def run(self, ips, imgs, para=None):
from cellpose import models, utils
from cellpose.plot import mask_overlay
use_GPU = models.use_gpu()
if not para['slice']: imgs = [ips.img]
imgs = [i.reshape((i.shape + (-1, ))[:3]) for i in imgs]
model = models.Cellpose(gpu=use_GPU, model_type=para['model'])
channels = [para['cytoplasm'], para['nucleus']]
self.setValue = lambda x: self.progress(x, 100)
masks, flows, styles, diams = model.eval(imgs,
diameter=para['diameter'],
rescale=None,
channels=channels,
progress=self)
self.app.show_img(masks, ips.title + '-cp_mask')
if para['flow']:
self.app.show_img([i[0] for i in flows], ips.title + '-cp_flow')
if para['overlay']:
for i in range(len(imgs)):
maski = masks[i].copy().astype(np.uint8)
imgi = imgs[i].copy()
overlayi = mask_overlay(imgi, maski)
self.app.show_img([overlayi], ips.title + '-overlay')
if para['diams']:
self.app.show_table(pd.DataFrame({'diams': diams}),
ips.title + '-cp_diams')
def do_check_gpu(self):
import importlib.util
torch_installed = importlib.util.find_spec('torch') is not None
if models.use_gpu(istorch=torch_installed):
message = "GPU appears to be working correctly!"
else:
message = "GPU test failed. There may be something wrong with your configuration."
import wx
wx.MessageBox(message, caption="GPU Test")
mask = lut[lab].ravel()[rst].reshape(shp)
return hist, lut[lab], mask
if __name__ == '__main__':
from skimage.io import imread, imsave
from skimage.data import coins, gravel
from skimage.segmentation import find_boundaries
import matplotlib.pyplot as plt
from time import time
import cellpose
from cellpose import models, utils
img = gravel()
use_GPU = models.use_gpu()
model = models.Cellpose(gpu=use_GPU, model_type='cyto')
channels = [0, 0]
mask, flow, style, diam = model.eval(
img, diameter=30, rescale=None, channels=[0,0])
start = time()
water, core, msk = flow2msk(flow[1].transpose(1,2,0), None, 1.0, 20, 100)
print('flow to mask cost:', time()-start)
ax1, ax2, ax3, ax4, ax5, ax6 =\
[plt.subplot(230+i) for i in (1,2,3,4,5,6)]
ax1.imshow(img)
ax2.imshow(flow[0])
ax3.imshow(np.log(water+1))
ax4.imshow(core)
ax5.imshow(msk)
ax6.imshow(~find_boundaries(msk)*img)
def test_gpu_check():
from cellpose import models
models.use_gpu()
