diff --git a/training/.gitignore b/training/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..916db7be6d9b28c9afbbb449836696585bf7b70d --- /dev/null +++ b/training/.gitignore @@ -0,0 +1,131 @@ +.vscode/ + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +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/ diff --git a/training/Engine/__init__.py b/training/Engine/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/training/Engine/evaluate.py b/training/Engine/evaluate.py new file mode 100644 index 0000000000000000000000000000000000000000..59ce60a350509e7907f8cf26249db9e9190d8c19 --- /dev/null +++ b/training/Engine/evaluate.py @@ -0,0 +1,105 @@ +import platform +import torch as T +import nibabel +import numpy as np + +from monai.networks.nets.unet import UNet +from monai.data import DataLoader, Dataset +from monai.metrics import compute_meandice +from monai.transforms import ( + AddChanneld, + Compose, + LoadImaged, + NormalizeIntensityd, + ToTensord, + Resized, + AsDiscrete, + ThresholdIntensityd, + KeepLargestConnectedComponent +) +from Engine.utils import ( + read_yaml, + load_model, + store_output +) + +def init_eval_file(directory): + with open(directory + "/evaluate.csv", "w+") as file: + file.write("epoch,train_loss,val_loss,dice_score\n") + +def append_eval(eval_path, input_filename, segment_filename, val_loss, dice_score): + with open(eval_path, 'a') as file: + file.write(f"{input_filename},{segment_filename},{val_loss},{dice_score}\n") + +def evaluate(model, loss_function, loader, device, evaluate_config): + + model.eval() + losses = [] + dices = [] + + transform = KeepLargestConnectedComponent([1], connectivity = 3) + + + with T.no_grad(): + for image in loader: + inp, boxes, label = image["image"].to(device), image["boxes"].to(device), image["label"].to(device) + directory_split = '\\' if platform.system() == 'Windows' else '/' + output = model(inp) + + original_filename = image['image_meta_dict']['filename_or_obj'][0] + segmentation_filename = f"{evaluate_config['save_directory']}{directory_split}seg_{original_filename.split(directory_split)[-1]}" + + original_image = nibabel.load(original_filename) + + loss = loss_function(output, label).item() + + output = output.cpu() + output[output >= evaluate_config['output_threshold']] = 1 + output[output < evaluate_config['output_threshold']] = 0 + output = output.to(device) + + output = transform(output) + + if(evaluate_config['save_segmentations']): + store_output(output, original_image, segmentation_filename, image['image_meta_dict']['affine'].squeeze(0).numpy()) + + dice = compute_meandice(output, label).item() + + + append_eval(evaluate_config['save_directory']+"evaluate.csv", original_filename, segmentation_filename, loss, dice) + losses.append(loss) + dices.append(dice) + + append_eval(evaluate_config['save_directory']+"evaluate.csv", 'Total', '', sum(losses)/len(losses), sum(dices)/len(dices)) + +def initiate(config_file): + config = read_yaml(config_file) + device = T.device(config["device"]) + + data = read_yaml(config["data"]["train_dataset"]) + + image_shape = (config["data"]["scale_dim"]["d_0"], config["data"]["scale_dim"]["d_1"], config["data"]["scale_dim"]["d_2"]) + + for i, d in enumerate(data['data']): + data['data'][i]['image'] = data['image_prefix'] + d['label'] + data['data'][i]['boxes'] = data['boxes_prefix'] + d['label'] + data['data'][i]['label'] = data['label_prefix'] + d['label'] + + transform = Compose( + [ + LoadImaged(keys=["image", "boxes", "label"]), + AddChanneld(keys=["image", "boxes", "label"]), + ToTensord(keys=["image", "boxes", "label"]), + ] + ) + + dataset = Dataset(data['data'], transform) + loader = T.utils.data.DataLoader(dataset, 1) + + model, loss = load_model(config['model'], eval = True) + model.load_state_dict(T.load(config["model"]["weights"])) + model.to(device) + + init_eval_file(config['evaluate']['save_directory']) + + evaluate(model, loss, loader, device, config['evaluate']) diff --git a/training/Engine/inference.py b/training/Engine/inference.py new file mode 100644 index 0000000000000000000000000000000000000000..d6b9fcea8319bcdc5f5318e3bf67a45c0786b820 --- /dev/null +++ b/training/Engine/inference.py @@ -0,0 +1,72 @@ +import platform +import nibabel +import torch as T +from monai.data import DataLoader, Dataset +from monai.transforms import ( + AddChanneld, + Compose, + LoadImaged, + NormalizeIntensityd, + Resized, + ThresholdIntensityd, + ToTensord +) + +from Engine.utils import ( + load_model, + read_yaml, + store_output +) + +def infer(model, loader, device, infer_config): + + model.eval() + + with T.no_grad(): + for image in loader: + inp, boxes = image["image"].to(device), image["boxes"].to(device) + directory_split = '\\' if platform.system() == 'Windows' else '/' + output = model(inp) + + original_filename = image['image_meta_dict']['filename_or_obj'][0] + segmentation_filename = f"{infer_config['save_directory']}{directory_split}seg_{original_filename.split(directory_split)[-1]}" + + original_image = nibabel.load(original_filename) + upsample = T.nn.Upsample(original_image.shape, mode='trilinear', align_corners = False) + output = upsample(output) + + print(image['image_meta_dict']['affine']) + store_output(output, original_image, segmentation_filename, image['image_meta_dict']['affine'].squeeze(0).numpy()) + + +def initiate(config_file): + config = read_yaml(config_file) + device = T.device(config["device"]) + + data = read_yaml(config["data"]["dataset"]) + + image_shape = (config["data"]["scale_dim"]["d_0"], config["data"]["scale_dim"]["d_1"], config["data"]["scale_dim"]["d_2"]) + + for i, d in enumerate(data['test']): + data['test'][i]['image'] = data['image_prefix'] + d['image'] + data['test'][i]['boxes'] = data['boxes_prefix'] + d['boxes'] + + + transform = Compose( + [ + LoadImaged(keys=["image", "boxes"]), + AddChanneld(keys=["image", "boxes"]), + ToTensord(keys=["image", "boxes"]), + ] + ) + + dataset = Dataset(data['data'], transform) + loader = T.utils.data.DataLoader(dataset, 1) + + model = load_model(config['model'], infer = True) + model.load_state_dict(T.load(config["model"]["weights"])) + model.to(device) + + logger.LogInfo("Starting inference!", [str(data)]) + infer(model, loader, device, config['inference']) + logger.LogMilestone("Inference finished!", []) diff --git a/training/Engine/seg_test.py b/training/Engine/seg_test.py new file mode 100644 index 0000000000000000000000000000000000000000..e7770cb6877c90fabd6ff75cf5d9e558e3f4f75e --- /dev/null +++ b/training/Engine/seg_test.py @@ -0,0 +1,112 @@ +import torch as T +import yaml +import nibabel +import sys +from monai.losses import DiceLoss + +from monai.networks.nets.unet import UNet + +import numpy as np +import torch as T +from monai.data import (DataLoader, Dataset) +from monai.metrics import compute_meandice +from monai.transforms import ( + AddChanneld, + Compose, + LoadImaged, + NormalizeIntensityd, + ToTensord, + Resized, + RandFlipd, + RandRotate90d, + ThresholdIntensityd +) + +from Engine.utils import ( + load_model, + read_yaml +) + +from Networks.UNet4 import UNet4 + +def init_plot_file(plot_path): + with open(plot_path, "w+") as file: + file.write("step,loss\n") + +def append_metrics(plot_path, epoch, loss): + with open(plot_path, 'a') as file: + file.write(f"{epoch},{loss}\n") + +def main(): + path = "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/full_size.yaml" + plot_path = "/cluster/work/sosevle/metrics/t_test3.csv" + model_loc = "/cluster/work/sosevle/models/t_test3/" + dim = (128,128,128) + if sys.platform == "win32": + path = "D:\\Repos\\LungTumorSegmentation\\Resources\\Test\\data_test_train.yaml" + plot_path = "D:\\Repos\\LungTumorSegmentation\\m_test\\test.csv" + model_loc = "D:\\Repos\\LungTumorSegmentation\\m_test\\" + dim = (32,32,32) + + data = read_yaml(path) + + for i, d in enumerate(data['train']): + data['train'][i]['image'] = data['image_prefix'] + d['image'] + data['train'][i]['boxes'] = data['boxes_prefix'] + d['boxes'] + data['train'][i]['label'] = data['label_prefix'] + d['label'] + + train_transform = Compose( + [ + LoadImaged(keys=["image", "boxes", "label"]), + ThresholdIntensityd(keys=["image"], above=False, threshold=1024, cval=1024), + NormalizeIntensityd(keys=["image"], nonzero=True, channel_wise=True), + AddChanneld(keys=["image", "boxes", "label"]), + Resized(keys=["image", "boxes", "label"], spatial_size=dim), + RandFlipd(keys=["image", "boxes", "label"], prob=0.1, spatial_axis=0), + RandFlipd(keys=["image", "boxes", "label"], prob=0.1, spatial_axis=1), + RandFlipd(keys=["image", "boxes", "label"], prob=0.1, spatial_axis=2), + RandRotate90d(keys=["image", "boxes", "label"], prob=0.1, spatial_axes=(0, 1)), + ToTensord(keys=["image", "boxes", "label"]), + ] + ) + + train_dataset = Dataset(data['train'], train_transform) + train_loader = T.utils.data.DataLoader(train_dataset, 1, shuffle=True) + + device = T.device("cuda") + + #model = T.nn.Sequential(UNet(3, 1, 1, (32, 64, 128, 256), (2, 2, 2)), T.nn.Sigmoid()) + model = UNet4(32, 2) + + loss_criterion = DiceLoss() + optimizer = T.optim.Adam(model.parameters(), 0.0005) + + model.to(device) + model.train() + + init_plot_file(plot_path) + + optimizer.zero_grad() + + for i in range(500): + print(f"Epoch {i}") + epoch_loss = 0 + + for j in train_loader: + inputs, boxes, labels = j["image"].to(device), j["boxes"].to(device), j["label"].to(device) + forwarded = model.forward(inputs) + train_loss = loss_criterion(forwarded, labels) + train_loss.backward() + optimizer.step() + + epoch_loss += train_loss.item() + print(f"loss: {train_loss.item()}") + + append_metrics(plot_path, i, epoch_loss / len(train_loader)) + + if (i % 10 == 2): + T.save(model.state_dict(), model_loc + f"m_{i}.pth") + + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/training/Engine/train.py b/training/Engine/train.py new file mode 100644 index 0000000000000000000000000000000000000000..d008b4254d486055ceaf52e9948f467ba7ca8f81 --- /dev/null +++ b/training/Engine/train.py @@ -0,0 +1,201 @@ +import numpy as np +import torch as T +from monai.data import (DataLoader, Dataset) +from monai.metrics import compute_meandice +from monai.transforms import ( + AddChanneld, + Compose, + LoadImaged, + NormalizeIntensityd, + ToTensord, + Resized, + RandFlipd, + RandRotate90d, + ThresholdIntensityd, + ScaleIntensityRanged +) + +from Engine.utils import ( + load_model, + read_yaml +) + + +from Engine.utils import ( + load_model, + read_yaml +) + +from Engine.utils import ( + load_model, + read_yaml +) + + +def init_plot_file(plot_path): + with open(plot_path, "w+") as file: + file.write("step,train_loss,val_loss,dice_score\n") + +def append_metrics(plot_path, epoch, train_loss, val_loss, dice_score): + with open(plot_path, 'a') as file: + file.write(f"{epoch},{train_loss},{val_loss},{dice_score}\n") + +def train(model, loss_function, optimizer, train_loader, val_loader, device, train_config): + best_val_loss = float('inf') + val_loss = float('inf') + total_steps = 0 + dcs_metric = 0 + step_loss = 0 + + optimizer.zero_grad() + + for epoch in range(train_config['max_epochs']): + print("-" * 10) + print(f"epoch {epoch + 1}/{train_config['max_epochs']}") + model.train() + train_loss = 0 + step = 0 + accumulated_loss = 0 + + if((epoch + 1) % train_config['save_frequency'] == 0): + T.save(model.state_dict(), train_config['model_directory'] + f"model_{epoch + 1}.pth") + + for batch_data in train_loader: + total_steps += 1 + step += 1 + inputs, boxes, labels = batch_data["image"].to(device), batch_data["boxes"].to(device), batch_data["label"].to(device) + loss = model.train_step(inputs, labels, loss_function, boxes) + loss.backward() + optimizer.step() + + train_loss += loss.detach().item() + step_loss += loss.detach().item() + + print( + f"step {step}/{len(train_loader.dataset) // train_loader.batch_size}, " + f"train_loss: {loss.item():.6f}") + epoch_len = len(train_loader.dataset) // train_loader.batch_size + accumulated_loss += loss + + if(total_steps % train_config['batch_size'] == 0): + + accumulated_loss = 0 + step_loss /= train_config['batch_size'] + append_metrics(train_config['metric_path'], total_steps, step_loss, val_loss, dcs_metric) + step_loss = 0 + + train_loss /= len(train_loader.dataset) + print(f"epoch {epoch + 1} average loss: {train_loss:.6f}") + + + + if((epoch + 1) % train_config['val_frequency'] == 0): + model.eval() + + + print("Start eval") + + step = 0 + val_loss = 0 + dcs_metric = 0 + + with T.no_grad(): + for batch_data in val_loader: + step += 1 + inputs, boxes, labels = batch_data["image"].to(device), batch_data["boxes"].to(device), batch_data["label"].to(device) + outputs = model(inputs) + + loss = loss_function(outputs, labels) + + outputs = outputs.cpu() + + outputs[outputs >= train_config['output_threshold']] = 1 + outputs[outputs < train_config['output_threshold']] = 0 + outputs = outputs.to(device) + + dcs_metric += T.mean(compute_meandice(outputs.unsqueeze(0), labels.unsqueeze(0))).item() + val_loss += loss.item() + + dcs_metric /= len(val_loader.dataset) + + + val_loss /= step + + if(val_loss < best_val_loss): + best_val_loss = val_loss + T.save(model.state_dict(), train_config['model_directory'] + f"model_best.pth") + + print(f"epoch {epoch + 1} validation loss: {val_loss:.6f}") + print(f"epoch {epoch + 1} validation dice score: {dcs_metric:.6f}") + + + T.save(model.state_dict(), train_config['model_directory'] + f"model_last.pth") + +def initiate(config_path): + config = read_yaml(config_path) + init_plot_file(config['train']['metric_path']) + data_paths = config["data"]["train_dataset"] + image_shape = (config["data"]["scale_dim"]["d_0"], config["data"]["scale_dim"]["d_1"], config["data"]["scale_dim"]["d_2"]) + + combined_train = [] + combined_val = [] + + for data in data_paths: + prefixes = read_yaml(data) + + for i, d in enumerate(read_yaml(data)['train']): + instance = { + 'image' : prefixes['image_prefix'] + d['label'], + 'label' : prefixes['label_prefix'] + d['label'], + 'boxes' : prefixes['boxes_prefix'] + d['label'] + } + combined_train.append(instance) + + for data in data_paths: + prefixes = read_yaml(data) + + for i, d in enumerate(read_yaml(data)['train']): + instance = { + 'image' : prefixes['image_prefix'] + d['label'], + 'label' : prefixes['label_prefix'] + d['label'], + 'boxes' : prefixes['boxes_prefix'] + d['label'] + } + combined_val.append(instance) + + train_transform = Compose( + [ + LoadImaged(keys=["image", "boxes", "label"]), + AddChanneld(keys=["image", "boxes", "label"]), + RandFlipd(keys=["image", "boxes", "label"], prob=config["data"]["aug_prob"], spatial_axis=0), + RandFlipd(keys=["image", "boxes", "label"], prob=config["data"]["aug_prob"], spatial_axis=1), + RandFlipd(keys=["image", "boxes", "label"], prob=config["data"]["aug_prob"], spatial_axis=2), + RandRotate90d(keys=["image", "boxes", "label"], prob=config["data"]["aug_prob"], spatial_axes=(0, 1)), + RandRotate90d(keys=["image", "boxes", "label"], prob=config["data"]["aug_prob"], spatial_axes=(0, 2)), + RandRotate90d(keys=["image", "boxes", "label"], prob=config["data"]["aug_prob"], spatial_axes=(1, 2)), + ToTensord(keys=["image", "boxes", "label"]), + ] + ) + + val_transform = Compose( + [ + LoadImaged(keys=["image", "boxes", "label"]), + AddChanneld(keys=["image", "boxes", "label"]), + ToTensord(keys=["image", "boxes", "label"]), + ] + ) + + train_dataset = Dataset(combined_train, train_transform) + train_loader = T.utils.data.DataLoader(train_dataset, 1, shuffle = True) + + val_dataset = Dataset(combined_val, val_transform) + val_loader = T.utils.data.DataLoader(val_dataset, 1) + + device = T.device(config["device"]) + + model, loss, optimizer = load_model(config['model']) + if (config["model"]["weights"]): + model.load_state_dict(T.load(config["model"]["weights"])) + model.to(device) + + print("initiates training!") + train(model, loss, optimizer, train_loader, val_loader, device, config['train']) diff --git a/training/Engine/utils.py b/training/Engine/utils.py new file mode 100644 index 0000000000000000000000000000000000000000..5567f3a4169d41376f679e7a78c7f65ee15b4d09 --- /dev/null +++ b/training/Engine/utils.py @@ -0,0 +1,79 @@ +import torch as T +import yaml +import nibabel + +from monai.losses import DiceLoss, GeneralizedDiceLoss, FocalLoss, TverskyLoss +from Networks.UNet4 import UNet4 +from Networks.UNet5_filter_teacher import UNet5_filter_teacher +from Networks.UNet5_decoder_teacher import UNet5_decoder_teacher +from Networks.UNet_test import UNet_student +from Networks.UNet_concat_double_student import UNet_concat_student +from monai.networks.nets.unet import UNet +from Networks.monai_student import UNet_double +from Networks.monai_unet import UNet_single + + +def load_model(model_config, infer = False, eval = False): + model, loss, optim = None, None, None + model_name = model_config["architecture"] + base = model_config["filter_base"] + expansion = model_config["filter_expansion"] + + filter_layers = model_config["filters"] + + if(model_name == 'UNet_decoder'): + model = UNet5_decoder_teacher(base, expansion) + elif(model_name == 'UNet_filter'): + model = UNet5_filter_teacher(base, expansion) + elif(model_name == 'UNet_con_double'): + model = UNet_concat_student(base, expansion) + elif(model_name == 'UNet_monai'): + model = UNet_single(3, 1, 1, tuple(filter_layers), tuple([2 for i in range(len(filter_layers) - 1)])) + elif(model_name == 'UNet_monai_double'): + model = UNet_double(3, 1, 1, tuple(filter_layers), tuple([2 for i in range(len(filter_layers) - 1)])) + elif(model_name == 'UNet4'): + model = UNet4(base, expansion) + else: + print("Architecture not found...") + exit(1) + + if(infer): + return model + + loss_name = model_config["loss"] + if(loss_name == 'BCE'): + loss = T.nn.BCELoss() + elif(loss_name == 'DiceLoss'): + loss = DiceLoss() + elif(loss_name == "GenDice"): + loss = GeneralizedDiceLoss() + elif(loss_name == "Tversky"): + loss = TverskyLoss(alpha=2.0, beta=10.0) + else: + print("Loss not found...") + exit(1) + + if(eval): + return model, loss + + optim_name = model_config['optimizer']['name'] + if(optim_name == 'Adam'): + optim = T.optim.Adam(model.parameters(), model_config['optimizer']['lr']) + else: + print("Optimizer not found...") + exit(1) + + return model, loss, optim + +def read_yaml(yaml_path): + with open(yaml_path, 'r') as file: + config = yaml.load(file, Loader = yaml.FullLoader) + return config + +def store_output(output, original_image, directory, affine): + + headers = original_image.header + output = output.squeeze(0).squeeze(0) + save = nibabel.Nifti1Image(output.cpu().numpy(), affine, headers) + + nibabel.save(save, directory) diff --git a/training/LICENSE b/training/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..df5792de4c6f11ff9b5c39e8a9f00c4ad4d5cdd6 --- /dev/null +++ b/training/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2021 Vemund Fredriksen + +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. diff --git a/training/Networks/UNet4.py b/training/Networks/UNet4.py new file mode 100644 index 0000000000000000000000000000000000000000..0e7b2d32c5d3653a7abb312de01617c6ac35189e --- /dev/null +++ b/training/Networks/UNet4.py @@ -0,0 +1,115 @@ +import torch as T +import torch.nn as nn +from Networks.network import Network + +class UNet4(Network): + def __init__(self, base, expansion): + super(UNet4, self).__init__() + self._build(base, expansion) + + def forward(self, image, segbox=None): + layer_0, layer_1, layer_2 = self._analysis(image) + return self._synthesis(layer_0, layer_1, layer_2, self._bridge(layer_2)) + + def train_step(self, image, segment, criterion, segbox = None): + output = self.forward(image) + + loss = criterion(output, segment) + return loss + + def _analysis(self, x): + layer_0 = self.analysis_0(x) + layer_1 = self.analysis_1(layer_0) + layer_2 = self.analysis_2(layer_1) + + return layer_0, layer_1, layer_2 + + def _bridge(self, layer_2): + return self.bridge(layer_2) + + def _synthesis(self, layer_0, layer_1, layer_2, layer_3): + concat_2 = T.cat((layer_2, layer_3), dim = 1) + concat_1 = T.cat((layer_1, self.synthesis_2(concat_2)), dim = 1) + concat_0 = T.cat((layer_0, self.synthesis_1(concat_1)), dim = 1) + + return self.synthesis_0(concat_0) + + def _build(self, base, expansion): + layer_0_count = int(base) + layer_1_count = int(base * expansion) + layer_2_count = int(base * (expansion ** 2)) + layer_3_count = int(base * (expansion ** 3)) + + self.analysis_0 = nn.Sequential( + nn.Conv3d(1, layer_0_count, 3, 1, 1), + nn.BatchNorm3d(layer_0_count), + nn.LeakyReLU(), + nn.Conv3d(layer_0_count, layer_0_count, 3, 1, 1), + nn.BatchNorm3d(layer_0_count), + nn.LeakyReLU(), + ) + + self.analysis_1 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(layer_0_count, layer_1_count, 3, 1, 1), + nn.BatchNorm3d(layer_1_count), + nn.LeakyReLU(), + nn.Conv3d(layer_1_count, layer_1_count, 3, 1, 1), + nn.BatchNorm3d(layer_1_count), + nn.LeakyReLU(), + ) + + self.analysis_2 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(layer_1_count, layer_2_count, 3, 1, 1), + nn.BatchNorm3d(layer_2_count), + nn.LeakyReLU(), + nn.Conv3d(layer_2_count, layer_2_count, 3, 1, 1), + nn.BatchNorm3d(layer_2_count), + nn.LeakyReLU(), + ) + + self.bridge = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(layer_2_count, layer_3_count, 3, 1, 1), + nn.BatchNorm3d(layer_3_count), + nn.LeakyReLU(), + nn.Conv3d(layer_3_count, layer_3_count, 3, 1, 1), + nn.BatchNorm3d(layer_3_count), + nn.LeakyReLU(), + nn.ConvTranspose3d(layer_3_count, layer_3_count, 2, 2, 0) + ) + + self.synthesis_2 = nn.Sequential( + nn.Conv3d(layer_2_count + layer_3_count, layer_2_count, 3, 1, 1), + nn.BatchNorm3d(layer_2_count), + nn.LeakyReLU(), + nn.Conv3d(layer_2_count,layer_2_count, 3, 1, 1), + nn.BatchNorm3d(layer_2_count), + nn.LeakyReLU(), + nn.ConvTranspose3d(layer_2_count, layer_2_count, 2, 2, 0) + ) + + self.synthesis_1 = nn.Sequential( + nn.Conv3d(layer_1_count + layer_2_count, layer_1_count, 3, 1, 1), + nn.BatchNorm3d(layer_1_count), + nn.LeakyReLU(), + nn.Conv3d(layer_1_count,layer_1_count, 3, 1, 1), + nn.BatchNorm3d(layer_1_count), + nn.LeakyReLU(), + nn.ConvTranspose3d(layer_1_count, layer_1_count, 2, 2, 0) + ) + + self.synthesis_0 = nn.Sequential( + nn.Conv3d(layer_0_count + layer_1_count, layer_0_count, 3, 1, 1), + nn.BatchNorm3d(layer_0_count), + nn.LeakyReLU(), + nn.Conv3d(layer_0_count,layer_0_count, 3, 1, 1), + nn.BatchNorm3d(layer_0_count), + nn.LeakyReLU(), + nn.Conv3d(layer_0_count, layer_0_count, 3, 1, 1), + nn.BatchNorm3d(layer_0_count), + nn.LeakyReLU(), + nn.Conv3d(layer_0_count, 1, 3, 1, 1), + nn.Sigmoid() + ) diff --git a/training/Networks/UNet5_Teacher.py b/training/Networks/UNet5_Teacher.py new file mode 100644 index 0000000000000000000000000000000000000000..ad903e387ca4be406b6ee791e28ebfc7f68d09a5 --- /dev/null +++ b/training/Networks/UNet5_Teacher.py @@ -0,0 +1,121 @@ +import torch as T +import torch.nn as nn +from Networks.network import Network + +class UNet5_Teacher(Network): + def __init__(self, base, expansion): + super(UNet5_Teacher, self).