first commit

.gitignore

@@ -0,0 +1,145 @@
+# Custom
+*.svs
+*.xml
+*.csv
+*.xcf
+*.zip
+*.json
+*.state
+*.tiff
+*.tif
+.idea
+*.jpeg
+*.jpg
+**/data/
+**/patches/
+classification_stuff/Transfer-Learning-Library
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
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+.eggs/
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+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

DigiCertHighAssuranceEVCA-1.pem

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+-----END CERTIFICATE-----

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Amir Hossein
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,3 @@
+# Thyroid-Project-Using-DL
+
+Developing a neural network to classify thyroid carcinoma using H&E slides

classifications_efforts/test_methods/test_fda/fda.py

@@ -0,0 +1,19 @@
+# from dalib.translation.fourier_transform import FourierTransform
+import importlib.util
+import sys
+
+from PIL import Image
+
+fourier_transform_address = "E:\\Documentwork\\sharif\\CE Project\\future\\Thyroid Project\\Thyroid-Project-Using-DL\\classification_stuff\\Transfer-Learning-Library\\dalib\\translation\\fourier_transform.py"
+spec = importlib.util.spec_from_file_location("module.name", fourier_transform_address)
+foo = importlib.util.module_from_spec(spec)
+sys.modules["module.name"] = foo
+spec.loader.exec_module(foo)
+FourierTransform = foo.FourierTransform
+image_list = ["bio_tile (1).jpeg", "bio_tile (2).jpeg", "bio_tile (3).jpeg", "bio_tile (4).jpeg", "bio_tile (4).jpeg"]
+amplitude_dir = "amplitude_dir"
+fourier_transform = FourierTransform(image_list, amplitude_dir, beta=0, rebuild=False)
+source_image = Image.open("tile2.jpeg")  # image form source domain
+source_image_in_target_style = fourier_transform(source_image)
+
+source_image_in_target_style.save("out_fda.jpeg")

classifications_efforts/test_methods/test_model_for_bengin_malignant/albumentations_mixup.py

@@ -0,0 +1,62 @@
+import random
+
+import cv2
+import torch
+import torch.nn as nn
+from albumentations.augmentations.utils import read_rgb_image
+from albumentations.core.transforms_interface import BasicTransform, to_tuple
+
+
+class Mixup(BasicTransform):
+    def __init__(self, mixups, read_fn=read_rgb_image, beta_limit=0.3, **kwargs):
+        super().__init__(**kwargs)
+        self.mixups = mixups
+        self.read_fn = read_fn
+        self.beta_limit = to_tuple(beta_limit, low=0)
+
+    def apply(self, image, mixup_image=None, beta=0.1, **params):
+        img_type = image.dtype
+        image = ((1 - beta) * image + beta * mixup_image).astype(img_type)
+        return image
+
+    def apply_to_target(self, target, beta=0.1, mixup_target=-1, **params):
+        target = {"img": target, "mixup": mixup_target, "beta": beta}
+        return target
+
+    def get_params_dependent_on_targets(self, params):
+        img = params["image"]
+        mixup = random.choice(self.mixups)
+        mixup_image = self.read_fn(mixup[0])
+        vertical_pad = max(0, (img.shape[0] - mixup_image.shape[0]) // 2)
+        horizontal_pad = max(0, (img.shape[1] - mixup_image.shape[1]) // 2)
+        try:
+            mixup_image = cv2.copyMakeBorder(mixup_image, vertical_pad, vertical_pad, horizontal_pad, horizontal_pad,
+                                             cv2.BORDER_REFLECT)
+        except Exception as e:
+            print(e)
+        mixup_image = cv2.resize(mixup_image, dsize=(img.shape[1], img.shape[0]))
+        return {"mixup_image": mixup_image, "mixup_target": mixup[1]}
+
+    def get_params(self):
+        return {"beta": random.uniform(self.beta_limit[0], self.beta_limit[1])}
+
+    @property
+    def targets(self):
+        return {
+            "image": self.apply,
+            "target": self.apply_to_target,
+        }
+
+    @property
+    def targets_as_params(self):
+        return ["image"]
+
+
+def mixup_loss(output, target):
+    if type(target) == torch.Tensor:
+        loss = nn.CrossEntropyLoss()
+        return loss(output, target)
+    else:  # mixup has been used
+        loss = nn.CrossEntropyLoss(reduction="none")
+        return ((1 - target["beta"]) * loss(output, target["img"]) + target["beta"] * loss(output,
+                                                                                           target["mixup"])).mean()

classifications_efforts/test_methods/test_model_for_bengin_malignant/fragment_splitter.py

@@ -0,0 +1,162 @@
+import csv
+import glob
+import os
+import random
+
+from tqdm import tqdm
+
+from config import Config
+
+
+class CustomFragmentLoader:
+    def __init__(self, datasets_folder_name):
+        self._datasets_folder_name = datasets_folder_name
+        self._database_slide_dict = {}
+        self._load_csv_files_to_dict()
+
+    def _load_csv_files_to_dict(self):
+        databases_directory = "../../../database_crawlers/"
+        list_dir = [os.path.join(databases_directory, o, "patches") for o in self._datasets_folder_name
+                    if os.path.isdir(os.path.join(databases_directory, o, "patches"))]
+        for db_dir in list_dir:
+            csv_dir = os.path.join(db_dir, "patch_labels.csv")
+            with open(csv_dir, "r") as csv_file:
+                csv_reader = csv.reader(csv_file)
+                header = next(csv_reader, None)
+                for row in csv_reader:
+                    if row:
+                        database_id = row[0]
+                        image_id = row[1]
+                        slide_frag_folder_name = [o for o in os.listdir(db_dir) if image_id.startswith(o)]
+                        if slide_frag_folder_name:
+                            slide_frag_folder_name = slide_frag_folder_name[0]
+                        else:
+                            continue
+                        slide_path = os.path.join(db_dir, slide_frag_folder_name)
+                        image_paths = glob.glob(os.path.join(slide_path, "*.jpeg"))
+                        if image_paths:
+                            d = self._database_slide_dict.get(database_id, {})
+                            d[image_id] = [image_paths] + [row[3], row[2]]
+                            self._database_slide_dict[database_id] = d
+
+    def load_image_path_and_labels_and_split(self, test_percent=20, val_percent=10):
+        train_images, val_images, test_images = [], [], []
+        for database_name, slides_dict in self._database_slide_dict.items():
+            image_paths_by_slide = [(len(v[0]), v[0], v[1], v[2]) for v in slides_dict.values()]
+            random.shuffle(image_paths_by_slide)
+            # image_paths_by_slide.sort()
+            class_slides_dict = {}
+            for item in image_paths_by_slide:
+                class_name = None
+                if database_name == "NationalCancerInstitute":
+                    normal_percent = int(item[2].strip(r"(|)|\'").split("\', \'")[0])
+                    tumor_percent = int(item[2].strip(r"(|)|\'").split("\', \'")[1])
+                    stormal_percent = int(item[2].strip(r"(|)|\'").split("\', \'")[2])
+                    if stormal_percent == 0:
+                        if tumor_percent == 100:
+                            class_name = "MALIGNANT"
+                        elif normal_percent == 100:
+                            class_name = "BENIGN"
+                        else:
+                            class_name = str(tumor_percent)
+                elif database_name == "BioAtlasThyroidSlideProvider":
+                    if "papillary" in item[3].lower():
+                        class_name = "MALIGNANT"
+                    elif "normal" in item[3].lower():
+                        class_name = "BENIGN"
+                class_name = class_name if class_name else item[2]
+                if class_name in Config.class_names:
+                    class_slides_dict[class_name] = class_slides_dict.get(class_name, []) + [
+                        (item[0], item[1], class_name)]
+
+            # split test val train because they must not share same slide id fragment
+
+            for thyroid_class, slide_frags in class_slides_dict.items():
+                dataset_train_images, dataset_val_images, dataset_test_images = [], [], []
+                total_counts = sum([item[0] for item in slide_frags])
+                test_counts = total_counts * test_percent // 100
+                val_counts = total_counts * val_percent // 100
+                train_counts = total_counts - test_counts - val_counts
+                for i, slide_frags_item in enumerate(slide_frags):
+                    if len(dataset_train_images) + slide_frags_item[0] <= train_counts:
+                        dataset_train_images += slide_frags_item[1]
+                    elif len(dataset_val_images) + slide_frags_item[0] <= val_counts:
+                        dataset_val_images += slide_frags_item[1]
+                    else:
+                        dataset_test_images += slide_frags_item[1]
+                train_images += [(i, thyroid_class) for i in dataset_train_images]
+                val_images += [(i, thyroid_class) for i in dataset_val_images]
+                test_images += [(i, thyroid_class) for i in dataset_test_images]
+
+        return train_images, val_images, test_images
+
+    def national_cancer_image_and_labels_splitter_per_slide(self, test_percent=20, val_percent=10):
+        train_images, val_images, test_images = [], [], []
+        for database_name, slides_dict in self._database_slide_dict.items():
+            print(database_name)
+            image_paths_by_slide = [(len(v[0]), v[0], v[1], v[2], k) for k, v in slides_dict.items()]
+            random.shuffle(image_paths_by_slide)
+            # image_paths_by_slide.sort()
+            class_slides_dict = {}
+            for item in tqdm(image_paths_by_slide):
+                class_name = None
+                normal_percent = int(item[2].strip(r"(|)|\'").split("\', \'")[0])
+                tumor_percent = int(item[2].strip(r"(|)|\'").split("\', \'")[1])
+                stormal_percent = int(item[2].strip(r"(|)|\'").split("\', \'")[2])
+                if stormal_percent == 0:
+                    if tumor_percent == 100:
+                        class_name = 100
+                    elif normal_percent == 100:
+                        class_name = 0
+                    else:
+                        class_name = tumor_percent
+                class_name = class_name if class_name is not None else item[2]
+                if class_name in Config.class_names:
+                    class_slides_dict[class_name] = class_slides_dict.get(class_name, []) + [
+                        (item[0], item[1], class_name, item[4])]
+
+            # split test val train because they must not share same slide id fragment
+
+            for thyroid_class, slide_frags in class_slides_dict.items():
+                dataset_train_images, dataset_val_images, dataset_test_images = [], [], []
+                total_counts = sum([item[0] for item in slide_frags])
+                test_counts = total_counts * test_percent // 100
+                val_counts = total_counts * val_percent // 100
+                train_counts = total_counts - test_counts - val_counts
+                for i, slide_frags_item in enumerate(slide_frags):
+                    items_paths = [(item_path, slide_frags_item[3]) for item_path in slide_frags_item[1]]
+                    if len(dataset_train_images) + slide_frags_item[0] <= train_counts:
+                        dataset_train_images += items_paths
+                    elif len(dataset_val_images) + slide_frags_item[0] <= val_counts:
+                        dataset_val_images += items_paths
+                    else:
+                        dataset_test_images += items_paths
+                train_images += [(i, (thyroid_class, j)) for i, j in dataset_train_images]
+                val_images += [(i, (thyroid_class, j)) for i, j in dataset_val_images]
+                test_images += [(i, (thyroid_class, j)) for i, j in dataset_test_images]
+
+        return train_images, val_images, test_images
+
+
+if __name__ == '__main__':
+    # datasets_folder = ["national_cancer_institute"]
+    datasets_folder = ["papsociaty"]
+    # datasets_folder = ["stanford_tissue_microarray"]
+    # datasets_folder = ["bio_atlas_at_jake_gittlen_laboratories"]
+    train, val, test = CustomFragmentLoader(datasets_folder).load_image_path_and_labels_and_split(
+        val_percent=Config.val_percent,
+        test_percent=Config.test_percent)
+    benign_train = [i for i in train if i[1] == "BENIGN"]
+    mal_train = [i for i in train if i[1] == "MALIGNANT"]
+    print(f"train: {len(train)}={len(benign_train)}+{len(mal_train)}")
+    benign_val = [i for i in val if i[1] == "BENIGN"]
+    mal_val = [i for i in val if i[1] == "MALIGNANT"]
+    print(f"val: {len(val)}={len(benign_val)}+{len(mal_val)}")
+    benign_test = [i for i in test if i[1] == "BENIGN"]
+    mal_test = [i for i in test if i[1] == "MALIGNANT"]
+    print(f"test: {len(test)}={len(benign_test)}+{len(mal_test)}")
+
+    print(set(train) & set(test))
+    print(set(train) & set(val))
+    print(set(test) & set(val))
+    print(len(set(val) & set(val)))

classifications_efforts/test_methods/test_model_for_bengin_malignant/model_train_logger.py

@@ -0,0 +1,20 @@
+import os
+
+
+def set_config_for_logger(config_label):
+    import logging
+    trains_state_dir = "./train_state"
+    if not os.path.isdir(trains_state_dir):
+        os.mkdir(trains_state_dir)
+    config_train_dir = os.path.join(trains_state_dir, config_label)
+    if not os.path.isdir(config_train_dir):
+        os.mkdir(config_train_dir)
+    log_file = os.path.join(config_train_dir, "console.log")
+    logger = logging.getLogger(config_label)
+    logger.setLevel(logging.DEBUG)
+    fh = logging.FileHandler(log_file)
+    formatter = logging.Formatter('%(asctime)s|%(levelname)s|%(message)s', datefmt='%Y-%m-%d %H:%M:%S')
+    fh.setFormatter(formatter)
+    fh.setLevel(logging.DEBUG)
+    logger.addHandler(fh)
+    return logger

classifications_efforts/test_methods/test_model_for_bengin_malignant/model_training.py

