In [1]:
#imports
import numpy as np
from skimage.measure import label, regionprops
from skimage.draw import line, set_color
import imageio
import cv2
import operator
import math
import matplotlib.pyplot as plt
%matplotlib inline
import time
from tqdm import tqdm_notebook
from PIL import Image
import argparse
# from Tkinter import *
In [2]:
#Find homography
source_pts = np.array([[100, 90], [475, 70], [425, 370], [75, 470]], dtype = 'float32') #pixels!
dst_pts = np.array([[0, 0], [100, 0], [80, 80], [0, 100]], dtype = 'float32') #cm
homography_matrix, _ = cv2.findHomography(source_pts, dst_pts, cv2.RANSAC, 5.0) #not sure what the 5.0 is really doing seems to work though
POINTMOO = np.array([[75,470]],dtype = 'float32')
POINTMOO = np.array([POINTMOO])
dst_pt = cv2.perspectiveTransform(POINTMOO, homography_matrix)
#print(dst_pt[0][0][0])
#print(dst_pt[0][0][1])
#print(dst_pt)
In [3]:
#Locations of objects and distance thresholds (how close does the rat have to be to be near it)
familiarObject_center_x = 380
familiarObject_center_y = 160
realWorld_famObj_center = cv2.perspectiveTransform(np.array([np.array([[familiarObject_center_x,familiarObject_center_y]], dtype='float32')]), homography_matrix)
familiarObject_center_x_realWorld = realWorld_famObj_center[0][0][0]
familiarObject_center_y_realWorld = realWorld_famObj_center[0][0][1]
DistanceThreshold_familiarObject = 22;
numFrames_FamiliarObject = 0;
novelObject_center_x = 210
novelObject_center_y = 320
realWorld_novelObj_center = cv2.perspectiveTransform(np.array([np.array([[novelObject_center_x,novelObject_center_y]],dtype='float32')]), homography_matrix)
novelObject_center_x_realWorld = realWorld_novelObj_center[0][0][0]
novelObject_center_y_realWorld = realWorld_novelObj_center[0][0][1]
DistanceThrehshold_NovelObject = 22;
numFrames_NovelObject = 0;
In [4]:
#setup for background model and foreground tracking
if 'fgbg' not in locals():
fgbg = cv2.createBackgroundSubtractorKNN()
morph_size = 2
shadowValue = 127
learnBG = False
showShadow = False
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE,(morph_size,morph_size))
In [28]:
#File IO
numFrames_FamiliarObject = 0
numFrames_NovelObject = 0
reader = imageio.get_reader('Round2/Day3/Test-2-cropped.mkv')
fps = reader.get_meta_data()['fps']
print('input video file length is {} seconds'.format(reader.get_length()/(fps)))
print('input video file has a framerate of {} fps'.format(fps))
writer = imageio.get_writer('test-out.mp4', fps=fps)
# def click(event, x, y, flags, param):
# # grab references to the global variables
# global refPt
# # if the left mouse button was clicked, record the starting
# # (x, y) coordinates and indicate that cropping is being
# # performed
# if event == cv2.EVENT_LBUTTONDOWN:
# refPt = [(x, y)]
# posx = refPt[0]
# posy = refPt[1]
# return posx, posy
# click(cv2.EVENT_LBUTTONDOWN)
class Position:
def __init__(self, m, n):
self.coordinates = np.zeros((m, n))
self.click = False
def select_coordinates(self, event, x, y, flags, param):
if event == cv2.EVENT_LBUTTONDOWN:
#Set coordinates to mouse position
self.coordinates[i, :] = [x, y]
self.clickcoords = [x,y]
print (self.clickcoords[0], self.clickcoords[1])
self.click = True
position = Position(reader.get_length(), 2)
cv2.namedWindow('im', flags=cv2.WINDOW_AUTOSIZE)
cv2.setMouseCallback('im', position.select_coordinates)
centers1 = {}
centers2 = {}
def dist_pts(y,x,yy,xx):