__init__() + self._build(base, expansion) + + def forward(self, image, segbox): + x_new = T.cat((image, segbox), dim = 1) + layer_0, layer_1, layer_2, layer_3 = self._analysis(x_new) + + return self._synthesis(layer_0, layer_1, layer_2, layer_3, self._bridge(layer_3)) + + def train_step(self, image, segment, criterion, segbox = None): + output = self.forward(image, segbox) + + loss = criterion(output, segment) + return loss + + def _analysis(self, x): + layer_0 = self.analysis_0(x) + layer_1 = self.analysis_1(layer_0) + layer_2 = self.analysis_2(layer_1) + layer_3 = self.analysis_3(layer_2) + + return layer_0, layer_1, layer_2, layer_3 + + def _bridge(self, layer_3): + return self.bridge(layer_3) + + def _synthesis(self, l0, l1, l2, l3, l4): + c_3 = T.cat((l3, l4), dim = 1) + c_2 = T.cat((l2, self.synthesis_3(c_3)), dim = 1) + c_1 = T.cat((l1, self.synthesis_2(c_2)), dim = 1) + c_0 = T.cat((l0, self.synthesis_1(c_1)), dim = 1) + + return self.synthesis_0(c_0) + + def _build(self, base, expansion): + fl_0 = int(base) + fl_1 = int(base * expansion) + fl_2 = int(base * (expansion ** 2)) + fl_3 = int(base * (expansion ** 3)) + fl_4 = int(base * (expansion ** 4)) + + self.analysis_0 = nn.Sequential( + nn.Conv3d(2, fl_0, 3, 1, 1), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_0, 3, 1, 1), + nn.LeakyReLU(), + ) + + self.analysis_1 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_0, fl_1, 3, 1, 1), + nn.LeakyReLU(), + nn.Conv3d(fl_1, fl_1, 3, 1, 1), + nn.LeakyReLU(), + ) + + self.analysis_2 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_1, fl_2, 3, 1, 1), + nn.LeakyReLU(), + nn.Conv3d(fl_2, fl_2, 3, 1, 1), + nn.LeakyReLU(), + ) + + self.analysis_3 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_2, fl_3, 3, 1, 1), + nn.LeakyReLU(), + nn.Conv3d(fl_3, fl_3, 3, 1, 1), + nn.LeakyReLU(), + ) + + self.bridge = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_3, fl_3, 3, 1, 1), + nn.LeakyReLU(), + nn.Conv3d(fl_3, fl_3, 3, 1, 1), + nn.LeakyReLU(), + nn.ConvTranspose3d(fl_3, fl_3, 2, 2, 0), + ) + + self.synthesis_3 = nn.Sequential( + nn.Conv3d(fl_3 + fl_3, fl_2, 3, 1, 1), + nn.LeakyReLU(), + nn.Conv3d(fl_2, fl_2, 3, 1, 1), + nn.LeakyReLU(), + nn.ConvTranspose3d(fl_2, fl_2, 2, 2, 0), + ) + + self.synthesis_2 = nn.Sequential( + nn.Conv3d(fl_2 + fl_2, fl_1, 3, 1, 1), + nn.LeakyReLU(), + nn.Conv3d(fl_1, fl_1, 3, 1, 1), + nn.LeakyReLU(), + nn.ConvTranspose3d(fl_1, fl_1, 2, 2, 0), + ) + + self.synthesis_1 = nn.Sequential( + nn.Conv3d(fl_1 + fl_1, fl_0, 3, 1, 1), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_0, 3, 1, 1), + nn.LeakyReLU(), + nn.ConvTranspose3d(fl_0, fl_0, 2, 2, 0), + ) + + self.synthesis_0 = nn.Sequential( + nn.Conv3d(fl_0 + fl_0, fl_0, 3, 1, 1), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_0, 3, 1, 1), + nn.LeakyReLU(), + nn.Conv3d(fl_0, 1, 3, 1, 1), + nn.Conv3d(1, 1, 1, 1, 0), + nn.Sigmoid() + ) + diff --git a/training/Networks/UNet5_decoder_teacher.py b/training/Networks/UNet5_decoder_teacher.py new file mode 100644 index 0000000000000000000000000000000000000000..0d1f97d832e11a5506d77482ef9a07637f1a4f2e --- /dev/null +++ b/training/Networks/UNet5_decoder_teacher.py @@ -0,0 +1,180 @@ +import torch as T +import torch.nn as nn +from Networks.network import Network + +class UNet5_decoder_teacher(Network): + def __init__(self, base, expansion): + super(UNet5_decoder_teacher, self).__init__() + self._build(base, expansion) + + def forward(self, image, segbox): + layer_0, layer_1, layer_2, layer_3 = self._analysis(image) + s_0, s_1, s_2, s_3 = self._box_scale(segbox) + + inp_layer_0 = T.cat((layer_0, self.analyse_box_0(s_0)), dim = 1) + inp_layer_1 = T.cat((layer_1, self.analyse_box_1(s_1)), dim = 1) + inp_layer_2 = T.cat((layer_2, self.analyse_box_2(s_2)), dim = 1) + inp_layer_3 = T.cat((layer_3, self.analyse_box_3(s_3)), dim = 1) + + return self._synthesis(inp_layer_0, inp_layer_1, inp_layer_2, inp_layer_3, self._bridge(layer_3)) + + def train_step(self, image, segment, criterion, segbox = None): + output = self.forward(image, segbox) + + loss = criterion(output, segment) + return loss + + def _analysis(self, x): + layer_0 = self.analysis_0(x) + layer_1 = self.analysis_1(layer_0) + layer_2 = self.analysis_2(layer_1) + layer_3 = self.analysis_3(layer_2) + + return layer_0, layer_1, layer_2, layer_3 + + def _bridge(self, layer_3): + return self.bridge(layer_3) + + def _synthesis(self, l0, l1, l2, l3, l4): + c_3 = T.cat((l3, l4), dim = 1) + c_2 = T.cat((l2, self.synthesis_3(c_3)), dim = 1) + c_1 = T.cat((l1, self.synthesis_2(c_2)), dim = 1) + c_0 = T.cat((l0, self.synthesis_1(c_1)), dim = 1) + + return self.synthesis_0(c_0) + + def _box_scale(self, b): + s_0 = b + s_1 = nn.functional.interpolate(s_0, scale_factor = (0.5, 0.5, 0.5)) + s_2 = nn.functional.interpolate(s_1, scale_factor = (0.5, 0.5, 0.5)) + s_3 = nn.functional.interpolate(s_2, scale_factor = (0.5, 0.5, 0.5)) + return s_0, s_1, s_2, s_3 + + def _build(self, base, expansion): + fl_0 = int(base) + fl_1 = int(base * expansion) + fl_2 = int(base * (expansion ** 2)) + fl_3 = int(base * (expansion ** 3)) + + self.analyse_box_0 = nn.Sequential( + nn.Conv3d(1, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.Sigmoid(), + ) + + self.analyse_box_1 = nn.Sequential( + nn.Conv3d(1, 128, 3, 1, 1), + nn.BatchNorm3d(128), + nn.Sigmoid(), + ) + + self.analyse_box_2 = nn.Sequential( + nn.Conv3d(1, 256, 3, 1, 1), + nn.BatchNorm3d(256), + nn.Sigmoid(), + ) + + self.analyse_box_3 = nn.Sequential( + nn.Conv3d(1, 512, 3, 1, 1), + nn.BatchNorm3d(512), + nn.Sigmoid(), + ) + + self.analysis_0 = nn.Sequential( + nn.Conv3d(1, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.LeakyReLU(), + nn.Conv3d(64, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.LeakyReLU(), + ) + + self.analysis_1 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(64, 128, 3, 1, 1), + nn.BatchNorm3d(128), + nn.LeakyReLU(), + nn.Conv3d(128, 128, 3, 1, 1), + nn.BatchNorm3d(128), + nn.LeakyReLU(), + ) + + self.analysis_2 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(128, 256, 3, 1, 1), + nn.BatchNorm3d(256), + nn.LeakyReLU(), + nn.Conv3d(256, 256, 3, 1, 1), + nn.BatchNorm3d(256), + nn.LeakyReLU(), + ) + + self.analysis_3 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(256, 512, 3, 1, 1), + nn.BatchNorm3d(512), + nn.LeakyReLU(), + nn.Conv3d(512, 512, 3, 1, 1), + nn.BatchNorm3d(512), + nn.LeakyReLU(), + ) + + self.bridge = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(512, 512, 3, 1, 1), + nn.BatchNorm3d(512), + nn.LeakyReLU(), + nn.Conv3d(512, 512, 3, 1, 1), + nn.BatchNorm3d(512), + nn.LeakyReLU(), + nn.ConvTranspose3d(512, 512, 2, 2, 0), + ) + + self.synthesis_3 = nn.Sequential( + nn.Conv3d(512 + 512 + 512, 256, 3, 1, 1), + nn.BatchNorm3d(256), + nn.LeakyReLU(), + nn.Conv3d(256, 256, 3, 1, 1), + nn.BatchNorm3d(256), + nn.LeakyReLU(), + nn.ConvTranspose3d(256, 256, 2, 2, 0), + ) + + self.synthesis_2 = nn.Sequential( + nn.Conv3d(256 + 256 + 256, 128, 3, 1, 1), + nn.BatchNorm3d(128), + nn.LeakyReLU(), + nn.Conv3d(128, 128, 3, 1, 1), + nn.BatchNorm3d(128), + nn.LeakyReLU(), + nn.ConvTranspose3d(128, 128, 2, 2, 0), + ) + + self.synthesis_1 = nn.Sequential( + nn.Conv3d(128 + 128 + 128, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.LeakyReLU(), + nn.Conv3d(64, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.LeakyReLU(), + nn.ConvTranspose3d(64, 64, 2, 2, 0), + ) + + self.synthesis_0 = nn.Sequential( + nn.Conv3d(64 + 64 + 64, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.LeakyReLU(), + nn.Conv3d(64, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.LeakyReLU(), + nn.Conv3d(64, 1, 3, 1, 1), + nn.Sigmoid() + ) + +if __name__ == "__main__": + s = UNet_teacher() + f = T.randn((1,1,64,64,64)) + a = s._box_scale(f) + + print(a[3].shape) + diff --git a/training/Networks/UNet5_filter_teacher.py b/training/Networks/UNet5_filter_teacher.py new file mode 100644 index 0000000000000000000000000000000000000000..31339c01feaa6245433fff5d51e0147622d4c8d8 --- /dev/null +++ b/training/Networks/UNet5_filter_teacher.py @@ -0,0 +1,137 @@ +import torch as T +import torch.nn as nn +from Networks.network import Network + +class UNet5_filter_teacher(Network): + def __init__(self, base, expansion): + super(UNet5_filter_teacher, self).