@@ -0,0 +1,399 @@
+import os
+import random
+import time
+from typing import cast
+import numpy as np
+import matplotlib.pyplot as plt
+import timm
+import torch
+import torchvision
+from sklearn.metrics import confusion_matrix, roc_curve, roc_auc_score
+from torch import nn, optim
+from torch.utils.data import DataLoader
+from tqdm import tqdm
+
+from config import Config
+from fragment_splitter import CustomFragmentLoader
+from model_train_logger import set_config_for_logger
+from thyroid_dataset import ThyroidDataset
+from thyroid_ml_model import ThyroidClassificationModel
+from transformation import get_transformation
+
+
+@torch.no_grad()
+def validate(model, data_loader, loss_function=None, show_tqdm=False):
+    class_set = sorted(data_loader.dataset.class_to_idx_dict.values())
+
+    loss_values = []
+    y_preds = []
+    y_targets = []
+    y_positive_scores = []
+
+    for images, labels in (data_loader if not show_tqdm else tqdm(data_loader)):
+        images = images.to(Config.available_device)
+        labels = labels.to(Config.available_device)
+        x = model(images, validate=True)
+        if loss_function:
+            loss_values.append(loss_function(x, labels))
+        values, preds = torch.max(x, 1)
+
+        y_positive_scores += x[:, 1].cpu()
+        y_preds += preds.cpu()
+        y_targets += labels.cpu()
+
+    cf_matrix = confusion_matrix(y_targets, y_preds, normalize="true")
+
+    class_accuracies = [cf_matrix[c][c] for c in class_set]
+    acc = sum(class_accuracies)
+    acc /= len(class_set)
+    # TN|FN
+    # FP|TP
+    fpr, tpr, _ = roc_curve(y_targets, y_positive_scores)
+    auc = roc_auc_score(y_targets, y_positive_scores)
+    if loss_function:
+        loss = sum(loss_values)
+        loss /= len(loss_values)
+        return acc * 100, cf_matrix, (fpr, tpr, auc), loss
+    return acc * 100, cf_matrix, (fpr, tpr, auc)
+
+
+def get_save_state_dirs(config_label, epoch=None):
+    trains_state_dir = "./train_state"
+    if not os.path.isdir(trains_state_dir):
+        os.mkdir(trains_state_dir)
+    config_train_dir = os.path.join(trains_state_dir, config_label)
+    if not os.path.isdir(config_train_dir):
+        os.mkdir(config_train_dir)
+    if epoch is not None:
+        save_state_dir = os.path.join(config_train_dir, f"epoch-{epoch}")
+        if not os.path.isdir(save_state_dir):
+            os.mkdir(save_state_dir)
+    else:
+        save_state_dir = None
+    return trains_state_dir, config_train_dir, save_state_dir
+
+
+def plot_and_save_model_per_epoch(epoch,
+                                  model_to_save,
+                                  val_acc_list,
+                                  train_acc_list,
+                                  val_loss_list,
+                                  train_loss_list,
+                                  config_label):
+    trains_state_dir, config_train_dir, save_state_dir = get_save_state_dirs(config_label, epoch)
+
+    fig_save_path = os.path.join(config_train_dir, "val_train_acc.jpeg")
+    plt.plot(range(len(val_acc_list)), val_acc_list, label="validation")
+    plt.plot(range(len(train_acc_list)), train_acc_list, label="train")
+    plt.legend(loc="lower right")
+    plt.xlabel('Epoch')
+    plt.ylabel('Balanced Accuracy')
+    plt.savefig(fig_save_path)
+    plt.clf()
+
+    fig_save_path = os.path.join(config_train_dir, "val_train_loss.jpeg")
+    plt.plot(range(len(val_loss_list)), val_loss_list, label="validation")
+    plt.plot(range(len(train_loss_list)), train_loss_list, label="train")
+    plt.legend(loc="lower right")
+    plt.xlabel('Epoch')
+    plt.ylabel('Loss')
+    plt.savefig(fig_save_path)
+    plt.clf()
+
+    if model_to_save:
+        model_save_path = os.path.join(save_state_dir, "model.state")
+        model_to_save.save_model(model_save_path)
+
+
+def save_auc_roc_chart_for_test(test_fpr, test_tpr, test_auc_score, config_label, epoch):
+    trains_state_dir, config_train_dir, save_dir = get_save_state_dirs(config_label, epoch)
+    fig_save_path = os.path.join(save_dir, f"test_roc_{time.time()}.jpeg")
+    plt.plot(test_fpr, test_tpr, label="test, auc=" + str(test_auc_score))
+    plt.legend(loc="lower right")
+    plt.xlabel('FPR')
+    plt.ylabel('TPR')
+    plt.savefig(fig_save_path)
+    plt.clf()
+
+
+def calculate_test(image_model, epoch, test_data_loader, logger, config_name, show_tqdm=False):
+    image_model.eval()
+    test_acc, test_c_acc, (test_FPR, test_TPR, test_auc_score) = validate(image_model,
+                                                                          test_data_loader,
+                                                                          show_tqdm=show_tqdm)
+    test_acc = float(test_acc)
+
+    save_auc_roc_chart_for_test(test_FPR, test_TPR, test_auc_score, config_name, epoch)
+    logger.info(f'Test|Epoch:{epoch}|Accuracy:{round(test_acc, 4)}, {test_c_acc}%')
+
+
+def train_model(base_model, config_base_name, train_val_test_data_loaders, augmentation,
+                adaptation_sample_dataset=None,
+                train_model_flag=True,
+                load_model_from_dir=None):
+    config_name = f"{config_base_name}-{augmentation}-{','.join(Config.class_idx_dict.keys())}"
+
+    logger = set_config_for_logger(config_name)
+    logger.info(f"training config: {config_name}")
+    try:
+        _is_inception = type(base_model) == torchvision.models.inception.Inception3
+        train_data_loader, val_data_loader, test_data_loader = train_val_test_data_loaders
+        logger.info(
+            f"train valid test splits:" +
+            f" {len(train_data_loader.dataset.samples) if train_data_loader else None}," +
+            f" {len(val_data_loader.dataset.samples) if val_data_loader else None}," +
+            f" {len(test_data_loader.dataset.samples) if test_data_loader else None}")
+
+        # MODEL
+        if load_model_from_dir:
+            # Load model from file
+            model_path = os.path.join(load_model_from_dir, 'model.state')
+            image_model = ThyroidClassificationModel(base_model).load_model(model_path).to(Config.available_device)
+        else:
+            image_model = ThyroidClassificationModel(base_model).to(Config.available_device)
+
+        if train_model_flag:
+            # TRAIN
+            transformation = get_transformation(augmentation=augmentation, base_dataset=adaptation_sample_dataset)
+            train_dataset = cast(ThyroidDataset, train_data_loader.dataset)
+            train_dataset.transform = transformation
+
+            cec = nn.CrossEntropyLoss(weight=torch.tensor(train_dataset.class_weights).to(Config.available_device))
+            optimizer = optim.Adam(image_model.parameters(), lr=Config.learning_rate)
+            my_lr_scheduler = torch.optim.lr_scheduler.ExponentialLR(optimizer=optimizer, gamma=Config.decay_rate)
+
+            val_acc_history = []
+            train_acc_history = []
+            train_y_preds = []
+            train_y_targets = []
+            best_epoch_val_acc = 0
+
+            for epoch in range(Config.n_epoch):
+                # variables to calculate train acc
+                class_set = sorted(train_data_loader.dataset.class_to_idx_dict.values())
+
+                for images, labels in tqdm(train_data_loader, colour="#0000ff"):
+                    if len(images) >= Config.batch_size // 2:
+                        image_model.train()
+                        images = images.to(Config.available_device)
+                        labels = labels.to(Config.available_device)
+                        optimizer.zero_grad()
+                        pred = image_model(images)
+                        # pred label: torch.max(pred, 1)[1], labels
+                        if _is_inception:
+                            pred, aux_pred = pred
+                            loss, aux_loss = cec(pred, labels), cec(aux_pred, labels)
+                            loss = loss + 0.4 * aux_loss
+                        else:
+                            loss = cec(pred, labels)
+                        loss.backward()
+                        optimizer.step()
+
+                        # train preds and labels
+                        values, preds = torch.max(pred, 1)
+                        train_y_preds.extend(preds.cpu())
+                        train_y_targets.extend(labels.cpu())
+
+                # Epoch level
+                # validation data
+                image_model.eval()
+
+                train_cf_matrix = confusion_matrix(train_y_targets, train_y_preds, normalize="true")
+
+                class_accuracies = [train_cf_matrix[c][c] for c in class_set]
+                train_acc = sum(class_accuracies)
+                train_acc /= len(class_set)
+
+                train_acc = (100 * sum(class_accuracies) / len(class_set)).item()
+                train_acc_history.append(train_acc)
+                logger.info(f'Train|E:{epoch}|Balanced Accuracy:{round(train_acc, 4)}%,\n{train_cf_matrix}')
+
+                val_acc, val_cf_matrix, _, val_loss = validate(image_model,
+                                                               val_data_loader,
+                                                               cec)
+                val_acc = float(val_acc)
+                val_acc_history.append(val_acc)
+                logger.info(f'Val|E:{epoch}|Balanced Accuracy:{round(val_acc, 4)}%,\n{val_cf_matrix}')
+
+                save_model = False
+                is_last_epoch = epoch == Config.n_epoch
+                is_a_better_epoch = val_acc >= best_epoch_val_acc
+                is_a_better_epoch &= abs(train_acc - val_acc) < Config.train_val_acc_max_distance_for_best_epoch
+                if is_a_better_epoch or is_last_epoch:
+                    save_model = True
+                    calculate_test(image_model, epoch, test_data_loader, logger, config_name, show_tqdm=False)
+                plot_and_save_model_per_epoch(epoch if save_model else None,
+                                              image_model if save_model else None,
+                                              val_acc_history,
+                                              train_acc_history,
+                                              [],
+                                              [],
+                                              config_label=config_name)
+                my_lr_scheduler.step()
+        else:
+            # JUST EVALUATE
+            calculate_test(image_model, 0, test_data_loader, logger, config_name,
+                           show_tqdm=True)
+    except Exception as e:
+        print(e)
+        logger.error(str(e))
+        raise e
+
+
+def load_datasets(datasets_folders, test_percent=Config.test_percent, val_percent=Config.val_percent, sample_percent=1,
+                  is_nci_per_slide=False):
+    if is_nci_per_slide:
+        l_train, l_val, l_test = CustomFragmentLoader(
+            datasets_folders).national_cancer_image_and_labels_splitter_per_slide(
+            test_percent=test_percent,
+            val_percent=val_percent)
+    else:
+        l_train, l_val, l_test = CustomFragmentLoader(datasets_folders).load_image_path_and_labels_and_split(
+            test_percent=test_percent,
+            val_percent=val_percent)
+
+    l_train = random.choices(l_train, k=int(sample_percent * len(l_train)))
+    l_val = random.choices(l_val, k=int(sample_percent * len(l_val)))
+    l_test = random.choices(l_test, k=int(sample_percent * len(l_test)))
+
+    l_train_ds = ThyroidDataset(l_train, Config.class_idx_dict)
+    l_val_ds = ThyroidDataset(l_val, Config.class_idx_dict)
+    l_test_ds = ThyroidDataset(l_test, Config.class_idx_dict)
+
+    l_train_data_loader = None
+    if l_train:
+        l_train_data_loader = DataLoader(l_train_ds, batch_size=Config.batch_size, shuffle=True)
+    l_val_data_loader = None
+    if l_val:
+        l_val_data_loader = DataLoader(l_val_ds, batch_size=Config.eval_batch_size, shuffle=True)
+    l_test_data_loader = None
+    if l_test:
+        l_test_data_loader = DataLoader(l_test_ds, batch_size=Config.eval_batch_size, shuffle=True)
+
+    return (l_train, l_val, l_test), (l_train_ds, l_val_ds, l_test_ds), (
+        l_train_data_loader, l_val_data_loader, l_test_data_loader)
+
+
+@torch.no_grad()
+def evaluate_nci_dataset_per_slide(config_base_name, augmentation, base_model, data_loader,
+                                   load_model_from_dir):
+    config_name = f"{config_base_name}-{augmentation}-tumor-percent"
+
+    logger = set_config_for_logger(config_name)
+    logger.info(f"training config: {config_name}")
+    _is_inception = type(base_model) == torchvision.models.inception.Inception3
+    logger.info(
+        f"test:" +
+        f" {len(data_loader.dataset.samples) if data_loader else None}")
+
+    # MODEL
+    # Load model from file
+    model_path = os.path.join(load_model_from_dir, 'model.state')
+    model = ThyroidClassificationModel(base_model).load_model(model_path).to(Config.available_device)
+
+    y_positive_scores = []
+    slides_preds = {}
+    slide_labels = {}
+    for images, (labels, slides) in tqdm(data_loader):
+        images = images.to(Config.available_device)
+
+        x = model(images, validate=True).cpu()
+        preds = x[:, 1]
+        logger.info("zero and 1000 percent")
+        logger.info(x[:, 0])
+        logger.info(x[:, 1])
+        for row_index in range(len(labels)):
+            slide_id = slides[row_index]
+            slide_label = labels[row_index]
+            slide_labels[slide_id] = slide_label
+            slides_preds[slide_id] = slides_preds.get(slide_id, []) + [preds[row_index].item()]
+        y_positive_scores += x[:, 1].cpu()
+
+    y_targets = []
+    y_preds = []
+    for key, value in slides_preds.items():
+        slides_preds[key] = (sum(slides_preds[key]) / len(slides_preds[key])) * 100
+        y_preds.append(slides_preds[key])
+        y_targets.append(int(slide_labels[key]))
+
+    y_targets_rounded = [int(round(x / 100, 1) * 100) for x in y_targets]
+    y_preds_rounded = [int(round(x / 100, 1) * 100) for x in y_preds]
+    cf_matrix = confusion_matrix(y_targets_rounded, y_preds_rounded, labels=Config.class_names, normalize="true")
+
+    class_accuracies = [cf_matrix[c][c] for c in range(len(cf_matrix))]
+    class_weights = [sum(cf_matrix[c]) for c in range(len(cf_matrix))]
+    acc = sum([class_accuracies[i] * class_weights[i] for i in range(len(class_accuracies))])
+    acc /= sum(class_weights)
+    # TN|FN
+    # FP|TP
+    # fpr, tpr, _ = roc_curve(y_targets, y_positive_scores)
+    # auc = roc_auc_score(y_targets, y_positive_scores)
+    logger.info(f"target rounded:{y_targets_rounded}")
+    logger.info(f"pred rounded:{y_preds_rounded}")
+    logger.info(f"Results| acc:{acc * 100}\ncf:{cf_matrix}")
+    return acc * 100, cf_matrix
+
+
+##########
+## Runs ##
+##########
+# train_phase block
+if __name__ == '__main__' and Config.train_phase:
+    _, (train_ds, _, _), (train_data_loader, val_data_loader, test_data_loader) = load_datasets(
+        ["national_cancer_institute"],
+        sample_percent=1)
+
+    # Domain adaptation dataset on small real datasets
+    # _, (_, _, domain_sample_test_dataset), _ = load_datasets(["stanford_tissue_microarray",
+    #                                                           "papsociaty"],
+    #                                                          sample_percent=0.5,
+    #                                                          test_percent=100,
+    #                                                          val_percent=0)
+
+    for c_base_name, model, augmentations in [
+        (f"resnet101_{Config.learning_rate}_{Config.decay_rate}_nci_final",
+         torchvision.models.resnet101(pretrained=True, progress=True), [
+             "mixup",
+             # "jit",
+             # "fda",
+             # "jit-fda-mixup",
+             # "shear",
+             # "std"
+         ]),
+    ]:
+        for aug in augmentations:
+            Config.reset_random_seeds()
+            train_model(model, c_base_name, (train_data_loader, val_data_loader, test_data_loader),
+                        augmentation=aug, adaptation_sample_dataset=train_ds)
+# evaluate_phase block
+if __name__ == '__main__' and Config.evaluate_phase:
+    # Main data
+    Config.class_names = [i for i in range(101)]
+    Config.class_idx_dict = {i: i for i in range(101)}
+    _, (train_ds, _, _), (_, _, test_data_loader) = load_datasets(
+        ["national_cancer_institute",
+         ],
+        sample_percent=1, test_percent=100, val_percent=0, is_nci_per_slide=True)
+
+    for c_base_name, model, aug_best_epoch_list in [
+        (f"resnet101_{Config.learning_rate}_{Config.decay_rate}_nci_eval",
+         torchvision.models.resnet101(pretrained=True, progress=True), [
+             ("mixup", "train_state/resnet101_0.0001_1_nci_final-mixup-BENIGN,MALIGNANT/epoch-19/"),
+         ]),
+        # (f"resnet101_{Config.learning_rate}_{Config.decay_rate}_test_nci_eval",
+        #  torchvision.models.resnet101(pretrained=True, progress=True), [
+        #      ("fda",
+        #       "train_state/runs_0.0001_1_nic_test_benign_mal/resnet101_0.0001_1_nci-fda-BENIGN,MALIGNANT/epoch-3/"),
+        #      ("mixup",
+        #       "train_state/runs_0.0001_1_nic_test_benign_mal/resnet101_0.0001_1_nci-mixup-BENIGN,MALIGNANT/epoch-3/"),
+        #      ("jit",
+        #       "train_state/runs_0.0001_1_nic_test_benign_mal/resnet101_0.0001_1_nci-jit-BENIGN,MALIGNANT/epoch-3/"),
+        #      ("jit-fda-mixup",
+        #       "train_state/runs_0.0001_1_nic_test_benign_mal/resnet101_0.0001_1_nci-jit-fda-mixup-BENIGN,MALIGNANT/epoch-3/"),
+        #  ]),
+
+    ]:
+        for aug, best_epoch in aug_best_epoch_list:
+            Config.reset_random_seeds()
+            evaluate_nci_dataset_per_slide(c_base_name, aug, model, test_data_loader,
+                                           load_model_from_dir=best_epoch)

