def main():
plt.style.use(['seaborn-white', 'seaborn-notebook'])
directory = "/Users/st659/Google Drive/Meth Blue Glucose 12-10-16"
paths = get_data_paths(directory)
print(paths)
sub_bw_anti_3, bw_anti_3, legend1 = calculate_graph_data(paths[3:6])
sub_bw_noanti_3, bw_noanti_3, legend2 = calculate_graph_data(paths[6:9])
sub_pk_anti_3, pk_anti_3, legend3 = calculate_graph_data(paths[10:12])
sub_pk_noanti_3, pk_noanti_3, legend4 = calculate_graph_data(paths[12:15])
bw_mean = np.array([bw_anti_3[1], bw_noanti_3[1]])
pk_mean = np.array([pk_anti_3[1], pk_noanti_3[1]])
total_mean_matrix = np.array(
[bw_anti_3[1], bw_noanti_3[1], pk_noanti_3[1], pk_anti_3[1]])
mean_var = np.var(total_mean_matrix, axis=0)
bw_var = np.var(bw_mean, axis=0)
pk_var = np.var(pk_mean, axis=0)
print(len(mean_var))
figure_var = plt.figure()
ax_var = figure_var.add_subplot(111)
ax_var.plot(bw_noanti_3[0], bw_var, label='BW')
ax_var.plot(bw_noanti_3[0], pk_var, label='PK')
plt.legend(loc='upper right')
figure1 = plt.figure()
ax1 = figure1.add_subplot(211)
ax1.errorbar(sub_bw_anti_3[0],
sub_bw_anti_3[1],
sub_bw_anti_3[2],
label=legend1)
ax1.errorbar(sub_bw_noanti_3[0],
sub_bw_noanti_3[1],
sub_bw_noanti_3[2],
label=legend2)
ax1.set_ylabel('Current (mA)')
ax1.set_xlabel('Voltage (V)')
plt.legend(loc='upper left')
ax2 = figure1.add_subplot(212)
ax2.errorbar(sub_pk_anti_3[0],
sub_pk_anti_3[1],
sub_pk_anti_3[2],
label=legend3)
ax2.errorbar(sub_pk_noanti_3[0],
sub_pk_noanti_3[1],
sub_pk_noanti_3[2],
label=legend4)
ax2.set_ylabel('Current (mA)')
ax2.set_xlabel('Voltage (V)')
plt.legend(loc='upper left')
plt.show()
def cv_difference(directory):
paths = get_data_paths(directory)
sub_bw_anti, bw_anti, bw_anti_max_volt, legend1 = calculate_graph_data(
paths[3:6])
sub_bw_noanti, bw_noanti, bw_noanti_max_volt, legend2 = calculate_graph_data(
paths[6:9])
sub_pk_anti, pk_anti, pk_anti_max_volt, legend3 = calculate_graph_data(
paths[10:12])
sub_pk_noanti, pk_noanti, pk_noanti_max_volt, legend4 = calculate_graph_data(
paths[12:15])
diff_bw = np.subtract(sub_bw_anti[1], sub_bw_noanti[1])
diff_bw_std = np.sqrt(
np.add(np.square(sub_bw_anti[2]), np.square(sub_bw_noanti[2])))
diff_pk = np.subtract(sub_pk_anti[1], sub_pk_noanti[1])
diff_pk_std = np.sqrt(
np.add(np.square(sub_pk_anti[2]), np.square(sub_pk_noanti[2])))
return [sub_bw_anti[0], diff_bw, diff_bw_std, diff_pk, diff_pk_std]
mg6_paths = paths3[2:]
print(mg6_paths)
print(mg5_paths)
print(mg4_paths)
paths_list = [blank, mg4_paths, mg6_paths]
fig2 = plt.figure()
legends = ['Blank', 'E.coli MG1655 $10^{4}$ cfu/ml', 'E.coli MG1655 $10^{6}$ cfu/ml']
ax2 = fig2.add_subplot(111)
data_list = list()
for path in paths_list:
sub_data_2, data, legend = calculate_graph_data(path)