__init__() + self._build(base, expansion) + + def forward(self, image, segbox): + x_new = T.cat((image, segbox), dim = 1) + layer_0, layer_1, layer_2, layer_3 = self._analysis(x_new) + + return self._synthesis(layer_0, layer_1, layer_2, layer_3, self._bridge(layer_3)) + + def train_step(self, image, segment, criterion, segbox = None): + output = self.forward(image, segbox) + + loss = criterion(output, segment) + return loss + + def _analysis(self, x): + layer_0 = self.analysis_0(x) + layer_1 = self.analysis_1(layer_0) + layer_2 = self.analysis_2(layer_1) + layer_3 = self.analysis_3(layer_2) + + return layer_0, layer_1, layer_2, layer_3 + + def _bridge(self, layer_3): + return self.bridge(layer_3) + + def _synthesis(self, l0, l1, l2, l3, l4): + c_3 = T.cat((l3, l4), dim = 1) + c_2 = T.cat((l2, self.synthesis_3(c_3)), dim = 1) + c_1 = T.cat((l1, self.synthesis_2(c_2)), dim = 1) + c_0 = T.cat((l0, self.synthesis_1(c_1)), dim = 1) + + return self.synthesis_0(c_0) + + def _build(self, base, expansion): + fl_0 = int(base) + fl_1 = int(base * expansion) + fl_2 = int(base * (expansion ** 2)) + fl_3 = int(base * (expansion ** 3)) + + self.analysis_0 = nn.Sequential( + nn.Conv3d(2, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + ) + + self.analysis_1 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_0, fl_1, 3, 1, 1), + nn.BatchNorm3d(fl_1), + nn.LeakyReLU(), + nn.Conv3d(fl_1, fl_1, 3, 1, 1), + nn.BatchNorm3d(fl_1), + nn.LeakyReLU(), + ) + + self.analysis_2 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_1, fl_2, 3, 1, 1), + nn.BatchNorm3d(fl_2), + nn.LeakyReLU(), + nn.Conv3d(fl_2, fl_2, 3, 1, 1), + nn.BatchNorm3d(fl_2), + nn.LeakyReLU(), + ) + + self.analysis_3 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_2, fl_3, 3, 1, 1), + nn.BatchNorm3d(fl_3), + nn.LeakyReLU(), + nn.Conv3d(fl_3, fl_3, 3, 1, 1), + nn.BatchNorm3d(fl_3), + nn.LeakyReLU(), + ) + + self.bridge = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_3, fl_3, 3, 1, 1), + nn.BatchNorm3d(fl_3), + nn.LeakyReLU(), + nn.Conv3d(fl_3, fl_3, 3, 1, 1), + nn.BatchNorm3d(fl_3), + nn.LeakyReLU(), + nn.ConvTranspose3d(fl_3, fl_3, 2, 2, 0), + ) + + self.synthesis_3 = nn.Sequential( + nn.Conv3d(fl_3 + fl_3, fl_2, 3, 1, 1), + nn.BatchNorm3d(fl_2), + nn.LeakyReLU(), + nn.Conv3d(fl_2, fl_2, 3, 1, 1), + nn.BatchNorm3d(fl_2), + nn.LeakyReLU(), + nn.ConvTranspose3d(fl_2, fl_2, 2, 2, 0), + ) + + self.synthesis_2 = nn.Sequential( + nn.Conv3d(fl_2 + fl_2, fl_1, 3, 1, 1), + nn.BatchNorm3d(fl_1), + nn.LeakyReLU(), + nn.Conv3d(fl_1, fl_1, 3, 1, 1), + nn.BatchNorm3d(fl_1), + nn.LeakyReLU(), + nn.ConvTranspose3d(fl_1, fl_1, 2, 2, 0), + ) + + self.synthesis_1 = nn.Sequential( + nn.Conv3d(fl_1 + fl_1, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + nn.ConvTranspose3d(fl_0, fl_0, 2, 2, 0), + ) + + self.synthesis_0 = nn.Sequential( + nn.Conv3d(fl_0 + fl_0, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + nn.Conv3d(fl_0, 1, 3, 1, 1), + nn.Sigmoid() + ) + diff --git a/training/Networks/UNet_concat_double_student.py b/training/Networks/UNet_concat_double_student.py new file mode 100644 index 0000000000000000000000000000000000000000..d01658a053b1c214510bd2e4dfda975d2b72ce1c --- /dev/null +++ b/training/Networks/UNet_concat_double_student.py @@ -0,0 +1,198 @@ +import torch as T +import torch.nn as nn +from Networks.network import Network + +class UNet_concat_student(Network): + def __init__(self, base, expansion): + super(UNet_concat_student, self).__init__() + self._build(base, expansion) + + def forward(self, image, segbox = None, eval_mode = True): + layer_0, layer_1, layer_2, layer_3 = self._analysis(image) + + inter_output, s_3, s_2, s_1 = self._synthesis(layer_0, layer_1, layer_2, layer_3, self._bridge(layer_3)) + output_0 = self.output_0(inter_output) + + u_0 = self._upsample(s_3, s_2, s_1, inter_output) + output_1 = self.output_1(u_0) + + if (eval_mode): + return output_0 + return output_0, output_1 + + def train_step(self, image, segment, criterion, segbox = None): + seg_out, box_out = self.forward(image, eval_mode=False) + + seg_loss = criterion(seg_out, segment) + box_loss = criterion(box_out, segbox) + return seg_loss + box_loss + + def _analysis(self, x): + layer_0 = self.analysis_0(x) + layer_1 = self.analysis_1(layer_0) + layer_2 = self.analysis_2(layer_1) + layer_3 = self.analysis_3(layer_2) + + return layer_0, layer_1, layer_2, layer_3 + + def _bridge(self, layer_3): + return self.bridge(layer_3) + + def _synthesis(self, l0, l1, l2, l3, l4): + c_3 = T.cat((l3, l4), dim = 1) + s_3 = self.synthesis_3(c_3) + c_2 = T.cat((l2, self.up_conv_3(s_3)), dim = 1) + s_2 = self.synthesis_2(c_2) + c_1 = T.cat((l1, self.up_conv_2(s_2)), dim = 1) + s_1 = self.synthesis_1(c_1) + c_0 = T.cat((l0, self.up_conv_1(s_1)), dim = 1) + + return self.synthesis_0(c_0), s_3, s_2, s_1 + + def _upsample(self, s_3, s_2, s_1, inter): + u_3 = self.up_sample_3(s_3) + u_2 = self.up_sample_2(s_2) + u_1 = self.up_sample_1(s_1) + + return T.cat((u_3, u_2, u_1, inter), dim = 1) + + def _build(self, base, expansion): + fl_i1 = int(base / (expansion ** 2)) + fl_i0 = int(base / expansion) + fl_0 = int(base) + fl_1 = int(base * expansion) + fl_2 = int(base * (expansion ** 2)) + fl_3 = int(base * (expansion ** 3)) + + self.analysis_0 = nn.Sequential( + nn.Conv3d(1, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + ) + + self.analysis_1 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_0, fl_1, 3, 1, 1), + nn.BatchNorm3d(fl_1), + nn.LeakyReLU(), + nn.Conv3d(fl_1, fl_1, 3, 1, 1), + nn.BatchNorm3d(fl_1), + nn.LeakyReLU(), + ) + + self.analysis_2 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_1, fl_2, 3, 1, 1), + nn.BatchNorm3d(fl_2), + nn.LeakyReLU(), + nn.Conv3d(fl_2, fl_2, 3, 1, 1), + nn.BatchNorm3d(fl_2), + nn.LeakyReLU(), + ) + + self.analysis_3 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_2, fl_3, 3, 1, 1), + nn.BatchNorm3d(fl_3), + nn.LeakyReLU(), + nn.Conv3d(fl_3, fl_3, 3, 1, 1), + nn.BatchNorm3d(fl_3), + nn.LeakyReLU(), + ) + + self.bridge = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(fl_3, fl_3, 3, 1, 1), + nn.BatchNorm3d(fl_3), + nn.LeakyReLU(), + nn.Conv3d(fl_3, fl_3, 3, 1, 1), + nn.BatchNorm3d(fl_3), + nn.LeakyReLU(), + nn.ConvTranspose3d(fl_3, fl_3, 2, 2, 0), + ) + + self.synthesis_3 = nn.Sequential( + nn.Conv3d(fl_3 + fl_3, fl_2, 3, 1, 1), + nn.BatchNorm3d(fl_2), + nn.LeakyReLU(), + nn.Conv3d(fl_2, fl_2, 3, 1, 1), + nn.BatchNorm3d(fl_2), + nn.LeakyReLU(), + ) + + self.synthesis_2 = nn.Sequential( + nn.Conv3d(fl_2 + fl_2, fl_1, 3, 1, 1), + nn.BatchNorm3d(fl_1), + nn.LeakyReLU(), + nn.Conv3d(fl_1, fl_1, 3, 1, 1), + nn.BatchNorm3d(fl_1), + nn.LeakyReLU(), + ) + + self.synthesis_1 = nn.Sequential( + nn.Conv3d(fl_1 + fl_1, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + ) + + self.up_conv_3 = nn.Sequential( + nn.ConvTranspose3d(fl_2, fl_2, 2, 2, 0), + ) + + self.up_conv_2 = nn.Sequential( + nn.ConvTranspose3d(fl_1, fl_1, 2, 2, 0), + ) + + self.up_conv_1 = nn.Sequential( + nn.ConvTranspose3d(fl_0, fl_0, 2, 2, 