classifications_efforts/test_methods/test_model_for_bengin_malignant/run_splitter.sh

@@ -0,0 +1,3 @@
+export PYTHONPATH="${PYTHONPATH}:../../../";
+export PYTHONPATH="${PYTHONPATH}:./";
+python fragment_splitter.py;

classifications_efforts/test_methods/test_model_for_bengin_malignant/run_test_models.sh

@@ -0,0 +1,3 @@
+export PYTHONPATH="${PYTHONPATH}:../../../";
+export PYTHONPATH="${PYTHONPATH}:./";
+python model_training.py;

classifications_efforts/test_methods/test_model_for_bengin_malignant/thyroid_dataset.py

@@ -0,0 +1,83 @@
+import os
+
+import numpy as np
+from PIL import Image
+from torch.utils.data import Dataset
+
+from config import Config
+from fragment_splitter import CustomFragmentLoader
+from transformation import get_transformation
+from utils import show_and_wait
+
+
+class ThyroidDataset(Dataset):
+    def __init__(self, image_paths_labels_list, class_to_index, transform=None, force_to_size_with_padding=512):
+        super().__init__()
+        self.class_to_idx_dict = class_to_index
+        self.force_to_size_with_padding = force_to_size_with_padding
+        self.transform = transform
+        self.samples = self._make_dataset(image_paths_labels_list)
+        self.class_weights = self._calculate_class_weights(image_paths_labels_list)
+
+    def _calculate_class_weights(self, image_paths_labels_list):
+        class_counts = {}
+        for image_path, (label, slide) in image_paths_labels_list:
+            class_counts[label] = class_counts.get(label, 0) + 1
+
+        class_weights = [
+            (self.class_to_idx_dict.get(c, None), len(image_paths_labels_list) / (len(class_counts) * v)) for c, v
+            in
+            class_counts.items()]
+        class_weights.sort()
+        return [item[1] for item in class_weights]
+
+    def _make_dataset(self, image_paths_labels_list):
+        images = []
+        for image_path, (label, slide) in image_paths_labels_list:
+            if not os.path.exists(os.path.abspath(image_path)):
+                raise (RuntimeError(f"{image_path} not found."))
+            item = (image_path, (self.class_to_idx_dict.get(label, "Unknown label"), slide))
+            images.append(item)
+        return images
+
+    def __len__(self):
+        return len(self.samples)
+
+    def __getitem__(self, index):
+        path, target = self.samples[index]
+        image = Image.open(path)
+        image = image.convert('RGB')
+        image = self.add_margin(image)
+        image = np.array(image)
+        if self.transform is not None:
+            # show_and_wait(image, name=f"./transformations/{index}-original", wait=False, save=True)
+            image = self.transform(image=image)['image']
+            # image_show = np.moveaxis(image.cpu().detach().numpy(), 0, -1)
+            # show_and_wait(image_show, name=f"./transformations/{index}-transformed", save=True)
+        else:
+            transform = get_transformation(augmentation="min")
+
+            image = transform(image=image)['image']
+
+        return image, target
+
+    def add_margin(self, pil_img):
+        width, height = pil_img.size
+        new_width = self.force_to_size_with_padding
+        new_height = self.force_to_size_with_padding
+        result = Image.new("RGB", (new_width, new_height), (0, 0, 0))
+        top_padding = (new_height - height) // 2
+        left_padding = (new_width - width) // 2
+        result.paste(pil_img, (left_padding, top_padding))
+        return result
+
+
+if __name__ == '__main__':
+    class_idx_dict = Config.class_idx_dict
+    datasets_folder = ["stanford_tissue_microarray", "papsociaty"]
+    train, val, test = CustomFragmentLoader(datasets_folder).load_image_path_and_labels_and_split()
+    train_ds = ThyroidDataset(train, class_idx_dict)
+    test_ds = ThyroidDataset(test, class_idx_dict)
+    val_ds = ThyroidDataset(val, class_idx_dict)
+    res = train_ds.__getitem__(0)
+    print(res)

classifications_efforts/test_methods/test_model_for_bengin_malignant/thyroid_ml_model.py

@@ -0,0 +1,47 @@
+import torch
+import torchvision
+from torch import nn
+
+
+class ThyroidClassificationModel(nn.Module):
+    def __init__(self, base_model):
+        super().__init__()
+        self.base_model = base_model
+        self.classifier = nn.Sequential(
+            nn.Linear(1000, 500),
+            nn.BatchNorm1d(500),
+            nn.ReLU(),
+            nn.Linear(500, 100),
+            nn.BatchNorm1d(100),
+            nn.ReLU(),
+            nn.Linear(100, 2),
+            nn.BatchNorm1d(2),
+            nn.Softmax(dim=-1)
+        )
+        self._is_inception3 = type(base_model) == torchvision.models.inception.Inception3
+        if self._is_inception3:
+            self.classifier2 = nn.Sequential(
+                nn.Linear(1000, 500),
+                nn.BatchNorm1d(500),
+                nn.ReLU(),
+                nn.Linear(500, 100),
+                nn.BatchNorm1d(100),
+                nn.ReLU(),
+                nn.Linear(100, 2),
+                nn.BatchNorm1d(2),
+                nn.Softmax(dim=-1)
+            )
+
+    def forward(self, x, validate=False):
+        output = self.base_model(x.float())
+        if self._is_inception3 and not validate:
+            return self.classifier(output[0]), self.classifier2(output[1])
+        return self.classifier(output)
+
+    def save_model(self, path):
+        torch.save(self.state_dict(), path)
+
+    def load_model(self, path):
+        self.load_state_dict(torch.load(path))
+        self.eval()
+        return self

classifications_efforts/test_methods/test_model_for_bengin_malignant/transformation.py

@@ -0,0 +1,82 @@
+import albumentations as A
+from albumentations.pytorch import ToTensorV2
+
+from albumentations_mixup import Mixup
+
+
+def get_transformation(augmentation, crop_size=299, base_dataset=None):
+    scaled_center_crop_size = int(crop_size * 1.25)
+
+    def random_crop_transformation(x):
+        return A.RandomCrop(x, x, always_apply=True)
+
+    def get_flip_rotate__custom__noise_transform(transform_list, random_scale=True):
+        return A.Compose([
+                             A.Flip(p=0.25),
+                             A.Rotate(p=0.25),
+                             A.RandomScale(scale_limit=0.5, p=0.5 if random_scale else 0),
+                             A.PadIfNeeded(min_height=scaled_center_crop_size, min_width=scaled_center_crop_size,
+                                           always_apply=True),
+                             A.CenterCrop(scaled_center_crop_size, scaled_center_crop_size),
+                             random_crop_transformation(crop_size),
+                         ] + transform_list + [
+                             A.Blur(p=0.25, blur_limit=2),
+                             A.GaussNoise(p=0.25, var_limit=10),
+                             ToTensorV2()
+                         ])
+
+    if augmentation == "min":
+        trans = A.Compose([
+            A.PadIfNeeded(min_height=scaled_center_crop_size, min_width=scaled_center_crop_size, always_apply=True),
+            A.CenterCrop(scaled_center_crop_size, scaled_center_crop_size),
+            random_crop_transformation(crop_size),
+            ToTensorV2()
+        ])
+
+    elif augmentation == "std":
+        trans = get_flip_rotate__custom__noise_transform([])
+    elif augmentation == "jit-nrs":
+        trans = get_flip_rotate__custom__noise_transform([
+            A.ColorJitter(p=0.5, hue=.5)
+        ], random_scale=False)
+    elif augmentation == "jit":
+        trans = get_flip_rotate__custom__noise_transform([
+            A.ColorJitter(p=0.5, hue=.5)
+        ])
+    elif augmentation == "fda":
+        fda_image_paths = [sample[0] for sample in base_dataset.samples]
+        trans = get_flip_rotate__custom__noise_transform([
+            A.domain_adaptation.FDA(fda_image_paths, beta_limit=0.1, p=0.5)
+        ])
+    elif augmentation == "mixup":
+        mixups = [sample[0:2] for sample in base_dataset.samples]
+        trans = get_flip_rotate__custom__noise_transform([
+            Mixup(mixups=mixups, p=0.5, beta_limit=(0.1)),
+        ])
+    elif augmentation == "jit-fda-mixup":
+        p = 0.16
+        fda_image_paths = [sample[0] for sample in base_dataset.samples]
+        mixups = [sample[0:2] for sample in base_dataset.samples]
+        trans = get_flip_rotate__custom__noise_transform([
+            A.domain_adaptation.FDA(fda_image_paths, beta_limit=0.1, p=p),
+            Mixup(mixups=mixups, p=p, beta_limit=(0.1)),
+            A.ColorJitter(p=p, hue=.5)
+        ])
+    elif augmentation == "jit-fda-mixup-nrs":
+        p = 0.16
+        fda_image_paths = [sample[0] for sample in base_dataset.samples]
+        mixups = [sample[0:2] for sample in base_dataset.samples]
+        trans = get_flip_rotate__custom__noise_transform([
+            A.domain_adaptation.FDA(fda_image_paths, beta_limit=0.1, p=p),
+            Mixup(mixups=mixups, p=p, beta_limit=(0.1)),
+            A.ColorJitter(p=p, hue=.5)
+        ], random_scale=False)
+    elif augmentation == "shear":
+        trans = get_flip_rotate__custom__noise_transform([
+            A.Affine(shear={"x": (-10, 10), "y": (-10, 10)}, p=0.5)
+        ], random_scale=False)
+
+
+    else:
+        raise ValueError(f"Augmentation unknown: {augmentation}")
+    return trans

config.py

@@ -0,0 +1,45 @@
+import random
+
+import torch
+
+
+class Config:
+    DEBUG = False
+
+    batch_size = 32
+    eval_batch_size = 128
+
+    test_percent = 20
+    val_percent = 10
+
+    learning_rate = 0.0001
+    decay_rate = 1  # 0.99**50=0.6, 0.99**100=0.36
+    n_epoch = 2 if DEBUG else 20
+
+    available_device = "cuda" if torch.cuda.is_available() and not DEBUG else "cpu"
+    print(f"Device: {available_device}")
+
+    workers = 1 if DEBUG else 40
+
+    # learned from evaluate_image_patcher_and_visualize.py
+    laplacian_threshold = 298
+
+    # RANDOM SEED
+    seed = 115
+
+    @staticmethod
+    def reset_random_seeds():
+        random.seed(Config.seed)
+        torch.manual_seed(Config.seed)
+
+    class_names = ["BENIGN", "MALIGNANT"]
+    class_idx_dict = {"BENIGN": 0, "MALIGNANT": 1}
+
+    train_val_acc_max_distance_for_best_epoch = 6  # Percent
+    n_epoch_for_image_patcher = 60
+
+    train_phase = False
+    evaluate_phase = False
+
+
+Config.reset_random_seeds()

