def vPrep(fname, saveDir, check=True):
fileName = va.getFileName(fname)
aviProps = va.getAVIinfo(fname)
plt.ion()
# fBackground frames
# -----------------
# Default values
nFrames = 10
bgOK = False
bgFile = saveDir + "/bg.npy"
if os.path.isfile(bgFile):
print("Background file exists, loading...")
bg = np.load(bgFile)
else:
print("Generating background with default settings...")
bg = va.getBg(fname, aviProps, nFrames)
if check:
while not bgOK:
plt.figure()
plt.imshow(bg)
plt.set_cmap('gray')
plt.show()
uDecision = raw_input("Background OK? [y]es; [n]o ")
if uDecision == 'y':
bgOK = True
else:
uframes = raw_input("Select number of frames ")
bg = va.getBg(fname, aviProps, int(uframes))
np.save(saveDir + 'bg', bg)
print('Background file saved')
# Threshold
# --------------
# Default values
ths = 40
morphDiameter = 10
pmtsFileExists = False
thsOK = False
pmtsFile = saveDir + "/pmts.npy"
if os.path.isfile(pmtsFile):
print("Parameters file exists, loading...")
pmtsFileExists = True
filePmts = np.load(pmtsFile)
ths, morphDiameter = va.setThreshold(fname, aviProps, bg,
filePmts[0][0], filePmts[1][0])
else:
print("Generating threshold with default settings...")
ths, morphDiameter = va.setThreshold(fname, aviProps, bg, ths,
morphDiameter)
if check:
while not thsOK:
uDecision = raw_input("Threshold OK? [y]es; [n]o ")
if uDecision == 'y':
thsOK = True
else:
while True:
try:
print "Current threshold is", ths
uths = int(raw_input("Select new threshold "))
print "Current diameter is", morphDiameter
umorph = int(
raw_input(
"Select new diameter to erode and dilate "))
break
except ValueError:
print("Invalid number, please try again ")
ths, morphDiameter = va.setThreshold(fname, aviProps, bg, uths,
umorph)
# Arena areas
# --------------
# Default values
nestPos = [125, 220]
nestArea = [(1, 320), (225, 320), (120, 125)]
arenaCenter = [600, 244]
foodArea = [(785, 360), (960, 360), (860, 185)]
plt.ioff()
arenaOk = False
if pmtsFileExists:
print("Using parameters file...")
va.plotArena(aviProps, filePmts, bg)
pmts = [[ths], [morphDiameter], filePmts[2], filePmts[3], filePmts[4],
filePmts[5]]
else:
print("Generating arena with default settings...")
pmts = [[ths], [morphDiameter], nestPos, nestArea, arenaCenter,
foodArea]
va.plotArena(aviProps, pmts, bg)
if check:
while not arenaOk:
uDecision = raw_input("Arena OK? [y]es; [n]o ")
if uDecision == 'y':
arenaOk = True
else:
print("Select new arena ")
points = va.setPoints(fname, aviProps, bg)
pmts = [[ths], [morphDiameter], points[0], points[1],
points[2], points[3]]
#print pmts[0], pmts[1]
#fsaveName = saveDir + fileName.rstrip(".avi") + "_pmts"
np.save(saveDir + 'pmts', pmts)
print('Parameters file saved')
def vPrep(fname, saveDir, check=True):
fileName = va.getFileName(fname)
aviProps = va.getAVIinfo(fname)
plt.ion()
# fBackground frames
# -----------------
# Default values
nFrames = 10
bgOK = False
bgFile = saveDir + "/bg.npy"
if os.path.isfile(bgFile):
print("Background file exists, loading...")
bg = np.load(bgFile)
else:
print("Generating background with default settings...")
bg = va.getBg(fname, aviProps, nFrames)
if check:
while not bgOK:
plt.figure()
plt.imshow(bg)
plt.set_cmap('gray')
plt.show()
uDecision = raw_input("Background OK? [y]es; [n]o ")
if uDecision=='y':
bgOK = True
else:
uframes = raw_input("Select number of frames ")
bg = va.getBg(fname, aviProps, int(uframes))
np.save(saveDir + 'bg', bg)
print('Background file saved')
# Threshold
# --------------
# Default values
ths = 40
morphDiameter = 10
pmtsFileExists = False
thsOK = False
pmtsFile = saveDir + "/pmts.npy"
if os.path.isfile(pmtsFile):
print("Parameters file exists, loading...")