0), + ) + + self.synthesis_0 = nn.Sequential( + nn.Conv3d(fl_0 + fl_0, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + ) + + self.output_0 = nn.Sequential( + nn.Conv3d(fl_0, fl_i0, 3, 1, 1), + nn.BatchNorm3d(fl_i0), + nn.LeakyReLU(), + nn.Conv3d(fl_i0, 1, 3, 1, 1), + nn.Sigmoid() + ) + + self.up_sample_3 = nn.Sequential( + nn.ConvTranspose3d(fl_2, fl_0, 8, 8, 0), + ) + + self.up_sample_2 = nn.Sequential( + nn.ConvTranspose3d(fl_1, fl_i0, 4, 4, 0), + ) + + self.up_sample_1 = nn.Sequential( + nn.ConvTranspose3d(fl_0, fl_i1, 2, 2, 0), + ) + + self.output_1 = nn.Sequential( + nn.Conv3d(fl_0 + fl_0 + fl_i0 + fl_i1, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_0, 3, 1, 1), + nn.BatchNorm3d(fl_0), + nn.LeakyReLU(), + nn.Conv3d(fl_0, fl_i0, 3, 1, 1), + nn.BatchNorm3d(fl_i0), + nn.LeakyReLU(), + nn.Conv3d(fl_i0, 1, 3, 1, 1), + nn.Sigmoid() + ) + diff --git a/training/Networks/UNet_test.py b/training/Networks/UNet_test.py new file mode 100644 index 0000000000000000000000000000000000000000..7078bff4a95bafad22de89abfb0ef79b79c395ea --- /dev/null +++ b/training/Networks/UNet_test.py @@ -0,0 +1,205 @@ +import torch as T +import torch.nn as nn +from Networks.network import Network +from monai.networks.nets.unet import UNet + +class UNet_student(Network): + def __init__(self): + super(UNet_student, self).__init__() + #self._build() + self.model = T.nn.Sequential(UNet(3, 1, 1, (32, 64, 128, 256), (2, 2, 2)), T.nn.Sigmoid()) + + def forward(self, image): + return self.model(image) + + def train_step(self, image, segment, criterion, segbox): + fo = self.forward(image) + loss = criterion(image, segment) + return loss + + + """ + def forward(self, image, segbox = None, eval_mode = True): + + + layer_0, layer_1, layer_2, layer_3 = self._analysis(image) + + inter_output, s_3, s_2, s_1 = self._synthesis(layer_0, layer_1, layer_2, layer_3, self._bridge(layer_3)) + seg_out = self.output_0(inter_output) + + u_0 = self._upsample(s_3, s_2, s_1, inter_output) + box_out = self.output_1(u_0) + + if (eval_mode): + return seg_out + return seg_out, box_out + + def train_step(self, image, segment, criterion, segbox = None): + seg_out, box_out = self.forward(image, eval_mode=False) + + seg_loss = criterion(seg_out, segment) + box_loss = criterion(box_out, segbox) + return seg_loss + box_loss + + def _analysis(self, x): + layer_0 = self.analysis_0(x) + layer_1 = self.analysis_1(layer_0) + layer_2 = self.analysis_2(layer_1) + layer_3 = self.analysis_3(layer_2) + + return layer_0, layer_1, layer_2, layer_3 + + def _bridge(self, layer_3): + return self.bridge(layer_3) + + def _synthesis(self, l0, l1, l2, l3, l4): + c_3 = T.cat((l3, l4), dim = 1) + s_3 = self.synthesis_3(c_3) + c_2 = T.cat((l2, self.up_conv_3(s_3)), dim = 1) + s_2 = self.synthesis_2(c_2) + c_1 = T.cat((l1, self.up_conv_2(s_2)), dim = 1) + s_1 = self.synthesis_1(c_1) + c_0 = T.cat((l0, self.up_conv_1(s_1)), dim = 1) + + return self.synthesis_0(c_0), s_3, s_2, s_1 + + def _upsample(self, s_3, s_2, s_1, inter): + u_3 = self.up_sample_3(s_3) + u_2 = self.up_sample_2(s_2) + u_1 = self.up_sample_1(s_1) + + return T.cat((u_3, u_2, u_1, inter), dim = 1) + + def _build(self): + self.analysis_0 = nn.Sequential( + nn.Conv3d(1, 16, 3, 1, 1), + nn.BatchNorm3d(16), + nn.LeakyReLU(), + nn.Conv3d(16, 24, 3, 1, 1), + nn.BatchNorm3d(24), + nn.LeakyReLU(), + ) + + self.analysis_1 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(24, 40, 3, 1, 1), + nn.BatchNorm3d(40), + nn.LeakyReLU(), + nn.Conv3d(40, 48, 3, 1, 1), + nn.BatchNorm3d(48), + nn.LeakyReLU(), + ) + + self.analysis_2 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(48, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.LeakyReLU(), + nn.Conv3d(64, 86, 3, 1, 1), + nn.BatchNorm3d(86), + nn.LeakyReLU(), + ) + + self.analysis_3 = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(86, 110, 3, 1, 1), + nn.BatchNorm3d(110), + nn.LeakyReLU(), + nn.Conv3d(110, 128, 3, 1, 1), + nn.BatchNorm3d(128), + nn.LeakyReLU(), + ) + + self.bridge = nn.Sequential( + nn.MaxPool3d(2), + nn.Conv3d(128, 128, 3, 1, 1), + nn.BatchNorm3d(128), + nn.LeakyReLU(), + nn.Conv3d(128, 128, 3, 1, 1), + nn.BatchNorm3d(128), + nn.LeakyReLU(), + nn.ConvTranspose3d(128, 128, 2, 2, 0), + ) + + self.synthesis_3 = nn.Sequential( + nn.Conv3d(128 + 128, 110, 3, 1, 1), + nn.BatchNorm3d(110), + nn.LeakyReLU(), + nn.Conv3d(110, 86, 3, 1, 1), + nn.BatchNorm3d(86), + nn.LeakyReLU(), + ) + + self.synthesis_2 = nn.Sequential( + nn.Conv3d(86 + 86, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.LeakyReLU(), + nn.Conv3d(64, 48, 3, 1, 1), + nn.BatchNorm3d(48), + nn.LeakyReLU(), + ) + + self.synthesis_1 = nn.Sequential( + nn.Conv3d(48 + 48, 40, 3, 1, 1), + nn.BatchNorm3d(40), + nn.LeakyReLU(), + nn.Conv3d(40, 24, 3, 1, 1), + nn.BatchNorm3d(24), + nn.LeakyReLU(), + ) + + self.up_conv_3 = nn.Sequential( + nn.ConvTranspose3d(86, 86, 2, 2, 0), + ) + + self.up_conv_2 = nn.Sequential( + nn.ConvTranspose3d(48, 48, 2, 2, 0), + ) + + self.up_conv_1 = nn.Sequential( + nn.ConvTranspose3d(24, 24, 2, 2, 0), + ) + + self.synthesis_0 = nn.Sequential( + nn.Conv3d(24 + 24, 16, 3, 1, 1), + nn.BatchNorm3d(16), + nn.LeakyReLU(), + nn.Conv3d(16, 16, 3, 1, 1), + nn.BatchNorm3d(16), + nn.LeakyReLU(), + ) + + self.output_0 = nn.Sequential( + nn.Conv3d(16, 8, 3, 1, 1), + nn.BatchNorm3d(8), + nn.LeakyReLU(), + nn.Conv3d(8, 1, 3, 1, 1), + nn.Sigmoid() + ) + + self.up_sample_3 = nn.Sequential( + nn.ConvTranspose3d(86, 32, 8, 8, 0), + ) + + self.up_sample_2 = nn.Sequential( + nn.ConvTranspose3d(48, 16, 4, 4, 0), + ) + + self.up_sample_1 = nn.Sequential( + nn.ConvTranspose3d(24, 8, 2, 2, 0), + ) + + self.output_1 = nn.Sequential( + nn.Conv3d(72, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.LeakyReLU(), + nn.Conv3d(64, 64, 3, 1, 1), + nn.BatchNorm3d(64), + nn.LeakyReLU(), + nn.Conv3d(64, 32, 3, 1, 1), + nn.BatchNorm3d(32), + nn.LeakyReLU(), + nn.Conv3d(32, 1, 3, 1, 1), + nn.Sigmoid() + ) + """ \ No newline at end of file diff --git a/training/Networks/__init__.py b/training/Networks/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/training/Networks/monai_student.py b/training/Networks/monai_student.py new file mode 100644 index 0000000000000000000000000000000000000000..0c48f94ed6fcad135430cb0bf22b87b5844c7193 --- /dev/null +++ b/training/Networks/monai_student.py @@ -0,0 +1,162 @@ +from typing import Sequence, Union + +import torch +import torch.nn as nn + +from monai.networks.blocks.convolutions import Convolution, ResidualUnit +from monai.networks.layers.factories import Act, Norm +from monai.networks.layers.simplelayers import SkipConnection +from monai.utils import alias, export + +class UNet_double(nn.Module): + def __init__( + self, + dimensions: int, + in_channels: int, + out_channels: int, + channels: Sequence[int], + strides: Sequence[int], + kernel_size: Union[Sequence[int], int] = 3, + up_kernel_size: Union[Sequence[int], int] = 3, + num_res_units: int = 0, + act=Act.PRELU, + norm=Norm.INSTANCE, + dropout=0.0,) -> None: + + super().