database_crawlers/bio_atlas_at_jake_gittlen_laboratories/database_crawler.py

@@ -0,0 +1,64 @@
+import ssl
+import time
+from urllib.parse import urlparse
+from urllib.request import urlopen
+
+from bs4 import BeautifulSoup
+
+from database_crawlers.web_stain_sample import StainType, WebStainWSIOneDIndex
+
+ssl._create_default_https_context = ssl._create_unverified_context
+
+
+class BioAtlasAtJakeGittlenLaboratoriesImage(WebStainWSIOneDIndex):
+
+    def __init__(self, database_name, image_id, image_web_label, report, stain_type, is_wsi):
+        super().__init__(database_name, image_id, image_web_label, report, stain_type, is_wsi)
+
+    def _get_tile_url(self, zoom, partition=None, i=None, j=None):
+        return f"https://bio-atlas.psu.edu/human/tile.jpeg.php?s={self.image_id}&z={zoom}&i={partition}"
+
+    def get_slide_view_url(self):
+        return f"https://bio-atlas.psu.edu/human/view.php?s={self.image_id}"
+
+    def _get_file_path_name(self):
+        return self.save_path + self.image_id
+
+    def find_best_zoom(self):
+        return 0
+
+
+class BioAtlasThyroidSlideProvider:
+    page_link = "https://bio-atlas.psu.edu/human/search.php?q=Thyroid&organism%5B%5D=5&age_fr=&age_fr_units=1&age_to=&age_to_units=1&sex%5B%5D=all&thumbnails=on&rpp=30&as_sfid=AAAAAAW0RrspdnblpiFwz8osoAdvS8nafd1J9LG_ARQ-IF_NZ3aI2EXCMDBeqE_iD5rUo1QLg454tS63DMSgATSzgrksb4rMi-GWPl3O9f3JKlqGn8oXoqbOYok3__yZx69ewzg%3D&as_fid=6900aeb3e4cc9f39ef9738a2f11c2cefb8c3f37c#results"
+    database_name = "BioAtlasThyroidSlideProvider"
+    stain_type = StainType.H_AND_E
+    is_wsi = True
+
+    @classmethod
+    def get_web_stain_samples(cls):
+        print(cls.page_link)
+        try:
+            html_text = urlopen(cls.page_link).read()
+            soup = BeautifulSoup(html_text, 'html.parser')
+            search_results = soup.find_all("div", {"class": "shadow-box search-result-item search-result-slide"})
+            for result_item in search_results:
+                image_view_url = result_item.find("a").attrs['href']
+                query_param = urlparse(image_view_url).query.split("=")
+                if query_param[0] != "s": raise Exception("Query params does not contains image url")
+                image_id = query_param[1]
+                image_web_label = str(result_item.find("b", text="Diagnosis").next_sibling)
+                yield BioAtlasAtJakeGittlenLaboratoriesImage(cls.database_name, image_id, image_web_label, None,
+                                                             cls.stain_type, cls.is_wsi)
+        except Exception as e:
+            print(e)
+            time.sleep(2)
+            yield cls.get_web_stain_samples()
+
+
+if __name__ == '__main__':
+    bio_atlas_provider = BioAtlasThyroidSlideProvider()
+    for slide in bio_atlas_provider.get_web_stain_samples():
+        if slide.image_id == "687":
+            print(slide.image_id, slide.image_web_label, slide.get_slide_view_url())
+            slide.crawl_image_save_jpeg_and_json()
+            break

database_crawlers/bio_atlas_at_jake_gittlen_laboratories/run_bio_atlas_crawler.sh

@@ -0,0 +1,3 @@
+export PYTHONPATH="${PYTHONPATH}:../../";
+export PYTHONPATH="${PYTHONPATH}:./";
+python database_crawler.py;

database_crawlers/heidelberg_pathology/database_crawler.py

@@ -0,0 +1,61 @@
+import time
+from urllib.parse import urlparse
+from urllib.request import urlopen
+
+from bs4 import BeautifulSoup
+
+from database_crawlers.web_stain_sample import StainType, WebStainWSITwoDIndex
+
+
+class HeidelbergPathologyImage(WebStainWSITwoDIndex):
+
+    def __init__(self, database_name, image_id, image_web_label, report, stain_type, is_wsi):
+        super().__init__(database_name, image_id, image_web_label, report, stain_type, is_wsi)
+
+    def _get_tile_url(self, zoom, partition=None, i=None, j=None):
+        return f"https://eliph.klinikum.uni-heidelberg.de/dzi/atlas/05-schilddruese/05-{'%.2d' % int(self.image_id)}_files/{zoom}/{i}_{j}.jpeg"
+
+    def get_slide_view_url(self):
+        return f"https://eliph.klinikum.uni-heidelberg.de/atlas/?c=05-schilddruese&context=image&pg={self.image_id}"
+
+    def _get_file_path_name(self):
+        return self.save_path + self.image_id
+
+    def find_best_zoom(self):
+        # 16 -> 0
+        return 16
+
+
+class HeidelbergPathologyProvider:
+    page_link = "https://eliph.klinikum.uni-heidelberg.de/atlas/?c=05-schilddruese&context=image"
+    database_name = "HeidelbergPathology"
+    stain_type = StainType.H_AND_E
+    is_wsi = True
+
+    @classmethod
+    def get_web_stain_samples(cls):
+        print(cls.page_link)
+        try:
+            html_text = urlopen(cls.page_link).read()
+            soup = BeautifulSoup(html_text, 'html.parser')
+            search_results = soup.find_all("div", {"class": "casegrid"})
+            for result_item in search_results:
+                image_view_url = result_item.find("a").attrs['href']
+                query_param = urlparse(image_view_url).query.split("=")
+                if "image&pg" not in query_param: raise Exception("Query params does not contains image id")
+                image_id = query_param[-1]
+                image_web_label = str(result_item.find("b").next)
+                yield HeidelbergPathologyImage(cls.database_name, image_id, image_web_label, None,
+                                               cls.stain_type, cls.is_wsi)
+        except Exception as e:
+            print(e)
+            time.sleep(2)
+            yield cls.get_web_stain_samples()
+
+
+if __name__ == '__main__':
+    bio_atlas_provider = HeidelbergPathologyProvider()
+    for slide in bio_atlas_provider.get_web_stain_samples():
+        print(slide.image_id, slide.image_web_label, slide.get_slide_view_url())
+        slide.crawl_image_save_jpeg_and_json()
+        break

database_crawlers/image_patcher/bio_atlas_patcher.py

@@ -0,0 +1,7 @@
+from image_patcher import ImageAndSlidePatcher
+
+if __name__ == '__main__':
+    database_folder_name = "bio_atlas_at_jake_gittlen_laboratories"
+    database_directory = "../"
+    image_slide_patcher = ImageAndSlidePatcher()
+    image_slide_patcher.save_patches_in_folders(database_directory, database_folder_name)

database_crawlers/image_patcher/image_patcher.py

@@ -0,0 +1,287 @@
+import csv
+import json
+import os
+import os.path as os_path
+import random
+import re
+from math import ceil
+from os import listdir
+from os.path import isfile, join
+
+import cv2
+import tifffile
+import zarr as ZarrObject
+from tqdm import tqdm
+
+from config import Config
+from database_crawlers.web_stain_sample import ThyroidCancerLevel, WebStainImage
+from utils import show_and_wait
+
+
+class ThyroidFragmentFilters:
+    @staticmethod
+    def func_laplacian_threshold(threshold=Config.laplacian_threshold):
+        def wrapper(image_nd_array):
+            res = ThyroidFragmentFilters._empty_frag_with_laplacian_threshold(image_nd_array, threshold)
+            return res
+
+        return wrapper
+
+    @staticmethod
+    def _empty_frag_with_laplacian_threshold(image_nd_array, threshold=Config.laplacian_threshold,
+                                             return_variance=False):
+        gray = cv2.cvtColor(image_nd_array, cv2.COLOR_BGR2GRAY)
+        gray = cv2.GaussianBlur(gray, (3, 3), 0)
+
+        laplacian = cv2.Laplacian(gray, cv2.CV_64F, ksize=3, )
+        std = cv2.meanStdDev(laplacian)[1][0][0]
+
+        variance = std ** 2
+        if return_variance:
+            return variance >= threshold, variance
+        return variance >= threshold
+
+
+class ImageAndSlidePatcher:
+    @classmethod
+    def _check_magnification_from_description(cls, tiff_address):
+        try:
+            tif_file_obj = tifffile.TiffFile(tiff_address)
+            image_description = tif_file_obj.pages.keyframe.tags["ImageDescription"].value
+            app_mag = int(re.findall("(AppMag = [0-9]+)", image_description)[0].split(" = ")[-1])
+            return app_mag
+        except Exception as e:
+            return None
+
+    @classmethod
+    def _zarr_loader(cls, tiff_address, key=0):
+        image_zarr = tifffile.imread(tiff_address, aszarr=True, key=key, )
+        zarr = ZarrObject.open(image_zarr, mode='r')
+        return zarr
+
+    @classmethod
+    def _jpeg_loader(cls, jpeg_address):
+        im = cv2.imread(jpeg_address)
+        return im
+
+    @classmethod
+    def _json_key_loader(cls, json_file_address, key=None):
+        with open(json_file_address, 'rb') as file:
+            json_dict = json.loads(file.read())
+        if key:
+            return json_dict[key]
+        return json_dict
+
+    @classmethod
+    def _get_extension_from_path(cls, file_path):
+        return os_path.splitext(file_path)[-1]
+
+    @classmethod
+    def _get_file_name_from_path(cls, file_path):
+        return ".".join(os_path.split(file_path)[-1].split(".")[:-1])
+
+    @classmethod
+    def _get_number_of_initial_frags(cls, zarr_object, frag_size=512, frag_overlap=0.1):
+        zarr_shape = zarr_object.shape
+
+        step_size = int(frag_size * (1 - frag_overlap))
+        overlap_size = frag_size - step_size
+        w_range = list(range(0, ceil((zarr_shape[0] - overlap_size) / step_size) * step_size, step_size))
+        h_range = list(range(0, ceil((zarr_shape[1] - overlap_size) / step_size) * step_size, step_size))
+        return len(w_range) * len(h_range)
+
+    @classmethod
+    def _generate_raw_fragments_from_image_array_or_zarr(cls, image_object, frag_size=512, frag_overlap=0.1,
+                                                         shuffle=True):
+        def frag_picker(w_pos, h_pos):
+            end_w, end_h = min(zarr_shape[0], w_pos + frag_size), min(zarr_shape[1], h_pos + frag_size)
+            start_w, start_h = end_w - frag_size, end_h - frag_size
+            return image_object[start_w:end_w, start_h: end_h], (start_w, start_h)
+
+        if image_object is None:
+            return None
+        zarr_shape = image_object.shape
+
+        step_size = int(frag_size * (1 - frag_overlap))
+        overlap_size = frag_size - step_size
+        w_range = list(range(0, ceil((zarr_shape[0] - overlap_size) / step_size) * step_size, step_size))
+
+        h_range = list(range(0, ceil((zarr_shape[1] - overlap_size) / step_size) * step_size, step_size))
+
+        if shuffle:
+            pos_list = [None] * len(w_range) * len(h_range)
+            index = 0
+            for w in w_range:
+                for h in h_range:
+                    pos_list[index] = (w, h)
+                    index += 1
+            random.shuffle(pos_list)
+            for w, h in pos_list:
+                yield frag_picker(w, h)
+        else:
+            for w in w_range:
+                for h in h_range:
+                    yield frag_picker(w, h)
+
+    @classmethod
+    def _filter_frag_from_generator(cls, frag_generator, filter_func_list, return_all_with_condition=False,
+                                    all_frag_count=None, output_file=None):
+        for next_test_item, frag_pos in tqdm(frag_generator, total=all_frag_count, file=output_file,
+                                             postfix="Filtering", position=0):
+            condition = True
+            for function in filter_func_list:
+                condition &= function(next_test_item)
+            if return_all_with_condition:
+                yield next_test_item, frag_pos, condition
+            elif condition:
+                # show_and_wait(frag)
+                yield next_test_item, frag_pos
+
+    @classmethod
+    def _get_json_and_image_address_of_directory(cls, directory_path, ignore_json=False):
+        image_formats = [".jpeg", ".tiff", ".jpg"]
+        json_format = ".json"
+        files = [f for f in listdir(directory_path) if isfile(join(directory_path, f))]
+        files.sort()
+        pairs = {}
+        for file_path in files:
+            file_path = join(directory_path, file_path)
+            file_name = cls._get_file_name_from_path(file_path)
+            pairs[file_name] = pairs.get(file_name, [None, None])
+            if cls._get_extension_from_path(file_path) in image_formats:
+                pairs[file_name][1] = file_path
+            elif cls._get_extension_from_path(file_path) == json_format:
+                pairs[file_name][0] = file_path
+        if ignore_json:
+            return [value for key, value in pairs.values() if value is not None]
+        return [(key, value) for key, value in pairs.values() if key is not None and value is not None]
+
+    @staticmethod
+    def create_patch_dir_and_initialize_csv(database_path):
+        data_dir = os.path.join(database_path, "data")
+        patch_dir = os.path.join(database_path, "patches")
+        if not os.path.isdir(patch_dir):
+            os.mkdir(patch_dir)
+        label_csv_path = os.path.join(patch_dir, "patch_labels.csv")
+        csv_file = open(label_csv_path, "a+")
+        csv_writer = csv.writer(csv_file)
+        csv_file.seek(0)
+        if len(csv_file.read(100)) <= 0:
+            csv_writer.writerow(WebStainImage.sorted_json_keys())
+        return data_dir, patch_dir, csv_writer, csv_file
+
+    @classmethod
+    def save_image_patches_and_update_csv(cls, thyroid_type, thyroid_desired_classes, csv_writer, web_details,
+                                          image_path, slide_patch_dir, slide_id):
+        csv_writer.writerow(list(web_details.values()))
+
+        if cls._get_extension_from_path(image_path) in [".tiff", ".tif", ".svs"]:
+            zarr_object = cls._zarr_loader(image_path)
+            generator = cls._generate_raw_fragments_from_image_array_or_zarr(zarr_object)
+            total_counts = cls._get_number_of_initial_frags(zarr_object=zarr_object)
+        else:
+            jpeg_image = cls._jpeg_loader(image_path)
+            jpeg_image = cls.ask_image_scale_and_rescale(jpeg_image)
+            generator = cls._generate_raw_fragments_from_image_array_or_zarr(jpeg_image)
+            total_counts = cls._get_number_of_initial_frags(zarr_object=jpeg_image)
+        if generator is None:
+            return
+
+        if not os.path.isdir(slide_patch_dir):
+            os.mkdir(slide_patch_dir)
+        filters = [ThyroidFragmentFilters.func_laplacian_threshold(Config.laplacian_threshold)]
+        fragment_id = 0
+        slide_progress_file_path = os.path.join(slide_patch_dir, "progress.txt")
+        with open(slide_progress_file_path, "w") as file:
+            for fragment, frag_pos in cls._filter_frag_from_generator(generator, filters, all_frag_count=total_counts,
+                                                                      output_file=file):
+                fragment_file_path = os.path.join(slide_patch_dir, f"{slide_id}-{fragment_id}.jpeg")
+                cv2.imwrite(fragment_file_path, fragment)
+                fragment_id += 1
+        return fragment_id, total_counts
+
+    @classmethod
+    def save_patches_in_folders(cls, database_directory, dataset_dir=None):
+        thyroid_desired_classes = [ThyroidCancerLevel.MALIGNANT, ThyroidCancerLevel.BENIGN]
+        datasets_dirs = os.listdir(database_directory) if dataset_dir is None else [dataset_dir]
+        list_dir = [os.path.join(database_directory, o) for o in datasets_dirs
+                    if os.path.isdir(os.path.join(database_directory, o, "data"))]
+        for database_path in list_dir:
+            print("database path: ", database_path)
+            data_dir, patch_dir, csv_writer, csv_file = cls.create_patch_dir_and_initialize_csv(database_path)
+            for json_path, image_path in cls._get_json_and_image_address_of_directory(data_dir):
+                print("image path: ", image_path)
+                file_name = cls._get_file_name_from_path(image_path)
+                slide_id = str(hash(file_name))
+                slide_patch_dir = os.path.join(patch_dir, slide_id)
+                if os.path.isdir(slide_patch_dir):
+                    """
+                    it has already been patched
+                    """
+                    continue
+
+                web_details = cls._json_key_loader(json_path)
+                web_details["image_id"] = slide_id
+                web_label = web_details["image_web_label"]
+                thyroid_type = ThyroidCancerLevel.get_thyroid_level_from_diagnosis_label(web_label)
+                web_details["image_class_label"] = thyroid_type.value[1]
+
+                cls.save_image_patches_and_update_csv(thyroid_type, thyroid_desired_classes, csv_writer, web_details,
+                                                      image_path, slide_patch_dir, slide_id)
+            csv_file.close()
+
+    @classmethod
+    def save_papsociaty_patch(cls, database_path):
+        thyroid_desired_classes = [ThyroidCancerLevel.MALIGNANT, ThyroidCancerLevel.BENIGN]
+        print("database path: ", database_path)
+        for folder in Config.class_names:
+            group_path = os.path.join(database_path, "data", folder)
+            data_dir, patch_dir, csv_writer, csv_file = cls.create_patch_dir_and_initialize_csv(database_path)
+            for image_path in cls._get_json_and_image_address_of_directory(group_path, ignore_json=True):
+                print("image path: ", image_path)
+                file_name = cls._get_file_name_from_path(image_path)
+                slide_id = str(hash(file_name))
+                slide_patch_dir = os.path.join(patch_dir, slide_id)
+                if os.path.isdir(slide_patch_dir):
+                    """
+                    it has already been patched
+                    """
+                    continue
+                web_label = folder + "-" + file_name
+                thyroid_type = ThyroidCancerLevel.get_thyroid_level_from_diagnosis_label(web_label)
+                web_details = {"database_name": "PapSociety",
+                               "image_id": slide_id,
+                               "image_web_label": web_label,
+                               "image_class_label": thyroid_type.value[1],
+                               "report": None,
+                               "stain_type": "UNKNOWN",
+                               "is_wsi": False}
+                cls.save_image_patches_and_update_csv(thyroid_type, thyroid_desired_classes, csv_writer, web_details,
+                                                      image_path, slide_patch_dir, slide_id)
+
+            csv_file.close()
+
+    @classmethod
+    def ask_image_scale_and_rescale(cls, image):
+        # small: S, Medium: M, Large:L
+        show_and_wait(image)
+        res = input("how much plus pointer fill a cell(float, i:ignore, else repeat): ")
+        try:
+            if res == "i":
+                return None
+            elif re.match("[0-9]+(.[0-9]*)?", res):
+                scale = 1 / float(res)
+                return cv2.resize(image, (0, 0), fx=scale, fy=scale)
+            else:
+                return cls.ask_image_scale_and_rescale(image)
+        except Exception as e:
+            print(e)
+            return cls.ask_image_scale_and_rescale(image)
+
+
+if __name__ == '__main__':
+    random.seed(1)
+
+    database_directory = "./"
+    # ImageAndSlidePatcher.save_patches_in_folders(database_directory, dataset_dir=["stanford_tissue_microarray"])
+    # ImageAndSlidePatcher.save_papsociaty_patch(os.path.join(database_directory, "papsociaty"))

