scipy.ndimage.morphology.binary_fill_holes
scipy.ndimage.distance_transform_edt

PIL.Image.open

skimage.filters.threshold_otsu
skimage.measure.points_in_poly

m.bias.data.zero_
x.get
computeITCList
pid.self._annotations.inside_polygons
torch.bmm
self.layer4
set
torch.load
scipy.ndimage.distance_transform_edt
skimage.measure.points_in_poly
m.weight.data.normal_
time.strftime
FP_probs.append
args.patch_size.args.patch_size.args.level.y.x.slide.read_region.convert.save
self.layer3
Probs.append
numpy.float32.img.np.array.transpose.transpose
self._resolution.np.log2.is_integer
torch.norm
numpy.random.seed
i.positive_vertices.astype
self.bn2
numpy.transpose
numpy.where
open
compute_FP_TP_Probs
os.mkdir
numpy.zeros
numpy.float32.img.np.array.transpose
self.conv1
computeEvaluationMask
torch.nn.Sequential
logging.basicConfig
numpy.amax
line.strip.split
Thresh.unlisted_FPs.np.asarray.sum
matplotlib.pyplot.plot
args.level.slide.level_dimensions.args.level.slide.read_region.convert
matplotlib.pyplot.show
numpy.rot90
skimage.measure.label
Xcorr.append
numpy.round
copy.deepcopy
range
self.bn3
matplotlib.pyplot.xlabel
os.path.join
torch.nn.Linear
numpy.random.randint
numpy.asarray.append
wsi.data.annotation.Formatter.camelyon16xml2json
int.strip
numpy.interp
torch.nn.Parameter
json_dict.append
logits.sigmoid
skimage.filters.gaussian.max
opts_list.append
ckpt.cpu.numpy
self._preprocess
xml.etree.ElementTree.parse
self.fc
self.Bottleneck.super.__init__
numpy.random.rand
str
numpy.asarray
numpy.logical_not
self.maxpool
skimage.measure.regionprops
matplotlib.pyplot.figure
int.Y.X.np.round.astype.transpose
torch.nn.ReLU
self.avgpool
sys.path.append
math.sqrt
each.endswith
wsi.data.annotation.Annotation.from_json
self.ResNet.super.__init__
argparse.ArgumentParser
print
openslide.open_slide.read_region
open.write
inxml.ET.parse.getroot.findall
matplotlib.pyplot.imshow
multiprocessing.Pool.map
self._image_size.self._image_size.y.x.self._slide.read_region.convert
run
os.path.dirname
feats.view.view
Polygon.inside
skimage.color.rgb2hsv
float
sorted
self.downsample
format
torch.nn.MaxPool2d
list
int.Y.X.np.round.astype.transpose.tolist
torch.zeros
numpy.max
argparse.ArgumentParser.parse_args
self.BasicBlock.super.__init__
skimage.filters.gaussian
ckpt.cpu.numpy.reshape
torch.nn.Conv2d
i.negative_vertices.astype
openslide.OpenSlide.read_region
shutil.copyfile
csvDIR.open.readlines
multiprocessing.Pool
int.i.negative_vertices.astype.tolist
self._polygons_negative.append
os.path.abspath
numpy.fliplr
plotFROC
logging.info
inxml.ET.parse.getroot
Y.X.np.round.astype
matplotlib.pyplot.subplot
self._color_jitter
numpy.log2
self.layer1
self.crf
self.layer2
torch.nn.BatchNorm2d
Isolated_Tumor_Cells.append
torch.transpose
numpy.mean
sum
computeFROC
line.rstrip
self.CRF.super.__init__
args.patch_size.args.patch_size.args.level.y.x.slide.read_region.convert
sys.stdout.flush
len
self._make_layer
map
torchvision.transforms.ColorJitter
wsi.model.layers.CRF
numpy.load
argparse.ArgumentParser.add_argument
matplotlib.pyplot.figure.suptitle
Ycorr.append
line.strip
conv3x3
block
layers.append
self._slide.read_region
pow
Thresh.unlisted_TPs.np.asarray.sum
super
torch.sum
matplotlib.pyplot.ylabel
logits.clone
int
self.avgpool.size
readCSVContent
enumerate
os.path.exists
x.vertices
multiprocessing.Value
self._coords.append
self.bn1
PIL.Image.open
skimage.filters.threshold_otsu
line.rstrip.split
m.weight.data.fill_
numpy.save
self.avgpool.view
self.relu
total_TPs.append
json.load
self._polygons_positive.append
numpy.float32.img.np.array.transpose.rotate
ResNet
os.listdir
main
json.dump
numpy.array
annotation.findall
self.conv2
self.modules
torch.squeeze
scipy.ndimage.morphology.binary_fill_holes
self.conv3
torch.nn.AvgPool2d
openslide.OpenSlide
multiprocessing.Lock
torch.squeeze.view
torch.load.cpu
open.close
wsi.data.annotation.Annotation
Exception
Polygon
int.i.positive_vertices.astype.tolist
openslide.open_slide
isinstance