mednet.data.classify.padchest¶
Padchest database for computer-aided diagnosis.
A large chest x-ray image dataset with multi-label annotated reports. This dataset includes more than 160,000 images from 67,000 patients that were interpreted and reported by radiologists at Hospital San Juan (Spain) from 2009 to 2017, covering six different position views and additional information on image acquisition and patient demography.
We keep only postero-anterior “PA” images in our setup.
Reference: [BPSdlIV20]
Raw data input (on disk):
PNG grayscale 16-bit depth images
Resolution: varying resolution
Labels: [BPSdlIV20]
Output image:
Transforms:
Load raw 16-bit PNG with
PIL
Remove excess black borders
Convert image to 32-bit floats between 0. and 1.
Convert to tensor
Final specifications
Grayscale, encoded as a 1-plane 32-bit float image, square with varying resolutions depending on the raw input image
Labels, in order (some of which may not be present in all splits):
COPD signs
Chilaiditi sign
NSG tube
abnormal foreign body
abscess
adenopathy
air bronchogram
air fluid level
air trapping
alveolar pattern
aortic aneurysm
aortic atheromatosis
aortic button enlargement
aortic elongation
aortic endoprosthesis
apical pleural thickening
artificial aortic heart valve
artificial heart valve
artificial mitral heart valve
asbestosis signs
ascendent aortic elongation
atelectasis
atelectasis basal
atypical pneumonia
axial hyperostosis
azygoesophageal recess shift
azygos lobe
blastic bone lesion
bone cement
bone metastasis
breast mass
bronchiectasis
bronchovascular markings
bullas
calcified adenopathy
calcified densities
calcified fibroadenoma
calcified granuloma
calcified mediastinal adenopathy
calcified pleural plaques
calcified pleural thickening
callus rib fracture
cardiomegaly
catheter
cavitation
central vascular redistribution
central venous catheter
central venous catheter via jugular vein
central venous catheter via subclavian vein
central venous catheter via umbilical vein
cervical rib
chest drain tube
chronic changes
clavicle fracture
consolidation
costochondral junction hypertrophy
costophrenic angle blunting
cyst
dai
descendent aortic elongation
dextrocardia
diaphragmatic eventration
double J stent
dual chamber device
electrical device
emphysema
empyema
end on vessel
endoprosthesis
endotracheal tube
esophagic dilatation
exclude
external foreign body
fibrotic band
fissure thickening
flattened diaphragm
fracture
gastrostomy tube
goiter
granuloma
ground glass pattern
gynecomastia
heart insufficiency
heart valve calcified
hemidiaphragm elevation
hiatal hernia
hilar congestion
hilar enlargement
humeral fracture
humeral prosthesis
hydropneumothorax
hyperinflated lung
hypoexpansion
hypoexpansion basal
increased density
infiltrates
interstitial pattern
kerley lines
kyphosis
laminar atelectasis
lepidic adenocarcinoma
lipomatosis
lobar atelectasis
loculated fissural effusion
loculated pleural effusion
lung metastasis
lung vascular paucity
lymphangitis carcinomatosa
lytic bone lesion
major fissure thickening
mammary prosthesis
mass
mastectomy
mediastinal enlargement
mediastinal mass
mediastinal shift
mediastinic lipomatosis
metal
miliary opacities
minor fissure thickening
multiple nodules
nephrostomy tube
nipple shadow
nodule
non axial articular degenerative changes
normal
obesity
osteopenia
osteoporosis
osteosynthesis material
pacemaker
pectum carinatum
pectum excavatum
pericardial effusion
pleural effusion
pleural mass
pleural plaques
pleural thickening
pneumomediastinum
pneumonia
pneumoperitoneo
pneumothorax
post radiotherapy changes
prosthesis
pseudonodule
pulmonary artery enlargement
pulmonary artery hypertension
pulmonary edema
pulmonary fibrosis
pulmonary hypertension
pulmonary mass
pulmonary venous hypertension
reservoir central venous catheter
respiratory distress
reticular interstitial pattern
reticulonodular interstitial pattern
rib fracture
right sided aortic arch
round atelectasis
sclerotic bone lesion
scoliosis
segmental atelectasis
single chamber device
soft tissue mass
sternoclavicular junction hypertrophy
sternotomy
subacromial space narrowing
subcutaneous emphysema
suboptimal study
superior mediastinal enlargement
supra aortic elongation
surgery
surgery breast
surgery heart
surgery humeral
surgery lung
surgery neck
suture material
thoracic cage deformation
total atelectasis
tracheal shift
tracheostomy tube
tuberculosis
tuberculosis sequelae
unchanged
vascular hilar enlargement
vascular redistribution
ventriculoperitoneal drain tube
vertebral anterior compression
vertebral compression
vertebral degenerative changes
vertebral fracture
volume loss
This module contains the base declaration of common data modules and raw-data loaders for this database. All configured splits inherit from this definition.
Module Attributes
Pythonic name of this database. |
|
Key to search for in the configuration file for the root directory of this database. |
Classes
|
Padchest database for computer-aided diagnosis. |
A specialized raw-data-loader for the PadChest database. |
- mednet.data.classify.padchest.DATABASE_SLUG = 'padchest'¶
Pythonic name of this database.
- mednet.data.classify.padchest.CONFIGURATION_KEY_DATADIR = 'datadir.padchest'¶
Key to search for in the configuration file for the root directory of this database.
- class mednet.data.classify.padchest.RawDataLoader[source]¶
Bases:
RawDataLoader
A specialized raw-data-loader for the PadChest database.
- target(sample)[source]¶
Load only sample target from its raw representation.
- Parameters:
sample (
Any
) – A tuple containing the path suffix, within the dataset root folder, where to find the image to be loaded, and an integer, representing the sample target.- Return type:
- Returns:
The labels corresponding to all radiological signs present in the specified sample, encapsulated as a 1D torch float tensor.
- class mednet.data.classify.padchest.DataModule(split_path)[source]¶
Bases:
CachingDataModule
Padchest database for computer-aided diagnosis.
- Parameters:
split_path (
Path
|Traversable
) – Path or traversable (resource) with the JSON split description to load.