def find_ROI(p, filenames):
"""Uses template matching to find the region of interest (terminal bulb) in images."""
# define bulb template
templ = define_template(filenames[:20], p)
# find template location in all following images
filenames = filenames[p.START:p.END:p.INTRVL]
# initialize data arrays
time = np.arange(p.START,p.END,p.INTRVL)
spacing = np.array([p.INTRVL]*(len(time)-1)+[p.END - (len(time)-1)*p.INTRVL - p.START])
locs = np.zeros((len(filenames),2))
confs = np.zeros(len(filenames))
for cnt,fn in enumerate(filenames):
img=mpimg.imread(os.path.join(p.DIRC,fn))
if p.ROT:
img = np.transpose(img)
if p.CROP is not None:
img = img[:,p.CROP[0]:p.CROP[1]]
# find bulb by template matching
yr,xr, conf = find_bulb(img, templ)
confs[cnt] = conf
locs[cnt] = (yr,xr)
time, yroi, spacing = clean_auto_coords(p, time, locs, confs, spacing, n = 3)
xroi = np.ones(len(yroi))*img.shape[1]/2.
#write data to file
write_data(p.OUTDIR, "roi_"+p.BASENAME, zip(time,xroi,yroi, spacing), ncol=4)
def write_ROI(p, filenames):
"""writes all region of interests to file"""
plt.ion()
fig = plt.figure(figsize=(12,8), dpi=100,edgecolor='k',facecolor='w')
clicks=clickSaver()
clicks.reset_data()
fig.canvas.mpl_connect('button_press_event', clicks.onclick)
ax = fig.add_subplot(111)
plt.title("Click on the bulb, if worm is out of frame click outside of image.")
filenames = filenames[p.START:p.END:p.INTRVL]
time = np.arange(p.START,p.END,p.INTRVL)
spacing = [p.INTRVL]*(len(time)-1)+[p.END - (len(time)-1)*p.INTRVL - p.START]
try:
for cnt,fn in enumerate(filenames):
img=mpimg.imread(os.path.join(p.DIRC,fn))
if p.ROT:
img = np.transpose(img)
if p.CROP !=None:
img = img[:,p.CROP[0]:p.CROP[1]]
if cnt==0:
im=ax.imshow(img,cmap='gray', origin = 'lower')
text = plt.text(-1.5,0.9,"%s"%fn, transform = ax.transAxes)
text2 = plt.text(-1.5,0.8,"%i\%i"%(float(cnt),(len(filenames)-1)), transform = ax.transAxes)
plt.draw()
plt.tight_layout()
plt.waitforbuttonpress()
else:
im.set_data(img)
text.set_text("%s"%fn)
text2.set_text("%i\%i"%(float(cnt),(len(filenames)-1)))
plt.draw()
#plt.tight_layout()
plt.waitforbuttonpress()
except IOError:
print "Problem with image?"
pass
finally:
xroi, yroi, time = clean_roi(time,clicks.xroi, clicks.yroi)
#write data to file
write_data(p.OUTDIR, "roi_"+p.BASENAME, zip(time,xroi,yroi, spacing), ncol=4)
