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Commit 1fc01530 by 王肇一
Options

mrnet with VOC type dataset

parent 2a781f86
Showing with 692 additions and 122 deletions
.gitignore
__pycache__/
.idea/*
data/imgs/*
data/masks/*
data/output/*
data/train_imgs/*
data/train_masks/*
data/train_imgs_32/*
data
.ipynb_checkpoints/
runs
checkpoint
\ No newline at end of file
app.py
......@@ -16,6 +16,7 @@ import os
import re
from unet import UNet
from mrnet import MultiUnet
from utils.predict import predict_img
from resCalc import save_img, get_subarea_info, save_img_mask
......@@ -29,7 +30,7 @@ def step_1(net, args, device, list, position):
for fn in tqdm(list, position = position):
logging.info("\nPredicting image {} ...".format(fn[0] + '/' + fn[1]))
img = Image.open('data/imgs/' + fn[0] + '/' + fn[1])
mask = predict_img(net = net, full_img = img, scale_factor = args.scale, out_threshold = args.mask_threshold,
mask = predict_img(net = net, full_img = img, out_threshold = args.mask_threshold,
device = device)
result = (mask * 255).astype(np.uint8)
......@@ -100,7 +101,8 @@ def cli_main():
seperate_path = divide_list(path, args.process)
if args.step == 1:
net = UNet(n_channels = 1, n_classes = 1)
# net = UNet(n_channels = 1, n_classes = 1)
net = MultiUnet(n_channels = 1,n_classes = 1)
logging.info("Loading model {}".format(args.module))
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
logging.info(f'Using device {device}')
......
cli/json_to_voc.py
......@@ -15,15 +15,11 @@ import labelme
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument('input_dir', help='input annotated directory')
parser.add_argument('output_dir', help='output dataset directory')
parser.add_argument('--labels', help='labels file', required=True)
parser.add_argument(
'--noviz', help='no visualization', action='store_true'
)
parser = argparse.ArgumentParser(formatter_class = argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input_dir', help = 'input annotated directory')
parser.add_argument('output_dir', help = 'output dataset directory')
parser.add_argument('--labels', help = 'labels file', required = True)
parser.add_argument('--noviz', help = 'no visualization', action = 'store_true')
args = parser.parse_args()
if osp.exists(args.output_dir):
......@@ -34,9 +30,7 @@ def main():
os.makedirs(osp.join(args.output_dir, 'SegmentationClass'))
os.makedirs(osp.join(args.output_dir, 'SegmentationClassPNG'))
if not args.noviz:
os.makedirs(
osp.join(args.output_dir, 'SegmentationClassVisualization')
)
os.makedirs(osp.join(args.output_dir, 'SegmentationClassVisualization'))
print('Creating dataset:', args.output_dir)
class_names = []
......@@ -58,47 +52,49 @@ def main():
f.writelines('\n'.join(class_names))
print('Saved class_names:', out_class_names_file)
for label_file in glob.glob(osp.join(args.input_dir, '*.json')):
print('Generating dataset from:', label_file)
with open(label_file) as f:
base = osp.splitext(osp.basename(label_file))[0]
out_img_file = osp.join(
args.output_dir, 'JPEGImages', base + '.jpg')
out_lbl_file = osp.join(
args.output_dir, 'SegmentationClass', base + '.npy')
out_png_file = osp.join(
args.output_dir, 'SegmentationClassPNG', base + '.png')
if not args.noviz:
out_viz_file = osp.join(
args.output_dir,
'SegmentationClassVisualization',
base + '.jpg',
)
data = json.load(f)
img_file = osp.join(osp.dirname(label_file), data['imagePath'])
img = np.asarray(PIL.Image.open(img_file))
PIL.Image.fromarray(img).save(out_img_file)
lbl = labelme.utils.shapes_to_label(
img_shape=img.shape,
shapes=data['shapes'],
label_name_to_value=class_name_to_id,
)
labelme.utils.lblsave(out_png_file, lbl)
np.save(out_lbl_file, lbl)
if not args.noviz:
viz = imgviz.label2rgb(
label=lbl,
img=img,
font_size=15,
label_names=class_names,
loc='rb',
)
imgviz.io.imsave(out_viz_file, viz)
for path in os.listdir(args.input_dir):
for label_file in glob.glob(osp.join(args.input_dir + '/' + path, '*.json')):
print('Generating dataset from:', label_file)
with open(label_file) as f:
base = osp.splitext(osp.basename(label_file))[0]
out_img_file = osp.join(args.output_dir, 'JPEGImages', base + '.jpg')
out_lbl_file = osp.join(args.output_dir, 'SegmentationClass', base + '.npy')
out_png_file = osp.join(args.output_dir, 'SegmentationClassPNG', base + '.png')
if not args.noviz:
out_viz_file = osp.join(args.output_dir, 'SegmentationClassVisualization', base + '.jpg', )
data = json.load(f)
img_file = osp.join(osp.dirname(label_file), data['imagePath'])
img = np.asarray(PIL.Image.open(img_file))
PIL.Image.fromarray(img).save(out_img_file)
lbl = labelme.utils.shapes_to_label(img_shape = img.shape, shapes = data['shapes'],
label_name_to_value = class_name_to_id, )
lblsave(out_png_file, lbl)
np.save(out_lbl_file, lbl)
if not args.noviz:
viz = imgviz.label2rgb(label = lbl, img = img, font_size = 15, label_names = class_names,
loc = 'rb', )
imgviz.io.imsave(out_viz_file, viz)
def lblsave(filename, lbl):
if osp.splitext(filename)[1] != '.png':
filename += '.png'
# Assume label ranses [-1, 254] for int32,
# and [0, 255] for uint8 as VOC.
if lbl.min() >= -1 and lbl.max() < 255:
lbl = np.array([1 if lbl[x, y] > 0 else 0 for x in range(200) for y in range(200)]).reshape([200, 200])
lbl_pil = PIL.Image.fromarray(lbl.astype(np.uint8), mode = 'P')
colormap = imgviz.label_colormap()
lbl_pil.putpalette(colormap.flatten())
lbl_pil.save(filename)
else:
raise ValueError('[%s] Cannot save the pixel-wise class label as PNG. '
'Please consider using the .npy format.' % filename)
if __name__ == '__main__':
......
