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 postTag(self,parent,tag):
req = etree.Element ('request')
etree.SubElement (req, 'tag', name=str(tag.name), value=str(tag.value), type='string')
log.debug("REQ: " + etree.tostring(req))
resp, content = request(parent.uri, "POST", body = etree.tostring(req), headers={'content-type':'text/xml' }, userpass = self.userpass )
log.debug("RESP: " + str(content))
return resp
def loadImage(self, url):
resp, content = request(url, userpass = self.userpass)
log.debug ('itkGeodesicSegmentationPY - response: ' + str(content) + '||||||||||' +url)
response = etree.XML(content)
image = parseXml(root = response, factory = BQNodeFactory)
log.debug("GOT " + str(image.uri))
return image
def loadImage(self, url):
resp, content = request(url)
log.debug('itkModulePY - response: ' + str(content) + '||||||||||' +
url)
response = etree.XML(content)
image = parseXml(root=response, factory=BQNodeFactory)
log.debug("GOT " + str(image.uri))
return image
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)
def main(self):
print 'Running in main'
client_server = sys.argv[1]
image_url = sys.argv[2]
user = '******'
password = '******'
self.userpass = (user, password)
seedX = [81, 99, 56, 40]
seedY = [114, 114, 92, 90]
Sigma = [1.0, 1.0, 1.0, 1.0]
SigmoidAlpha = [-0.5, -0.5, -0.3, -0.3]
SigmoidBeta = [3.0, 3.0, 2.0, 2.0]
requesturl = client_server + '/ms/'
#run all the four segmentation processes sequentially
for i in range(0, len(seedX)):
# Initiate the mex
response = self.createXML(client_server, image_url, seedX[i],
seedY[i], Sigma[i], SigmoidAlpha[i],
SigmoidBeta[i])
resp, content = xmlrequest(requesturl,
method="POST",
body=etree.tostring(response),
userpass=self.userpass)
#print 'RESPONSE = ', str(resp)
#print 'CONTENT = ',str(content)
#print 'CONTENT LENGTH = ',len(content)
# Check mex status
#mex = etree.parse(content)
#print '\n\n parsing \n\n'
mex = etree.parse(StringIO.StringIO(content))
uri = mex.getroot().get('uri')
#print '\nURI = ' ,str(uri)
while 1:
resp, content = request(uri, userpass=self.userpass)
#print "###CONTENT = ",str(content)
mex = etree.parse(StringIO.StringIO(content))
if mex.getroot()[0].get('status') == 'FINISHED':
print 'Finished'
break
elif mex.getroot()[0].get('status') == 'FAILURE':
print 'Failure'
break
#else:
# print '### Waiting..'
# START COMMENT
# decide on the tag name to search
#if seedX in range(78,83):
# tagName= "Left_Ventricle_Mask"
#elif seedX in range(97,101):
# tagName = "Right_Ventricle_Mask"
#elif seedX in range(54,58):
# tagName = "White_Matter_Mask"
#elif seedX in range(38,42):
# tagName = "Grey_Matter_Mask"
#else:
# tagName = "Unknown_Region_Mask"
# Now the tag is created- search for the tag in the image url-tag
#resp, content = request(image_url, userpass=self.userpass)
#print 'image url CONTENT = ',str(content)
#tag = etree.parse(StringIO.StringIO(content))
#tag_url = tag.getroot()[0][0].get('uri')
#request for the tag values again
#resp, content = request(tag_url , userpass=self.userpass)
#print 'image url CONTENT = ',str(content)
#tag = etree.parse(StringIO.StringIO(content))
#tag_root = tag.getroot()
#now parse the xml
#i = 0;
#while tag_root[i] != None:
# name = tag_root[i].get('name')
# if(name == tagName):
# break
# else:
# i = i+1
#mask_url = tag_root[i].get('value')
#if mask_url=='':
# print '\nERROR: mask_url not found'
#print '\n\n', mask_url
#time.sleep(5)
#END COMMENT
tagName = [
'Left_Ventricle_Mask', 'Right_Ventricle_Mask', 'White_Matter_Mask',
'Grey_Matter_Mask'
]
requesturl = client_server + '/ms/'
#Start processing for program 2
for i in range(0, len(tagName)):
response = self.createXML2(client_server, image_url, tagName[i])
resp, content = xmlrequest(requesturl,
method="POST",
body=etree.tostring(response),
userpass=self.userpass)
#print 'RESPONSE = ', str(resp)
#print 'CONTENT = ',str(content)
#print 'CONTENT LENGTH = ',len(content)
mex = etree.parse(StringIO.StringIO(content))
uri = mex.getroot().get('uri')
#print '\nURI = ' ,str(uri)
condCount = 0
while 1:
resp, content = request(uri, userpass=self.userpass)
mex = etree.parse(StringIO.StringIO(content))
if mex.getroot()[0].get('status') == 'FINISHED':
print ' Finished module 2'
break
elif mex.getroot()[0].get('status') == 'FAILURE':
if condCount < 3:
print 'Failure module 2 == Retrying for a free engine', condCount
print 'Sleeping for 5 seconds'
time.sleep(5)
resp, content = xmlrequest(
requesturl,
method="POST",
body=etree.tostring(response),
userpass=self.userpass)
mex = etree.parse(StringIO.StringIO(content))
uri = mex.getroot().get('uri')
condCount += 1
else:
print 'Failure module 2'
break
