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added figure plot scripts
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@rgerum
rgerum committed Oct 27, 2020
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78 changes: 78 additions & 0 deletions figures/blebistatin.py
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# -*- coding: utf-8 -*-
"""
Created on Tue May 22 2020
@author: Ben
# This program reads a txt file with the analyzed cell position, shape (semi-major and semi-minor axis etc.),
# computes the cell strain and the fluid shear stress acting on each cell,
# plots the data (strain versus stress) for each cell using a kernel density estimate for the datapoint color,
# and fits a stress stiffening equation to the data
# The results such as maximum flow speed, cell mechanical parameters, etc. are stored in
# the file 'all_data.txt' located at the same directory as this script
"""

from scripts.helper_functions import load_all_data, fitStiffness
from scripts.helper_functions import plotStressStrain, plotStressStrainFit
import numpy as np
import matplotlib.pyplot as plt

import pylustrator

pylustrator.start()

data3, config3 = load_all_data([
r"\\131.188.117.96\biophysDS\emirzahossein\microfluidic cell rhemeter data\microscope_1\september_2020\2020_09_30_alginate2%_NIH3T3_blebbistatin\inlet\[0-9]\*_result.txt"
], pressure=3)

data3b, config3b = load_all_data([
r"\\131.188.117.96\biophysDS\emirzahossein\microfluidic cell rhemeter data\microscope_1\september_2020\2020_09_30_alginate2%_NIH3T3_DMSO\inlet\[0-9]\*_result.txt",
], pressure=3)

fitStiffness(data3, config3)
fitStiffness(data3b, config3b)

plt.subplot(121)
plotStressStrain(data3b, config3b)
plotStressStrainFit(data3b, config3b)
plt.title("DMSO")

plt.text(0.5, 0.5, f"k = {config3b['fit']['p'][0]:3.0f} Pa\n$\\alpha$ = {config3b['fit']['p'][1]:2.2f}")

plt.subplot(122)
plotStressStrain(data3, config3)
plotStressStrainFit(data3, config3)
plt.title("blebbistation")

plt.text(0.5, 0.5, f"k = {config3['fit']['p'][0]:3.0f} Pa\n$\\alpha$ = {config3['fit']['p'][1]:2.2f}")

print("p3b", config3b["fit"]["p"])
print("p3", config3["fit"]["p"])

#% start: automatic generated code from pylustrator
plt.figure(1).ax_dict = {ax.get_label(): ax for ax in plt.figure(1).axes}
import matplotlib as mpl
plt.figure(1).set_size_inches(12.000000/2.54, 5.530000/2.54, forward=True)
plt.figure(1).axes[0].set_position([0.111446, 0.213746, 0.345357, 0.672724])
plt.figure(1).axes[0].set_xlim(0.0, 300.0)
plt.figure(1).axes[0].set_ylim(-0.0, 1.0)
plt.figure(1).axes[0].set_yticklabels(["0.0", "0.2", "0.4", "0.6", "0.8", "1.0"], fontsize=10)
plt.figure(1).axes[0].set_yticks([0.0, 0.2, 0.4, 0.6000000000000001, 0.8, 1.0])
plt.figure(1).axes[0].spines['right'].set_visible(False)
plt.figure(1).axes[0].spines['top'].set_visible(False)
plt.figure(1).axes[0].lines[3].set_markersize(2.0)
plt.figure(1).axes[0].texts[0].set_position([249.328258, 0.049992])
plt.figure(1).axes[1].set_position([0.559253, 0.213746, 0.345357, 0.672724])
plt.figure(1).axes[1].set_xlim(0.0, 300.0)
plt.figure(1).axes[1].set_ylim(0.0, 1.0)
plt.figure(1).axes[1].set_yticklabels(["", "", "", "", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="right")
plt.figure(1).axes[1].set_yticks([0.0, 0.2, 0.4, 0.6000000000000001, 0.8, 1.0])
plt.figure(1).axes[1].spines['right'].set_visible(False)
plt.figure(1).axes[1].spines['top'].set_visible(False)
plt.figure(1).axes[1].lines[3].set_markersize(2.0)
plt.figure(1).axes[1].texts[0].set_position([260.352304, 0.049992])
plt.figure(1).axes[1].get_yaxis().get_label().set_text("")
#% end: automatic generated code from pylustrator
plt.savefig(__file__[:-3] + ".png", dpi=300)
plt.savefig(__file__[:-3] + ".pdf")
plt.show()
177 changes: 177 additions & 0 deletions figures/figure_angles.py
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# -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
from scripts.helper_functions import load_all_data, plotDensityScatter, plotBinnedData
import numpy as np
from scipy import stats

import pylustrator
pylustrator.start()

numbers = []
for row, name in enumerate(["inlet", "middle", "outlet"]):
for index, pressure in enumerate([1, 2, 3]):
ax = plt.subplot(3, 3, 3*row+index+1)