data_list.append(sub_data_2)
legend_str = path[0].split('/')[-1]
legend = legend_str.split('_')[0]
ax2.errorbar(sub_data_2[0], sub_data_2[1], sub_data_2[2], label = legend)
ax2.legend(legends, loc='lower right')
ax2.set_ylabel('Current (mA)')
ax2.set_xlabel('Voltage vs Ag/AgCl (V)')
plt.xlim((-0.6, 0))
plt.ylim((-0.06, 0.02))
#plt.savefig(os.path.join(directory2,'Resazurin_OnChip.png'), dpi=300)
plt.show()
def main():
directory = "/Users/st659/Google Drive/Meth Blue 12-09"
paths = get_data_paths(directory)
plt.style.use(['seaborn-white', 'seaborn-notebook'])
print(paths)
# sub_bw_anti_3, bw_anti_3, = calculate_graph_data(paths[0:3])
# sub_bw_noanti_3, bw_noanti_3 = calculate_graph_data(paths[3:6])
# sub_pk_anti_3, pk_anti_3 = calculate_graph_data(paths[6:9])
# sub_pk_noanti_3, pk_noanti_3 = calculate_graph_data(paths[9:12])
#
# figure1 = plt.figure()
# ax1 = figure1.add_subplot(111)
# ax1.errorbar(sub_bw_anti_3[0], sub_bw_anti_3[1], sub_bw_anti_3[2])
# ax1.errorbar(sub_bw_noanti_3[0], sub_bw_noanti_3[1], sub_bw_noanti_3[2])
# ax1.errorbar(sub_pk_anti_3[0], sub_pk_anti_3[1], sub_pk_anti_3[2])
# ax1.errorbar(sub_pk_noanti_3[0], sub_pk_noanti_3[1], sub_pk_noanti_3[2])
#
# plt.xlabel('Voltage vs reference (V)')
# plt.ylabel('Current (mA)')
# plt.xlim([-0.3, 0])
# plt.ylim([-0.02, 0.01])
# plt.legend(('BW25113 0$\mu g/ml$ Ampicillin', 'BW25133 50$\mu g/ml$ Ampicillin', 'BW25113 with PKD3 0$\mu g/ml$ Ampicillin', 'BW25113 with PKD3 50$\mu g/ml$ Ampicillin'),loc='lower right', fontsize = '10')
# plt.title(r'Antibiotic Susceptibility of $10^{3}$ Bacteria after 5 hours incubation')
# sub_bw_anti_4, bw_anti_4, l= calculate_graph_data(paths[12:15])
# sub_bw_noanti_4, bw_noanti_4, l = calculate_graph_data(paths[15:18])
# sub_pk_anti_4, pk_anti_4, l = calculate_graph_data(paths[18:21])
# sub_pk_noanti_4, pk_noanti_4, l = calculate_graph_data(paths[21:24])
#
# figure2 = plt.figure()
# ax2 = figure2.add_subplot(111)
# ax2.errorbar(sub_bw_anti_4[0], sub_bw_anti_4[1], sub_bw_anti_4[2])
# ax2.errorbar(sub_bw_noanti_4[0], sub_bw_noanti_4[1], sub_bw_noanti_4[2])
# ax2.errorbar(sub_pk_anti_4[0], sub_pk_anti_4[1], sub_pk_anti_4[2])
# ax2.errorbar(sub_pk_noanti_4[0], sub_pk_noanti_4[1], sub_pk_noanti_4[2])
#
# plt.xlabel('Voltage vs reference (V)')
# plt.ylabel('Current (mA)')
# plt.xlim([-0.3, 0])
# plt.ylim([-0.02, 0.01])
# plt.legend(('BW25113 50$\mu g/ml$ Ampicillin', 'BW25133 0$\mu g/ml$ Ampicillin', 'BW25113 with PKD3 50$\mu g/ml$ Ampicillin', 'BW25113 with PKD3 0$\mu g/ml$ Ampicillin'),loc='lower right', fontsize = '10')
# plt.title(r'Antibiotic Susceptibility of $10^{4}$ CFU/ml after 5 hours incubation')
# #plt.savefig(os.path.join(directory,'susceptibility 10_4.png'), dpi=1200)
#
