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opflowtester.py
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opflowtester.py
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import cv2
import numpy as np
import tifffile as tiff
import time
from skimage import io
t0 = time.time()
inputDirectory = "/Volumes/HDD/Huygens_SYNC/_SYNC/CollectiveMigrationAnalysis/Examplemovies/"
#filenames = ["Starve_serumFree_flow_diection.tif"]
filenames = ["160112_H2B_noStarve_Pos_000_005_Median_3_frames.tif",
"160115_H2B_Starve_serumFree_T0_10min_Pos_003_003_Median_3_frames.tif",
"160126_H2B_T0_1h_3ml_serum_Pos_002_005_Median_3_frames.tif"]
def makeFromCoorinates(ncols, nrows, frame_width, frame_height):
"""
Generates a list of ncols*nrows evenly spaced x/y coordinates.
Args:
ncols: (int) Number of horizontal arrows
nrows: (int) Number of vertical arrows
frame_width: (int) with of image in pixels
frame_height: (int) height of image in pixels
Returns:
list of tuples containing origin x/y coordinates for velocity vectors
"""
dx = frame_width/float(ncols)
dy = frame_height/float(nrows)
out = []
x = int(round(dx/2.0))
for c in xrange(ncols):
y = int(round(dy/2.0))
for r in xrange(nrows):
out.append((int(round(x)),int(round(y))))
y += dy
x += dx
return out
def makeToCoordinates(fromCoords, Uframe, Vframe, scale):
"""
Picks and the values from the component vector matrixes at fromCoords
:param fromCoords: list of from coordinates
:param Umatrix: U (x) component vector matrix
:param Vmatrix: V (y) component vector matrix
:param scale: scalar to multiply u/v values with
:return: list of tuples containing x/y coordinates
"""
out = []
for e in fromCoords:
x = e[0]
y = e[1]
toX = Uframe[x][y]
toY = Vframe[x][y]
out.append((int(round(x+toX*scale)),int(round(y+toY*scale))))
return out
def drawArrows(frame, fromCoords, toCoords, color, thickness, **kwargs):
"""
Draws arrows on an image
:param frame: image to draw arrows on
:param fromCoords: list of tuples containing from x/y coorinates
:param toCoords: list of tuples containing to x/y coorinates
:param color: color of arrows
:param thickness: arrow thicknes in pixels
:param **kwargs: extra aruments passed to cv2.arrowedLine
:return: None, edits image in place
"""
for i in xrange(len(toCoords)):
fromX,fromY = fromCoords[i]
toX, toY = toCoords[i]
cv2.arrowedLine(frame, (fromX,fromY), (toX,toY), color, thickness, **kwargs)
def vectorVizualizer(inputDirectory, filenames, outputDirectory, nrows =15, ncols = 15, scale = 15):
"""
Args:
inputDirectory: (str)
filenames: (list) filenames to analyze and draw
outputDirectory: (str) Where to place output
Returns:
"""
for filename in filenames:
raw = tiff.imread(inputDirectory+filename)
nframes, frame_width, frame_height = raw.shape
ncols, nrows = nrows, ncols
scale = scale
outStack = np.zeros((nframes-1, frame_width, frame_height), dtype='uint8')
for i in xrange(nframes-1):
t1 = time.time()
print "Start frame "+str(i)+"..."+filename
frame = raw[i]
next_frame = raw[i+1]
flow = cv2.calcOpticalFlowFarneback(frame, next_frame, None, 0.5, 3, 9, 3, 5, 1.2, 0)
Uframe = flow[...,0]
Vframe = flow[...,1]
fromCoords = makeFromCoorinates(ncols, nrows, frame_width, frame_height)
toCoords = makeToCoordinates(fromCoords, Uframe, Vframe, scale)
drawArrows(outStack[i], fromCoords, toCoords, 255, 1, tipLength=0.2, line_type=cv2.LINE_AA)
print "Finish frame "+str(i)+" in "+str(time.time()-t1)+" s."
#print outStack.shape
tiff.imsave(outputDirectory+filename+'_vectors.tif', outStack)
print "All done in "+str(time.time()-t0)+" s"
def draw_hsv(flow):
h, w = flow.shape[:2]
fx, fy = flow[:,:,0], flow[:,:,1]
ang = np.arctan2(fy, fx) + np.pi
v = np.sqrt(fx*fx+fy*fy)
hsv = np.zeros((h, w, 3), np.uint8)
hsv[...,0] = ang*(180/np.pi/2)
hsv[...,1] = 255
hsv[...,2] = np.minimum(v*4, 255)
bgr = cv2.cvtColor(hsv, cv2.COLOR_HSV2BGR)
return bgr
def HSVizualizer(inputDirectory, filenames, outputDirectory):
"""
Args:
inputDirectory: (str)
filenames: (list) filenames to analyze and draw
outputDirectory: (str) Where to place output
Returns:
"""
for filename in filenames:
raw = tiff.imread(inputDirectory+filename)
nframes, frame_width, frame_height = raw.shape
#outstack is in RGB color so we need an extra 3 dimensions
outStack = np.zeros((nframes-1, frame_width, frame_height, 3), dtype='uint8')
for i in xrange(nframes-1):
t1 = time.time()
print "Start frame "+str(i)+"..."+filename
frame = raw[i]
next_frame = raw[i+1]
flow = cv2.calcOpticalFlowFarneback(frame, next_frame, None, 0.5, 3, 8, 4, 7, 1.5, 0)
outStack[i] = draw_hsv(flow)
print "Finish frame "+str(i)+" in "+str(time.time()-t1)+" s."
#print outStack.shape
tiff.imsave(outputDirectory+filename+'_HSV.tif', outStack)
print "All done in "+str(time.time()-t0)+" s"
HSVizualizer(inputDirectory,filenames[1:2], inputDirectory)