#data, config = load_all_data(r"\\131.188.117.96\biophysDS\emirzahossein\microfluidic cell rhemeter data" +
# r"\microscope4\2020_july\2020_07_21_alginate2%_dmem_NIH_time_2\[0-9]\*_result.txt", pressure=pressure)
data, config = load_all_data([
rf"\\131.188.117.96\biophysDS\emirzahossein\microfluidic cell rhemeter data\microscope4\2020_july\2020_07_29_aslginate2%_NIH_diff_x_position_2\{name}\[0-9]\*_result.txt",
rf"\\131.188.117.96\biophysDS\emirzahossein\microfluidic cell rhemeter data\microscope4\2020_july\2020_07_29_aslginate2%_NIH_diff_x_position_3\{name}\[0-9]\*_result.txt",
], pressure=pressure)

x, y = np.array(data.stress), np.array(np.abs(data.angle))
plotDensityScatter(x, y)
plotBinnedData(x, y, np.arange(0, 300, 50))

numbers.append(len(data.rp))

print("numbers", numbers)

#plt.legend()
#% start: automatic generated code from pylustrator
plt.figure(1).ax_dict = {ax.get_label(): ax for ax in plt.figure(1).axes}
import matplotlib as mpl
plt.figure(1).set_size_inches(15.360000/2.54, 9.570000/2.54, forward=True)
plt.figure(1).axes[0].set_xlim(0.0, 300.0)
plt.figure(1).axes[0].set_ylim(0.0, 40.0)
plt.figure(1).axes[0].set_xticks([0.0, 100.0, 200.0])
plt.figure(1).axes[0].set_yticks([0.0, 20.0, 40.0])
plt.figure(1).axes[0].set_xticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="center")
plt.figure(1).axes[0].set_yticklabels(["0", "20", "40"], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="right")
plt.figure(1).axes[0].set_position([0.130165, 0.699295, 0.246468, 0.249562])
plt.figure(1).axes[0].set_xticklabels(["", "", ""], minor=True)
plt.figure(1).axes[0].set_xticks([50.0, 150.0, 250.0], minor=True)
plt.figure(1).axes[0].spines['right'].set_visible(False)
plt.figure(1).axes[0].spines['top'].set_visible(False)
plt.figure(1).axes[0].text(0.5, 0.5, 'New Text', transform=plt.figure(1).axes[0].transAxes) # id=plt.figure(1).axes[0].texts[0].new
plt.figure(1).axes[0].texts[0].set_ha("center")
plt.figure(1).axes[0].texts[0].set_position([0.500000, 1.040243])
plt.figure(1).axes[0].texts[0].set_text("1 bar")
plt.figure(1).axes[0].get_xaxis().get_label().set_text("radial position (µm)")
plt.figure(1).axes[0].get_yaxis().get_label().set_text("angle (deg)")
plt.figure(1).axes[1].set_xlim(0.0, 300.0)
plt.figure(1).axes[1].set_ylim(0.0, 40.0)
plt.figure(1).axes[1].set_xticks([0.0, 100.0, 200.0])
plt.figure(1).axes[1].set_yticks([0.0, 20.0, 40.0])
plt.figure(1).axes[1].set_xticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="center")
plt.figure(1).axes[1].set_yticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="right")
plt.figure(1).axes[1].set_position([0.416835, 0.699295, 0.246468, 0.249562])
plt.figure(1).axes[1].set_xticklabels(["", "", ""], minor=True)
plt.figure(1).axes[1].set_xticks([50.0, 150.0, 250.0], minor=True)
plt.figure(1).axes[1].spines['right'].set_visible(False)
plt.figure(1).axes[1].spines['top'].set_visible(False)
plt.figure(1).axes[1].xaxis.labelpad = 3.716691
plt.figure(1).axes[1].text(0.5, 0.5, 'New Text', transform=plt.figure(1).axes[1].transAxes) # id=plt.figure(1).axes[1].texts[0].new
plt.figure(1).axes[1].texts[0].set_ha("center")
plt.figure(1).axes[1].texts[0].set_position([0.500000, 1.040243])
plt.figure(1).axes[1].texts[0].set_text("2 bar")
plt.figure(1).axes[1].get_xaxis().get_label().set_text("radial position (µm)")
plt.figure(1).axes[2].set_xlim(0.0, 300.0)
plt.figure(1).axes[2].set_ylim(0.0, 40.0)
plt.figure(1).axes[2].set_xticks([0.0, 100.0, 200.0])
