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R6289/artifact_plot.py
05139327dccecluster_pipeline

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artifact_plot.py
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import matplotlib
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
from matplotlib.figure import Figure
from matplotlib import pyplot as plt
import numpy as np
from skimage import io
import os
import cv2
experiments = ['1_170426_fly1_013','2_170608_fly1_007','4_170609_fly1_000']
ls = [100,200,300,400,500,600,700,800,900,1000]
gs = [0,2,4,6,8,10,12,14,16,18,20]
results = np.zeros((len(experiments),11,10))
for experiment,eidx in zip(experiments,range(len(experiments))):
for l,i in zip(ls, range(11)):
for g,j in zip(gs, range(11)):
path = '/scratch/aymanns/Data_R57C10s/'+experiment+'/results/div_l{}g{}/'.format(l,g)
div = io.imread(path+'div_out.tif')
mask = np.where(div<-1.2)
z = np.zeros(div.shape,dtype=np.uint8)
z[mask] = 255
for frame in range(len(z)):
output = cv2.connectedComponentsWithStats(z[frame],8,cv2.CV_32S)
stats = output[2]
results[eidx,j,i] += sum((stats[1:,cv2.CC_STAT_AREA]>20))
vmin = min(results.flatten())
vmax = max(results.flatten())
print(vmin)
print(vmax)
for experiment,eidx in zip(experiments, range(len(experiments))):
#plt.figure()
fig,ax=plt.subplots()
im = ax.imshow(results[eidx], vmin=vmin, vmax=vmax)
cbar = ax.figure.colorbar(im, ax=ax)
cbar.ax.set_ylabel('Number of artifacts', rotation=-90, va="bottom")
ax.set_xticks(np.arange(len(ls)))
ax.set_yticks(np.arange(len(gs)))
ax.set_xticklabels(ls)
ax.set_yticklabels(gs)
ax.set_ylabel('gamma')
ax.set_xlabel('lambda')
plt.setp(ax.get_xticklabels(), rotation=45, ha="right", rotation_mode="anchor")
plt.savefig('artifacts_'+experiment+'.eps')
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