data/voc/train.txt 0 → 100644
Step size0Dwell time50 Clinical Sample K. p Tobramycin 16ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 16ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 128ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 8ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil ATCC25922 PBb Tobramycin 0.5ug 852nm 30mw 300mw tune 43.02 002
Step size0Dwell time50 E.faecium atcc 29212 Amp 1ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 1ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 1ug 852nm 30mw 300mw tune 43.02 003
Step size0Dwell time50 E.coil D2O 852nm 30mw 300mw tune 43.02 004
Step size0Dwell time50 E.coil atcc 25922 12.16 D2O 852nm 40mw 400mw tune 43.08 001-
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 2ug 852nm 30mw 300mw tune 43.02 002
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 0.25ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 P.a atcc27853 Gen 0.5ug 852nm 30mw 300mw tune 43.03 001
Step size0Dwell time50 S.a atcc 29213 1h d2o-2 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 P.a atcc27853 LB-11.29 852nm 30mw 300mw tune 43.06 001
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 16ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.125ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.125ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 4ug 852nm 30mw 300mw tune 43.02 001
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 16ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 S.a atcc 29213 1h d2o-2 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 0.25ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 2ug 852nm 30mw 300mw tune 43.02 003
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 2ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc 25922 12.12 TOB 0.25 852nm 40mw 400mw tune 43.11 003
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 32ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 P.a atcc 27853 Ceft 4ug 852nm 30mw 300mw tune 43.03 001
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 1ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 1ug 852nm 30mw 300mw tune 43.02 002
Step size0Dwell time50 E.coil atcc25922 Amipicillin 8ug 852nm 40mw 400mw tune43.08 60x oil obj 002
Step size0Dwell time50 E.faecium atcc 29212 Amp 2ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 8ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 32ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 128ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 E.coil atcc25922 Gentamicin 1ug 852nm 30mw 300mw tune 43.04 004
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 16ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 128ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 Clinical Sample K. p Tobramycin 16ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 E.coil ATCC25922 PBb Tobramycin 0.5ug 852nm 30mw 300mw tune 43.02 001
Step size0Dwell time50 E.faecium atcc 29212 Ery 0.25ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 1ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 2ug 852nm 30mw 300mw tune 43.02 001
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 0.25ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.faecium atcc 29212 Ampicillin D2O 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 P.a atcc 27853 Ceft 2ug 852nm 30mw 300mw tune 43.03 001
Step size0Dwell time50 S.a atcc 29213 Eryth 0.03125ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.125ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc25922 Imipenen 0.5ug 852nm 40mw 400mw tune43.08 60x oil obj 002
Step size0Dwell time50 E.coil atcc25922 Imipenen 0.5ug 852nm 40mw 400mw tune43.08 60x oil obj 003
Step size0Dwell time50 P.a atcc 27853 Ceft 1ug 852nm 30mw 300mw tune 43.03 001
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 16ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 S.a atcc 29213 Eryth 0.03125ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 P.a overnight Tob 1ug 852nm 30mw 300mw tune 43.05 004
Step size0Dwell time50 S.a atcc 29213 1h d2o-2 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 P.a atcc27853 D2O-11.29 852nm 30mw 300mw tune 43.06 002
Step size0Dwell time50 P.a atcc 27853 Ceft 4ug 852nm 30mw 300mw tune 43.03 002
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 1ug 852nm 30mw 300mw tune 43.02 001
Step size0Dwell time50 E.coil atcc25922 Imipenen 0.25ug 852nm 40mw 400mw tune43.08 60x oil obj 001
Step size0Dwell time50 E.coil atcc25922 Amipicillin 8ug 852nm 40mw 400mw tune43.08 60x oil obj 001
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 8ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 P.a atcc27853 Imipenen D2O 852nm 30mw 300mw tune 43.02 001
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 16ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 Clinical Sample K. p Tobramycin 16ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 32ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 64ug 40mw 400mw tune 43.08 001-1
Step size0Dwell time50 E.faecium atcc 29212 Amp 2ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.faecium atcc 29212 Ery 0.25ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.faecium atcc 29212 Amp 1ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 32ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil atcc 25922 12.12 TOB 0.25 852nm 40mw 400mw tune 43.11 004
Step size0Dwell time50 E.coil D2O 852nm 30mw 300mw tune 43.02 002
Step size0Dwell time50 E.coil atcc25922 Imipenen 0.25ug 852nm 40mw 400mw tune43.08 60x oil obj 011
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 1ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 2ug 852nm 30mw 300mw tune 43.02 004
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 0.25ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 2ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 16ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 P.a overnight Tob 2ug 852nm 30mw 300mw tune 43.05 001
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.25ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 1h d2o-2 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 16ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 E.coil atcc25922 Amipicillin 16ug 852nm 40mw 400mw tune43.08 60x oil obj 001
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.0625ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 E.coil atcc25922 Imipenen 0.25ug 852nm 40mw 400mw tune43.08 60x oil obj 004
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 1ug 852nm 30mw 300mw tune 43.02 004
Step size0Dwell time50 E.coil D2O 852nm 30mw 300mw tune 43.02 003
Step size0Dwell time50 E.faecium atcc 29212 Amp 1ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.faecium atcc 29212 Amp 2ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil ATCC25922 PBb Tobramycin 0.5ug 852nm 30mw 300mw tune 43.02 005
Step size0Dwell time50 K.p atcc700603 Imipenen 0.25ug 852nm 40mw 400mw tune43.08 002
Step size0Dwell time50 E.coil atcc25922 Gentamicin 2ug 852nm 30mw 300mw tune 43.04 003
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 16ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 32ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc25922 Gentamicin 1ug 852nm 30mw 300mw tune 43.04 002
Step size0Dwell time50 P.a atcc27853 Gen 4ug 852nm 30mw 300mw tune 43.03 002
Step size0Dwell time50 P.a overnight Tob 0.5ug 852nm 30mw 300mw tune 43.05 002
Step size0Dwell time50 Clinical Sample K. p Tobramycin 16ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 E.faecium atcc 29212 Ery 0.25ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 P.a atcc27853 Gen 2ug 852nm 30mw 300mw tune 43.03 002