plt.figure(1).axes[2].set_yticks([0.0, 20.0, 40.0])
plt.figure(1).axes[2].set_xticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="center")
plt.figure(1).axes[2].set_yticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="right")
plt.figure(1).axes[2].set_position([0.705302, 0.699295, 0.246468, 0.249562])
plt.figure(1).axes[2].set_xticklabels(["", "", ""], minor=True)
plt.figure(1).axes[2].set_xticks([50.0, 150.0, 250.0], minor=True)
plt.figure(1).axes[2].spines['right'].set_visible(False)
plt.figure(1).axes[2].spines['top'].set_visible(False)
plt.figure(1).axes[2].text(0.5, 0.5, 'New Text', transform=plt.figure(1).axes[2].transAxes) # id=plt.figure(1).axes[2].texts[0].new
plt.figure(1).axes[2].texts[0].set_ha("center")
plt.figure(1).axes[2].texts[0].set_position([0.500000, 1.040243])
plt.figure(1).axes[2].texts[0].set_text("3 bar")
plt.figure(1).axes[2].text(0.5, 0.5, 'New Text', transform=plt.figure(1).axes[2].transAxes) # id=plt.figure(1).axes[2].texts[1].new
plt.figure(1).axes[2].texts[1].set_ha("center")
plt.figure(1).axes[2].texts[1].set_position([1.015452, 0.430286])
plt.figure(1).axes[2].texts[1].set_rotation(90.0)
plt.figure(1).axes[2].texts[1].set_text("inlet")
plt.figure(1).axes[2].get_xaxis().get_label().set_text("radial position (µm)")
plt.figure(1).axes[3].set_xlim(0.0, 300.0)
plt.figure(1).axes[3].set_ylim(0.0, 40.0)
plt.figure(1).axes[3].set_xticks([0.0, 100.0, 200.0])
plt.figure(1).axes[3].set_yticks([0.0, 20.0, 40.0])
plt.figure(1).axes[3].set_xticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="center")
plt.figure(1).axes[3].set_yticklabels(["0", "20", "40"], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="right")
plt.figure(1).axes[3].set_position([0.130165, 0.417189, 0.246468, 0.249562])
plt.figure(1).axes[3].set_xticklabels(["", "", ""], minor=True)
plt.figure(1).axes[3].set_xticks([50.0, 150.0, 250.0], minor=True)
plt.figure(1).axes[3].spines['right'].set_visible(False)
plt.figure(1).axes[3].spines['top'].set_visible(False)
plt.figure(1).axes[3].get_yaxis().get_label().set_text("angle (deg)")
plt.figure(1).axes[4].set_xlim(0.0, 300.0)
plt.figure(1).axes[4].set_ylim(0.0, 40.0)
plt.figure(1).axes[4].set_xticks([0.0, 100.0, 200.0])
plt.figure(1).axes[4].set_yticks([0.0, 20.0, 40.0])
plt.figure(1).axes[4].set_xticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="center")
plt.figure(1).axes[4].set_yticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="right")
plt.figure(1).axes[4].set_position([0.416835, 0.417189, 0.246468, 0.249562])
plt.figure(1).axes[4].set_xticklabels(["", "", ""], minor=True)
plt.figure(1).axes[4].set_xticks([50.0, 150.0, 250.0], minor=True)
plt.figure(1).axes[4].spines['right'].set_visible(False)
plt.figure(1).axes[4].spines['top'].set_visible(False)
plt.figure(1).axes[5].set_xlim(0.0, 300.0)
plt.figure(1).axes[5].set_ylim(0.0, 40.0)
plt.figure(1).axes[5].set_xticks([0.0, 100.0, 200.0])
plt.figure(1).axes[5].set_yticks([0.0, 20.0, 40.0])
plt.figure(1).axes[5].set_xticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="center")
plt.figure(1).axes[5].set_yticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="right")
plt.figure(1).axes[5].set_position([0.705302, 0.417189, 0.246468, 0.249562])
plt.figure(1).axes[5].set_xticklabels(["", "", ""], minor=True)
plt.figure(1).axes[5].set_xticks([50.0, 150.0, 250.0], minor=True)
plt.figure(1).axes[5].spines['right'].set_visible(False)
plt.figure(1).axes[5].spines['top'].set_visible(False)