__init__() + + self.dimensions = dimensions + self.in_channels = in_channels + self.out_channels = out_channels + self.channels = channels + self.strides = strides + self.kernel_size = kernel_size + self.up_kernel_size = up_kernel_size + self.num_res_units = num_res_units + self.act = act + self.norm = norm + self.dropout = dropout + + def _create_block( + inc: int, outc: int, channels: Sequence[int], strides: Sequence[int], is_top: bool) -> nn.Sequential: + + c = channels[0] + s = strides[0] + + subblock: nn.Module + + if len(channels) > 2: + subblock1, subblock2 = _create_block(c, c, channels[1:], strides[1:], False) # continue recursion down + upc = c * 2 + else: + # the next layer is the bottom so stop recursion, create the bottom layer as the sublock for this layer + subblock = self._get_bottom_layer(c, channels[1]) + upc = c + channels[1] + + down = self._get_down_layer(inc, c, s, is_top) # create layer in downsampling path + up1 = self._get_up_layer(upc, outc, s, is_top) # create layer in upsampling path + up2 = self._get_up_layer(upc, outc, s, is_top) + + return nn.Sequential(down, SkipConnection(subblock), up1), nn.Sequential(down, SkipConnection(subblock), up2) + + down = self._get_down_layer(inc, c, s, is_top) # create layer in downsampling path + up1 = self._get_up_layer(upc, outc, s, is_top) # create layer in upsampling path + up2 = self._get_up_layer(upc, outc, s, is_top) + + return nn.Sequential(down, SkipConnection(subblock1), up1), nn.Sequential(down, SkipConnection(subblock2), up2) + + self.model1, self.model2 = _create_block(in_channels, out_channels, self.channels, self.strides, True) + self.activation = nn.Sigmoid() + + def _get_down_layer(self, in_channels: int, out_channels: int, strides: int, is_top: bool) -> nn.Module: + """ + Args: + in_channels: number of input channels. + out_channels: number of output channels. + strides: convolution stride. + is_top: True if this is the top block. + """ + if self.num_res_units > 0: + return ResidualUnit( + self.dimensions, + in_channels, + out_channels, + strides=strides, + kernel_size=self.kernel_size, + subunits=self.num_res_units, + act=self.act, + norm=self.norm, + dropout=self.dropout, + ) + return Convolution( + self.dimensions, + in_channels, + out_channels, + strides=strides, + kernel_size=self.kernel_size, + act=self.act, + norm=self.norm, + dropout=self.dropout, + ) + + def _get_bottom_layer(self, in_channels: int, out_channels: int) -> nn.Module: + """ + Args: + in_channels: number of input channels. + out_channels: number of output channels. + """ + return self._get_down_layer(in_channels, out_channels, 1, False) + + def _get_up_layer(self, in_channels: int, out_channels: int, strides: int, is_top: bool) -> nn.Module: + """ + Args: + in_channels: number of input channels. + out_channels: number of output channels. + strides: convolution stride. + is_top: True if this is the top block. + """ + conv: Union[Convolution, nn.Sequential] + + conv = Convolution( + self.dimensions, + in_channels, + out_channels, + strides=strides, + kernel_size=self.up_kernel_size, + act=self.act, + norm=self.norm, + dropout=self.dropout, + conv_only=is_top and self.num_res_units == 0, + is_transposed=True, + ) + + if self.num_res_units > 0: + ru = ResidualUnit( + self.dimensions, + out_channels, + out_channels, + strides=1, + kernel_size=self.kernel_size, + subunits=1, + act=self.act, + norm=self.norm, + dropout=self.dropout, + last_conv_only=is_top, + ) + conv = nn.Sequential(conv, ru) + + return conv + + def forward(self, x: torch.Tensor) -> torch.Tensor: + return self.activation(self.model1(x)) + + def train_step(self, image, segment, criterion, segbox = None): + forwarded = self.forward_train(image) + target = torch.cat((segment, segbox), dim = 1) + return criterion(forwarded, target) + + def forward_train(self, image): + x1 = self.model1(image) + x2 = self.model2(image) + return self.activation(torch.cat((x1, x2), dim = 1)) + diff --git a/training/Networks/monai_unet.py b/training/Networks/monai_unet.py new file mode 100644 index 0000000000000000000000000000000000000000..b7e3d8e88d61810a195f8204b0917eb7de3f1b9c --- /dev/null +++ b/training/Networks/monai_unet.py @@ -0,0 +1,160 @@ +from typing import Sequence, Union + +import torch +import torch.nn as nn + +from monai.networks.blocks.convolutions import Convolution, ResidualUnit +from monai.networks.layers.factories import Act, Norm +from monai.networks.layers.simplelayers import SkipConnection +from monai.utils import alias, export + +class UNet_single(nn.Module): + def __init__( + self, + dimensions: int, + in_channels: int, + out_channels: int, + channels: Sequence[int], + strides: Sequence[int], + kernel_size: Union[Sequence[int], int] = 3, + up_kernel_size: Union[Sequence[int], int] = 3, + num_res_units: int = 0, + act=Act.PRELU, + norm=Norm.INSTANCE, + dropout=0.0,) -> None: + + super().__init__() + + self.dimensions = dimensions + self.in_channels = in_channels + self.out_channels = out_channels + self.channels = channels + self.strides = strides + self.kernel_size = kernel_size + self.up_kernel_size = up_kernel_size + self.num_res_units = num_res_units + self.act = act + self.norm = norm + self.dropout = dropout + + def _create_block( + inc: int, outc: int, channels: Sequence[int], strides: Sequence[int], is_top: bool) -> nn.Sequential: + """ + Builds the UNet structure from the bottom up by recursing down to the bottom block, then creating sequential + blocks containing the downsample path, a skip connection around the previous block, and the upsample path. + + Args: + inc: number of input channels. + outc: number of output channels. + channels: sequence of channels. Top block first. + strides: convolution stride. + is_top: True if this is the top block. + """ + c = channels[0] + s = strides[0] + + subblock: nn.Module + + if len(channels) > 2: + subblock = _create_block(c, c, channels[1:], strides[1:], False) # continue recursion down + upc = c * 2 + else: + # the next layer is the bottom so stop recursion, create the bottom layer as the sublock for this layer + subblock = self._get_bottom_layer(c, channels[1]) + upc = c + channels[1] + + down = self._get_down_layer(inc, c, s, is_top) # create layer in downsampling path + up = self._get_up_layer(upc, outc, s, is_top) # create layer in upsampling path + + return nn.Sequential(down, SkipConnection(subblock), up) + + self.model = _create_block(in_channels, out_channels, self.channels, self.strides, True) + self.activation = nn.Sigmoid() + + def _get_down_layer(self, in_channels: int, out_channels: int, strides: int, is_top: bool) -> nn.Module: + """ + Args: + in_channels: number of input channels. + out_channels: number of output channels. + strides: convolution stride. + is_top: True if this is the top block. + """ + if self.num_res_units > 0: + return ResidualUnit( + self.dimensions, + in_channels, + out_channels, + strides=strides, + kernel_size=self.kernel_size, + subunits=self.num_res_units, + act=self.act, + norm=self.norm, + dropout=self.dropout, + ) + return Convolution( + self.dimensions, + in_channels, + out_channels, + strides=strides, + kernel_size=self.kernel_size, + act=self.act, + norm=self.norm, + dropout=self.dropout, + ) + + def _get_bottom_layer(self, in_channels: int, out_channels: int) -> nn.Module: + """ + Args: + in_channels: number of input channels. + out_channels: number of output channels. + """ + return self._get_down_layer(in_channels, out_channels, 1, False) + + def _get_up_layer(self, in_channels: int, out_channels: int, strides: int, is_top: bool) -> nn.Module: + """ + Args: + in_channels: number of input channels. + out_channels: number of output channels. + strides: convolution stride. + is_top: True if this is the top block. + """ + conv: Union[Convolution, nn.Sequential] + + conv = Convolution( + self.dimensions, + in_channels, + out_channels, + strides=strides, + kernel_size=self.up_kernel_size, + act=self.act, + norm=self.norm, + dropout=self.dropout, + conv_only=is_top and self.num_res_units == 0, + is_transposed=True, + ) + + if self.num_res_units > 0: + ru = ResidualUnit( + self.dimensions, + out_channels, + out_channels, + strides=1, + kernel_size=self.kernel_size, + subunits=1, + act=self.act, + norm=self.norm, + dropout=self.dropout, + last_conv_only=is_top, + ) + conv = nn.Sequential(conv, ru) + + return conv + + def forward(self, x: torch.Tensor) -> torch.Tensor: + return self.activation(self.model(x)) + + def train_step(self, image, segment, criterion, segbox = None): + forwarded = self.forward(image) + return criterion(forwarded, segment) + + diff --git a/training/Networks/network.py b/training/Networks/network.py new file mode 100644 index 0000000000000000000000000000000000000000..14526f6cd66dc87ad21b6c9b290fd50278420a14 --- /dev/null +++ b/training/Networks/network.py @@ -0,0 +1,11 @@ +import torch as T + +class Network(T.nn.Module): + def __init__(self): + super(Network, self).