pmtsFileExists = True
filePmts = np.load(pmtsFile)
ths, morphDiameter = va.setThreshold(fname, aviProps, bg, filePmts[0][0], filePmts[1][0])
else:
print("Generating threshold with default settings...")
ths, morphDiameter = va.setThreshold(fname, aviProps, bg, ths, morphDiameter)
if check:
while not thsOK:
uDecision = raw_input("Threshold OK? [y]es; [n]o ")
if uDecision=='y':
thsOK = True
else:
while True:
try:
print "Current threshold is", ths
uths = int(raw_input("Select new threshold "))
print "Current diameter is", morphDiameter
umorph = int(raw_input("Select new diameter to erode and dilate "))
break
except ValueError:
print("Invalid number, please try again ")
ths, morphDiameter = va.setThreshold(fname, aviProps, bg, uths, umorph)
# Arena areas
# --------------
# Default values
nestPos = [125, 220]
nestArea = [(1,320),(225,320),(120,125)]
arenaCenter = [600,244]
foodArea = [(785,360),(960,360),(860,185)]
plt.ioff()
arenaOk = False
if pmtsFileExists:
print("Using parameters file...")
va.plotArena(aviProps, filePmts, bg)
pmts = [[ths], [morphDiameter], filePmts[2], filePmts[3], filePmts[4], filePmts[5]]
else:
print("Generating arena with default settings...")
pmts = [[ths], [morphDiameter], nestPos, nestArea, arenaCenter, foodArea]
va.plotArena(aviProps, pmts, bg)
if check:
while not arenaOk:
uDecision = raw_input("Arena OK? [y]es; [n]o ")
if uDecision=='y':
arenaOk = True
else:
print("Select new arena ")
points = va.setPoints(fname, aviProps, bg)
pmts = [[ths], [morphDiameter], points[0], points[1], points[2], points[3]]
#print pmts[0], pmts[1]
#fsaveName = saveDir + fileName.rstrip(".avi") + "_pmts"
np.save(saveDir + 'pmts', pmts)
print('Parameters file saved')
if len(tAxis)>len(trackData): tAxis = np.delete(tAxis, -1)
if len(tAxis)<len(trackData): trackData = np.delete(trackData, -1)
smooth_trackData = smooth.smooth(trackData[:,1], window_len=50)
ax[ax2].plot(tAxis, trackData[:,1],'k',lw=1)
ax[ax2].plot(tAxis, smooth_trackData, colors[d], lw=1.5)
# Plot histogram
ax[ax3].hist(trackData[:,1], bins=30, orientation='horizontal', histtype='stepfilled', normed=True, color=colors[d])
ax[ax3].set_xlim([0,0.008])
# get and plot looms
#loomOnsets = da.getLoomOnsets(trackData, aviProps)
#for l in loomOnsets: ax[ax2].plot(l, 1150, marker='o', markerfacecolor='k', markeredgecolor='k')
plt.show()
return dataOut
# ------------------------------------------
data, props = [], []
for d in dirList:
fname = d + '/trackingData.txt'
movieFname = d + '/trackingMovie.avi'
data.append(np.loadtxt(fname))
props.append(va.getAVIinfo(fname))
dataOut = plotTrackingData(data, props)
times = [line.strip() for line in f]
except IOError:
print('times.txt does not exist')
minCpuTime = 10
#totalCpus = 100
cpus = int(totalCpus/len(fileList[1:]))
nfile = 1
print 'Using', cpus, 'cpus per file'
os.system('rm -f '+activeDir+'/file*.*')
os.system('rm -f '+activeDir+'/tracking*')
for f in fileList[1:]:
f = fileList[0]+'/'+f
aviProps = va.getAVIinfo(f)
if nfile==1:
startFrame = va.time2frame(int(times[0]), aviProps)
else:
startFrame = va.time2frame(0, aviProps)
if nfile==len(fileList[1:]):
endFrame = va.time2frame(int(times[1]), aviProps)
if endFrame>aviProps[6]: endFrame=aviProps[6]
else:
endFrame = aviProps[6]
if mode=='local':
framesPerCpu = np.ceil(float(endFrame-startFrame))
secPerCpu = va.frame2time(framesPerCpu, aviProps)
else:
framesPerCpu = np.ceil(float(endFrame-startFrame)/cpus)
