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labels.py

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+"""
+All target labels used in UMIE.
+
+Each label has a unique id, RadLex name, RadLex id, grade, and source names.
+Source names are the names of the labels used in the original datasets. They are meant to be helpful when translating labels from new source datasets to RadLex labels.
+Each of the target labels has a grade, which is an integer value that represents the intensity of the label ranging from 0 to 1.
+E.g. 0.25 - mild, 0.5 - moderate, 0.75 - severe, 1 - critical. If the grade is not specified, the default value is 1.
+Here in "grades", we store the information about how many grades the label has.
+"""
+
+from dataclasses import dataclass, field
+from typing import Optional
+
+
+@dataclass
+class Label:  # Name of the label should match RadLex name
+    """This class represents a target UMIE label."""
+
+    id: int  # Unique id of the label in UMIE
+    radlex_name: str  # name of the label in RadLex
+    radlex_id: str  # unique id of the label in RadLex
+    grades: Optional[int] = field(  # number of grades the label has (possible intensity levels of the label)
+        default_factory=int
+    )  # Grades of the label, some datasets come with intesity scale for the labels
+    source_names: Optional[dict] = field(
+        default_factory=dict
+    )  # Names used by other datasets, key - dataset name, value - source label name in this dataset
+
+
+# Use camel case for the labels names
+# We do not keep vague labels like "other" or "unknown"
+# One source label may correspond to multiple RadLex labels
+
+NormalityDecriptor = Label(
+    id=0,
+    radlex_name="NormalityDecriptor",
+    radlex_id="RID29001",
+    source_names={
+        "kits23": ["normal"],
+        "coronahack": ["Normal"],
+        "alzheimers": ["NonDemented"],
+        "covid19_detection": ["normal"],
+        "chestX-ray14": ["No Finding"],
+        "brain_tumor_classification": ["no_tumor"],
+        "brain_with_intracranial_hemorrhage": ["normal"],
+        "brain_tumor_detection": ["N"],
+        "lits": ["NormalityDescriptor"],
+    },
+)
+
+Neoplasm = Label(
+    id=1,
+    radlex_name="Neoplasm",
+    radlex_id="RID3957",
+    source_names={
+        "kits23": [
+            "angiomyolipoma",
+            "chromophobe",
+            "clear_cell_papillary_rcc",
+            "clear_cell_rcc",
+            "mest",
+            "multilocular_cystic_rcc",
+            "oncocytoma",
+            "papillary_rcc",
+            "rcc_unclassified",
+            "spindle_cell_neoplasm",
+            "urothelial",
+            "wilms",
+            "other",
+        ],
+        "pad_chest": ["adenocarcinoma"],
+        "brain_tumor_detection": ["Y"],
+        "lits": ["Neoplasm"],
+    },
+)
+
+RenalAdenocarcinoma = Label(
+    id=2,
+    radlex_name="RenalAdenocarcinoma",
+    radlex_id="RID4234",
+    source_names={
+        "kits23": [
+            "clear_cell_rcc",
+            "chromophobe_rcc",
+            "papillary_rcc",
+            "multilocular_cystic_rcc",
+            "rcc_unclassified",
+            "clear_cell_papillary",
+        ],
+    },
+)
+
+ClearCellAdenocarcinoma = Label(
+    id=3,
+    radlex_name="ClearCellAdenocarcinoma",
+    radlex_id="RID4235",
+    source_names={"kits23": ["clear_cell_rcc", "clear_cell_papillary"]},
+)
+
+ChromophobeAdenocarcinoma = Label(
+    id=4, radlex_name="ChromophobeAdenocarcinoma", radlex_id="RID4236", source_names={"kits23": ["chromophobe_rcc"]}
+)
+
+TransitionalCellCarcinoma = Label(
+    id=5,
+    radlex_name="TransitionalCellCarcinoma",
+    radlex_id="",
+    source_names={"kits23": ["transitional_cell_carcinoma"]},
+)
+
+PapillaryRenalAdenocarcinoma = Label(
+    id=6,
+    radlex_name="PapillaryRenalAdenocarcinoma",
+    radlex_id="RID4233",
+    source_names={"kits23": ["papillary_rcc", "clear_cell_papillary"]},
