def test(opt, test_loader, net, split):
start_time = time.time()
eva = Evaluator(opt.n_classes, opt.bg_err)
eva_crf = Evaluator(opt.n_classes, opt.bg_err)
ims = []
labels = []
net = net.eval()
for iteration, batch in enumerate(test_loader):
im, label = batch
im = im.cuda()
label = label.cuda()
out = net(im)
prob = F.softmax(out, dim=1)
for i in range(opt.batch_size):
prob_np = prob[i].detach().cpu().numpy()
label_np = label[i].cpu().numpy()
im_np = im[i].cpu().numpy()
ims.append(to_image(im[i, :3, :, :]))
labels.append(label_np)
eva.register(label_np, prob_np)
prob_crf = crf(prob_np, im_np, opt.sdims, opt.schan, opt.compat,
opt.iters)
eva_crf.register(label_np, prob_crf)
print(
str(iteration * opt.batch_size + i).zfill(2),
time.time() - start_time, 'seconds')
msa, preds_msa, miou, miiou, preds_miou = eva.evaluate()
msa_crf, preds_msa_crf, miou_crf, miiou_crf, preds_miou_crf = eva_crf.evaluate(
)
print('Pre-CRF: MSA: {} mIoU: {} miIoU: {}'.format(
round(msa * 100, 1), round(miou * 100, 1), round(miiou * 100, 1)))
print('Post-CRF: MSA: {} mIoU: {} miIoU: {}'.format(
round(msa_crf * 100, 1), round(miou_crf * 100, 1),
round(miiou_crf * 100, 1)))
for i, label in enumerate(labels):
pred_msa = preds_msa[i]
pred_msa_crf = preds_msa_crf[i]
pred_miou = preds_miou[i]
pred_miou_crf = preds_miou_crf[i]
vis_im = ims[i]
vis_label = colormap(label)
vis_pred_msa = colormap(pred_msa)
vis_pred_msa_crf = colormap(pred_msa_crf)
vis_pred_miou = colormap(pred_miou)
vis_pred_miou_crf = colormap(pred_miou_crf)
vis_all = np.concatenate(
(np.concatenate((vis_im, vis_label), axis=2),
np.concatenate((vis_pred_miou, vis_pred_miou_crf), axis=2)),
axis=1)
vis_all = vis_all.transpose((1, 2, 0))
io.imsave(
Path(opt.out_path) / split / (str(i).zfill(2) + '.png'), vis_all)
return msa, miou, miiou, msa_crf, miou_crf, miiou_crf
def train(opt, vis, epoch, train_loader, net, optimizer, scheduler):
net = net.train()
train_len = len(train_loader)
start_time = time.time()
scheduler.step()
for iteration, batch in enumerate(train_loader):
# Load Data
im, label = batch
im = im.cuda(non_blocking=True)
label = label.cuda(non_blocking=True)
# Forward Pass
out = net(im)
loss = F.cross_entropy(out, label)
# Backward Pass
optimizer.zero_grad()
loss.backward()
optimizer.step()
scheduler.batch_step()
# Logging
cur_time = time.time()
loss_scalar = float(loss.cpu().detach().numpy())
if iteration < opt.threads:
print('{} [{}]({}/{}) AvgTime:{:>4} Loss:{:>4}'.format(opt.env, epoch, iteration, train_len, \
round((cur_time - start_time) / (iteration + 1), 2), \
round(loss_scalar, 4)))
if iteration == opt.threads - 1:
start_time = cur_time
else:
print('{} [{}]({}/{}) AvgTime:{:>4} Loss:{:>4}'.format(opt.env, epoch, iteration, train_len, \
round((cur_time - start_time) / (iteration + 1 - opt.threads), 2), \
round(loss_scalar, 4)))
# Visualization
vis.iteration.append(epoch + iteration / train_len)
vis.nlogloss.append(-np.log(np.maximum(1e-6, loss_scalar)))
vis.plot_loss()
if opt.vis_iter <= 0 or iteration % opt.vis_iter > 0:
continue
prob, pred = torch.max(out, dim=1)
vis_rgb = to_image(im[0, 0:3, :, :] * 0.5)
vis_nir = to_image(im[0, 3:4, :, :] * 0.5)
vis_swir1 = to_image(im[0, 4:5, :, :] * 0.5)
vis_swir2 = to_image(im[0, -2:-1, :, :] * 0.5)
vis_label = colormap(label[0].cpu().numpy())
vis_pred = colormap(pred[0].cpu().numpy())
vis_im = np.concatenate((np.concatenate((vis_label, vis_pred), axis=1), \
np.concatenate((vis_rgb, vis_nir), axis=1), \
