poetry run emacs an.org
import tifffile as tff
import numpy as np
import aicsimageio
import matplotlib.pyplot as plt
import seaborn as sb
import impy
from pathlib import Path
import skimage
import scipy
import imageio
import pandas as pd
cd "/home/dati/dt-evolv/data/2022-11-16/13401/TimePoint_1"
cd "/home/dati/dt-evolv/data/2022-11-16/13401/TimePoint_1"
mkdir -p thumbs
fd _thumb -0 | xargs -0 mv -t ./thumbs
pwd
cd "/home/dati/dt-evolv/data/2022-11-16/13401/TimePoint_1"
fp2 = "/home/dati/dt-evolv/data/2022-11-16/13401/TimePoint_1/6w-20Xph1-SpikeTest6-DA_A01_s1_w2B3DEDFEB-FB52-4D83-8176-CC090AD62AC4.tif"
fp1 = "/home/dati/dt-evolv/data/2022-11-16/13401/TimePoint_1/6w-20Xph1-SpikeTest6-DA_A01_s1_w19A3DA0A6-B9DD-475E-ABED-27415F9DE6EB.tif"
i1 = impy.imread(fp1)
i2 = impy.imread(fp2)
skimage.io.imshow(i2)
p = Path(".")
out1 = Path("./1024")
out2 = Path("./512")
out1.mkdir()
out2.mkdir()
import utils
p = Path(".")
s_in = ["A01", "B01", "A02", "A03"]
s_out = ["A01", "B01", "A02", "A03"]
for ins, outs in zip(s_in, s_out):
for i in range(1, 901):
print(ins, outs, i)
fp1 = sorted(p.glob(f"*{ins}*s{i}_w1*"))[0]
fp2 = sorted(p.glob(f"*{ins}*s{i}_w2*"))[0]
c1 = tff.imread(fp1)
c2 = tff.imread(fp2)
# clip1 = int(utils.bg(c1)[0])
clip2 = int(utils.bg(c2)[0])
# c1r = skimage.util.img_as_ubyte(skimage.exposure.rescale_intensity(c1.clip(clip1, c1.max() * 0.95)))
# c2r = skimage.util.img_as_ubyte(skimage.exposure.rescale_intensity(c2.clip(clip2, c2.max() * 0.95)))
c1r = skimage.util.img_as_ubyte((c1))
c2r = skimage.util.img_as_ubyte(skimage.exposure.rescale_intensity(c2.clip(clip2,65000)))
cc = np.dstack((c2r, c1r, np.zeros_like(c1r)))
cc = skimage.transform.downscale_local_mean(cc, (4, 4, 1))
imageio.imwrite(out2 / f"{outs}_s{i}.png", cc)
cd "/home/dati/dt-evolv/data/2022-11-16/13401/TimePoint_1"
p = Path(".")
out2 = Path("./512n")
out2.mkdir()
import utils
p = Path(".")
s_in = ["A01", "B01", "A02", "A03"]
s_out = ["A01", "B01", "A02", "A03"]
for ins, outs in zip(s_in, s_out):
print(ins)
for i in range(1, 901):
fp1 = sorted(p.glob(f"*{ins}*s{i}_w1*"))[0]
fp2 = sorted(p.glob(f"*{ins}*s{i}_w2*"))[0]
c1 = tff.imread(fp1)
c2 = tff.imread(fp2)
c1 = skimage.transform.downscale_local_mean(c1, 4)
c2 = skimage.transform.downscale_local_mean(c2, 4)
clip1 = int(np.sum(utils.bg(c1)))
clip2 = int(np.sum(utils.bg(c2)))
c1r = skimage.util.img_as_ubyte(skimage.exposure.rescale_intensity(c1.clip(clip1, c1.max() * 0.95)))
c2r = skimage.util.img_as_ubyte(skimage.exposure.rescale_intensity(c2.clip(clip2, c2.max() * 0.95)))
cc = np.dstack((c2r, c1r, np.zeros_like(c1r)))
imageio.imwrite(out2 / f"{outs}_s{i}.png", cc)