+)
+
+MultilocularCysticRenalTumor = Label(
+    id=7,
+    radlex_name="MultilocularCysticRenalTumor",
+    radlex_id="RID4538",
+    source_names={"kits23": ["multilocular_cystic_rcc"]},
+)
+
+WilmsTumor = Label(id=8, radlex_name="WilmsTumor", radlex_id="RID4553", source_names={"kits23": ["wilms"]})
+
+Angiomyolipoma = Label(
+    id=9, radlex_name="Angiomyolipoma", radlex_id="RID4343", source_names={"kits23": ["angiomyolipoma"]}
+)
+
+Oncocytoma = Label(id=10, radlex_name="Oncocytoma", radlex_id="RID4515", source_names={"kits23": ["oncocytoma"]})
+
+RenalCyst = Label(id=11, radlex_name="RenalCyst", radlex_id="RID35811", source_names={"kits23": ["cyst"]})
+
+ViralInfection = Label(
+    id=12,
+    radlex_name="ViralInfection",
+    radlex_id="RID4687",
+    grades=5,
+    source_names={
+        "coronahack": ["PneumoniaVirus"],
+        "MosMedData": ["CT-1", "CT-2", "CT-3", "CT-4"],
+        "covid19_detection": ["pneumonia_viral"],
+    },
+)
+
+Pneumonia = Label(
+    id=13,
+    radlex_name="Pneumonia",
+    radlex_id="RID5350",
+    source_names={
+        "coronahack": ["PneumoniaVirus", "PneumoniaBacteria"],
+        "ChestX-ray14": ["Pneumonia"],
+        "PadChest": ["Pneumonia", "atypical pneumonia"],
+        "covid19_detection": ["pneumonia_bacterial", "pneumonia_viral"],
+    },
+)
+
+PneumoniaViral = Label(
+    id=14,
+    radlex_name="PneumoniaViral",
+    radlex_id="RID34769",
+    source_names={"coronahack": ["PneumoniaVirus"], "covid19_detection": ["pneumonia_viral"]},
+)
+
+Atelectasis = Label(
+    id=15,
+    radlex_name="Atelectasis",
+    radlex_id="RID28493",
+    source_names={"Chest_X-ray_Abnormalities_Detection": ["Atelectasis"], "ChestX-ray14": ["Atelectasis"]},
+)
+
+Calcification = Label(
+    id=16,
+    radlex_name="Calcification",
+    radlex_id="RID5196",
+    source_names={"Chest_X-ray_Abnormalities_Detection": ["Calcification"]},
+)
+
+BoxlikeHeart = Label(
+    id=17,
+    radlex_name="BoxlikeHeart",
+    radlex_id="RID35057",
+    source_names={"Chest_X-ray_Abnormalities_Detection": ["Cardiomegaly"], "ChestX-ray14": ["Cardiomegaly"]},
+)
+
+Consolidation = Label(
+    id=18,
+    radlex_name="Consolidation",
+    radlex_id="RID43255",
+    source_names={
+        "Chest_X-ray_Abnormalities_Detection": ["Consolidation", "Infiltration"],
+        "ChestX-ray14": ["Consolidation", "Infiltration"],
+    },
+)
+
+InterstitialLungDisease = Label(
+    id=19,
+    radlex_name="InterstitialLungDisease",
+    radlex_id="RID28799",
+    source_names={"Chest_X-ray_Abnormalities_Detection": ["ILD"]},
+)
+
+Opacity = Label(
+    id=20,
+    radlex_name="Opacity",
+    radlex_id="RID28530",
+    source_names={"Chest_X-ray_Abnormalities_Detection": ["Opacity"]},
+)
+
+Lesion = Label(
+    id=21,
+    radlex_name="Lesion",
+    radlex_id="RID38780",
+    source_names={
+        "Chest_X-ray_Abnormalities_Detection": ["Nodule/Mass", "Other Lesion"],
+        "ChestX-ray14": ["Mass", "Nodule"],
+    },
+)
+
+PleuralEffusion = Label(
+    id=22,
+    radlex_name="PleuralEffusion",
+    radlex_id="RID34539",
+    source_names={"Chest_X-ray_Abnormalities_Detection": ["Effusion"], "ChestX-ray14": ["Effusion"]},
+)
+
+Thickening = Label(
+    id=23,
+    radlex_name="Thickening",
+    radlex_id="RID5352",
+    source_names={
+        "Chest_X-ray_Abnormalities_Detection": ["Pleural_Thickening"],
+        "ChestX-ray14": ["Pleural_Thickening"],
+    },
+)
+
+Pneumothorax = Label(
+    id=24,
+    radlex_name="Pneumothorax",
+    radlex_id="RID5352",
+    source_names={"Chest_X-ray_Abnormalities_Detection": ["Pneumothorax"], "ChestX-ray14": ["Pneumothorax"]},
+)
+
+Fibrosis = Label(
+    id=25,
+    radlex_name="Fibrosis",
+    radlex_id="RID3820",
+    source_names={
+        "Chest_X-ray_Abnormalities_Detection": ["Pulmonary Fibrosis"],
+        "ChestX-ray14": ["Fibrosis"],