# ht = (int(yy)-int(y))**2
# wdth = (int(xx)-int(x))**2
# if ht == 0:
# dist = int(xx) - int(x)
# elif wdth == 0:
# dist = int(yy) - int(y)
# else:
# dist = math.sqrt(ht/wdth)
dist = math.hypot(xx - x, yy - y)
return dist
#Read in file frame by frame. Perform position tracking background subtraction
for i, im in enumerate(reader):
im = cv2.cvtColor(im, cv2.COLOR_RGB2BGR)
cv2.imshow('im', im)
#im = im[10:470, 20:480]
if learnBG:
fgmask = fgbg.apply(im)
else:
fgmask = fgbg.apply(im, learningRate=0)
fgmask = cv2.morphologyEx(fgmask, cv2.MORPH_OPEN, kernel)
fgmask = cv2.morphologyEx(fgmask, cv2.MORPH_CLOSE, cv2.getStructuringElement(cv2.MORPH_ELLIPSE,(8*morph_size,8*morph_size)))
bg = fgbg.getBackgroundImage()
# see https://www.mathworks.com/matlabcentral/answers/68696-how-can-i-extract-the-largest-blob-in-a-binary-image
label_img = label(fgmask)
regions = regionprops(label_img)
region_areas = []
for props in regions:
region_areas.append(props.area)
if len(region_areas) > 0:
largestBlobIndex, _ = max(enumerate(region_areas), key=operator.itemgetter(1))
# Find largest object in foreground
ratBlob = regions[largestBlobIndex]
# Find center coordinates of largest foreground object
y0, x0 = ratBlob.centroid
# Find angle between x axis and major axis of an ellipse around largest foreground object
orient_ratBlob = ratBlob.orientation
# Find coordinates of endpoints of major axis
x1 = x0 + math.cos(orient_ratBlob) * 0.5 * ratBlob.major_axis_length
y1 = y0 - math.sin(orient_ratBlob) * 0.5 * ratBlob.major_axis_length
x2 = x0 - math.sin(orient_ratBlob) * 0.75 * ratBlob.minor_axis_length
y2 = y0 - math.cos(orient_ratBlob) * 0.75 * ratBlob.minor_axis_length
x3 = x0 + math.sin(orient_ratBlob) * 0.75 * ratBlob.minor_axis_length
y3 = y0 + math.cos(orient_ratBlob) * 0.75 * ratBlob.minor_axis_length
rr1, cc1 = line(int(y0), int(x0), int(y2), int(x2))
rr2, cc2 = line(int(y0), int(x0), int(y3), int(x3))
rr3, cc3 = line(int(y0)+1, int(x0), int(y2)+1, int(x2))
rr4, cc4 = line(int(y0)+1, int(x0), int(y3)+1, int(x3))
set_color(fgmask, (rr1, cc1), (0), 1)
set_color(fgmask, (rr2, cc2), (0), 1)
set_color(fgmask, (rr3, cc3), (0), 1)
set_color(fgmask, (rr4, cc4), (0), 1)
label_halves = label(fgmask)
regions = regionprops(label_halves)
if len(regions) > 1:
rathalf1 = regions[0]
y01, x01 = rathalf1.centroid
x11 = x01 - math.cos(orient_ratBlob) * 0.5 * rathalf1.major_axis_length
y11 = y01 + math.sin(orient_ratBlob) * 0.5 * rathalf1.major_axis_length
x21 = x01 - math.sin(orient_ratBlob) * 0.75 * rathalf1.minor_axis_length
y21 = y01 - math.cos(orient_ratBlob) * 0.75 * rathalf1.minor_axis_length
x31 = x01 + math.sin(orient_ratBlob) * 0.75 * rathalf1.minor_axis_length
y31 = y01 + math.cos(orient_ratBlob) * 0.75 * rathalf1.minor_axis_length
rrh11, cch11 = line(int(y01), int(x01), int(y21), int(x21))
rrh12, cch12 = line(int(y01), int(x01), int(y31), int(x31))
rrh13, cch13 = line(int(y01)+1, int(x01), int(y21)+1, int(x21))
rrh14, cch14 = line(int(y01)+1, int(x01), int(y31)+1, int(x31))
set_color(fgmask, (rrh11, cch11), (0), 1)
set_color(fgmask, (rrh12, cch12), (0), 1)
set_color(fgmask, (rrh13, cch13), (0), 1)
set_color(fgmask, (rrh14, cch14), (0), 1)
label_quarters1 = label(fgmask)
regions1 = regionprops(label_quarters1)
ratquart1 = regions1[0]
ratquart2 = regions1[1]
rqx1, rqy1 = ratquart1.centroid
rqx2, rqy2 = ratquart2.centroid
#So you're getting the one that's further away from the center. Cool
#should immediately draw this point!