if len(tAxis) < len(trackData): trackData = np.delete(trackData, -1)
smooth_trackData = smooth.smooth(trackData[:, 1], window_len=50)
ax[ax2].plot(tAxis, trackData[:, 1], 'k', lw=1)
ax[ax2].plot(tAxis, smooth_trackData, colors[d], lw=1.5)
# Plot histogram
ax[ax3].hist(trackData[:, 1],
bins=30,
orientation='horizontal',
histtype='stepfilled',
normed=True,
color=colors[d])
ax[ax3].set_xlim([0, 0.008])
# get and plot looms
#loomOnsets = da.getLoomOnsets(trackData, aviProps)
#for l in loomOnsets: ax[ax2].plot(l, 1150, marker='o', markerfacecolor='k', markeredgecolor='k')
plt.show()
return dataOut
# ------------------------------------------
data, props = [], []
for d in dirList:
fname = d + '/trackingData.txt'
movieFname = d + '/trackingMovie.avi'
data.append(np.loadtxt(fname))
props.append(va.getAVIinfo(fname))
dataOut = plotTrackingData(data, props)
startFrame = int(sys.argv[3])
#tEnd = int(sys.argv[4])
nfile = sys.argv[4]
ncall = sys.argv[5]
if len(nfile) == 1:
nfile = '00' + nfile
elif len(nfile) == 2:
nfile = '0' + nfile
if len(ncall) == 1:
ncall = '00' + ncall
elif len(ncall) == 2:
ncall = '0' + ncall
secPerCpu = float(sys.argv[6])
nestThreshold = 10
aviProps = va.getAVIinfo(fname)
print fname, aviProps
fileName = va.getFileName(fname)
trackFname = saveDir + 'file' + str(nfile) + '_' + ncall + '.txt'
aviFname = saveDir + 'file' + str(nfile) + '_' + ncall + '.avi'
bgSubFname = saveDir + 'file' + str(nfile) + '_' + ncall
tStart = va.frame2time(startFrame, aviProps) + (int(ncall) - 1) * secPerCpu
tEnd = tStart + secPerCpu
print tStart, tEnd
while True:
try:
print(saveDir + "bg.npy")
bg = np.load(saveDir + "bg.npy")
print("Background file loaded")
except IOError:
with open(activeDir + '/times.txt', 'r') as f:
times = [line.strip() for line in f]
except IOError:
print('times.txt does not exist')
minCpuTime = 10
#totalCpus = 100
cpus = int(totalCpus / len(fileList[1:]))
nfile = 1
print 'Using', cpus, 'cpus per file'
os.system('rm -f ' + activeDir + '/file*.*')
os.system('rm -f ' + activeDir + '/tracking*')
for f in fileList[1:]:
f = fileList[0] + '/' + f
aviProps = va.getAVIinfo(f)
if nfile == 1:
startFrame = va.time2frame(int(times[0]), aviProps)
else:
startFrame = va.time2frame(0, aviProps)
if nfile == len(fileList[1:]):
endFrame = va.time2frame(int(times[1]), aviProps)
if endFrame > aviProps[6]: endFrame = aviProps[6]
else:
endFrame = aviProps[6]
if mode == 'local':
framesPerCpu = np.ceil(float(endFrame - startFrame))
secPerCpu = va.frame2time(framesPerCpu, aviProps)
else:
framesPerCpu = np.ceil(float(endFrame - startFrame) / cpus)
import numpy as np
import matplotlib.pylab as plt
import matplotlib.cm as colormap
import os.path
import tkFileDialog
import sys
import videoAnalysisLib as va
import dataAnalysisLib as da
#activeDir = '/lmb/home/tbranco/analysis/114491a_foraging'
activedir = sys.argv[1]
datafname = activedir+'/trackingData.txt'
avifname = activedir+'/trackingMovie.avi'
aviProps = va.getAVIinfo(avifname)
try:
bg = np.load(activedir+'/bg.npy')
print("Background file loaded")
except IOError:
print("Cannot find background file ")
try:
pmts = np.load(activedir+'/pmts.npy')
print("Parameters file loaded")
except IOError:
print("Cannot find parameters file ")
# Basic tracking data
print("Processing data...")
data, resultsDict, fig = va.analyseData(datafname, aviProps, bg, pmts)
va.writeDict(resultsDict, activedir+'/trackingAnalysis.txt')