database_crawlers/image_patcher/national_cancer_patcher.py

@@ -0,0 +1,60 @@
+import concurrent.futures
+import os
+import pathlib
+
+from tqdm import tqdm
+
+from config import Config
+from image_patcher import ImageAndSlidePatcher
+from national_cancer_institute.read_xml_file import get_slide_info_from_bcr_xml
+
+
+def save_national_cancer_institute_patch(database_path):
+    def patch_image(image_path):
+        try:
+            image_path = str(image_path)
+            print()
+            print("image path: ", image_path)
+            file_name = ImageAndSlidePatcher._get_file_name_from_path(image_path)
+            slide_id = file_name.split(".")[0]
+            slide_patch_dir = os.path.join(patch_dir, slide_id)
+            if os.path.isdir(slide_patch_dir):
+                print("it has already been patched")
+                return
+            web_label = slide_infos.get(slide_id, None)
+            if web_label is None:
+                print("Ignored")
+                return
+            web_details = {"database_name": "NationalCancerInstitute",
+                           "image_id": slide_id,
+                           "image_web_label": web_label,
+                           "image_class_label": web_label,
+                           "report": None,
+                           "stain_type": "H&E",
+                           "is_wsi": True}
+            return ImageAndSlidePatcher.save_image_patches_and_update_csv(web_label, None, csv_writer, web_details,
+                                                                          image_path, slide_patch_dir, slide_id)
+        except Exception as e:
+            print(e)
+
+    data_dir = os.path.join(database_path, "data")
+    slide_infos = {}
+    for xml_path in pathlib.Path(data_dir).glob("**/*.xml"):
+        slide_infos.update(get_slide_info_from_bcr_xml(str(xml_path)))
+
+    data_dir, patch_dir, csv_writer, csv_file = ImageAndSlidePatcher.create_patch_dir_and_initialize_csv(database_path)
+    csv_file.flush()
+
+    with concurrent.futures.ThreadPoolExecutor(max_workers=Config.workers) as executor:
+        image_paths = pathlib.Path(data_dir).glob("**/*.svs")
+        image_paths = [i for i in image_paths]
+        print()
+        for res in tqdm(executor.map(patch_image, image_paths), total=len(image_paths)):
+            if res:
+                csv_file.flush()
+    csv_file.flush()
+
+
+if __name__ == '__main__':
+    database_directory = "../"
+    save_national_cancer_institute_patch(os.path.join(database_directory, "national_cancer_institute"))

database_crawlers/image_patcher/run_bio_atlas_patcher.sh

@@ -0,0 +1,4 @@
+export PYTHONPATH="${PYTHONPATH}:../../";
+export PYTHONPATH="${PYTHONPATH}:../";
+export PYTHONPATH="${PYTHONPATH}:./";
+python bio_atlas_patcher.py;

database_crawlers/image_patcher/run_image_patcher.sh

@@ -0,0 +1,4 @@
+export PYTHONPATH="${PYTHONPATH}:../../";
+export PYTHONPATH="${PYTHONPATH}:../";
+export PYTHONPATH="${PYTHONPATH}:./";
+python image_patcher.py;

database_crawlers/image_patcher/run_national_image_patcher.sh

@@ -0,0 +1,4 @@
+export PYTHONPATH="${PYTHONPATH}:../../";
+export PYTHONPATH="${PYTHONPATH}:../";
+export PYTHONPATH="${PYTHONPATH}:./";
+python national_cancer_patcher.py;

database_crawlers/image_patcher/test_image_patcher/nci_svs_and_masks/evaluate_image_patcher_and_visualize.py