# diff = np.subtract(sub_bw_anti_4[1], sub_bw_noanti_4[1])
# diff_std = np.sqrt(np.add(np.square(sub_bw_anti_4[2]), np.square(sub_bw_noanti_4[2])))
# diff2 = np.subtract(sub_pk_anti_4[1], sub_pk_noanti_4[1])
# diff2_std = np.sqrt(np.add(np.square(sub_pk_anti_4[2]), np.square(sub_pk_noanti_4[2])))
#
# figure2 = plt.figure()
# ax3 = figure2.add_subplot(211)
# ax3.errorbar(sub_bw_anti_4[0], diff, diff_std, label='BW', color='b')
# ax3.set_ylabel('$\Delta$ Current (mA)')
#
# plt.legend(loc = 'upper left')
# ax4 = figure2.add_subplot(212)
# ax4.errorbar(sub_bw_anti_4[0], diff2, diff2_std, label='PK', color='g')
# ax4.set_ylabel('$\Delta$ Current (mA)')
# ax4.set_xlabel('Voltage (V)')
# plt.legend(loc = 'upper left')
#
#
#
#
# sub_bw_anti_5, bw_anti_5, l = calculate_graph_data(paths[24:27])
# sub_bw_noanti_5, bw_noanti_5, l = calculate_graph_data(paths[27:30])
# sub_pk_anti_5, pk_anti_5, l = calculate_graph_data(paths[30:33])
# sub_pk_noanti_5, pk_noanti_5, l = calculate_graph_data(paths[33:36])
#
# mean_matrix = np.array([bw_anti_5[1], bw_noanti_5[1], pk_noanti_5[1], pk_anti_5[1]])
# mean_var = np.var(mean_matrix, axis=0)
# print(len(mean_var))
#
# figure_var = plt.figure()
# ax_var = figure_var.add_subplot(111)
# ax_var.plot(bw_noanti_5[0], mean_var)
# plt.show()
# diff = np.subtract(sub_bw_anti_5[1], sub_bw_noanti_5[1])
# diff_std = np.sqrt(np.add(np.square(sub_bw_anti_5[2]), np.square(sub_bw_noanti_5[2])))
# diff2 = np.subtract(sub_pk_anti_5[1], sub_pk_noanti_5[1])
# diff2_std = np.sqrt(np.add(np.square(sub_pk_anti_5[2]), np.square(sub_pk_noanti_5[2])))
#
# figure3 = plt.figure()
# ax5 = figure3.add_subplot(211)
# ax5.errorbar(sub_bw_anti_4[0], diff, diff_std, label='BW', color='b')
# ax5.set_ylabel('$\Delta$ Current (mA)')
#
# plt.legend(loc = 'upper left')
# ax6 = figure3.add_subplot(212)
# ax6.errorbar(sub_bw_anti_4[0], diff2, diff2_std, label='PK', color='g')
# ax6.set_ylabel('$\Delta$ Current (mA)')
# ax6.set_xlabel('Voltage (V)')
# plt.legend(loc = 'upper left')
#
# figure3 = plt.figure()
# ax3 = figure3.add_subplot(111)
# ax3.errorbar(sub_bw_anti_5[0], sub_bw_anti_5[1], sub_bw_anti_5[2])
# ax3.errorbar(sub_bw_noanti_5[0], sub_bw_noanti_5[1], sub_bw_noanti_5[2])
# ax3.errorbar(sub_pk_anti_5[0], sub_pk_anti_5[1], sub_pk_anti_5[2])
# ax3.errorbar(sub_pk_noanti_5[0], sub_pk_noanti_5[1], sub_pk_noanti_5[2])
#
# plt.xlabel('Voltage vs reference (V)')
# plt.ylabel('Current (mA)')
# plt.xlim([-0.3, 0])
# plt.ylim([-0.02, 0.01])
# plt.legend(('BW25113 50$\mu g/ml$ Ampicillin', 'BW25133 00$\mu g/ml$ Ampicillin', 'BW25113 with PKD3 50$\mu g/ml$ Ampicillin', 'BW25113 with PKD3 0$\mu g/ml$ Ampicillin'),loc='lower right', fontsize = '10')
# plt.title(r'Antibiotic Susceptibility of $10^{5}$ CFU/ml after 5 hours incubation')
# #plt.savefig(os.path.join(directory,'susceptibility 10_5.png'), dpi=1200)
#
sub_bw_anti_6, bw_anti_6, leg= calculate_graph_data(paths[36:39])
