def process(srcDir, dstDir, currentDir, fileName, keepDirectories):
print "Processing:"
ROIpath, V1S1RL = os.path.split(currentDir)
# Opening the image
print "Open image file", fileName
imp = IJ.openImage(os.path.join(currentDir, fileName))
imp.show()
print "Compute F/F0"
IJ.run(imp, "F div F0", "6")
imp.close()
V1S1RL = "RoiSet " + V1S1RL + ".zip"
# Put your processing commands here!
ROIPath = ROIpath + "/" + V1S1RL
print "Open ROIS", ROIPath
rm = RoiManager.getInstance()
if not rm:
rm = RoiManager()
rm.reset()
rm.runCommand("open", ROIPath)
rm.runCommand("Show All")
print "Multi Measure"
imp = IJ.getImage()
rt = rm.multiMeasure(imp)
imp.close()
imp = IJ.getImage()
imp.close()
# Saving the image
saveDir = currentDir.replace(srcDir, dstDir) if keepDirectories else dstDir
if not os.path.exists(saveDir):
os.makedirs(saveDir)
print "Saving to", saveDir
rt.save(os.path.join(saveDir, fileName + '.csv'))
# IJ.saveAs(imp, "Tiff", os.path.join(saveDir, fileName));
imp.close()
def tethered_cell(image_path, frame_number=100, frame_rate=100.0, CCW=1):
"""
parameter setting; frame rate (frame/sec)
CCW = 1 : the motor rotation direction and the cell rotation direction on the image are same
CCW = -1: the motor rotation direction and the cell rotation direction on the image are different
"""
opener = Opener()
imp = opener.openImage(image_path)
image_slice_number = imp.getNSlices()
rm = RoiManager().getInstance()
if image_slice_number < frame_number: # too short movie
IJ.log('Number of frame of the movie is fewer than the number of frame that you selected')
return False
# create result directory
result_path = image_path + '_tethered_cell_result'
if os.path.lexists(result_path) is False:
os.mkdir(result_path)
#z projection; standard deviation, tethered cell shorws circle
IJ.run(imp, 'Subtract Background...', 'rolling=5 light stack')
IJ.run(imp, 'Median...', 'radius=2 stack')
IJ.run(imp, 'Z Project...', 'stop=500 projection=[Standard Deviation]')
zimp = IJ.getImage()
IJ.saveAs(zimp, 'bmp', os.path.join(result_path,'STD_DEV.bmp'))
# pick up tethered cell
IJ.setAutoThreshold(zimp, 'MaxEntropy dark')
IJ.run(zimp, 'Convert to Mask', '')
IJ.run('Set Measurements...', "area centroid bounding shape feret's limit redirect=None decimal=3")
IJ.run(zimp, 'Analyze Particles...', 'size=30-Infinity circularity=0.88-1.00 show=Nothing display exclude clear include')
zrt = ResultsTable.getResultsTable()
IJ.saveAs('Results', os.path.join(result_path,'RoiInfo.csv'))
#tcX and tcY are xy coordinates of tethered cell, tcdia is outer diameter of rotating tethered cell
#add ROI into stack image
for i in range(zrt.getCounter()):
tcX = zrt.getValue('X', i)
tcY = zrt.getValue('Y', i)
tcdia = zrt.getValue('Feret', i)
rm.add(imp, OvalRoi(tcX - tcdia/2.0, tcY - tcdia/2.0, tcdia + 1, tcdia + 1), i)
#calculate rotation speed by ellipse fitting
IJ.setAutoThreshold(imp, 'Li')
for roi_number in range(rm.getCount()):
t = []
XM = []
YM = []
theta = []
rotation_speed = []
area = []
imp.setRoi(rm.getRoi(roi_number))
cropped_imp = Duplicator().run(imp)
IJ.run('Set Measurements...', 'area mean center fit limit redirect=None decimal=3')
rm.select(roi_number)
rt = rm.multiMeasure(imp)
# check cell is present while analysis. Don't a cell gose anywhare?
for i in range(frame_number):
area.append(rt.getValue('Area1', i))
if 0 in area:
continue
for i in range(frame_number):
t.append((1/frame_rate)*i)
XM.append(rt.getValue('XM1', i))
YM.append(rt.getValue('YM1', i))
theta.append(rt.getValue('Angle1', i)/180.0*math.pi) # convert to radian
if i == 0:
rotation_speed.append(0)
else:
# phase treatment, theta should be -pi ~ pi
temp_rotation_speed = [theta[i] - theta[i-1],
theta[i] - theta[i-1] + math.pi,
theta[i] - theta[i-1] - math.pi,
theta[i] - theta[i-1] + 2*math.pi,
theta[i] - theta[i-1] - 2*math.pi]
temp_rotation_speed = sorted(temp_rotation_speed, key = lambda x :abs(x) )[0]
rotation_speed.append(CCW*temp_rotation_speed/(2.0*math.pi)*frame_rate)
# write csv
# earch columns indicate 1:index, 2:time(sec), 3:X-coordinate of center of mass(pixel), 4:Y-coordinate of center of mass (pixel), 5:Angle(Radian), 6:Rotation Speed(Hz)
with open(os.path.join(result_path,'Roi' + str(roi_number) + '.csv'), 'w') as f:
writer = csv.writer(f)
writer.writerow(['Index', 'time(s)', 'X', 'Y', 'Angle(rad)', 'Rotation Speed(Hz)'])
for i in range(len(t)):
writer.writerow([i, t[i], XM[i], YM[i], theta[i], rotation_speed[i]])
# plot x-y, t-x, t-y, t-rotation speed, save plot as bmp
plotRotation(roi_number, result_path, t, XM, YM, rotation_speed)
IJ.saveAs(cropped_imp, 'tiff', os.path.join(result_path,'Roi' + str(roi_number) + '.tiff'))
rt.reset()
# get analysis date and time
dt = datetime.datetime.today()
dtstr = dt.strftime('%Y-%m-%d %H:%M:%S')
# wtite analysis setting
with open(os.path.join(result_path,'analysis_setting.csv'), 'w') as f:
writer = csv.writer(f)
writer.writerow(['Analysis Date','frame number','frame rate','CCW direction', 'Method','Auto threshold', 'Subtruct Background', 'Median filter'])
writer.writerow([dtstr, frame_number, frame_rate, CCW, 'Ellipse', 'Li', '5.0', '2'])
# save roi
if rm.getCount() != 0:
rm.runCommand('Save', os.path.join(result_path, 'Roi.zip'))
zimp.close()
imp.close()
rm.close()
zrt.reset()