Step size0Dwell time50 E.coil atcc25922 Amipicillin 8ug 852nm 40mw 400mw tune43.08 60x oil obj 006
Step size0Dwell time50 E.faecium atcc 29212 Amp 1ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil D2O 852nm 30mw 300mw tune 43.02 001
Step size0Dwell time50 E.faecium atcc 29212 Ampicillin D2O 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil atcc25922 Amipicillin 16ug 852nm 40mw 400mw tune43.08 60x oil obj 003
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 2ug 852nm 40mw 400mw tune 43.08 006
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 16ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 P.a overnight Tob 2ug 852nm 30mw 300mw tune 43.05 002
Step size0Dwell time50 E.coil atcc25922 Imipenen 0.5ug 852nm 40mw 400mw tune43.08 60x oil obj 004
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.25ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 16ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.faecium atcc 29212 Ampicillin D2O 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.0625ug 852nm 40mw 400mw tune 43.08 006
Step size0Dwell time50 P.a overnight Tob 4ug 852nm 30mw 300mw tune 43.05 001
Step size0Dwell time50 E.coil atcc 25922 12.12 TOB 0.25 852nm 40mw 400mw tune 43.11 006
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 32ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 P.a atcc27853 Gen 1ug 852nm 30mw 300mw tune 43.03 002
Step size0Dwell time50 P.a overnight Tob 0.25ug 852nm 30mw 300mw tune 43.05 003
Step size0Dwell time50 E.faecium atcc 29212 Lb 852nm 40mw 400mw tune 43.08 0077
Step size0Dwell time50 E.faecium atcc 29212 Amp 2ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.faecium atcc 29212 Ery 0.25ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc700603 Imipenen 0.25ug 852nm 40mw 400mw tune43.08 001
Step size0Dwell time50 E.coil atcc25922 Gentamicin 1ug 852nm 30mw 300mw tune 43.04 001
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 32ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 256ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 S.a atcc 29213 Linezolid 16ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 4ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 P.a atcc27853 Amipicillin 16ug 852nm 30mw 300mw tune 43.03 001
Step size0Dwell time50 E.coil atcc 25922 12.16 D2O 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.125ug 852nm 40mw 400mw tune 43.08 006
Step size0Dwell time50 E.coil ATCC25922 PBb Tobramycin 0.25ug 852nm 30mw 300mw tune 43.02 004
Step size0Dwell time50 P.a 1h D2O 852nm 30mw 300mw tune 43.03 004
Step size0Dwell time50 E.coil atcc 25922 12.16 lb 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.faecium atcc 29212 Amp 0.25ug 852nm 40mw 400mw tune 43.08 002
191128-Step size0Dwell time50 P.a overnight LB 852nm 30mw 300mw tune 43.05 001
Step size0Dwell time50 P.a atcc27853 Levofloxacin-11.29 0.5ug 852nm 30mw 300mw tune 43.06 003
Step size0Dwell time50 E.faecium atcc 29212 Ery 2ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc25922 1h D2O 852nm 40mw 400mw tune43.08 60x oil obj 003
Step size0Dwell time50 P.a atcc27853 Gen 0.25ug 852nm 30mw 300mw tune 43.03 001
Step size0Dwell time50 E.faecium atcc 29212 Ery 1ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Linezolid 1ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 0.50.5ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.faecium atcc 29212 Ery 1ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.faecium atcc 29212 Ery 2ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 P.a atcc27853 Levofloxacin-11.29 0.5ug 852nm 30mw 300mw tune 43.06 002
Step size0Dwell time50 E.faecium atcc 29212 Amp 0.25ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Linezolid 4ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.faecium atcc 29212 Ery 4ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 8ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 S.a atcc 29213 Linezolid 16ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 256ug 852nm 30mw 300mw tune 43.00 005
Step size0Dwell time50 E.coil atcc25922 Gentamicin 0.5ug 852nm 30mw 300mw tune 43.04 006
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 8ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 P.a atcc27853 Amipicillin 16ug 852nm 30mw 300mw tune 43.03 002
Step size0Dwell time50 Clinical Sample K. p D2O 0ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 E.coil atcc 25922 12.16 D2O 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Linezolid 0.5ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.125ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 E.faecium atcc 29212 Amp 0.25ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.faecium atcc 29212 Ery 2ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 4ug 852nm 40mw 400mw tune43.08 60x oil obj 004
Step size0Dwell time50 Clinical Sample K. p Tobramycin 4ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 0.50.5ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 0.50.5ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.faecium atcc 29212 Ery 1ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 4ug 852nm 40mw 400mw tune43.08 60x oil obj 005
Step size0Dwell time50 Clinical Sample K. p Tobramycin 4ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 S.a atcc 29213 Linezolid 4ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.faecium atcc 29212 Ery 4ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 Clinical Sample K. p Tobramycin 64ug 852nm 30mw 300mw tune 43.00 003_over-exposure
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.125ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 S.a atcc 29213 Linezolid 0.5ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 1ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 8ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 S.a atcc 29213 Linezolid 16ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc25922 Gentamicin 0.5ug 852nm 30mw 300mw tune 43.04 003
Step size0Dwell time50 Clinical Sample K. p D2O 0ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 4ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Linezolid 0.5ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil ATCC25922 PBb Tobramycin 0.25ug 852nm 30mw 300mw tune 43.02 002
Step size0Dwell time30 P.a atcc27853 D2O OVERNIGHT 852nm 30mw 300mw tune 43.01 005
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 2ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 P.a atcc27853 Imipenen LB 852nm 30mw 300mw tune 43.02 007
Step size0Dwell time50 S.a atcc 29213 Linezolid 1ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 S.a atcc 29213 Linezolid 1ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 4ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Linezolid 2ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 Clinical Sample K. p LB 0ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 1ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil ATCC25922 PBb Tobramycin 0.25ug 852nm 30mw 300mw tune 43.02 003
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 4ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil atcc25922 1h D2O 852nm 30mw 300mw tune43.08 60x oil obj 002
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 256ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 S.a atcc 29213 Linezolid 16ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 64ug 852nm 30mw 300mw tune 43.00 003_over-exposure
