.image.ch) == 3):
# read image from Bisque system
resp, content = request(self.image.src + '?format=png', "GET", userpass = self.userpass )
print str(resp)
print len(content)
tempinfile = 'ac_in.png'
tempoutfile = 'ac_out.png'
f = open(tempinfile,'w')
f.write(content)
f.close()
print 'Done writing the file'
InitialDistance = 5.0
seg.doSegment(tempinfile,tempoutfile, self.seedX, self.seedY, InitialDistance, self.Sigma, self.SigmoidAlpha, self.SigmoidBeta,self.PropagationScaling)
print 'Segmentation done!'
buffer = open(tempoutfile,'r')
print ' posting the output to the server ..'
file = [('upload', tempoutfile, buffer.read())]
resp, content = post_files (self.client_server + '/bisquik/upload_raw_image', file, [], userpass = self.userpass,)
log.debug("RESP: " + str(content))
self.image_out_url = str(content)
def processImage(self):
log.debug("IMAGE: " + self.image.z + ',' + self.image.t + ',' +
self.image.ch)
print 'In process image'
if int(self.image.z) == 1 and int(self.image.t) == 1 and (int(
self.image.ch) == 1 or int(self.image.ch) == 3):
# read image from Bisque system
resp, content = request(self.image.src + '?format=tiff',
"GET",
userpass=self.userpass)
print str(resp)
print len(content)
tempinfile = 'in.tiff'
tempoutfile = 'out.tiff'
f = open(tempinfile, 'w')
f.write(content)
f.close()
print 'Done writing the file'
# define all the input values for now
#seedX = 81
#seedY = 114
#Sigma = 1.0
#SigmoidAlpha = -0.5
#SigmoidBeta = 3.0
TimeThreshold = 100
StoppingValue = 100
seg.doSegment(tempinfile, tempoutfile, self.seedX, self.seedY,
self.Sigma, self.SigmoidAlpha, self.SigmoidBeta,
TimeThreshold, StoppingValue)
print 'Segmentation done!'
#OutputPixelType = itk.UC
#OutputImageType = itk.Image[OutputPixelType, 2]
#WriterType = itk.ImageFileWriter[ OutputImageType ]
#writer = WriterType.New()
#writer.SetFileName('out.tiff')
#writer.SetInput( segm_out )
#writer.Update()
#print 'File Output done'
buffer = open(tempoutfile, 'r')
#buffer= cStringIO.StringIO(tempoutfile)
print ' posting the output to the server ..'
file = [('upload', tempoutfile, buffer.read())]
resp, content = post_files(
self.client_server + '/bisquik/upload_raw_image',
file,
[],
userpass=self.userpass,
)
log.debug("RESP: " + str(content))
self.image_out_url = str(content)
def processImage(self):
log.debug("IMAGE: " + self.image.z + ',' + self.image.t + ',' + self.image.ch)
print 'In process image'
if int(self.image.z) == 1 and int(self.image.t) == 1 and (int(self.image.ch) ==1 or int(self.image.ch) == 3):
# read image from Bisque system
resp, content = request(self.image.src + '?format=tiff', "GET", userpass = self.userpass )
# convert stream into Image
im = cStringIO.StringIO(content)
img = Image.open(im)
log.debug("IMAGE: " + str(img.format) + ',' + str(img.size) + ',' + str(img.mode))
''' IMAGE PROCESSING '''
# convert color image into grayscale image
grayimg = ImageOps.grayscale(img)
# convert Image into numpy array
in_im = asarray(grayimg)
# normalize image
norm_im = self.normalizeImage(in_im)
# set the threshold value
thNorm = double((double(self.thValue)/100.0))
# threshold image with thNorm value
th_im = norm_im < thNorm;
# label image with 8conn
structure = [[1,1,1], [1,1,1], [1,1,1]]
th_im = binary_erosion(~th_im,structure)
label_tuple = label(th_im,structure) #(data, dtype, number of labels)
label_im = label_tuple[0]-1
# wathershed
wh_im = watershed_ift(in_im, label_im)
# convert numpy array into Image
img_out = Image.fromarray(wh_im.astype('uint8'))
''' IMAGE PROCESSING '''
# convert Image into stream
buffer = StringIO.StringIO()
img_out.save(buffer, 'TIFF')
# upload image into Bisque system
buffer.seek(0)
buffer.name = 'file.tif'
fields = { 'file' : buffer }
resp, content = post_files (self.client_server + '/bisquik/upload_images', fields=fields, userpass = self.userpass,)
log.debug("RESP: " + str(content))
self.image_out_url = str(content)