plt.figure(1).axes[5].text(0.5, 0.5, 'New Text', transform=plt.figure(1).axes[5].transAxes) # id=plt.figure(1).axes[5].texts[0].new
plt.figure(1).axes[5].texts[0].set_ha("center")
plt.figure(1).axes[5].texts[0].set_position([1.015452, 0.375669])
plt.figure(1).axes[5].texts[0].set_rotation(90.0)
plt.figure(1).axes[5].texts[0].set_text("middle")
plt.figure(1).axes[6].set_xlim(0.0, 300.0)
plt.figure(1).axes[6].set_ylim(0.0, 40.0)
plt.figure(1).axes[6].set_xticks([0.0, 100.0, 200.0])
plt.figure(1).axes[6].set_yticks([0.0, 20.0, 40.0])
plt.figure(1).axes[6].set_xticklabels(["0", "100", "200"], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="center")
plt.figure(1).axes[6].set_yticklabels(["0", "20", "40"], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="right")
plt.figure(1).axes[6].set_position([0.130165, 0.135083, 0.246468, 0.249562])
plt.figure(1).axes[6].set_xticklabels(["", "", ""], minor=True)
plt.figure(1).axes[6].set_xticks([50.0, 150.0, 250.0], minor=True)
plt.figure(1).axes[6].spines['right'].set_visible(False)
plt.figure(1).axes[6].spines['top'].set_visible(False)
plt.figure(1).axes[6].get_xaxis().get_label().set_text("shear stress (Pa)")
plt.figure(1).axes[6].get_yaxis().get_label().set_text("angle (deg)")
plt.figure(1).axes[7].set_xlim(0.0, 300.0)
plt.figure(1).axes[7].set_ylim(0.0, 40.0)
plt.figure(1).axes[7].set_xticks([0.0, 100.0, 200.0])
plt.figure(1).axes[7].set_yticks([0.0, 20.0, 40.0])
plt.figure(1).axes[7].set_xticklabels(["0", "100", "200"], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="center")
plt.figure(1).axes[7].set_yticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="right")
plt.figure(1).axes[7].set_position([0.416835, 0.135083, 0.246468, 0.249562])
plt.figure(1).axes[7].set_xticklabels(["", "", ""], minor=True)
plt.figure(1).axes[7].set_xticks([50.0, 150.0, 250.0], minor=True)
plt.figure(1).axes[7].spines['right'].set_visible(False)
plt.figure(1).axes[7].spines['top'].set_visible(False)
plt.figure(1).axes[7].get_xaxis().get_label().set_text("shear stress (Pa)")
plt.figure(1).axes[8].set_xlim(0.0, 300.0)
plt.figure(1).axes[8].set_ylim(0.0, 40.0)
plt.figure(1).axes[8].set_xticks([0.0, 100.0, 200.0])
plt.figure(1).axes[8].set_yticks([0.0, 20.0, 40.0])
plt.figure(1).axes[8].set_xticklabels(["0", "100", "200"], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="center")
plt.figure(1).axes[8].set_yticklabels(["", "", ""], fontsize=10.0, fontweight="normal", color="black", fontstyle="normal", fontname="Arial", horizontalalignment="right")
plt.figure(1).axes[8].set_position([0.705302, 0.135083, 0.246468, 0.249562])
plt.figure(1).axes[8].set_xticklabels(["", "", ""], minor=True)
plt.figure(1).axes[8].set_xticks([50.0, 150.0, 250.0], minor=True)
plt.figure(1).axes[8].spines['right'].set_visible(False)
plt.figure(1).axes[8].spines['top'].set_visible(False)
plt.figure(1).axes[8].text(0.5, 0.5, 'New Text', transform=plt.figure(1).axes[8].transAxes) # id=plt.figure(1).axes[8].texts[0].new
plt.figure(1).axes[8].texts[0].set_ha("center")
plt.figure(1).axes[8].texts[0].set_position([1.015452, 0.400091])
plt.figure(1).axes[8].texts[0].set_rotation(90.0)
plt.figure(1).axes[8].texts[0].set_text("outlet")
plt.figure(1).axes[8].get_xaxis().get_label().set_text("shear stress (Pa)")
#% end: automatic generated code from pylustrator
plt.savefig(__file__[:-3]+".png", dpi=300)
plt.savefig(__file__[:-3]+".pdf")

plt.show()


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