sub_bw_noanti_6, bw_noanti_6, leg = calculate_graph_data(paths[39:42])
sub_pk_anti_6, pk_anti_6, leg = calculate_graph_data(paths[42:45])
sub_pk_noanti_6, pk_noanti_6, leg = calculate_graph_data(paths[45:48])
figure4 = plt.figure()
ax4 = figure4.add_subplot(111)
ax4.errorbar(sub_bw_anti_6[0], sub_bw_anti_6[1], sub_bw_anti_6[2])
ax4.errorbar(sub_bw_noanti_6[0], sub_bw_noanti_6[1], sub_bw_noanti_6[2])
ax4.errorbar(sub_pk_anti_6[0], sub_pk_anti_6[1], sub_pk_anti_6[2])
ax4.errorbar(sub_pk_noanti_6[0], sub_pk_noanti_6[1], sub_pk_noanti_6[2])
plt.xlabel('Voltage vs reference (V)')
plt.ylabel('Current (mA)')
plt.xlim([-0.3, 0])
plt.ylim([-0.02, 0.01])
plt.legend(('BW25113 50$\mu g/ml$ Ampicillin', 'BW25133 0$\mu g/ml$ Ampicillin', 'BW25113 with PKD3 50$\mu g/ml$ Ampicillin', 'BW25113 with PKD3 0$\mu g/ml$ Ampicillin'),loc='lower right', fontsize = '10')
plt.title(r'Antibiotic Susceptibility of $10^{6}$ CFU/ml after 5 hours incubation')
plt.savefig(os.path.join(directory,'susceptibility 10_6 300dpi.png'), dpi=300)
plt.style.use(['seaborn-white', 'seaborn-notebook'])
data_list = list()
data_list_2 = list()
# fig = plt.figure()
fig2 = plt.figure()
# ax = fig.add_subplot(111)
ax = fig2.add_subplot(111)
#ax2 = fig2.add_subplot(122)
# for path in paths_list:
for pb_path in paths:
print(pb_path)
no, pb, legend = calculate_graph_data(pb_path)
#esfe, shu, seg = calculate_graph_data(shu_path)
#legend_str = path[0].split('/')[-1]
#legend = legend_str.split('_')[0]
#ax.plot(shu[0], shu[1])
ax.plot(pb[0], pb[1])
#plt.xlim((-0.6,0))
#plt.ylim((-0.06, 0.02))
#plt.legend(loc = 'lower right')
#plt.title('E.coli MG1655 Pseudo starting at 10^5 CFU/ml after 5 hours Incubation with 1mM Resazurin')
ax.set_xlabel('Voltage vs AgAgCl (V)')
ax.set_ylabel('Current (mA)')
#ax2.set_xlabel('Voltage vs AgAgCl (V)')
data_list_2 = list()
# fig = plt.figure()
fig2 = plt.figure()
# ax = fig.add_subplot(111)
ax = fig2.add_subplot(121)
ax2 = fig2.add_subplot(122)
# for path in paths_list:
for pb_path, shu_path in zip(paths, paths_2):
no, pb, legend = calculate_graph_data(pb_path)
esfe, shu, seg = calculate_graph_data(shu_path)
#legend_str = path[0].split('/')[-1]
#legend = legend_str.split('_')[0]
ax.plot(shu[0], shu[1])
ax2.plot(pb[0], pb[1])
#plt.xlim((-0.6,0))
#plt.ylim((-0.06, 0.02))
#plt.legend(loc = 'lower right')
#plt.title('E.coli MG1655 Pseudo starting at 10^5 CFU/ml after 5 hours Incubation with 1mM Resazurin')
ax.set_xlabel('Voltage vs AgAgCl (V)')
ax.set_ylabel('Current (mA)')
ax2.set_xlabel('Voltage vs AgAgCl (V)')