@@ -0,0 +1,280 @@
+import concurrent.futures
+import math
+
+import cv2
+import matplotlib.pyplot as plt
+import numpy as np
+
+from config import Config
+from database_crawlers.image_patcher.image_patcher import ImageAndSlidePatcher, ThyroidFragmentFilters
+from utils import check_if_generator_is_empty
+
+
+def imul(a, b):
+    return math.ceil(a * b)
+
+
+def calculate_acc_and_sensitivity(image_path, zarr_loader_mask, zarr_loader, frag_generator, scaled_masked_image,
+                                  generated_mask_scale, laplacian_threshold, slide_patch_size,
+                                  save_generated_image=True):
+    def process_frag(args):
+        next_test_item, frag_pos, condition = args
+        frag_shape = next_test_item.shape
+        mask_scaled_frag_shape = list((imul(frag_shape[i], mask_scale) for i in range(2)))
+
+        mask_frag_pos = list((imul(frag_pos[i], mask_scale) for i in range(2)))
+        mask_w1, mask_w2 = mask_frag_pos[0], mask_frag_pos[0] + mask_scaled_frag_shape[0]
+        mask_h1, mask_h2 = mask_frag_pos[1], mask_frag_pos[1] + mask_scaled_frag_shape[1]
+        mask_item = zarr_loader_mask[mask_w1:mask_w2, mask_h1:mask_h2]
+        mask_item = cv2.resize(mask_item, dsize=(0, 0), fx=1 / mask_scale, fy=1 / mask_scale)
+
+        fragment_size = next_test_item.shape
+        scaled_frag_size = (imul(fragment_size[0], generated_mask_scale), imul(fragment_size[1], generated_mask_scale))
+        scaled_frag = cv2.resize(next_test_item[:, :, :3], dsize=scaled_frag_size, interpolation=cv2.INTER_CUBIC)
+        scaled_frag_size = scaled_frag.shape
+
+        if next_test_item is not None:
+            mask_item = mask_item[:, :, 0]
+            masked = mask_item.mean() > 256 * .3
+            if condition and masked:
+                background_dict["TP"] += 1
+            elif condition and not masked:
+                background_dict["FP"] += 1
+            elif not condition and masked:
+                background_dict["FN"] += 1
+                # show_and_wait(next_test_item)
+                # show_and_wait(mask_item)
+            elif not condition and not masked:
+                background_dict["TN"] += 1
+        else:
+            return None
+        if not condition:
+            # background patches get dark
+            scaled_frag = (scaled_frag * 0.3).astype(np.int8)
+        scaled_pos = list((imul(frag_pos[i], generated_mask_scale) for i in range(2)))
+        try:
+            mask_g_w1, mask_g_w2 = scaled_pos[0], scaled_pos[0] + scaled_frag_size[0]
+            mask_g_h1, mask_g_h2 = scaled_pos[1], scaled_pos[1] + scaled_frag_size[1]
+            scaled_masked_image[mask_g_w1:mask_g_w2, mask_g_h1:mask_g_h2] = scaled_frag
+        except Exception as e:
+            print(e)
+        return True
+
+    mask_scale = zarr_loader_mask.shape[0] / zarr_loader.shape[0]
+
+    filter_func_list = [ThyroidFragmentFilters.func_laplacian_threshold(laplacian_threshold)]
+    background_dict = {"TP": 0, "FP": 0, "TN": 0, "FN": 0}
+    total_frags = slide_patch_size if slide_patch_size else ImageAndSlidePatcher._get_number_of_initial_frags(
+        zarr_loader)
+    frag_filtered = ImageAndSlidePatcher._filter_frag_from_generator(frag_generator, filter_func_list,
+                                                                     return_all_with_condition=True,
+                                                                     all_frag_count=total_frags)
+    with concurrent.futures.ThreadPoolExecutor(max_workers=Config.workers) as executor:
+        futures = []
+        patch_count = 0
+        for args in frag_filtered:
+            patch_count += 1
+            future_res = executor.submit(process_frag, args)
+            futures.append(future_res)
+            if len(futures) >= Config.workers or patch_count == slide_patch_size:
+                for future in concurrent.futures.as_completed(futures):
+                    future.result()
+                futures = []
+                if patch_count == slide_patch_size:
+                    break
+
+    if save_generated_image:
+        masked_image_path = ".".join(image_path.split(".")[:-1]) + "_generated_mask.jpg"
+        cv2.imwrite(masked_image_path, scaled_masked_image)
+
+    return background_dict
+
+
+def score_calculator(accuracy, specificity, acc_w=0.75):
+    return accuracy * acc_w + specificity * (1 - acc_w)
+
+
+def get_zarr_loaders_and_generators():
+    zarr_loaders_and_generators = []
+    for _img_mask_path, _img_path in image_lists:
+        _zarr_loader_mask = ImageAndSlidePatcher._zarr_loader(_img_mask_path)
+        _zarr_loader = ImageAndSlidePatcher._zarr_loader(_img_path)
+        _frag_generator = ImageAndSlidePatcher._generate_raw_fragments_from_image_array_or_zarr(_zarr_loader,
+                                                                                                shuffle=True)
+        _zarr_shape = _zarr_loader.shape
+
+        _generated_mask_scale = 10 / 512
+        _scaled_zarr_shape = (
+            imul(_zarr_shape[0], _generated_mask_scale) + 5, imul(_zarr_shape[1], _generated_mask_scale) + 5, 3)
+        _scaled_masked_image = np.zeros(_scaled_zarr_shape)
+
+        zarr_loaders_and_generators.append([
+            _zarr_loader_mask, _zarr_loader, _frag_generator, _scaled_masked_image, _generated_mask_scale
+        ])
+    return zarr_loaders_and_generators
+
+
+def update_and_find_best_threshold(initial_thresh, learn_threshold_and_log_cf_matrix_per_patch=True):
+    initial_threshold_jump_size_const = 120
+    threshold_jump_size = initial_threshold_jump_size_const
+    decay_const = 0.85
+    decay_count = 0
+
+    threshold_jump_increase = 1
+
+    threshold_score = None
+    # update after initial run
+    laplacian_threshold = initial_thresh
+
+    threshold_history = []
+    score_history = []
+    for epoch in range((Config.n_epoch_for_image_patcher if learn_threshold_and_log_cf_matrix_per_patch else 1)):
+        print("New Epoch")
+        zarr_loaders_and_generators = get_zarr_loaders_and_generators()
+        whole_background_dict_per_slide = [{} for i in range(len(zarr_loaders_and_generators))]
+        whole_background_dict = {}
+
+        while sum([item is not None for item in zarr_loaders_and_generators]) >= 1:
+            none_empty_generators = [i for i in range(len(zarr_loaders_and_generators)) if
+                                     zarr_loaders_and_generators[i] is not None]
+
+            if learn_threshold_and_log_cf_matrix_per_patch:
+                whole_background_dict = {}
+            if len(none_empty_generators) >= 6 or not learn_threshold_and_log_cf_matrix_per_patch:
+                for slide_pick in none_empty_generators:
+                    img_path = image_lists[slide_pick][1]
+                    zarr_loader_mask = zarr_loaders_and_generators[slide_pick][0]
+                    zarr_loader = zarr_loaders_and_generators[slide_pick][1]
+                    frag_generator = zarr_loaders_and_generators[slide_pick][2]
+
+                    generated_scaled_mask_image = zarr_loaders_and_generators[slide_pick][3]
+                    generated_mask_scale = zarr_loaders_and_generators[slide_pick][4]
+
+                    group_dict = calculate_acc_and_sensitivity(img_path,
+                                                               zarr_loader_mask,
+                                                               zarr_loader,
+                                                               frag_generator,
+                                                               generated_scaled_mask_image,
+                                                               generated_mask_scale,
+                                                               laplacian_threshold,
+                                                               slide_patch_size=2000,
+                                                               save_generated_image=not learn_threshold_and_log_cf_matrix_per_patch)
+                    for i in range(len(zarr_loaders_and_generators)):
+                        if zarr_loaders_and_generators[i]:
+                            generator = check_if_generator_is_empty(zarr_loaders_and_generators[i][2])
+                            if generator:
+                                zarr_loaders_and_generators[i][2] = generator
+                            else:
+                                zarr_loaders_and_generators[i] = None
+
+                    for key, value in group_dict.items():
+                        whole_background_dict[key] = whole_background_dict.get(key, 0) + value
+                        whole_background_dict_per_slide[slide_pick][key] = whole_background_dict_per_slide[
+                                                                               slide_pick].get(key, 0) + value
+
+                if learn_threshold_and_log_cf_matrix_per_patch:
+                    e = .000001
+                    total_preds = (sum(list(whole_background_dict.values())) + e)
+                    acc = (whole_background_dict["TP"] + whole_background_dict["TN"]) / total_preds
+                    positive_preds = (whole_background_dict["TP"] + whole_background_dict["FP"] + e)
+                    precision = whole_background_dict["TP"] / positive_preds
+                    next_score = score_calculator(acc, precision)
+                    if threshold_score is None:
+                        threshold_score = next_score
+                    else:
+                        threshold_history.append(laplacian_threshold)
+                        score_history.append(next_score)
+                        if next_score > threshold_score:
+                            threshold_score = next_score
+
+                            laplacian_threshold += threshold_jump_increase * threshold_jump_size
+                        elif next_score <= threshold_score:
+                            threshold_score = next_score
+
+                            threshold_jump_increase *= -1
+                            threshold_jump_size *= decay_const
+
+                            laplacian_threshold += threshold_jump_increase * threshold_jump_size
+                            decay_count += 1
+                        save_threshold_and_score_chart(threshold_history, score_history)
+
+                    acc = round(acc, 3)
+                    precision = round(precision, 3)
+                    threshold_score_rounded = round(threshold_score, 3)
+                    print(
+                        f"acc:{acc},precision:{precision},score:{threshold_score_rounded},table:{whole_background_dict}" +
+                        f"thresh:{laplacian_threshold},jump_size:{threshold_jump_size}")
+                else:
+                    print(f"table:{whole_background_dict},table_per_slide:{whole_background_dict_per_slide}" +
+                          f"threshold:{laplacian_threshold},jump_size:{threshold_jump_size}")
+            else:
+                break
+    return laplacian_threshold
+
+
+def save_threshold_and_score_chart(threshold_history, score_history):
+    fig_save_path = "laplacian_threshold_history_chart.jpeg"
+    plt.plot(range(len(threshold_history)), threshold_history)
+    plt.xlabel('Batch')
+    plt.ylabel('Laplacian threshold')
+    plt.savefig(fig_save_path)
+    plt.clf()
+
+    fig_save_path = "laplacian_threshold_score_history_chart.jpeg"
+    plt.plot(range(len(score_history)), score_history)
+    plt.xlabel('Batch')
+    plt.ylabel('Objective function - Sore')
+    plt.savefig(fig_save_path)
+    plt.clf()
+
+
+if __name__ == '__main__':
+    image_lists = [
+        (  # "('0', '100', '0')"
+            "./TCGA-BJ-A3F0-01A-01-TSA.728CE583-95BE-462B-AFDF-FC0B228DF3DE__3_masked.tiff",
+            "./TCGA-BJ-A3F0-01A-01-TSA.728CE583-95BE-462B-AFDF-FC0B228DF3DE__3.svs"
+        ),
+        (  # "('0', '100', '0')"
+            "./TCGA-DJ-A1QG-01A-01-TSA.04c62c21-dd45-49ea-a74f-53822defe097__2000_masked.tiff",
+            "./TCGA-DJ-A1QG-01A-01-TSA.04c62c21-dd45-49ea-a74f-53822defe097__2000.svs"
+        ),
+        # (  # "('0', '100', '0')"
+        #     "./TCGA-EL-A3ZQ-01A-01-TS1.344610D2-AB50-41C6-916E-FF0F08940BF1__2000_masked.tiff",
+        #     "./TCGA-EL-A3ZQ-01A-01-TS1.344610D2-AB50-41C6-916E-FF0F08940BF1__2000.svs"
+        # ),
+        (  # "('45', '55', '0')"
+            "./TCGA-ET-A39N-01A-01-TSA.C38FCE19-9558-4035-9F0B-AD05B9BE321D___198_masked.tiff",
+            "./TCGA-ET-A39N-01A-01-TSA.C38FCE19-9558-4035-9F0B-AD05B9BE321D___198.svs"
+        ),
+        # (  # "('0', '40', '60')"
+        #     "./TCGA-J8-A42S-01A-01-TSA.7B80CBEB-7B85-417E-AA0C-11C79DE40250__0_masked.tiff",
+        #     "./TCGA-J8-A42S-01A-01-TSA.7B80CBEB-7B85-417E-AA0C-11C79DE40250__0.svs"
+        # ),
+        (  # "('0', '90', '10')"
+            "./TCGA-ET-A39O-01A-01-TSA.3829C900-7597-4EA9-AFC7-AA238221CE69_7000_masked.tiff",
+            "./TCGA-ET-A39O-01A-01-TSA.3829C900-7597-4EA9-AFC7-AA238221CE69_7000.svs"
+        ),
+        (  # "('100', '0', '0')"
+            "./TCGA-EL-A4K7-11A-01-TS1.C08B59AA-87DF-4ABB-8B70-25FEF9893C7F__70_masked.tiff",
+            "./TCGA-EL-A4K7-11A-01-TS1.C08B59AA-87DF-4ABB-8B70-25FEF9893C7F__70.svs"
+        ),
+        (  # "('100', '0', '0')"
+            "./TCGA-EL-A3TB-11A-01-TS1.6E0966C9-1552-4B30-9008-8ACF737CA8C3__2000_masked.tiff",
+            "./TCGA-EL-A3TB-11A-01-TS1.6E0966C9-1552-4B30-9008-8ACF737CA8C3__2000.svs"
+        ),
+    ]
+
+    learned_threshold = update_and_find_best_threshold(500, learn_threshold_and_log_cf_matrix_per_patch=True)
+    update_and_find_best_threshold(learned_threshold, learn_threshold_and_log_cf_matrix_per_patch=False)
+
+# Start with 500 with jump size 120 and decay 0.85
+# table:{'TP': 15018, 'FP': 412, 'TN': 66898, 'FN': 2389},
+# table_per_slide:[
+# {'TP': 460, 'FP': 0, 'TN': 19618, 'FN': 1426},
+# {'TP': 4624, 'FP': 126, 'TN': 14100, 'FN': 226},
+# {'TP': 1138, 'FP': 4, 'TN': 6671, 'FN': 492},
+# {'TP': 7615, 'FP': 92, 'TN': 20871, 'FN': 234},
+# {'TP': 78, 'FP': 18, 'TN': 1880, 'FN': 4},
+# {'TP': 1103, 'FP': 172, 'TN': 3758, 'FN': 7}
+# ]
+# threshold:298.86314585743395,jump_size:120

database_crawlers/image_patcher/test_image_patcher/nci_svs_and_masks/run_patch_evaluator_and_visualizer.sh

@@ -0,0 +1,6 @@
+export PYTHONPATH="${PYTHONPATH}:../../../../";
+export PYTHONPATH="${PYTHONPATH}:../../../";
+export PYTHONPATH="${PYTHONPATH}:../../";
+export PYTHONPATH="${PYTHONPATH}:../";
+export PYTHONPATH="${PYTHONPATH}:./";
+python evaluate_image_patcher_and_visualize.py;

database_crawlers/image_patcher/test_image_patcher/run_patch_distribution.sh

@@ -0,0 +1,4 @@
+export PYTHONPATH="${PYTHONPATH}:../../";
+export PYTHONPATH="${PYTHONPATH}:../";
+export PYTHONPATH="${PYTHONPATH}:./";
+python patcher_distribution.py;

database_crawlers/national_cancer_institute/cells_chart.py

@@ -0,0 +1,18 @@
+import pathlib
+
+import matplotlib.pyplot as plt
+
+from national_cancer_institute.read_xml_file import get_slide_info_from_bcr_xml
+
+if __name__ == '__main__':
+    data_dir = "data/"
+    slide_infos = {}
+    for xml_path in pathlib.Path(data_dir).glob("**/*.xml"):
+        slide_infos.update(get_slide_info_from_bcr_xml(str(xml_path)))
+    cell_percents = [int(item[1]) for item in slide_infos.values() if int(item[2]) == 0]
+    print("tumor:", len([i for i in cell_percents if i == 100]))
+    print("normal", len([i for i in cell_percents if i == 0]))
+    print([i for i in cell_percents if i != 0 and i != 100])
+    print(len(cell_percents))
+    plt.hist(cell_percents, bins=150)
+    plt.savefig("tumor_cell_distribution.jpeg")

database_crawlers/national_cancer_institute/patch_distribution.py

@@ -0,0 +1,65 @@
+import concurrent.futures
+import os
+import pathlib
+
+import matplotlib.pyplot as plt
+from tqdm import tqdm
+
+from config import Config
+from image_patcher import ImageAndSlidePatcher
+
+
+def save_patch_distribution(database_path):
+    def patch_image(image_path):
+        try:
+            image_path = str(image_path)
+            file_name = ImageAndSlidePatcher._get_file_name_from_path(image_path)
+            slide_id = file_name.split(".")[0]
+            slide_patch_dir = os.path.join(patch_dir, slide_id)
+
+            if ImageAndSlidePatcher._get_extension_from_path(image_path) in [".tiff", ".tif", ".svs"]:
+                zarr_object = ImageAndSlidePatcher._zarr_loader(image_path)
+                total_counts = ImageAndSlidePatcher._get_number_of_initial_frags(zarr_object=zarr_object)
+            else:
+                jpeg_image = ImageAndSlidePatcher._jpeg_loader(image_path)
+                jpeg_image = ImageAndSlidePatcher.ask_image_scale_and_rescale(jpeg_image)
+                total_counts = ImageAndSlidePatcher._get_number_of_initial_frags(zarr_object=jpeg_image)
+            if os.path.exists(slide_patch_dir):
+                fragment_id = len([i for i in pathlib.Path(slide_patch_dir).glob("*.jpeg")])
+                return fragment_id, total_counts
+        except Exception as e:
+            print("error")
+            print(e)
+            raise e
+
+    res_patch_counts = []
+
+    data_dir = os.path.join(database_path, "data")
+
+    patch_dir = os.path.join(database_path, "patches")
+
+    with concurrent.futures.ThreadPoolExecutor(max_workers=Config.workers) as executor:
+        image_paths = pathlib.Path(data_dir).glob("**/*.svs")
+        image_paths = [i for i in image_paths]
+        print()
+        for res in tqdm(executor.map(patch_image, image_paths), total=len(image_paths)):
+            if res:
+                frags, total = res
+                res_patch_counts.append(res)
+    print(res_patch_counts)
+    plt.hist([i[0] for i in res_patch_counts], bins=100)
+    plt.xlabel("Patch per slide")
+    plt.ylabel("Frequency")
+    plt.savefig("patch_distribution.jpeg")
+    plt.clf()
+
+    plt.hist([round(i[0] / (i[1] + 0.00001), 5) * 100 for i in res_patch_counts], bins=100)
+    plt.xlabel("Patch per slide percent")
+    plt.ylabel("Frequency")
+    plt.savefig("patch_percent_distribution.jpeg")
+    plt.clf()
+
+
+if __name__ == '__main__':
+    database_directory = "../"
+    save_patch_distribution(os.path.join(database_directory, "national_cancer_institute"))

database_crawlers/national_cancer_institute/read_xml_file.py

@@ -0,0 +1,26 @@
+from xml.dom import minidom
+
+
+def get_slide_info_from_bcr_xml(xml_path):
+    file = minidom.parse(xml_path)
+    patient = file.childNodes[0].getElementsByTagName("bio:patient")[0]
+    data_dict = {}
+    try:
+        for i in range(10):
+            percent_tumor_cells = patient.getElementsByTagName("bio:percent_tumor_cells")[i].childNodes[
+                0].data.strip()
+            percent_normal_cells = patient.getElementsByTagName("bio:percent_normal_cells")[i].childNodes[
+                0].data.strip()
+            percent_stormal_cells = patient.getElementsByTagName("bio:percent_stromal_cells")[i].childNodes[
+                0].data.strip()
+            slide_barcode = patient.getElementsByTagName("shared:bcr_slide_barcode")[i].childNodes[0].data.strip()
+            data_dict[slide_barcode] = (percent_normal_cells, percent_tumor_cells, percent_stormal_cells)
+    except Exception as e:
+        pass
+    return data_dict
+
+
+if __name__ == '__main__':
+    path = "../national_cancer_institute/data/1aea8f2a-f809-4f19-bed3-1365e9aab33b/nationwidechildrens.org_biospecimen.TCGA-BJ-A28X.xml"
+    res = get_slide_info_from_bcr_xml(path)
+    print(res)

database_crawlers/national_cancer_institute/run_cell_distribution.sh

@@ -0,0 +1,4 @@
+export PYTHONPATH="${PYTHONPATH}:../../";
+export PYTHONPATH="${PYTHONPATH}:../";
+export PYTHONPATH="${PYTHONPATH}:./";
+python cells_chart.py;

database_crawlers/national_cancer_institute/run_patch_distribution.sh

@@ -0,0 +1,5 @@
+export PYTHONPATH="${PYTHONPATH}:../../";
+export PYTHONPATH="${PYTHONPATH}:../";
+export PYTHONPATH="${PYTHONPATH}:../image_patcher";
+export PYTHONPATH="${PYTHONPATH}:./";
+python patch_distribution.py;