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 256ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 P.a 1h d2o 852nm 30mw 300mw tune 43.06 002
Step size0Dwell time50 Clinical Sample K. p D2O 0ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 P.a atcc27853 Levofloxacin-11.29 8ug 852nm 30mw 300mw tune 43.06 001
Step size0Dwell time50 S.a atcc 29213 Linezolid 0.5ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc 25922 12.16 D2O 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil ATCC25922 PBb Tobramycin 0.25ug 852nm 30mw 300mw tune 43.02 001
Step size0Dwell time50 S.a atcc 29213 Linezolid 4ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 E.faecium atcc 29212 Ery 0.5ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 2ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 4ug 852nm 40mw 400mw tune43.08 60x oil obj 002
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 0.50.5ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 4ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 4ug 852nm 40mw 400mw tune43.08 60x oil obj 003
Step size0Dwell time50 Clinical Sample K. p Tobramycin 4ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 P.a atcc27853 LB-12.2 852nm 30mw 300mw tune 43.01 002
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 2ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 Clinical Sample K. p Tobramycin 64ug 852nm 30mw 300mw tune 43.00 002_over-exposure
Step size0Dwell time50 E.faecium atcc 29212 Ery 0.5ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 1ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Linezolid 4ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil atcc25922 1h D2O 852nm 30mw 300mw tune43.08 60x oil obj 001
Step size0Dwell time50 Clinical Sample K. p D2O 0ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 E.faecium atcc 29212 Amp 0.5ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 2ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 8ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 0.25ug 852nm 40mw 400mw tune43.08 60x oil obj 003
Step size0Dwell time50 S.a atcc 29213 Eryth 0.25ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 Clinical Sample K. p Tobramycin 32ug 852nm 30mw 300mw tune 43.00 002_over-exposure
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 2ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.25ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 Clinical Sample K. p Tobramycin 4ug 852nm 30mw 300mw tune 43.00 001_over-exposure
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 8ug40mw 400mw tune 43.08 004
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 16ug40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 16ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.5ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 128ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 K.p atcc700603 Imipenen 0.5ug 852nm 40mw 400mw tune43.08 003
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 2ug 852nm 40mw 400mw tune43.08 60x oil obj 001
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.0625 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.25ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 0.5ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 0.25ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.125ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.125ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 0.25ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 0.5ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc700603 Imipenen 0.5ug 852nm 40mw 400mw tune43.08 002
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.5ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 P.a atcc 27853 Ceft 0.5ug 852nm 30mw 300mw tune 43.03 002
191128-Step size0Dwell time50 P.a overnight Gen 4ug 852nm 30mw 300mw tune 43.05 001
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 16ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 0.25ug 852nm 30mw 300mw tune 43.02 001
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 2ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 P.a atcc 29213 Gen-r 2ug 852nm 30mw 300mw tune43.05 010
Step size0Dwell time50 E.faecium atcc 29212 Amp 16ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 0.25ug 852nm 40mw 400mw tune43.08 60x oil obj 002
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 8ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.faecium atcc 29212 Amp 0.5ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 P.a overnight LB 852nm 30mw 300mw tune 43.05 001
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 2ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.25ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 16ug40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 2ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 P.a atcc 29213 Gen 0.25ug 852nm 30mw 300mw tune43.05 003
Step size0Dwell time50 S.a atcc 29213 Vancomycin D2O 852nm 40mw 400mw tune 43.08 0088
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 128ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.25ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 2ug 852nm 40mw 400mw tune43.08 60x oil obj 002
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.125ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 0.5ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 P.a atcc27853 Amipicillin 64ug 852nm 30mw 300mw tune 43.03 002
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 2ug 852nm 40mw 400mw tune43.08 60x oil obj 003
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.25ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Vancomycin D2O 852nm 40mw 400mw tune 43.08 0089
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 128ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 K.p atcc700603 Imipenen 0.5ug 852nm 40mw 400mw tune43.08 001
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.5ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 16ug40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 2ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 16ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 0.25ug 852nm 30mw 300mw tune 43.02 002
Step size0Dwell time50 S.a atcc 29213 Eryth 0.25ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc25922 Amipicillin 2ug 852nm 40mw 400mw tune43.08 60x oil obj 002
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 2ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 0.25ug 852nm 40mw 400mw tune43.08 60x oil obj 001
Step size0Dwell time10 E.coil atcc25922 1h d2o 852nm 30mw 300mw tune 43.04 0088
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 0.25ug 852nm 40mw 400mw tune43.08 60x oil obj 005
Step size0Dwell time50 S.a atcc 29213 Eryth 0.0625ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.faecium atcc 29212 Amp 16ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.0625ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 D2O 40mw 400mw tune 43.08 0077
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 8ug40mw 400mw tune 43.08 002
Step size0Dwell time50 Clinical Sample K. p Tobramycin 128ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 S.a atcc 29213 Eryth 1ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.125ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil atcc25922 Amipicillin 1ug 852nm 40mw 400mw tune43.08 60x oil obj 001
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.0625 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 S.a atcc 29213 Eryth 2ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.125ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 P.a atcc27853 Imipenen 0.5ug 852nm 30mw 300mw tune 43.06 003