+        "PadChest": ["Pulmonary Fibrosis"],
+    },
+)
+
+Mass = Label(id=26, radlex_name="Mass", radlex_id="RID3874", source_names={"ChestX-ray14": ["Mass"]})
+
+PulmonaryEdema = Label(
+    id=27,
+    radlex_name="PulmonaryEdema",
+    radlex_id="RID4866",
+    source_names={"ChestX-ray14": ["Edema"], "PadChest": ["Pulmonary Edema"]},
+)
+
+Emphysema = Label(
+    id=28,
+    radlex_name="Emphysema",
+    radlex_id="RID4799",
+    source_names={"ChestX-ray14": ["Emphysema"], "PadChest": ["Emphysema"]},
+)
+
+Hernia = Label(id=29, radlex_name="Hernia", radlex_id="RID4895", source_names={"ChestX-ray14": ["Hernia"]})
+
+ChronicObstructivePulmonaryDisease = Label(
+    id=30,
+    radlex_name="ChronicObstructivePulmonaryDisease",
+    radlex_id="RID5317",
+    source_names={"PadChest": ["COPD signs"]},
+)
+
+Tubeculosis = Label(
+    id=31,
+    radlex_name="Tuberculosis",
+    radlex_id="RID29116",
+    source_names={"PadChest": ["Tuberculosis", "Tuberculosis seqelae"]},
+)
+
+Metastasis = Label(
+    id=32,
+    radlex_name="Metastasis",
+    radlex_id="RID5231",
+    source_names={"PadChest": ["Lung metastasis", "Bone metastasis"]},
+)
+
+Pneumonitis = Label(
+    id=33, radlex_name="Pneumonitis", radlex_id="RID3541", source_names={"PadChest": ["post radiotherapy changes"]}
+)
+
+PulmonaryHypertension = Label(
+    id=34,
+    radlex_name="PulmonaryHypertension",
+    radlex_id="RID3299",
+    source_names={"PadChest": ["Pulmonary artery hypertension"]},
+)
+
+AdultRespiratoryDistressSyndrome = Label(
+    id=35,
+    radlex_name="AdultRespiratoryDistressSyndrome",
+    radlex_id="RID5319",
+    source_names={"PadChest": ["Respiratory distress syndrome"]},
+)
+
+Asbestosis = Label(
+    id=36, radlex_name="Asbestosis", radlex_id="RID5346", source_names={"PadChest": {"Asbestosis signs"}}
+)
+
+Carcinomatosis = Label(
+    id=37, radlex_name="Carcinomatosis", radlex_id="RID5231", source_names={"PadChest": ["lymphangitis carcinomatosa"]}
+)
+
+Adenocarcinoma = Label(
+    id=38,
+    radlex_name="Adenocarcinoma",
+    radlex_id="RID4226",
+    source_names={
+        "kits23": [
+            "clear_cell_rcc",
+            "chromophobe_rcc",
+            "papillary_rcc",
+            "multilocular_cystic_rcc",
+            "rcc_unclassified",
+            "clear_cell_papillary",
+        ],
+        "PadChest": ["adenocarcinoma"],
+    },
+)
+
+Glioma = Label(
+    id=39, radlex_name="Glioma", radlex_id="RID4026", source_names={"brain_tumor_classification": ["glioma_tumor"]}
+)
+
+Meningioma = Label(
+    id=40,
+    radlex_name="Meningioma",
+    radlex_id="RID4088",
+    source_names={"brain_tumor_classification": ["meningioma_tumor"]},
+)
+
+Pituitary = Label(
+    id=41,
+    radlex_name="Pituitary",
+    radlex_id="RID28679",
+    source_names={"brain_tumor_classification": ["pituitary_tumor"]},
+)
+
+Osteoarthritis = Label(
+    id=42,
+    radlex_name="Osteoarthritis",
+    radlex_id="RID3555",
+    grades=4,
+    source_names={
+        "knee_osteoarthritis": [
+            "DoubtfulOsteoarthritis",
+            "MinimalOsteoarthritis",
+            "ModerateOsteoarthritis",
+            "SevereOsteoarthritis",
+        ]
+    },
+)
+
+Hemorrhage = Label(
+    id=43,
+    radlex_name="Hemorrhage",
+    radlex_id="RID4700",
+    source_names={"Brain_with_hemorrhage": ["brain_hemorrhage"]},
+)
+
+Dementia = Label(
+    id=44,
+    radlex_name="Dementia",
+    radlex_id="RID5136",
+    grades=3,
+    source_names={"alzheimers": ["VeryMildDemented", "MildDemented", "ModerateDemented"]},
+)
+
+HeartFailure = Label(
+    id=45,
+    radlex_name="HeartFailure",
+    radlex_id="RID34795",
+    source_names={"PadChest": ["heart insufficiency"]},
+)
+
+all_labels = [obj for name, obj in globals().items() if isinstance(obj, Label)]

masks.py

@@ -0,0 +1,106 @@
+"""
+This file contains the masks used in the datasets. The masks are defined as mask dataclasses.
