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from .BaseReport import BaseReport
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.ndimage as ndi
class FocusReport(BaseReport):
def __init__(self,imgstack_files,coord_infos,fov,out_csv):
super().__init__(imgstack_files,coord_infos)
self.fov_name = fov
self.imgstack = self.imgstack #(y,x,wvs,irs,zs)
self.peak_idx = np.zeros((self.imgstack.shape[2],self.imgstack.shape[3]))
self.out_csv = out_csv
def f_measure(self,img):
filter = np.array([ [1],
[0],
[-1],
[0],
[0]])
res = ndi.convolve(img,filter,mode='reflect')
res = np.power(res,2)
return res.sum()
#Reports-----
def f_measure_report(self):
#create an empty matrix with dimensions of ir x wv x z (rows v cols v depth)
#Populate the matrix in the loop
#Then imshow and add text
focus_matrix = np.zeros((len(self.coords['irs']),
len(self.coords['wvs']),
len(self.coords['zs']))
)
for iir,ir in enumerate(self.coords['irs']):
for iwv,wv in enumerate(self.coords['wvs']):
for iz,z in enumerate(self.coords['zs']):
focus_matrix[iir,iwv,iz] = self.f_measure(self.imgstack[:,:,iwv,iir,iz])
viz_focus_matrix = np.argmax(focus_matrix,axis=2)
f, ax = plt.subplots()
im = ax.imshow(viz_focus_matrix)
ax.set_xticks(np.arange(len(self.coords['wvs'])), self.coords['wvs'])
ax.set_yticks(np.arange(len(self.coords['irs'])), self.coords['irs'])
ax.set_xlabel("Wavelength (nm)")
ax.set_ylabel("Imaging Round")
plt.setp(ax.get_xticklabels(), rotation=45, ha="right", rotation_mode="anchor")
for iir in range(len(self.coords['irs'])):
for iwv in range(len(self.coords['wvs'])):
text = ax.text(iwv, iir, viz_focus_matrix[iir, iwv], ha="center", va="center", color="w")
plt.tight_layout()
self.pdf.savefig()
plt.close(f)
#Save the pk idx to a csv information for each imaging round
df = pd.DataFrame()
for iwv,wv in enumerate(self.coords['wvs']):
df[str(wv)] = viz_focus_matrix[:,iwv] # each imaging round is a row
df["FOV"] = len(viz_focus_matrix[:,0])*[self.fov_name]
df["IR"] = self.coords['irs']
df.to_csv(self.out_csv)
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