database_crawlers/papsociaty/duplicate_image.txt

@@ -0,0 +1,29 @@
+1811210076455461803,BENIGN-BTNpap-hyperplZC04-10370x4_0
+7845783054062606488,BENIGN-Dan_Colloid1_0
+7637345021064072354,BENIGN-FTH468BTN_sheets_follicles_1_0
+814792220375115888,BENIGN-GD40T
+2888555316355101926,BENIGN-gd-fn20_0
+-8312464544528256569,BENIGN-gd10p_0
+-2254510488499374008,BENIGN-gd20g_0
+2271447961045108683,MALIGNANT-ATC20L_0
+7269337178939971574,MALIGNANT-ATC20b_0
+-9073528708751422131,MALIGNANT-ATC40BB_0
+-8571937763202005072,MALIGNANT-ATC40FC_0
+-8610450256188951874,MALIGNANT-ATC40J_0
+-7854679564093375561,MALIGNANT-ATC40p_0
+-4977783033606377395,MALIGNANT-ATC5A_0
+1342853015262631578,MALIGNANT-Atc63w_0
+431837691807971266,MALIGNANT-C03-54313A_0
+8004646368797684873,MALIGNANT-C03-54313B_0
+8041832687277297518,MALIGNANT-C03-54313C_0
+6449521961463025237,MALIGNANT-C03-54313D_0
+-8688277356782858138,MALIGNANT-C03-54313E_0
+-9068734717515564721,MALIGNANT-C03-54313F_0
+-5752120463987418399,MALIGNANT-C03-54313G_0
+8889530878367993817,MALIGNANT-Ed82C_1_0
+2934951614446666978,"MALIGNANT-Follicular_neoplasm2,_low_power,_confirmed_FVPTC_DQ_SM_0"
+-1541914789037593200,"MALIGNANT-Pap_CA,_excellent_inclusion,_DQ_0"
+-1717557305576530323,"MALIGNANT-Pap_CA,_powdery_nuclei,_small_nucleoli_and_small_inclusion,_PAP_hp_0"
+947862089311894766,"MALIGNANT-Papillary_CA,_giant_cell,_DQ_lp_0"
+-8520432463383972777,"MALIGNANT-Papillary_CA,_giant_cell_and_tumor_sheets,_PAP_lp2_0"
+-4759582710547943524,"MALIGNANT-Papillary_CA,_high_cellularity_3,_PAP_lp_0"

database_crawlers/papsociaty/remove_duplicate_patches.py

@@ -0,0 +1,13 @@
+import os
+import shutil
+if __name__ == '__main__':
+    duplicate_info_file_path = "duplicate_image.txt"
+    with open(duplicate_info_file_path, "r") as file:
+        for line in file.readlines():
+            folder_id = line.split(",")[0]
+            folder_path = os.path.join("./patches", folder_id)
+            if os.path.exists(folder_path):
+                shutil.rmtree(folder_path)
+                print("deleted")
+            else:
+                print("no")

database_crawlers/stanford_tissue_microarray/database_crawler.py

@@ -0,0 +1,64 @@
+import json
+from urllib.parse import urlparse
+from urllib.request import urlretrieve
+
+import requests
+from bs4 import BeautifulSoup
+
+from database_crawlers.web_stain_sample import WebStainImage, StainType
+
+
+class StanfordTissueMicroArrayStainSample(WebStainImage):
+
+    def __init__(self, database_name, image_id, image_web_label, report, stain_type, is_wsi):
+        super().__init__(database_name, image_id, image_web_label, report, stain_type, is_wsi)
+
+    def get_slide_view_url(self):
+        return f"https://storage.googleapis.com/jpg.tma.im/{self.image_id}"
+
+    def get_file_name(self):
+        image_raw_id = self.image_id.replace("/", "_")
+        image_raw_id = ".".join(image_raw_id.split(".")[:len(image_raw_id.split(".")) - 1])
+        return self.save_path + image_raw_id
+
+    def get_relative_image_path(self):
+        return self.get_file_name() + ".jpeg"
+
+    def get_relative_json_path(self):
+        return self.get_file_name() + ".json"
+
+    def crawl_image_save_jpeg(self):
+        urlretrieve(self.get_slide_view_url(), self.get_relative_image_path())
+        json_object = json.dumps(self.to_json())
+        with open(self.get_relative_json_path(), "w") as outfile:
+            outfile.write(json_object)
+
+
+class StanfordTissueMicroArraySlideProvider:
+    page_link = "https://tma.im/cgi-bin/selectImages.pl?organ=thyroid"
+    database_name = "StanfordTissueMicroArray"
+    stain_type = StainType.UNKNOWN
+    is_wsi = False
+
+    @classmethod
+    def get_web_stain_samples(cls):
+        payload = {'250 small images': '250 small images'}
+        files = []
+        headers = {
+            'Cookie': 'DAD_ATTEMPTS=0; DAD_SID=36d77eb69e009b1cf1ebc9c3d7866546; DAD_USERID=WORLD'
+        }
+        html_text = requests.post(cls.page_link, files=files, headers=headers, data=payload).content.decode("utf-8")
+        soup = BeautifulSoup(html_text, 'html.parser')
+        search_results = soup.find_all("div", {"class": "iDiv0", "style": "width: 86px; height: 260px;"})
+        for result_item in search_results:
+            image_url = result_item.find("a", {"target": "_blank"}).attrs['href']
+            image_id = "/".join(urlparse(image_url).path.strip("/").split("/")[1:])
+            image_web_label = list(result_item.find_all("p", {"class": "iDiv1"}))[-2].text
+            yield StanfordTissueMicroArrayStainSample(cls.database_name, image_id, image_web_label, None,
+                                                      cls.stain_type, cls.is_wsi)
+
+
+if __name__ == '__main__':
+    for slide in StanfordTissueMicroArraySlideProvider.get_web_stain_samples():
+        print(slide.image_id, slide.image_web_label, slide.get_slide_view_url())
+        slide.crawl_image_save_jpeg()

database_crawlers/utils.py

@@ -0,0 +1,87 @@
+import concurrent.futures
+import concurrent.futures
+import time
+from urllib.error import HTTPError
+from urllib.request import urlretrieve
+
+from torch.utils.data import IterableDataset
+from tqdm import tqdm
+
+from config import Config
+
+
+def find_in_log_n(start, end, func, bias=0.3):
+    if end - start <= 1:
+        return start
+    mid = int(start * (1 - bias) + end * bias)
+    if start == mid:
+        mid += 1
+    if func(mid):
+        return find_in_log_n(mid, end, func)
+    else:
+        return find_in_log_n(start, mid, func)
+
+
+def fetch_tile_content(tile_url, retry=15):
+    for i in range(retry):
+        try:
+            image_path = urlretrieve(tile_url)[0]
+            with open(image_path, "rb") as file:
+                return file.read()
+        except Exception as e:
+            print("e", end="|")
+            time.sleep(2 ** (0.3 * (i + 1)))
+            if i == retry - 1:
+                if input("continue") == "y":
+                    return fetch_tile_content(tile_url, retry)
+                raise e
+    raise HTTPError("Not able for fetch image tile", code=500, msg="", hdrs={}, fp=None)
+
+
+def download_urls_in_thread(url_and_index_list):
+    def download(args):
+        url, index = args
+        file_content = fetch_tile_content(url)
+        return file_content, index
+
+    with concurrent.futures.ThreadPoolExecutor(max_workers=Config.workers) as executor:
+        for tile, i in tqdm(executor.map(download, url_and_index_list), total=len(url_and_index_list)):
+            yield tile, i
+
+
+def _get_alignment_sore_and_percent(seq1, seq2, match_score=2, mismatch_score=-1, gap_score=-1):
+    from alignment.sequence import Sequence
+    from alignment.sequencealigner import SimpleScoring, GlobalSequenceAligner
+    from alignment.vocabulary import Vocabulary
+    a = Sequence(seq1)
+    b = Sequence(seq2)
+
+    v = Vocabulary()
+    aEncoded = v.encodeSequence(a)
+    bEncoded = v.encodeSequence(b)
+
+    scoring = SimpleScoring(match_score, mismatch_score)
+    aligner = GlobalSequenceAligner(scoring, gap_score)
+    score = aligner.align(aEncoded, bEncoded, backtrace=False)
+
+    return score
+
+
+def get_normalized_score(seq1, seq2):
+    score = _get_alignment_sore_and_percent(seq1, seq2)
+    return score / (len(seq2) + len(seq1))
+
+
+class DatasetWithGenerator(IterableDataset):
+    def __init__(self, generator):
+        self.generator = generator
+
+    def __iter__(self):
+        return self.generator
+
+
+if __name__ == '__main__':
+    import math
+
+    print(math.log2(1000 * 1000))
+    print(find_in_log_n(0, 100, lambda x: x <= 76))

database_crawlers/web_stain_sample.py

@@ -0,0 +1,296 @@
+import enum
+import json
+import time
+from io import BytesIO
+from urllib.request import Request, urlopen
+
+import cv2
+import numpy as np
+from PIL import Image
+from tifffile import TiffWriter
+
+from database_crawlers.utils import find_in_log_n, fetch_tile_content, download_urls_in_thread
+
+
+class StainType(enum.Enum):
+    H_AND_E = 0, "H&E"
+    UNKNOWN = 1, "UNKNOWN"
+
+
+class ThyroidCancerLevel(enum.Enum):
+    UNKNOWN = -1, "UNKNOWN"
+    MALIGNANT = 0, "MALIGNANT"
+    BENIGN = 1, "BENIGN"
+
+    @staticmethod
+    def get_thyroid_level_from_diagnosis_label(label: str):
+        label = label.lower()
+        if "malignant" in label:
+            return ThyroidCancerLevel.MALIGNANT
+        elif "benign" in label:
+            return ThyroidCancerLevel.BENIGN
+        else:
+            return ThyroidCancerLevel.UNKNOWN
+
+
+class ThyroidType(enum.Enum):
+    UNKNOWN = -1, "UNKNOWN"
+    NORMAL = 0, "NORMAL"
+    PAPILLARY_CARCINOMA = 1, "PAPILLARY_CARCINOMA"
+    GRAVES_DISEASE = 2, "GRAVES_DISEASE"
+    NODULAR_GOITER = 3, "NODULAR_GOITER"
+    HASHIMOTO_THYROIDITIS = 4, "HASHIMOTO_THYROIDITIS"
+    FOLLICULAR_CARCINOMA = 5, "FOLLICULAR_CARCINOMA"
+    FOLLICULAR_ADENOMA = 6, "FOLLICULAR_ADENOMA"
+    COLLOID_GOITER = 7, "COLLOID_GOITER"
+
+    @staticmethod
+    def get_thyroid_type_from_diagnosis_label(label: str):
+        label = label.lower()
+        if "normal" in label:
+            return ThyroidType.NORMAL
+        elif "papillary" in label:
+            return ThyroidType.PAPILLARY_CARCINOMA
+        elif "grave" in label:
+            return ThyroidType.GRAVES_DISEASE
+        elif "nodular" in label and "goiter" in label:
+            return ThyroidType.NODULAR_GOITER
+        elif "hashimoto" in label:
+            return ThyroidType.HASHIMOTO_THYROIDITIS
+        elif "follicular" in label:
+            if "adenoma" in label:
+                return ThyroidType.FOLLICULAR_ADENOMA
+            else:
+                return ThyroidType.FOLLICULAR_CARCINOMA
+        elif "colloid" in label and "goiter" in label:
+            return ThyroidType.COLLOID_GOITER
+        else:
+            return ThyroidType.UNKNOWN
+
+
+class WebStainImage:
+    save_path = "data/"
+
+    def __init__(self, database_name, image_id, image_web_label, report, stain_type, is_wsi):
+        self.database_name = database_name
+        self.image_id = image_id
+        self.image_web_label = image_web_label
+        self.report = report
+        self.stain_type = stain_type
+        self.is_wsi = is_wsi
+
+    def to_json(self):
+        return {"database_name": self.database_name,
+                "image_id": self.image_id,
+                "image_web_label": self.image_web_label,
+                "image_class_label": self.image_class_label,
+                "report": self.report,
+                "stain_type": self.stain_type.value[1],
+                "is_wsi": self.is_wsi}
+
+    @staticmethod
+    def sorted_json_keys():
+        return ["database_name",
+                "image_id",
+                "image_web_label",
+                "image_class_label",
+                "report",
+                "stain_type",
+                "is_wsi"]
+
+    @property
+    def image_class_label(self):
+        return ThyroidType.get_thyroid_type_from_diagnosis_label(self.image_web_label).value[1]
+
+    def get_slide_view_url(self):
+        raise NotImplemented("get_slide_view_url")
+
+    def crawl_image_save_jpeg_and_json(self):
+        raise NotImplemented("crawl_image_get_jpeg")
+
+    def _get_file_path_name(self):
+        return self.save_path + self.image_id
+
+    def _get_relative_image_path(self):
+        return self._get_file_path_name() + ".jpeg"
+
+    def _get_relative_tiff_image_path(self):
+        return self._get_file_path_name() + ".tiff"
+
+    def _get_relative_json_path(self):
+        return self._get_file_path_name() + ".json"
+
+    def _save_json_file(self):
+        json_object = json.dumps(self.to_json())
+        with open(self._get_relative_json_path(), "w") as outfile:
+            outfile.write(json_object)
+
+
+class WebStainWSI(WebStainImage):
+    def __init__(self, database_name, image_id, image_web_label, report, stain_type, is_wsi):
+        super().__init__(database_name, image_id, image_web_label, report, stain_type, is_wsi)
+
+    def _get_tile_url(self, zoom, partition=None, i=None, j=None):
+        raise NotImplemented("_get_tile_url")
+
+    def _generate_tile_urls(self):
+        raise NotImplemented("generate tile urls")
+
+    def find_best_zoom(self):
+        return 0
+
+    def _find_first_tile_width(self):
+        image_content = fetch_tile_content(self._get_tile_url(self.find_best_zoom(), partition=0, i=0, j=0))
+        img = Image.open(BytesIO(image_content))
+        return img.size[0], img.size[1]
+
+    def _fetch_all_tiles(self):
+        batch = []
+        index = 0
+        for url in self._generate_tile_urls():
+            batch.append((url, index))
+            # DONE
+            index += 1
+        # download last batch
+        if len(batch) != 0:
+            for content, downloaded_index in download_urls_in_thread(batch):
+                yield content, downloaded_index
+        print("Slide download tiles done!!!")
+
+    def crawl_image_save_jpeg_and_json(self):
+        raise NotImplemented("crawl_image_save_jpeg_and_json")
+
+
+class WebStainWSIOneDIndex(WebStainWSI):
+    def __init__(self, database_name, image_id, image_web_label, report, stain_type, is_wsi):
+        super().__init__(database_name, image_id, image_web_label, report, stain_type, is_wsi)
+        self.last_partition = None
+
+    def _find_last_partition(self):
+        print("Finding last partition: ", end="")
+
+        def func(partition, retry=3):
+            print(partition, end="")
+            for i in range(retry):
+                try:
+                    request = Request(self._get_tile_url(self.find_best_zoom(), partition=partition), method='HEAD')
+                    resp = urlopen(request)
+                    headers = resp.info()
+                    print("<", end=", ")
+                    return True
+                except Exception as e:
+                    print("e", end="")
+                    time.sleep(2 ** (0.1 * (i + 1)))
+            print(">", end=", ")
+            return False
+
+        return find_in_log_n(0, 1000 * 1000, func)
+
+    def _generate_tile_urls(self):
+        for partition in range(self.last_partition + 1):
+            yield self._get_tile_url(self.find_best_zoom(), partition=partition)
+
+    def crawl_image_save_jpeg_and_json(self):
+        def generator():
+            while True:
+                if first_temp_rows:
+                    yield first_temp_rows[0]
+                    del first_temp_rows[0]
+                else:
+                    res = next(content_fetcher, -1)
+                    if res == -1:
+                        break
+                    img = cv2.imdecode(np.frombuffer(res[0], np.uint8), -1)
+                    if len(img.shape) == 2:
+                        img = cv2.cvtColor(img, cv2.COLOR_GRAY2BGR)
+                    yield img
+
+        first_image_width, first_image_height = self._find_first_tile_width()
+        first_temp_rows = []
+        column_tiles, row_tiles = None, None
+        self.last_partition = self._find_last_partition()
+        content_fetcher = self._fetch_all_tiles()
+        with TiffWriter(self._get_relative_tiff_image_path(), bigtiff=True) as tif:
+            while column_tiles is None:
+                content, index = content_fetcher.__next__()
+                image_array = cv2.imdecode(np.frombuffer(content, np.uint8), cv2.IMREAD_COLOR)
+                first_temp_rows.append(image_array)
+                if image_array.shape[1] != first_image_width:
+                    column_tiles = index + 1
+                    row_tiles = (self.last_partition + 1) // column_tiles
+            shape = (first_image_height * row_tiles, first_image_width * column_tiles, 3)
+            tif.write(generator(), subfiletype=1, tile=(first_image_height, first_image_width), shape=shape,
+                      dtype=np.uint8,
+                      compression='JPEG',  # TODO
+                      photometric='rgb')
+
+        """
+        Save json file
+        """
+        self._save_json_file()
+
+
+class WebStainWSITwoDIndex(WebStainWSI):
+    def __init__(self, database_name, image_id, image_web_label, report, stain_type, is_wsi):
+        super().__init__(database_name, image_id, image_web_label, report, stain_type, is_wsi)
+        self.last_i = None
+        self.last_j = None
+
+    def _generate_tile_urls(self):
+        for j in range(self.last_j + 1):
+            for i in range(self.last_i + 1):
+                yield self._get_tile_url(self.find_best_zoom(), i=i, j=j)
+
+    def _find_last_i_and_j(self):
+        def func(i, j, retry=3):
+            print(f"{i}-{j}", end="")
+            for r in range(retry):
+                try:
+                    request = Request(self._get_tile_url(self.find_best_zoom(), i=i, j=j), method='HEAD')
+                    resp = urlopen(request)
+                    headers = resp.info()
+                    print("<", end=", ")
+                    return True
+                except Exception as e:
+                    print("e", end="")
+                    time.sleep(2 ** (0.1 * (r + 1)))
+            print(">", end=", ")
+            return False
+
+        print("Finding last i: ", end="")
+        i_func = lambda i: func(i=i, j=0)
+        last_i = find_in_log_n(0, 1000, i_func)
+        print("\nFinding last j: ")
+        j_func = lambda j: func(i=0, j=j)
+        last_j = find_in_log_n(0, 1000, j_func)
+        return last_i, last_j
+
+    def crawl_image_save_jpeg_and_json(self):
+        def generator():
+            while True:
+                res = next(content_fetcher, -1)
+                if res == -1:
+                    break
+                res = cv2.imdecode(np.frombuffer(res[0], np.uint8), -1)
+                if max(res.shape) >= 260:
+                    raise Exception(f"warning shape: {res.shape}")
+                res = cv2.resize(res, (min(res.shape[1], 256), min(res.shape[0], 256)))
+                yield res
+
+        first_image_width = 256
+        first_image_height = 256
+        self.last_i, self.last_j = self._find_last_i_and_j()
+        content_fetcher = self._fetch_all_tiles()
+        with TiffWriter(self._get_relative_tiff_image_path(), bigtiff=True) as tif:
+            shape = (first_image_height * (self.last_j + 1), first_image_width * (self.last_i + 1), 3)
+            tif.write(generator(), subfiletype=1,
+                      tile=(first_image_height, first_image_width),
+                      shape=shape,
+                      dtype=np.uint8,
+                      compression='JPEG',  # TODO
+                      photometric='rgb')
+
+        """
+        Save json file
+        """
+        self._save_json_file()