+
+Each mask has the following attributes:
+- id: int - the id of the mask
+- radlex_name: str - the name of the mask in RadLex
+- color: int - the color of the mask
+- radlex_id: str - the id of the mask in RadLex
+- source_names: dict - the names of the mask in other datasets, meant to be helpful when translating new source dataset masks to UMIE.
+"""
+from dataclasses import dataclass, field
+from typing import Optional
+
+
+@dataclass
+class Mask:
+    """This class represents a mask."""
+
+    id: int  # The unique id of the mask in UMIE (also the value of the mask in the mask image)
+    radlex_name: str  # The name of the mask in RadLex
+    color: int  # The color of the mask in the mask image
+    radlex_id: str  # The id of the mask in RadLex
+    source_names: Optional[dict] = field(
+        default_factory=dict
+    )  # How the mask is named in other datasets, key - dataset name, value - source mask name in this dataset
+
+
+Background = Mask(
+    id=0, radlex_name="Background", color=0, radlex_id=""
+)  # Actually there is no radlex for backgroud ofc but "Normality descriptor" didnt fit either
+
+Kidney = Mask(
+    id=1, radlex_name="Kidney", color=1, radlex_id="RID205", source_names={"kits23": ["kidney"], "ct_org": ["Kidney"]}
+)
+
+Neoplasm = Mask(
+    id=2,
+    radlex_name="Neoplasm",
+    color=2,
+    radlex_id="RID3957",
+    source_names={"kits23": ["kidney tumor"], "brain_tumor_progression": ["Brain tumor"], "lits": ["liver_tumor"]},
+)
+RenalCyst = Mask(id=3, radlex_name="RenalCyst", color=3, radlex_id="RID35811", source_names={"kits23": ["cyst"]})
+ViralInfection = Mask(
+    id=4, radlex_name="ViralInfection", color=4, radlex_id="RID4687", source_names={"mos_med_data": ["CT-1"]}
+)
+
+Lung = Mask(
+    id=5,
+    radlex_name="Lung",
+    color=5,
+    radlex_id="RID1301",
+    source_names={
+        "ct_org": ["lungs"],
+        "chest_xray_masks_and_label": ["Lungs"],
+        "finding_and_measuring_lungs": ["lungs"],
+    },
+)
+
+BoneOrgan = Mask(id=6, radlex_name="BoneOrgan", color=6, radlex_id="RID13197", source_names={"ct_org": ["Bones"]})
+
+Liver = Mask(id=7, radlex_name="Liver", color=7, radlex_id="RID58", source_names={"ct_org": ["liver"]})
+
+UrinaryBladder = Mask(
+    id=8, radlex_name="UrinaryBladder", color=8, radlex_id="RID237", source_names={"ct_org": ["bladder"]}
+)
+
+Brain = Mask(id=9, radlex_name="Brain", color=9, radlex_id="RID6434", source_names={"ct_org": ["Brain"]})
+
+Nodule = Mask(
+    id=10,
+    radlex_name="Nodule",
+    color=10,
+    radlex_id="RID3875",
+    source_names={"lidc_idri": ["Nodule>=3mm", "Nodule<3mm"]},
+)
+
+Lesion = Mask(
+    id=11, radlex_name="Lesion", color=11, radlex_id="RID38780", source_names={"lidc_idri": ["Non-nodule>=3mm"]}
+)  # That is not a nodule
+
+CalciumScore = Mask(
+    id=12,
+    radlex_name="CalciumScore",
+    color=12,
+    radlex_id="RID28808",
+    source_names={"coca": ["coronary_artery_calcium"]},
+)
+
+Metastasis = Mask(
+    id=13,
+    radlex_name="Metastasis",
+    color=13,
+    radlex_id="RID5231",
+    source_names={"brain_met_share": ["brain_metastasis"]},
+)
+
+Hemorrhage = Mask(
+    id=14,