191128-Step size0Dwell time50 P.a overnight d2o 852nm 30mw 300mw tune 43.05 00191128-5
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.5ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 P.a atcc 27853 Ceft D2O that day cultured 852nm 30mw 300mw tune 43.03 001
Step size0Dwell time50 P.a atcc 29213 Gen 1ug 852nm 30mw 300mw tune43.05 001-1
Step size0Dwell time50 E.faecium atcc 29212 Amp 8ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 8ug40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.0625ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Eryth 0.0625ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.faecium atcc 29212 Amp 0.5ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 2ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil atcc25922 Ceftazidime 0.25ug 852nm 40mw 400mw tune43.08 60x oil obj 006
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 8ug40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 2ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.faecium atcc 29212 Amp 8ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 Clinical Sample K. p Tobramycin 128ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 128ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 S.a atcc 29213 Eryth 1ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.25ug 852nm 40mw 400mw tune 43.08 003-1
Step size0Dwell time50 E.coil atcc25922 Amipicillin 1ug 852nm 40mw 400mw tune43.08 60x oil obj 002
Step size0Dwell time50 S.a atcc 29213 Eryth 2ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.25ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 S.a atcc 29213 Eryth 2ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc25922 Amipicillin 1ug 852nm 40mw 400mw tune43.08 60x oil obj 003
Step size0Dwell time50 E.coil atcc 25922 12.16 Tob 0.25ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 S.a atcc 29213 Eryth 1ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 Clinical Sample K. p Tobramycin 128ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 E.faecium atcc 29212 Amp 8ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 P.a atcc27853 Amipicillin 32ug 852nm 30mw 300mw tune 43.03 001
Step size0Dwell time50 S.a atcc 29213 Ampicillin 0.0625ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc25922 Amipicillin 2ug 852nm 40mw 400mw tune43.08 60x oil obj 004
Step size0Dwell time50 E.faecium atcc 29212 Amp 0.5ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 128ug40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc700603 Imipenen 2ug 852nm 40mw 400mw tune43.08 004
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 64ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 E.coil ATCC25922 PBb Tobramycin 1ug 852nm 30mw 300mw tune 43.02 002
Step size0Dwell time50 S.a atcc 29213 Linezolid 8ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 1ug 40mw 400mw tune 43.08 005
Step size0Dwell time50 E.faecium atcc 29212 Ery 8ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 S.a atcc 29213 Eryth 0.125ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 P.a 1h d2o 852nm 30mw 300mw tune 43.05 003
Step size0Dwell time50 S.a atcc 29213 Ampicillin 2ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 0.5ug 852nm 30mw 300mw tune 43.02 004
Step size0Dwell time50 Clinical Sample K. p Tobramycin 8ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.0625ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time10 E.coil atcc25922 Gentamicin 0.5ug 852nm 30mw 300mw tune 43.04 002
Step size0Dwell time50 S.a atcc 29213 Eryth 0.5ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 4ug 40mw 400mw tune 43.08 006
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 64ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 E.coil ATCC25922 LB 852nm 30mw 300mw tune 43.02 001
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 4ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 K.p atcc 700603 12.16 D2O 40mw 400mw tune 43.08 001
Step size0Dwell time50 Clinical Sample K. p Tobramycin 64ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 Clinical Sample K. p Tobramycin 32ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 E.coil atcc25922 Imipenen 2ug 852nm 40mw 400mw tune43.08 60x oil obj 003
Step size0Dwell time50 E.coil atcc 25922 12.16 D2O 852nm 40mw 400mw tune 43.08 003-
Step size0Dwell time50 P.a atcc27853 Levofloxacin-11.29 4ug 852nm 30mw 300mw tune 43.06 004
Step size0Dwell time50 S.a atcc 29213 Ampicillin 1ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc25922 Imipenen 1ug 852nm 40mw 400mw tune43.08 60x oil obj 004
Step size0Dwell time50 S.a atcc 29213 Eryth 0.125ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 64ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 S.a atcc 29213 Ampicillin 4ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 128ug40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 128ug40mw 400mw tune 43.08 001
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 64ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 S.a atcc 29213 Linezolid 8ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 16ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil ATCC25922 PBb Tobramycin 1ug 852nm 30mw 300mw tune 43.02 001
Step size0Dwell time50 S.a atcc 29213 Vancomycin LB 852nm 40mw 400mw tune 43.08 0089
Step size0Dwell time50 E.faecium atcc 29212 Ery 8ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Eryth 0.125ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc700603 Imipenen 4ug 852nm 40mw 400mw tune43.08 005
Step size0Dwell time50 S.a atcc 29213 Ampicillin 2ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 32ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 E.coil atcc25922 Ceftazime 1ug 852nm 40mw 400mw tune43.08 60x oil obj 004
Step size0Dwell time50 S.a atcc 29213 Ampicillin 1ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time10 E.coil atcc25922 Gentamicin 0.5ug 852nm 30mw 300mw tune 43.04 001
Step size0Dwell time50 Clinical Sample K. p Tobramycin 8ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 E.coil atcc25922 Imipenen 1ug 852nm 40mw 400mw tune43.08 60x oil obj 006
Step size0Dwell time50 S.a atcc 29213 Eryth 0.5ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc25922 Imipenen 0.25ug 852nm 40mw 400mw tune43.08 60x oil obj 009
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 32ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 E.coil atcc25922 Gentamicin 0.25ug 852nm 30mw 300mw tune 43.04 003
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 64ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 512ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 256ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 64ug 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil ATCC25922 LB 852nm 30mw 300mw tune 43.02 002
Step size0Dwell time50 K.p atcc 700603 12.16 D2O 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Linezolid 0.25ug 852nm 40mw 400mw tune 43.08 005
Step size0Dwell time50 S.a atcc 29213 Linezolid 0.25ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 K.p atcc 700603 12.16 D2O 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil ATCC25922 LB 852nm 30mw 300mw tune 43.02 003
Step size0Dwell time50 E.coil atcc25922 Gentamicin 0.25ug 852nm 30mw 300mw tune 43.04 002
Step size0Dwell time50 E.coil atcc25922 Imipenen 1ug 852nm 40mw 400mw tune43.08 60x oil obj 007