datasets_sample_view/convert_to_jpeg.py

@@ -0,0 +1,20 @@
+from PIL import Image
+import zarr
+import tifffile
+
+def convert_tif_to_jpeg():
+    input_address = "data/test/1672.tiff"
+    # outfile = "data/test/out.jpeg"
+    outfile = "data/test/out.zarr"
+    image_zarr = tifffile.imread(input_address, aszarr=True, key=0)
+    zarr_image = zarr.open(image_zarr, mode='r')
+    zarr.save(outfile, zarr_image)
+    ## RAM PROBLEM
+    # im = Image.open()
+    # out = im.convert("RGB")
+    # out.save(outfile, "JPEG", quality=90)
+
+
+if __name__ == '__main__':
+    Image.MAX_IMAGE_PIXELS = 1000 * 1000 * 256 * 256
+    convert_tif_to_jpeg()

datasets_sample_view/dataset_sample_view.py

@@ -0,0 +1,50 @@
+# import libtiff
+# import pytiff
+import cv2
+import tifffile
+
+
+def show_tif_image(address, name, key=0, w_from=0, h_from=0, size=700, whole_image=False):
+    import zarr
+    image_zarr = tifffile.imread(address, aszarr=True, key=key)
+    zarr = zarr.open(image_zarr, mode='r')
+    if not whole_image:
+        image_frag = zarr[w_from:min(w_from + size, zarr.shape[0]), h_from:min(h_from + size, zarr.shape[1])]
+    else:
+        image_frag = zarr[0:zarr.shape[0], 0:zarr.shape[1]]
+    cv2.imshow(f"name:{name} - shape:{image_frag.shape} - page:{key}", image_frag)
+    print(f"name: {name}, shape: {zarr.shape}")
+    image_zarr.close()
+
+
+def show_CAMELYON16_sample_view():
+    # show_tif_image('data/CAMELYON16/tumor_084.tif', "CAMELYON16", key=7)
+    show_tif_image('data/CAMELYON16/tumor_084.tif', "CAMELYON16", key=0, w_from=10000, h_from=50000)
+
+
+def show_CAMELYON17_sample_view():
+    show_tif_image('data/CAMELYON17/patient_083_node_4.tif', "CAMELYON17", key=7)
+
+
+def show_Papsociety_sample_view():
+    image_frag = cv2.imread(
+        'data/Papsociety/Follicular_neoplasm2,_low_power,_confirmed_FVPTC_DQ_SM.jpg')
+    cv2.imshow(f"Papsociety - {image_frag.shape}", image_frag)
+
+
+def show_test(name, ):
+    # show_tif_image('data/CAMELYON16/tumor_084.tif', "CAMELYON16", key=7)
+    show_tif_image('data/test/1272.tiff', name, key=0, w_from=1300, h_from=0, size=1000)
+
+
+
+if __name__ == '__main__':
+    # show_CAMELYON16_sample_view()
+    # show_CAMELYON17_sample_view()
+    # show_Papsociety_sample_view()
+    show_tif_image('data/test/1272.tiff', "1", key=0, w_from=1000, h_from=100, size=1000)
+    show_tif_image('data/test/1272.tiff', "2", key=0, w_from=1000, h_from=1000, size=1000)
+
+    while True:
+        if cv2.waitKey(1) == ord('q'):
+            break

requirements.txt

@@ -0,0 +1,180 @@
+absl-py==1.0.0
+aiohttp==3.8.1
+aiosignal==1.2.0
+alignment==1.0.10
+appdirs==1.4.4
+argon2-cffi==20.1.0
+asgiref==3.2.10
+astunparse==1.6.3
+async-generator==1.10
+async-timeout==4.0.2
+attrs==21.2.0
+backcall==0.2.0
+bleach==3.3.0
+blis==0.7.5
+cachetools==4.2.4
+catalogue==2.0.6
+certifi==2021.10.8
+cffi==1.14.5
+charset-normalizer==2.0.8
+click==8.0.3
+colorama==0.4.4
+convertapi==1.4.0
+cryptography==3.4.7
+cycler==0.11.0
+cymem==2.0.6
+Cython==0.29.23
+decorator==5.0.9
+defusedxml==0.7.1
+distlib==0.3.2
+dj-database-url==0.5.0
+Django==3.1.2
+django-crispy-forms==1.9.2
+django-heroku==0.3.1
+django-rest==0.8.7
+djangorestframework==3.13.1
+djangorestframework-simplejwt==5.0.0
+entrypoints==0.3
+et-xmlfile==1.1.0
+factory-boy==3.2.1
+Faker==12.3.0
+filelock==3.0.12
+flatbuffers==2.0
+fonttools==4.28.2
+frozenlist==1.3.0
+gast==0.4.0
+gensim==4.1.2
+google-auth==2.3.3
+google-auth-oauthlib==0.4.6
+google-pasta==0.2.0
+grpcio==1.42.0
+gunicorn==20.0.4
+h5py==3.6.0
+hazm==0.7.0
+huggingface-hub==0.6.0
+idna==3.3
+importlib-metadata==4.8.2
+ipykernel==5.5.5
+ipython==7.24.1
+ipython-genutils==0.2.0
+ipywidgets==7.6.3
+jedi==0.18.0
+Jinja2==3.0.1
+joblib==1.0.1
+jsonschema==3.2.0
+jupyter==1.0.0
+jupyter-client==6.1.12
+jupyter-console==6.4.0
+jupyter-core==4.7.1
+jupyterlab-pygments==0.1.2
+jupyterlab-widgets==1.0.0
+keras==2.7.0
+Keras-Preprocessing==1.1.2
+kiwisolver==1.3.2
+langcodes==3.3.0
+libclang==12.0.0
+libtiff==0.4.2
+Markdown==3.3.6
+MarkupSafe==2.0.1
+matplotlib==3.5.0
+matplotlib-inline==0.1.2
+mistune==0.8.4
+multidict==6.0.2
+murmurhash==1.0.6
+nbclient==0.5.3
+nbconvert==6.0.7
+nbformat==5.1.3
+nest-asyncio==1.5.1
+nltk==3.3
+notebook==6.4.0
+numpy==1.20.3
+oauthlib==3.1.1
+opencv-python==4.5.2.54
+openpyxl==3.0.7
+opt-einsum==3.3.0
+packaging==20.9
+pandas==1.2.4
+pandocfilters==1.4.3
+parso==0.8.2
+pathy==0.6.1
+pickleshare==0.7.5
+Pillow==8.4.0
+preshed==3.0.6
+prometheus-client==0.11.0
+prompt-toolkit==3.0.18
+protobuf==3.19.1
+psycopg2==2.8.6
+pyaes==1.6.1
+pyaml==21.10.1
+pyasn1==0.4.8
+pyasn1-modules==0.2.8
+pycparser==2.20
+pydantic==1.8.2
+Pygments==2.9.0
+PyJWT==2.3.0
+pynput==1.7.5
+pyOpenSSL==20.0.1
+pyparsing==2.4.7
+pyrsistent==0.17.3
+pyTelegramBotAPI==4.4.0
+python-dateutil==2.8.1
+python-decouple==3.6
+pytz==2020.1
+PyWavelets==1.1.1
+pywin32==301
+pywinpty==1.1.1
+PyYAML==6.0
+pyzmq==22.1.0
+qtconsole==5.1.0
+QtPy==1.9.0
+regex==2022.4.24
+requests==2.26.0
+requests-oauthlib==1.3.0
+rsa==4.8
+scikit-learn==0.24.2
+scipy==1.7.0
+Send2Trash==1.5.0
+setuptools-scm==6.3.2
+six==1.16.0
+sklearn==0.0
+smart-open==5.2.1
+spacy==3.2.1
+spacy-legacy==3.0.8
+spacy-loggers==1.0.1
+sqlparse==0.4.1
+srsly==2.4.2
+Telethon==1.24.0
+tensorboard==2.7.0
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.0
+tensorflow==2.7.0
+tensorflow-estimator==2.7.0
+tensorflow-io-gcs-filesystem==0.22.0
+termcolor==1.1.0
+terminado==0.10.0
+testpath==0.5.0
+thinc==8.0.13
+threadpoolctl==2.2.0
+tokenizers==0.12.1
+tomli==1.2.2
+torch==1.10.1
+torchtext==0.11.1
+torchvision==0.11.1
+tornado==6.1
+tqdm==4.62.3
+traitlets==5.0.5
+transformers==4.19.2
+typer==0.4.0
+typing_extensions==4.0.1
+urllib3==1.26.7
+virtualenv==20.4.7
+wasabi==0.9.0
+wcwidth==0.2.5
+webencodings==0.5.1
+Werkzeug==2.0.2
+whitenoise==5.2.0
+widgetsnbextension==3.5.1
+wrapt==1.13.3
+xlrd==2.0.1
+yarl==1.7.2
+zipp==3.6.0

utils.py

@@ -0,0 +1,21 @@
+import itertools
+
+import cv2
+
+
+def show_and_wait(img, name="img", wait=True, save=False):
+    cv2.imshow(name, img)
+    if wait:
+        while cv2.waitKey() != ord('q'):
+            continue
+        cv2.destroyAllWindows()
+    if save:
+        cv2.imwrite(f"{name}.jpeg", img)
+
+
+def check_if_generator_is_empty(generator):
+    try:
+        first = next(generator)
+    except StopIteration:
+        return None
+    return itertools.chain([first], generator)