+    radlex_name="Hemorrhage",
+    color=14,
+    radlex_id="RID4700",
+    source_names={"brain_with_intracranial_hemorrhage": ["brain_hemorrhage"]},
+)
+
+all_masks = [obj for name, obj in globals().items() if isinstance(obj, Mask)]

pos_weights.json

@@ -0,0 +1 @@
+{"label_counts": {"NormalityDecriptor": 1.1057690645367633, "Neoplasm": 0.09583273355405211, "RenalAdenocarcinoma": 0.054858642325462566, "ClearCellAdenocarcinoma": 0.04114881613813146, "ChromophobeAdenocarcinoma": 0.00594213132151514, "TransitionalCellCarcinoma": 0, "PapillaryRenalAdenocarcinoma": 0.007627272877682368, "MultilocularCysticRenalTumor": 9.03171775060964e-05, "WilmsTumor": 0, "Angiomyolipoma": 0.0003120739779577222, "Oncocytoma": 0.004200520221444501, "RenalCyst": 0, "ViralInfection": 0.01151410716880852, "Pneumonia": 0.03661655383122769, "PneumoniaViral": 0.01151410716880852, "Atelectasis": 0.04981275506466307, "Calcification": 0, "BoxlikeHeart": 0.011526707414297104, "Consolidation": 0.11212662122740781, "InterstitialLungDisease": 0, "Opacity": 0, "Lesion": 0.052325104213913905, "PleuralEffusion": 0.05782683648080038, "Thickening": 0.014091073710677162, "Pneumothorax": 0.022248705445939255, "Fibrosis": 0.0069691884161010575, "Mass": 0.024311891887346213, "PulmonaryEdema": 0.009543938169536479, "Emphysema": 0.010435850214855739, "Hernia": 0.0009326940065165316, "ChronicObstructivePulmonaryDisease": 0, "Tuberculosis": 0, "Metastasis": 0, "Pneumonitis": 0, "PulmonaryHypertension": 0, "AdultRespiratoryDistressSyndrome": 0, "Asbestosis": 0, "Carcinomatosis": 0, "Adenocarcinoma": 0.054858642325462566, "Glioma": 0.0038156929644555426, "Meningioma": 0.003861194786356837, "Pituitary": 0.003712295071835588, "Osteoarthritis": 0.024945409565001537, "Hemorrhage": 0.002617585565414945, "Dementia": 0.013310705134604505, "HeartFailure": 0}, "mask_counts": {"Background": 0, "Kidney": 0.1532667717638816, "Neoplasm": 0.08602303933806484, "RenalCyst": 0.019574688926928693, "ViralInfection": 0, "Lung": 0.001097225703847687, "BoneOrgan": 0, "Liver": 0.08524893973413165, "UrinaryBladder": 0, "Brain": 0, "Nodule": 0, "Lesion": 0, "CalciumScore": 0.015244842675557408, "Metastasis": 0, "Hemorrhage": 0.002617585565414945}, "label_counts_list": [1.1057690645367633, 0.09583273355405211, 0.054858642325462566, 0.04114881613813146, 0.00594213132151514, 0, 0.007627272877682368, 9.03171775060964e-05, 0, 0.0003120739779577222, 0.004200520221444501, 0, 0.01151410716880852, 0.03661655383122769, 0.01151410716880852, 0.04981275506466307, 0, 0.011526707414297104, 0.11212662122740781, 0, 0, 0.052325104213913905, 0.05782683648080038, 0.014091073710677162, 0.022248705445939255, 0.0069691884161010575, 0.024311891887346213, 0.009543938169536479, 0.010435850214855739, 0.0009326940065165316, 0, 0, 0, 0, 0, 0, 0, 0, 0.054858642325462566, 0.0038156929644555426, 0.003861194786356837, 0.003712295071835588, 0.024945409565001537, 0.002617585565414945, 0.013310705134604505, 0], "mask_counts_list": [0, 0.1532667717638816, 0.08602303933806484, 0.019574688926928693, 0, 0.001097225703847687, 0, 0.08524893973413165, 0, 0, 0, 0, 0.015244842675557408, 0, 0.002617585565414945]}