Step size0Dwell time50 S.a atcc 29213 Ampicillin 1ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 Clinical Sample K. p Tobramycin 8ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 P.a atcc 29213 Gen 0.5ug 852nm 30mw 300mw tune43.05 001
Step size0Dwell time50 S.a atcc 29213 Ampicillin 2ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.faecium atcc 29212 Ery 8ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Linezolid 8ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Ampicillin 4ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc700603 Imipenen 2ug 852nm 40mw 400mw tune43.08 002
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 64ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 128ug40mw 400mw tune 43.08 004
Step size0Dwell time50 K.p atcc700603 Imipenen 1ug 852nm 40mw 400mw tune43.08 003
Step size0Dwell time50 E.coil ATCC25922 PBb Tobramycin 1ug 852nm 30mw 300mw tune 43.02 004
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 32ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 4ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.0625ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 32ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 E.coil atcc25922 Ceftazime 1ug 852nm 40mw 400mw tune43.08 60x oil obj 001
Step size0Dwell time50 E.coil atcc25922 Imipenen 2ug 852nm 40mw 400mw tune43.08 60x oil obj 004
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 32ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 Clinical Sample K. p Tobramycin 32ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.5ug 852nm 40mw 400mw tune 43.08 0089
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 256ug 852nm 30mw 300mw tune 43.00 001
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 64ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.25ug 852nm 40mw 400mw tune 43.08 0089
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 64ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 4ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.5ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 4ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Linezolid 0.25ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.25ug 852nm 40mw 400mw tune 43.08 0088
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 4ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 E.coil atcc 25922 12.16 levo 0.5ug 852nm 40mw 400mw tune 43.08 0088
Step size0Dwell time50 Clinical Sample K. p Tobramycin 32ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 P.a atcc27853 Levofloxacin-11.29 4ug 852nm 30mw 300mw tune 43.06 002
Step size0Dwell time50 E.coil atcc25922 Imipenen 1ug 852nm 40mw 400mw tune43.08 60x oil obj 002
Step size0Dwell time50 P.a atcc27853 Amipicillin 128ug 852nm 30mw 300mw tune 43.03 001
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 4ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 E.coil ATCC25922 PBb Levofloxacin 0.5ug 852nm 30mw 300mw tune 43.02 003
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.0625ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 32ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc700603 Imipenen 4ug 852nm 40mw 400mw tune43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 1ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 K.p atcc700603 Imipenen 1ug 852nm 40mw 400mw tune43.08 002
Step size0Dwell time50 K.p atcc700603 Imipenen 2ug 852nm 40mw 400mw tune43.08 003
Step size0Dwell time50 K.p atcc700603 Imipenen 2ug 852nm 40mw 400mw tune43.08 001
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 512ug 852nm 30mw 300mw tune 43.00 001_over-expousre
Step size0Dwell time50 E.faecium atcc 29212 Ery 8ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 S.a atcc 29213 Linezolid 8ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 P.a atcc27853 D2O-12.2 852nm 30mw 300mw tune 43.01 001
Step size0Dwell time50 S.a atcc 29213 Ampicillin 2ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 64ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.0625ug 852nm 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc 700603 12.16 Gentsmincin 4ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 Clinical Sample K. p Tobramycin 8ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 32ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 E.coil atcc25922 Ceftazime 1ug 852nm 40mw 400mw tune43.08 60x oil obj 002
Step size0Dwell time50 K.p atcc 700603 12.16 LB 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Eryth 0.5ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil atcc 25922 12.16 D2O 852nm 40mw 400mw tune 43.08 002-
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 32ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 4ug 40mw 400mw tune 43.08 003
data/voc/traineval.txt 0 → 100644
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 256ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 64ug 40mw 400mw tune 43.08 002
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 512ug 852nm 30mw 300mw tune 43.00 002
Step size0Dwell time50 P.a atcc27853 Levofloxacin-11.29 2ug 852nm 30mw 300mw tune 43.06 002
Step size0Dwell time50 S.a atcc 29213 Linezolid 0.25ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 Tobramycin 4ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 P.a atcc27853 Levofloxacin-11.29 1ug 852nm 30mw 300mw tune 43.06 003
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.5ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 S.a atcc 29213 Levofloxacin 0.5ug 852nm 40mw 400mw tune 43.08 003
Step size0Dwell time50 S.a atcc 29213 Linezolid 0.25ug 852nm 40mw 400mw tune 43.08 002
Step size0Dwell time50 P.a atcc27853 Levofloxacin-11.29 2ug 852nm 30mw 300mw tune 43.06 003
Step size0Dwell time50 Clinical Sample K. p Tobramycin 64ug 852nm 30mw 300mw tune 43.00 004
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 512ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 K.p atcc 700603 12.16 Ampicillin 64ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 256ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 P.a 1h lb 852nm 30mw 300mw tune 43.03 005
Step size0Dwell time50 Clinical Sample K. p Ceftazidime 32ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 P.a atcc27853 Levofloxacin-11.29 4ug 852nm 30mw 300mw tune 43.06 001
Step size0Dwell time50 K.p atcc 700603 12.16 LB 40mw 400mw tune 43.08 002
Step size0Dwell time50 E.coil atcc25922 Ceftazime 1ug 852nm 40mw 400mw tune43.08 60x oil obj 003
Step size0Dwell time50 Clinical Sample K. p Ampicillcin 32ug 852nm 30mw 300mw tune 43.00 003
Step size0Dwell time50 S.a atcc 29213 Ampicillin 1ug 852nm 40mw 400mw tune 43.08 004
Step size0Dwell time50 E.coil atcc25922 Imipenen 1ug 852nm 40mw 400mw tune43.08 60x oil obj 001
Step size0Dwell time50 K.p atcc 700603 12.16 Ceftazidime 64ug 40mw 400mw tune 43.08 003
Step size0Dwell time50 K.p atcc 700603 12.16 Levofloxacin 1ug 40mw 400mw tune 43.08 001
Step size0Dwell time50 K.p atcc700603 Imipenen 1ug 852nm 40mw 400mw tune43.08 001
mrnet/mrnet_module.py
......@@ -3,7 +3,7 @@
import torch
from torch import nn
from .mrnet_parts import MultiResBlock,ResPath,TransCompose
from .mrnet_parts import MultiResBlock, ResPath, TransCompose
class MultiUnet(nn.Module):
......@@ -40,8 +40,11 @@ class MultiUnet(nn.Module):
self.res9 = MultiResBlock(self.up9.outc*2, 32)
self.pool = nn.MaxPool2d(2)
self.outconv = nn.Conv2d(self.res9.outc, n_classes, kernel_size = 3, padding = 1)
# self.outconv = nn.Sequential(
# nn.Conv2d(self.res9.outc, n_classes, kernel_size = 1),
# nn.Sigmoid()
# )
self.outconv = nn.Conv2d(self.res9.outc, n_classes,kernel_size = 1)
def forward(self, x):
x = self.inconv(x)
......