if dist_pts(rqx1, rqy1, x0, y0) > dist_pts(rqx2, rqy2, x0, y0):
hx1 = rqx1
hy1 = rqy1
else:
hx1 = rqx2
hy1 = rqy2
rathalf2 = regions[1]
y02, x02 = rathalf2.centroid
x12 = x02 - math.cos(orient_ratBlob) * 0.5 * rathalf2.major_axis_length
y12 = y02 + math.sin(orient_ratBlob) * 0.5 * rathalf2.major_axis_length
x22 = x02 - math.sin(orient_ratBlob) * 0.75 * rathalf2.minor_axis_length
y22 = y02 - math.cos(orient_ratBlob) * 0.75 * rathalf2.minor_axis_length
x32 = x02 + math.sin(orient_ratBlob) * 0.75 * rathalf2.minor_axis_length
y32 = y02 + math.cos(orient_ratBlob) * 0.75 * rathalf2.minor_axis_length
rrh21, cch21 = line(int(y02), int(x02), int(y22), int(x22))
rrh22, cch22 = line(int(y02), int(x02), int(y32), int(x32))
rrh23, cch23 = line(int(y02)+1, int(x02), int(y22)+1, int(x22))
rrh24, cch24 = line(int(y02)+1, int(x02), int(y32)+1, int(x32))
set_color(fgmask, (rrh21, cch21), (0), 1)
set_color(fgmask, (rrh22, cch22), (0), 1)
set_color(fgmask, (rrh23, cch23), (0), 1)
set_color(fgmask, (rrh24, cch24), (0), 1)
label_quarters2 = label(fgmask)
regions2 = regionprops(label_quarters2)
#how do you know these are the other two quarters? Maybe draw the centroid?
ratquart3 = regions2[0]
ratquart4 = regions2[1]
rqx3, rqy3 = ratquart3.centroid
rqx4, rqy4 = ratquart4.centroid
#so you should have both ends of the rat blob
#what you should do is draw the "dot" on both ends in different colors
#that'll make sure that you have access to both ends
#or that you're actually identifying both ends
if dist_pts(rqx3, rqy3, x0, y0) > dist_pts(rqx4, rqy4, x0, y0):
hx2 = rqx3
hy2 = rqy3
else:
hx2 = rqx4
hy2 = rqy4
#okay so the closest one to the previous location is taken here
#logic looks fine
#just need the previous part/comment and make sure that's good
if dist_pts(hx1, hy1, position.coordinates[i - 1, 0], position.coordinates[i - 1, 1]) \
> dist_pts(hx2, hy2, position.coordinates[i - 1, 0], position.coordinates[i - 1, 1]):
position.coordinates[i, : ] = [hx2, hy2]
else:
position.coordinates[i, : ] = [hx1, hy1]
# dist = lambda pt1, pt2: math.hypot(pt2[0]-pt1[0], pt2[1]-pt1[1])
# dist(centers,centers)
# def ptdiff(lst):
# return lambda p1,p2: (math.hypot(p1[0]-p2[0], p1[1]-p2[1]))
# diff = ptdiff(centers)
# print (diff)
# diffcent = {}
# diff = {}
# for cent1 in centers1:
# for cent2 in centers2:
# dist = math.hypot(centers1[cent1][0]-centers2[cent2][0], centers1[cent1][1] - centers2[cent2][1])
# diffcent[cent2] = dist
# diff[cent1] = max(diffcent)
# furthest_quarters = max(diff)
# print (furthest_quarters)
if position.click:
cv2.circle(im,(int(position.clickcoords[0]),int(position.clickcoords[1])),10,(255,255,255),-11)
cv2.circle(im,(int(position.clickcoords[0]),int(position.clickcoords[1])),11,(0,0,255),1) # draw circle
cv2.ellipse(im, (int(position.clickcoords[0]),int(position.clickcoords[1])), (10,10), 0, 0, 90,(0,255,255),-1 )
cv2.ellipse(im, (int(position.clickcoords[0]),int(position.clickcoords[1])), (10,10), 0, 180, 270,(0,255,255),-1 )
cv2.circle(im,(int(position.clickcoords[0]),int(position.clickcoords[1])),1,(0,255,0),1) # draw center
print ("hi I'm iin here")
cv2.imshow('imtracker',im)
# time.sleep(10)
position.click = False
else:
#draw tracking "dot"
cv2.circle(im,(int(position.coordinates[i, 1]),int(position.coordinates[i, 0])),10,(255,255,255),-11)
cv2.circle(im,(int(position.coordinates[i, 1]),int(position.coordinates[i, 0])),11,(0,0,255),1) # draw circle
cv2.ellipse(im, (int(position.coordinates[i, 1]),int(position.coordinates[i, 0])), (10,10), 0, 0, 90,(0,0,255),-1 )
cv2.ellipse(im, (int(position.coordinates[i, 1]),int(position.coordinates[i, 0])), (10,10), 0, 180, 270,(0,0,255),-1 )