np.concatenate((vis_swir1, vis_swir2), axis=1)), axis=2)
vis.plot_image(vis_im, 0)
def get_seg_label_by_name(ImgName,
mc,
max_size=(640, 640),
default_ImgLoc='./VOCdevkit/VOC2012/JPEGImages/'):
#should read original images here, and do not resize it here
MEAN_PIXEL = np.array([103.939, 116.779, 123.68])
ImgName_ = ImgName.split('.')[0] + '.jpg'
FileName = default_ImgLoc + ImgName_
orign_img = cv2.imread(FileName)
im = orign_img - MEAN_PIXEL
seg = cv2.imread('./VOCdevkit/VOC2012/SegmentationClass/' +
ImgName)[:, :, ::-1] #utils.get_seg_by_name(ImgName)
#print(seg)
#print(seg.shape)
#seg = seg[:,:,::-1]
#print('segment shape',seg.shape)
gray_to_rgb, rgb_to_gray = utils.colormap()
#rgb_to_gray = utils.label_colormap()
#print(rgb_to_gray.shape)
#print(rgb_to_gray)
#rgb_to_gray = [rgb_to_gray,]# * mc.BATCH_SIZE#rgb_to_gray * mc.BATCH_SIZE
#print(len(rgb_to_gray))
row, col, _ = im.shape
im_blob = np.zeros((max_size[0], max_size[1], 3))
im_blob[0:row, 0:col, :] = im
seg_blob = np.zeros((max_size[0], max_size[1], 1))
mask = np.zeros_like(seg_blob)
for i in xrange(row):
for j in xrange(col):
seg_blob[i, j] = rgb_to_gray[tuple(seg[i, j, :])]
# Discard 255 edge class
if seg_blob[i, j] != 255:
mask[i, j] = 1
else:
seg_blob[i, j] = 0
#print(seg_blob)
cv2.imwrite('res_img_seg.png', seg_blob)
"""
seg_blob = np.zeros((max_size[0], max_size[1],1))
mask = np.zeros_like(seg_blob)
row, col, _ = orign_img.shape
seg_gray = np.zeros((row, col))
#print(rgb_to_gray[tuple(seg[0,0,:])])
for i in xrange(row):
for j in xrange(col):
#print(np.asarray(seg[i,j]))
seg_gray[i,j] = rgb_to_gray[tuple(seg[i,j])]
seg_blob = cv2.resize(seg_gray, max_size, interpolation=cv2.INTER_NEAREST)
for i in xrange(max_size[0]):
for j in xrange(max_size[1]):
if seg_blob[i,j] != 255:
mask[i,j] = 1
else:
seg_blob[i,j] = 0
#print(seg_blob.shape, mask.shape)
seg_blob = np.array([seg_blob]).transpose((1,2,0))
mask = np.array([mask]).transpose((1,2,0))
"""
return im_blob, seg_blob, mask
def rview(img, seg=None, overlay=None, colors=None, binary="rview"):
"""
Launches rview.
"""
if isinstance(img, Image):
if overlay is not None and seg is not None:
print "You cannot specify both seg and overlay"
return
if overlay is not None and colors is None:
colors = 'jet' # default colormap
if colors is not None and overlay is None:
overlay = img.rescale() # we want to see img in colors
img = zeros(img.get_header(), dtype='int16')
if isinstance(colors, str):
colors = utils.get_colormap(colors)
if seg is not None and colors is None:
colors = utils.random_colormap(seg.max())
# now, seg == overlay
if overlay is not None:
seg = overlay
if seg is not None and not isinstance(seg, Image):
seg = Image(seg, img.get_header())
handle, filename = tempfile.mkstemp(suffix=".nii")
garbage.append(filename)
imwrite(filename, img.astype('int16')) # rview reads in "short" anyway
args = [binary, filename]
if seg is not None:
handle, seg_filename = tempfile.mkstemp(suffix=".nii")
garbage.append(seg_filename)
handle, colors_filename = tempfile.mkstemp(suffix=".txt")
garbage.append(colors_filename)
imwrite(seg_filename, seg.astype('int16'))
args.extend(["-seg", seg_filename])
utils.colormap(colors, colors_filename)
args.extend(["-lut", colors_filename])
if overlay is not None:
args.append("-labels")
# launch rview as an independant process
subprocess.Popen(args)
def rview( img, seg=None, overlay=None, colors=None, binary="rview" ):
"""
Launches rview.