mrnet/mrnet_parts.py
......@@ -4,6 +4,21 @@ import torch
import torchvision
import torch.nn as nn
import torch.nn.functional as F
import torchsnooper
def conv(in_channel, out_channel):
return nn.Sequential(
nn.Conv2d(in_channels = in_channel, out_channels = out_channel, kernel_size = 3, stride = 1,
padding = 1),
nn.BatchNorm2d(out_channel),
nn.ReLU(inplace = True))
def shortcut(in_channels, out_channels):
return nn.Sequential(
nn.Conv2d(in_channels = in_channels, out_channels = out_channels, kernel_size = 1, stride = 1),
nn.BatchNorm2d(out_channels))
class MultiResBlock(nn.Module):
......@@ -13,26 +28,26 @@ class MultiResBlock(nn.Module):
self.W = U * alpha
self.inc = in_channels
self.outc = int(self.W * 0.167) + int(self.W * 0.333) + int(self.W * 0.5)
self.shortcut = shortcut(self.inc,self.outc)
def conv(self, in_channel, out_channel, kernel_size):
return nn.Sequential(
nn.Conv2d(in_channels = in_channel, out_channels = out_channel, kernel_size = kernel_size, stride = 1,padding = 1),
nn.BatchNorm2d(out_channel), nn.ReLU(inplace = True))
self.conv3 = conv(self.inc, int(self.W * 0.167))
self.conv5 = conv(int(self.W * 0.167), int(self.W * 0.333))
self.conv7 = conv(int(self.W * 0.333), int(self.W * 0.5))
self.norm = nn.BatchNorm2d(self.outc)
self.seq = nn.Sequential(nn.ReLU(inplace = True), nn.BatchNorm2d(self.outc))
#@torchsnooper.snoop()
def forward(self, x):
shortcut = nn.Sequential(
nn.Conv2d(in_channels = self.inc, out_channels = self.outc, kernel_size = 1, stride = 1),
nn.BatchNorm2d(self.outc))(x)
shortcut = self.shortcut(x)
conv3 = self.conv(self.inc, int(self.W * 0.167), 3)(x)
conv5 = self.conv(int(self.W * 0.167), int(self.W * 0.333), 3)(conv3)
conv7 = self.conv(int(self.W * 0.333), int(self.W * 0.5), 3)(conv5)
result = torch.cat([conv3, conv5, conv7], 1)
result = nn.BatchNorm2d(self.outc)(result)
conv3 = self.conv3(x)
conv5 = self.conv5(conv3)
conv7 = self.conv7(conv5)
result = torch.add(result, shortcut)
result = nn.Sequential(nn.ReLU(inplace = True), nn.BatchNorm2d(self.outc))(result)
return result
comb = torch.cat([conv3, conv5, conv7], 1)
result = self.norm(comb)
return self.seq(torch.add(result, shortcut))
class TransCompose(nn.Module):
......@@ -40,12 +55,12 @@ class TransCompose(nn.Module):
super().__init__()
self.inc = in_channels
self.outc = out_channels
self.proc = nn.Sequential(
nn.ConvTranspose2d(in_channels = self.inc, out_channels = self.outc, kernel_size = 2, stride = 2),
nn.BatchNorm2d(self.outc))
def forward(self, x):
return nn.Sequential(
nn.ConvTranspose2d(in_channels = self.inc, out_channels = self.outc, kernel_size = 2, stride = 2),
nn.BatchNorm2d(self.outc)
)(x)
return self.proc(x)
class ResPath(nn.Module):
......@@ -55,20 +70,16 @@ class ResPath(nn.Module):
self.inc = in_channels
self.outc = out_channels
def unit(self, in_channels, out_channels, x):
shortcut = nn.Sequential(
nn.Conv2d(in_channels = in_channels, out_channels = out_channels, kernel_size = 1, stride = 1),
nn.BatchNorm2d(self.outc))(x)
conv = nn.Sequential(
nn.Conv2d(in_channels = in_channels, out_channels = out_channels, kernel_size = 3, stride = 1, padding = 1),
nn.BatchNorm2d(out_channels),
nn.ReLU(inplace = True))(x)
self.shortcut1 = shortcut(self.inc,self.outc)
self.conv1 = conv(self.inc,self.outc)
self.shortcut = shortcut(self.outc, self.outc)
self.conv = conv(self.outc, self.outc)
result = torch.add(conv, shortcut)
return nn.Sequential(nn.ReLU(inplace = True), nn.BatchNorm2d(out_channels))(result)
self.seq = nn.Sequential(nn.ReLU(inplace = True), nn.BatchNorm2d(out_channels))
def forward(self, x):
x = self.unit(self.inc, self.outc, x)
x = self.seq(torch.add(self.conv1(x), self.shortcut1(x)))
for i in range(self.length - 1):
x = self.unit(self.outc, self.outc, x)
x = self.seq(torch.add(self.conv(x), self.shortcut(x)))
return x
mrnet/train.py
......@@ -7,9 +7,10 @@ from tqdm import tqdm
import torch
import torch.nn as nn
from torch import optim
from torchvision import transforms
from torch.utils.data import DataLoader, random_split
from utils.dataset import BasicDataset
from utils.dataset import BasicDataset,VOCSegmentation
from utils.eval import eval_net
......@@ -18,47 +19,61 @@ dir_mask = 'data/train_masks/'
dir_checkpoint = 'checkpoint/'
def train_net(net, device, epochs = 5, batch_size = 1, lr = 0.1, val_percent = 0.1, img_scale = 0.5):
dataset = BasicDataset(dir_img, dir_mask, img_scale)
n_val = int(len(dataset) * val_percent)
n_train = len(dataset) - n_val
train, val = random_split(dataset, [n_train, n_val])
train_loader = DataLoader(train, batch_size = batch_size, shuffle = True, num_workers = 8, pin_memory = True)
val_loader = DataLoader(val, batch_size = batch_size, shuffle = False, num_workers = 8, pin_memory = True)
def train_net(net, device, epochs = 5, batch_size = 1, lr = 0.1, val_percent = 0.1):
# dataset = BasicDataset(dir_img, dir_mask)
# n_val = int(len(dataset) * val_percent)
# n_train = len(dataset) - n_val
# train, val = random_split(dataset, [n_train, n_val])
# train_loader = DataLoader(train, batch_size = batch_size, shuffle = True, num_workers = 8, pin_memory = True)
# val_loader = DataLoader(val, batch_size = batch_size, shuffle = False, num_workers = 8, pin_memory = True)
trans = transforms.Compose([
transforms.Resize(256),
transforms.ToTensor()
])
trainset = VOCSegmentation('data', 'train', trans, trans)
evalset = VOCSegmentation('data', 'traineval', trans, trans)
n_train = len(trainset)
n_val = len(evalset)
train_loader = DataLoader(trainset, batch_size = batch_size, shuffle = True, num_workers = 8, pin_memory = True)
val_loader = DataLoader(evalset, batch_size = batch_size, shuffle = False, num_workers = 8, pin_memory = True)
optimizer = optim.Adam(net.parameters(), lr = lr)
criterion = nn.BCEWithLogitsLoss()
for epoch in tqdm(range(epochs)):
for epoch in range(epochs):
net.train()
epoch_loss = 0
with tqdm(total = n_train, desc = f'Epoch {epoch + 1}/{epochs}', unit = 'img') as pbar:
for batch in train_loader:
imgs = batch['image']
true_masks = batch['mask']
for imgs, true_masks in train_loader:
# imgs = batch['image']
# true_masks = batch['mask']
imgs = imgs.to(device = device, dtype = torch.float32)
mask_type = torch.float32 if net.n_classes == 1 else torch.long
true_masks = true_masks.to(device = device, dtype = mask_type)
optimizer.zero_grad()
masks_pred = net(imgs)
loss = criterion(masks_pred, true_masks)
epoch_loss += loss.item()
pbar.set_postfix(**{'loss (batch)': loss.item()})
optimizer.zero_grad()
loss.backward()
optimizer.step()
pbar.update(imgs.shape[0])
val_score = eval_net(net, val_loader, device, n_val)
logging.info('Validation cross entropy: {}'.format(val_score))
try:
os.mkdir(dir_checkpoint)
logging.info('Created checkpoint directory')
except OSError:
pass
torch.save(net.state_dict(), dir_checkpoint + f'CP_epoch{epoch + 1}.pth')
logging.info('Validation : {}'.format(val_score))
if epoch % 5 == 0:
try:
os.mkdir(dir_checkpoint)
logging.info('Created checkpoint directory')
except OSError:
pass
torch.save(net.state_dict(), dir_checkpoint + f'CP_epoch{epoch + 1}.pth')
logging.info(f'Checkpoint {epoch + 1} saved !')
