https://github.com/maartenpaul/DBD_tracking
Revision fe1884d1a8f83faa68c789c30a839b3874986713 authored by Maarten Paul on 24 November 2022, 07:54:07 UTC, committed by GitHub on 24 November 2022, 07:54:07 UTC
fix hard coded variable for track length
1 parent 36f032f
Tip revision: fe1884d1a8f83faa68c789c30a839b3874986713 authored by Maarten Paul on 24 November 2022, 07:54:07 UTC
Update MSD_fit.R
Update MSD_fit.R
Tip revision: fe1884d
mss.py
import os
os.environ['QT_QPA_PLATFORM_PLUGIN_PATH'] = 'C:/Users/maart/Anaconda3/Library/plugins/platforms'
# Three possible plots: gamma versus p, log(Cp) versus p and D versus p
# Specify which plots to produce (by setting True or False):
plotGvsP = True # Plot gamma versus p
plotCvsP = False # Plot log(Cp) versus p
plotDvsP = False # Plot D versus p
if 1 != 1:
print('Run section 4 first!')
else:
# print('Folder: ' + str(np.array(foldername)) + ' (' + str(len(filename)) + ' files) \n')
numPmsd = 4
numPmss = 4
minLen = 10
p = np.linspace(0.5, 6, 12) # power
b = 'unknown' # b can be set to 'zero' if MSD (ax + b) needs to be calculated with b = 0. Default is b = 'unknown'.
# Calculations for whole dataset
goodX = []
goodY = []
xD = []
yD = []
for xx, yy in zip(x, y):
if len(xx) > max(numPmsd, numPmss, minLen):
diff, _, Smss, _ = getMSDandMSS([xx], [yy], numPmsd, numPmss, p, b = b)
if (diff >= 0) and (Smss >= 0):
goodX.append(xx)
goodY.append(yy)
if (Smss <= 0.6) and (Smss >= 0.4):
xD.append(xx)
yD.append(yy)
diff, MSS, C, cD, Smss, intercept = getMSDandMSSandC(goodX, goodY, numPmsd, numPmss, p, b = b)
# Calculations per state
x0, y0, x1, y1, x2, y2 = getTrackPieces(x, y, allStates)
goodX0 = []
goodY0 = []
xD0 = []
yD0 = []
for xx0, yy0 in zip(x0, y0):
if len(xx0) > max(numPmsd, numPmss, minLen):
diff0, _, Smss0, _ = getMSDandMSS([xx0], [yy0], numPmsd, numPmss, p, b = b)
if (diff0 >= 0) and (Smss0 >= 0):
goodX0.append(xx0)
goodY0.append(yy0)
goodX1 = []
goodY1 = []
xD1 = []
yD1 = []
for xx1, yy1 in zip(x1, y1):
if len(xx1) > max(numPmsd, numPmss, minLen):
diff1, _, Smss1, _ = getMSDandMSS([xx1], [yy1], numPmsd, numPmss, p, b = b)
if (diff1 >= 0) and (Smss1 >= 0):
goodX1.append(xx1)
goodY1.append(yy1)
goodX2 = []
goodY2 = []
xD2 = []
yD2 = []
for xx2, yy2 in zip(x2, y2):
if len(xx2) > max(numPmsd, numPmss, minLen):
diff2, _, Smss2, _ = getMSDandMSS([xx2], [yy2], numPmsd, numPmss, p, b = b)
if (diff2 >= 0) and (Smss2 >= 0):
goodX2.append(xx2)
goodY2.append(yy2)
diff0, MSS0, C0, cD0, Smss0, intercept0 = getMSDandMSSandC(goodX0, goodY0, numPmsd, numPmss, p, b = b)
diff1, MSS1, C1, cD1, Smss1, intercept1 = getMSDandMSSandC(goodX1, goodY1, numPmsd, numPmss, p, b = b)
diff2, MSS2, C2, cD2, Smss2, intercept2 = getMSDandMSSandC(goodX2, goodY2, numPmsd, numPmss, p, b = b)
print('Fast\t\tMSD: D = %.4f \t\tMSS: Smss = %.4f, Intercept = %.4f' \
%(diff0, Smss0, intercept0))
print('Slow\t\tMSD: D = %.4f \t\tMSS: Smss = %.4f, Intercept = %.4f' \
%(diff1, Smss1, intercept1))
print('Immobile\tMSD: D = %.4f \t\tMSS: Smss = %.4f, Intercept = %.4f\n' \
%(diff2, Smss2, intercept2))
# Plotting
plt.style.use(['classic', 'seaborn-darkgrid'])
plt.rcParams['figure.figsize'] = (7, 6)
if plotGvsP == True:
plt.figure(1)
plt.fill_between(p, p / 2.0, p, facecolor = 'slateblue', edgecolor = 'none', alpha = 0.1, \
label = 'Regions from diffusion to linear motion')
plt.plot(p, MSS, '-o', color = 'darkorange', label = r'MSS total, $S_\mathrm{MSS}$ = %.2f' %(Smss))
plt.plot(p, MSS0, '-o', color = 'red', label = r'MSS fast, $S_\mathrm{MSS}$ = %.2f' %(Smss0))
plt.plot(p, MSS1, '-o', color = 'royalblue', label = r'MSS slow, $S_\mathrm{MSS}$ = %.2f' %(Smss1))
plt.plot(p, MSS2, '-o', color = 'darkblue', label = r'MSS immobile, $S_\mathrm{MSS}$ = %.2f' %(Smss2))
(plt.gca()).set_ylim(0, 3.2)
(plt.gca()).set_xlim(p[0], p[-1])
plt.xlabel(r'$p$', labelpad = 10, fontdict = font, size = 'large')
plt.ylabel(r'$\mathrm{\gamma_p}$', labelpad = 10, fontdict = font, size = 'x-large')
plt.legend(loc = 'upper left', bbox_to_anchor = (1, 1.02))
if plotCvsP == True:
plt.figure(2)
plt.plot(p, C, '-o', color = 'darkorange', label = 'Total')
plt.plot(p, C0, '-o', color = 'red', label = 'Fast')
plt.plot(p, C1, '-o', color = 'royalblue', label = 'Slow')
plt.plot(p, C2, '-o', color = 'darkblue', label = 'Immobile')
(plt.gca()).set_xlim(p[0], p[-1])
plt.xlabel(r'$p$', labelpad = 10, fontdict = font, size = 'large')
plt.ylabel(r'$\mathrm{log} \ C_\mathrm{p}$', labelpad = 10, fontdict = font, size = 'large')
plt.legend(loc = 'upper left', bbox_to_anchor = (1, 1.02))
if plotDvsP == True:
plt.figure(3)
plt.plot(p, np.array(cD) * pixSize ** 2 / t, '-o', color = 'darkorange', label = 'Total')
plt.plot(p, np.array(cD0) * pixSize ** 2 / t, '-o', color = 'red', label = 'Fast')
plt.plot(p, np.array(cD1) * pixSize ** 2 / t, '-o', color = 'royalblue', label = 'Slow')
plt.plot(p, np.array(cD2) * pixSize ** 2 / t, '-o', color = 'darkblue', label = 'Immobile')
(plt.gca()).set_xlim(p[0], p[-1])
plt.xlabel(r'$p$', labelpad = 10, fontdict = font, size = 'large')
plt.ylabel(r'$D \ \mathrm{[\mu m^2/s]}$', labelpad = 10, fontdict = font, size = 'large')
plt.legend(loc = 'upper left', bbox_to_anchor = (1, 1.02))
plt.show()
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