"""
if isinstance( img, Image ):
if overlay is not None and seg is not None:
print "You cannot specify both seg and overlay"
return
if overlay is not None and colors is None:
colors = 'jet' # default colormap
if colors is not None and overlay is None:
overlay = img.rescale() # we want to see img in colors
img = zeros(img.get_header(), dtype='int16')
if isinstance( colors, str ):
colors = utils.get_colormap( colors )
if seg is not None and colors is None:
colors = utils.random_colormap(seg.max())
# now, seg == overlay
if overlay is not None:
seg = overlay
if seg is not None and not isinstance(seg, Image):
seg = Image( seg, img.get_header() )
handle,filename = tempfile.mkstemp(suffix=".nii")
garbage.append(filename)
imwrite( filename, img.astype('int16') ) # rview reads in "short" anyway
args = [ binary, filename ]
if seg is not None:
handle,seg_filename = tempfile.mkstemp(suffix=".nii")
garbage.append(seg_filename)
handle,colors_filename = tempfile.mkstemp(suffix=".txt")
garbage.append(colors_filename)
imwrite( seg_filename, seg.astype('int16') )
args.extend( ["-seg", seg_filename])
utils.colormap( colors, colors_filename )
args.extend( ["-lut", colors_filename])
if overlay is not None:
args.append("-labels")
# launch rview as an independant process
subprocess.Popen( args )
#!/usr/bin/env python3
import collections, functools, itertools, logging, multiprocessing, random
import matplotlib.cm
import matplotlib.patches
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.optimize
import scipy.special
import plot_fit, utils
import plot_fit
CMAP_VIRIDIS = matplotlib.cm.get_cmap("viridis")
CMAP_FOLDED_VIRIDIS = utils.colormap(
"folded_viridis",
np.concatenate([CMAP_VIRIDIS(np.linspace(0.0, 1.0, 100)),
CMAP_VIRIDIS(np.linspace(1.0, 0.0, 100))]))
CMAP_FOLDED_PINK = utils.colormap(
"folded_pink",
["#ffffff", "#ec7ca3", "#ffffff"])
# scaling transformations
TRANSFORM_LOG_ABS = lambda x: np.log(abs(x)), lambda x: np.exp(x)
TRANSFORM_ID = lambda x: x, lambda x: x
def gather_fit_data_inner(group, fit_count, maxfev):
badness_threshold = plot_fit.LOGDERIV_BADNESS_THRESHOLD
(label, interaction, num_filled, freq, method), gg = group
logging.info(f"{(label, interaction, num_filled, freq, method)}")
gg = gg.rename(columns={"num_shells": "x", "energy": "y"})
#!/usr/bin/env python3
import functools, random
import matplotlib.cm
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.optimize
import scipy.special
import fits, utils
CMAP_VIRIDIS = matplotlib.cm.get_cmap("viridis")
CMAP_FOLDED_VIRIDIS = utils.colormap(
"folded_viridis",
np.concatenate([CMAP_VIRIDIS(np.linspace(0.0, 1.0, 100)),
CMAP_VIRIDIS(np.linspace(1.0, 0.0, 100))]))
CMAP_FOLDED_PINK = utils.colormap(
"folded_pink",
["#ffffff", "#ec7ca3", "#ffffff"])
# scaling transformations
TRANSFORM_LOG_ABS = lambda x: np.log(abs(x)), lambda x: np.exp(x)
TRANSFORM_ID = lambda x: x, lambda x: x
def parse_bin(s):
# why Pandas converts bins to strings, no-one knows
return (tuple(map(float, s[1:-1].split(","))))
def parse_binned_groups(stream):
return ((parse_bin(k), v) for k, v in stream)