torch.save(net.state_dict(), 'MODEL.pth')
train.py
......@@ -63,8 +63,7 @@ if __name__ == '__main__':
# cudnn.benchmark = True
try:
mrnet.train_net(net = net, device = device, epochs = args.epochs, batch_size = args.batchsize, lr = args.lr,
img_scale = args.scale, val_percent = args.val / 100)
mrnet.train_net(net = net, device = device, epochs = args.epochs, batch_size = args.batchsize, lr = args.lr, val_percent = args.val / 100)
except KeyboardInterrupt:
torch.save(net.state_dict(), 'INTERRUPTED.pth')
logging.info('Saved interrupt')
......
utils/__init__.py 0 → 100644
#!/usr/bin/env python
# -*- coding:utf-8 -*-
\ No newline at end of file
utils/dataset.py
#!/usr/bin/env python
# -*- coding:utf-8 -*-
from os.path import splitext
from os import listdir
import numpy as np
......@@ -7,13 +9,15 @@ from torch.utils.data import Dataset
import logging
from PIL import Image
import os
from torchvision.datasets.vision import VisionDataset
class BasicDataset(Dataset):
def __init__(self, imgs_dir, masks_dir, scale=1):
self.imgs_dir = imgs_dir
self.masks_dir = masks_dir
self.scale = scale
#assert 0 < scale <= 1, 'Scale must be between 0 and 1'
self.ids = [splitext(file)[0] for file in listdir(imgs_dir)
if not file.startswith('.')]
......@@ -24,8 +28,6 @@ class BasicDataset(Dataset):
@classmethod
def preprocess(cls, pil_img):
#newW, newH = 256,256 #int(scale * w), int(scale * h)
#assert newW > 0 and newH > 0, 'Scale is too small'
pil_img = pil_img.resize((256, 256))
img_nd = np.array(pil_img)
......@@ -59,3 +61,68 @@ class BasicDataset(Dataset):
mask = self.preprocess(mask)
return {'image': torch.from_numpy(img), 'mask': torch.from_numpy(mask)}
class VOCSegmentation(VisionDataset):
def __init__(self, root, image_set = 'train', transform = None, target_transform = None, transforms = None):
super(VOCSegmentation, self).__init__(root, transforms, transform, target_transform)
base_dir = 'voc'
voc_root = os.path.join(self.root, base_dir)
image_dir = os.path.join(voc_root, 'JPEGImages')
mask_dir = os.path.join(voc_root, 'SegmentationClassPNG')
if not os.path.isdir(voc_root):
raise RuntimeError('Dataset not found or corrupted.' + ' You can use download=True to download it')
split_f = os.path.join(voc_root, image_set.rstrip('\n') + '.txt')
with open(os.path.join(split_f), "r") as f:
file_names = [x.strip() for x in f.readlines()]
self.images = [os.path.join(image_dir, x + ".jpg") for x in file_names]
self.masks = [os.path.join(mask_dir, x + ".png") for x in file_names]
assert (len(self.images) == len(self.masks))
@classmethod
def preprocess(cls, pil_img):
pil_img = pil_img.resize((256, 256))
img_nd = np.array(pil_img)
if len(img_nd.shape) == 2:
img_nd = np.expand_dims(img_nd, axis = 2)
# HWC to CHW
img_trans = img_nd.transpose((2, 0, 1))
if img_trans.max() > 1:
img_trans = img_trans / 255
return img_trans
def __getitem__(self, index):
"""
Args:
index (int): Index
Returns:
tuple: (image, target) where target is the image segmentation.
"""
img = Image.open(self.images[index]).convert('L')
target = Image.open(self.masks[index]).convert('L')
pim = target.load()
for i in range(200):
for j in range(200):
pim[i, j] = 1 if pim[i,j] >0 else 0
if self.transforms is not None:
img, target = self.transforms(img, target)
# img = self.preprocess(img)
# target = self.preprocess(target)
return img, target
#return {'image':torch.from_numpy(np.asarray(img)), 'mask':torch.from_numpy(np.asarray(target))}
def __len__(self):
return len(self.images)
utils/predict.py
......@@ -4,9 +4,10 @@ from torchvision import transforms
from utils.dataset import BasicDataset
def predict_img(net, full_img, device, scale_factor = 1, out_threshold = 0.5):
def predict_img(net, full_img, device, out_threshold = 0.5):
net.eval()
img = torch.from_numpy(BasicDataset.preprocess(full_img, scale_factor))
img = torch.from_numpy(BasicDataset.preprocess(full_img))
img = img.unsqueeze(0)
img = img.to(device = device, dtype = torch.float32)
......
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