cv2.circle(im,(int(position.coordinates[i, 1]),int(position.coordinates[i, 0])),1,(0,255,0),1) # draw center
# #cv2.putText(OriImage,pid,(int(cx)+10,int(cy)-10),cv2.FONT_HERSHEY_COMPLEX_SMALL,1,(255,180,180))
# 'dot' location of familiar object
cv2.circle(im,(familiarObject_center_x,familiarObject_center_y),1,(0,0,0),10)
# 'dot' location of novel object
cv2.circle(im,(novelObject_center_x,novelObject_center_y),1,(0,0,0),10)
realWorldPoint = cv2.perspectiveTransform(np.array([np.array([[x0,y0]],dtype='float32')]), homography_matrix)
realWorldX = realWorldPoint[0][0][0]
realWorldY = realWorldPoint[0][0][1]
distanceFromNovelObject = math.hypot(novelObject_center_x_realWorld - realWorldX, novelObject_center_y_realWorld - realWorldY)
distanceFromFamiliarObject = math.hypot(familiarObject_center_x_realWorld - realWorldX, familiarObject_center_y_realWorld - realWorldY)
if(distanceFromNovelObject < DistanceThrehshold_NovelObject):
numFrames_NovelObject = numFrames_NovelObject + 1
cv2.circle(im,(novelObject_center_x,novelObject_center_y),1,(0,255,0),10)
if(distanceFromFamiliarObject < DistanceThreshold_familiarObject):
numFrames_FamiliarObject = numFrames_FamiliarObject + 1
cv2.circle(im,(familiarObject_center_x,familiarObject_center_y),1,(0,255,0),10)
cv2.imshow('fgmask',fgmask)
cv2.imshow('imtracker',im)
# cv2.imshow('bg',bg)
im = cv2.cvtColor(im, cv2.COLOR_BGR2RGB) # imageio writer takes RGB
writer.append_data(im)
k = cv2.waitKey(1) & 0xff
# if k!= 255:
# print(k)
if k == 32: # 'space'
if learnBG:
learnBG = False
print('background learning OFF')
else:
learnBG = True
print('background learning ON')
if k == 115: # 's'
if showShadow:
showShadow = False
shadowValue = 0
print('shadows OFF')
else:
showShadow = True
shadowValue = 127
print('shadows ON')
#fgbg.setDetectShadows(showShadow)
fgbg.setShadowValue(shadowValue)
if k == 171 or k == 43: # '+'
if morph_size < 20:
morph_size +=5
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE,(morph_size,morph_size))
if k == 173 or k == 45: # '-'
if morph_size > 2:
morph_size -=1
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE,(morph_size,morph_size))
if k == 27:
break
print("Total amount of time spent with objects: {} seconds".format((numFrames_FamiliarObject/fps)+(numFrames_NovelObject/fps)))
print("Percentage of time spent with objects that was spent with the novel object: {}%".format((numFrames_NovelObject*100/fps)/((numFrames_FamiliarObject/fps)+(numFrames_NovelObject/fps))))
writer.close()
cv2.destroyAllWindows()
print('exited gracefully')
timeSpentFamObject = numFrames_FamiliarObject/fps
timeSpentNovObject = numFrames_NovelObject/fps
timeSpent = ('Familiar', 'Novel')
n_groups = len(timeSpent)
index = np.arange(n_groups)
bar_width = 0.1
plt.bar(index, [timeSpentFamObject, timeSpentNovObject], bar_width, color='blue', align='center', alpha=0.6)
plt.title("Time Spent with Objects")
plt.xticks(index, ('Familiar', 'Novel'))
plt.xlabel("Object")
plt.ylabel("Time (Seconds)")
plt.show()
In [6]:
centers = []
centers.append(ratBlob.centroid)
centers.append(rathalf1.centroid)
centers.append(rathalf2.centroid)
centers.append(ratquart1.centroid)
# print(centers)
diffs = []
centlst = []
centlst.append(zip(centers[0], centers[1]))
centlst.append(zip(centers[0], centers[2]))
centlst.append(zip(centers[0], centers[3]))
centlst.append(zip(centers[1], centers[2]))
centlst.append(zip(centers[1], centers[3]))
centlst.append(zip(centers[2], centers[3]))
def ptdiff(lst):
return lambda p1,p2: (math.hypot(p1[0]-p2[0], p1[1]-p2[1]))
diff = ptdiff(centlst)
print (diff)
In [ ]: