It is possible to orientate chromosomes vertically with a morphological "rose des directions" using successive erosions. The larger the particle is, the longer the operation is. However, the iterations can be reduced by submitting not the particle itself, but a Top-Hat version of the image, or the particle skeleton or the particle contour yielding similar results with a reduced cost.
The first rose-des-directions was obtained with the original particle, I didn't compute the total amount of erosion, but finding the principal orientation around 120° required around 50 successive erosions, whereas only 16 erosions are necessary if the particle skeleton is analysed, 30 erosions with the Top-Hat filtered image or 20 with the contour.
With a more complex image, the "rose des directions" detects the orientation of the larger chromosome.
I am not too satisfied of the result. The interaction is not too convenient (key board+mouse), but for a first trial, that does the job. To rotate the chromosome, hit the r key of the keyboard to toggle between the drag-and-drop and the rotation modes.
Here is the script:
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 5 15:44:42 2011
@author: jean-pat
"""
#!/usr/bin/env python
#
import os, pygame
import ConfigParser as CfgP
from pygame.locals import*
#def makeCfgFile():
# config = CfgP.RawConfigParser()
# config.add_section('shape classifier')
# config.set('shape classifier', 'ref', '')
# config.set('shape classifier', 'shape type', '')
# return config
#def saveCfgFile(cfgfile,IKromList):
# #building a config file
# for s in IKromList:
# print "saving config"
# cref=s.ref
# ctype=s.type
# config.add_section(cref)
# config.set(cref,'shape type', ctype)
# config.write(open('shape.cfg','w'))
# print "config saved"
def readconfiguration():
"""
read path to particles to classify:
[Fluorochrome]
Counter stain='DAPI'
Probes=('Cy3','Cy5,'FITC')
[Images Path]
work dir=...
user=...
slide=...
field list=...
[Classifier]
screen size=(1024,768)
category number=4
category list=(single chromosome,touching chromosomes,nuclei,dust)
box size=(200,100)
first box=(5,650)
box hspacing=30
"""
def load_image(name, colorkey=None):
fullname=os.path.join("data", name)
try:
image=pygame.image.load(fullname)
except pygame.error, message:
print "Impossible de charger l'image:",name
raise SystemExit, message
image = image.convert()
if colorkey is not None:
if colorkey is -1:
colorkey = image.get_at((0, 0))
image.set_colorkey(colorkey, RLEACCEL)
return image, image.get_rect()
class Ichrom(pygame.sprite.Sprite):
def __init__(self,image,ref,initpos):
pygame.sprite.Sprite.__init__(self)
self.ref=ref#particule name
self.type=""
self.pos = initpos
self.image,self.rect=image
self.original=image
self.rotation=0
self.mode="translation"
#print "self.rect",self.rect,"-self.image:",self.image
self.button=(0,0,0)#mouse buttons not pressed
#self.selected = 0
self.mouseover=False
self.focused=False
self.rect.topleft=initpos
print "init chrom at ",self.pos
def rollover(self,rotationmode):
"""Test if the mouse fly over the chromosome
self.mouseover==True if mouse flying over the chrom,
False if not"""
mpos=pygame.mouse.get_pos()#mouseposition
#test if mouse roll over the sprite
if rotationmode==0:
self.mode="translation"
if rotationmode==1:
self.mode="rotation"
print pygame.mouse.get_rel()
if self.rect.collidepoint(mpos):
self.mouseover=True
else:
self.mouseover=False
def update(self,classifiergroup,background):
self.button=pygame.mouse.get_pressed()
mpos = pygame.mouse.get_pos()
self.selected=self.rect.collidepoint(mpos)
#the mouse flies over a chromosome
if (self.mouseover):
if self.mode=="translation":
#print "mouse pos:",mpos
collision=pygame.sprite.spritecollide(self,classifiergroup,False)
#collision should contains only one element
if len(collision)>0:
#print collision[0].category
self.type=collision[0].category
print "particle "+self.ref+" is classified to "+self.type
if self.button==(1,0,0):
pos = pygame.mouse.get_pos()
self.rect.center = pos
elif self.mode=="rotation":
#test mouse movement
mrel=pygame.mouse.get_rel()
if self.rotation>=360:
self.rotation=0
self.image=self.original
elif mrel[0]>0:
self.rotation=self.rotation+10
self.image=pygame.transform.rotate(self.original[0],self.rotation)
self.rect=self.image.get_rect(center=self.rect.center)
elif mrel[0]<0:
self.rotation=self.rotation-10
self.image=pygame.transform.rotate(self.original[0],self.rotation)
self.rect=self.image.get_rect(center=self.rect.center)
class Classifier(pygame.sprite.Sprite):
'''When a chrom is moved is moved into a category '''
def __init__(self,initpos,category):
pygame.sprite.Sprite.__init__(self)
self.category=category
self.image = pygame.Surface((100,100))
self.image.set_colorkey((0,0,0))
self.image = self.image.convert_alpha()
self.rect= self.image.get_rect()
#pygame.draw.rect(screen, color, (x,y,width,height), thickness)
pygame.draw.rect(self.image, (255,0,0,255), (0,0,100,100),1)
self.rect.topleft= initpos
def update(self):
pass
def main():
pygame.init()
screen = pygame.display.set_mode((320,300))
pygame.display.set_caption("Karyotyper")
pygame.mouse.set_visible(True)
background = pygame.Surface(screen.get_size())
background = background.convert()
background.fill((0, 0, 0))
screen.blit(background,(0, 0))
pygame.display.flip()
i1=load_image("/home/claire/Applications/ImagesTest/jp/Jpp48/13/DAPI/particules/part15.png", -1)
i2=load_image("/home/claire/Applications/ImagesTest/jp/Jpp48/13/DAPI/particules/part12.png", -1)
chr1 = Ichrom(i1,"part15",(0,0))
#chr1 = Krom(i1,(0,0))
chr2=Ichrom(i2,"part12",(30,30))
#chr2=Krom(i2,(30,30))
categ1=Classifier((5,150),"single")
categ2=Classifier((110,150),"overlapping")
categ3=Classifier((215,150),"other stuff")
allsprites = pygame.sprite.RenderPlain((chr1,chr2))
allcategories=pygame.sprite.RenderPlain((categ1,categ2,categ3))
clock = pygame.time.Clock()
config = CfgP.RawConfigParser()
spritelist=(chr1,chr2)
rotationmode=0
while 1:
clock.tick(60)
for event in pygame.event.get():
if event.type == QUIT:
return
elif event.type == KEYDOWN and event.key == K_ESCAPE:
#spritelist=(chr1,chr2)
#building a config file
#saveCfgFile(config,spritelist)
for s in spritelist:
print "saving config"
cref=s.ref
ctype=s.type
config.add_section(cref)
config.set(cref,'shape type', ctype)
config.write(open('shape.cfg','w'))
print "config saved"
return
elif event.type == KEYDOWN and event.key == K_r:
rotationmode=rotationmode+1
if rotationmode==1:
print "rotation ON"
if rotationmode==2:
print "rotation OFF"
rotationmode=0
if event.type ==pygame.MOUSEBUTTONDOWN:
#need to be modified to handle a list of chromosomes
chr1.rollover(rotationmode)
chr2.rollover(rotationmode)
allsprites.update(allcategories,background)
allcategories.update()
##
##Search which chromosome is moved
##into which category and classify
##that chromosome in that category
# collision=pygame.sprite.groupcollide(allcategories,allsprites,False,False,None)
# for classified in collision.keys():
# print classified
screen.blit(background,(0,0))
allsprites.draw(screen)
allcategories.draw(screen)
pygame.display.flip()
if __name__ == '__main__': main()