__init__() + + def forward(self, image, segbox): + pass + + def train_step(self, image, segment, criterion, segbox): + pass \ No newline at end of file diff --git a/training/README.md b/training/README.md new file mode 100644 index 0000000000000000000000000000000000000000..47b7194050f032ae501dd83c12f4b2056d0b55aa --- /dev/null +++ b/training/README.md @@ -0,0 +1,101 @@ +# Lung Tumor 3D Segmentation - Mixed Supervision + +End to end code base for lung tumor segmentation from CT-scan using mixed supervision for deep convolutional neural network. Takes 3D CT scans as input and outputs 3D segmentation of primary tumor. Project aims to utilize multiple different datasets with different label types (classification labels, bounding boxes, rough segmentations and fine segmentations). + +## Installation + +Requires python >= 3.6 + +Install python dependencies with pip. The requirements file is located in */Resources/* +``` +pip install -r requirements.txt +``` + +Build repository files as packages using setuptools. If you alter the code, remember to run the setup again. +``` +python setupy.py install +``` + +## Docker Integration +*To be specified* + +## Usage + +**Initiate Training:** `python .\Runable\Test\test_sevlus.py` + +The training is initiated from the .\Resources\Test\test_train.yaml file that looks like this: +``` +device: 'cuda' + +data: + train_dataset: "D:\\Repos\\LungTumorSegmentation\\Resources\\Test\\data_test_train.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 32 + d_1: 32 + d_2: 32 + +model: + architecture: UNet_con_double + loss: DiceLoss + filter_base: 64 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.001 + +train: + max_epochs: 3 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "D:\\Repos\\LungTumorSegmentation\\metrics.csv" + save_frequency: 5 + model_directory: "D:\\Repos\\LungTumorSegmentation\\models\\" + steps_per_plot: 10 +``` + +The paths would need to be updated. + +**Plot Training Metric File**: `python interface.py plot ` + +Store the plot by specifying the store location: `python interface.py plot -store_file -steps_per_epoch ` Example: `python interface.py plot ./metrics.csv -store_file plot.png -steps_per_epoch 120` + +**Evaluate Network**: `python .\Runable\Evaluate\eval.py` + +Evaluates the network on specified test images with labels. The configuration file (which here is the file at .\Resources\Windows_Files\win_eval.yaml) should contain network information as well as a reference to the data to evaluate the network on. + +The evaluation config should look similar to this + +``` +device: 'cuda' + +data: + train_dataset: "D:\\Repos\\LungTumorSegmentation\\Resources\\Windows_Files\\evaluate_data_msd.yaml" + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet_filter + weights: "D:\\idun_models\\1\\model_last_128.pth" + loss: DiceLoss + filter_base: 128 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.01 + +evaluate: + save_segmentations: True + save_directory: 'D:\\Repos\\LungTumorSegmentation\\m_128\\' + output_threshold: 0.5 +``` + +In this case, the paths would also need to be updated. + +## Authors +[Vemund Fredrksen](https://github.com/VemundFredriksen) & [Svein Ole M. Sevle](https://github.com/sosevle) + +## License +[MIT](https://choosealicense.com/licenses/mit/) diff --git a/training/Resources/Evaluate/malvik.yaml b/training/Resources/Evaluate/malvik.yaml new file mode 100644 index 0000000000000000000000000000000000000000..89a9abebcf0c8b98ae9d76de3880efaa15e75ba9 --- /dev/null +++ b/training/Resources/Evaluate/malvik.yaml @@ -0,0 +1,23 @@ +device: 'cuda' + +data: + train_dataset: "/home/tumor/LungTumorSegmentation/Resources/Inference/malvik_inference_data2.yaml" + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet_test + weights: "" + loss: DiceLoss + filter_base: 32 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.01 + +evaluate: + save_segmentations: True + save_directory: '' + output_threshold: 0.5 \ No newline at end of file diff --git a/training/Resources/Idun_Train_1/cropped.yaml b/training/Resources/Idun_Train_1/cropped.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a4b0f3fe70af32e772eb8973469020e0451b597d --- /dev/null +++ b/training/Resources/Idun_Train_1/cropped.yaml @@ -0,0 +1,320 @@ +image_prefix: "/cluster/work/sosevle/MSD_Cropped/Images/" +boxes_prefix: "/cluster/work/sosevle/MSD_Cropped/Boxes/" +label_prefix: "/cluster/work/sosevle/MSD_Cropped/Labels/" + +train: + [ + { + 'image' : 'lung_001.nii', + 'boxes' : 'lung_001.nii', + 'label' : 'lung_001.nii' + }, + { + 'image' : 'lung_003.nii', + 'boxes' : 'lung_003.nii', + 'label' : 'lung_003.nii' + }, + { + 'image' : 'lung_004.nii', + 'boxes' : 'lung_004.nii', + 'label' : 'lung_004.nii' + }, + { + 'image' : 'lung_005.nii', + 'boxes' : 'lung_005.nii', + 'label' : 'lung_005.nii' + }, + { + 'image' : 'lung_006.nii', + 'boxes' : 'lung_006.nii', + 'label' : 'lung_006.nii' + }, + { + 'image' : 'lung_009.nii', + 'boxes' : 'lung_009.nii', + 'label' : 'lung_009.nii' + }, + { + 'image' : 'lung_010.nii', + 'boxes' : 'lung_010.nii', + 'label' : 'lung_010.nii' + }, + { + 'image' : 'lung_014.nii', + 'boxes' : 'lung_014.nii', + 'label' : 'lung_014.nii' + }, + { + 'image' : 'lung_015.nii', + 'boxes' : 'lung_015.nii', + 'label' : 'lung_015.nii' + }, + { + 'image' : 'lung_016.nii', + 'boxes' : 'lung_016.nii', + 'label' : 'lung_016.nii' + }, + { + 'image' : 'lung_018.nii', + 'boxes' : 'lung_018.nii', + 'label' : 'lung_018.nii' + }, + { + 'image' : 'lung_020.nii', + 'boxes' : 'lung_020.nii', + 'label' : 'lung_020.nii' + }, + { + 'image' : 'lung_022.nii', + 'boxes' : 'lung_022.nii', + 'label' : 'lung_022.nii' + }, + { + 'image' : 'lung_023.nii', + 'boxes' : 'lung_023.nii', + 'label' : 'lung_023.nii' + }, + { + 'image' : 'lung_025.nii', + 'boxes' : 'lung_025.nii', + 'label' : 'lung_025.nii' + }, + { + 'image' : 'lung_026.nii', + 'boxes' : 'lung_026.nii', + 'label' : 'lung_026.nii' + }, + { + 'image' : 'lung_027.nii', + 'boxes' : 'lung_027.nii', + 'label' : 'lung_027.nii' + }, + { + 'image' : 'lung_028.nii', + 'boxes' : 'lung_028.nii', + 'label' : 'lung_028.nii' + }, + { + 'image' : 'lung_029.nii', + 'boxes' : 'lung_029.nii', + 'label' : 'lung_029.nii' + }, + { + 'image' : 'lung_031.nii', + 'boxes' : 'lung_031.nii', + 'label' : 'lung_031.nii' + }, + { + 'image' : 'lung_033.nii', + 'boxes' : 'lung_033.nii', + 'label' : 'lung_033.nii' + }, + { + 'image' : 'lung_034.nii', + 'boxes' : 'lung_034.nii', + 'label' : 'lung_034.nii' + }, + { + 'image' : 'lung_036.nii', + 'boxes' : 'lung_036.nii', + 'label' : 'lung_036.nii' + }, + { + 'image' : 'lung_037.nii', + 'boxes' : 'lung_037.nii', + 'label' : 'lung_037.nii' + }, + { + 'image' : 'lung_038.nii', + 'boxes' : 'lung_038.nii', + 'label' : 'lung_038.nii' + }, + { + 'image' : 'lung_041.nii', + 'boxes' : 'lung_041.nii', + 'label' : 'lung_041.nii' + }, + { + 'image' : 'lung_042.nii', + 'boxes' : 'lung_042.nii', + 'label' : 'lung_042.nii' + }, + { + 'image' : 'lung_043.nii', + 'boxes' : 'lung_043.nii', + 'label' : 'lung_043.nii' + }, + { + 'image' : 'lung_044.nii', + 'boxes' : 'lung_044.nii', + 'label' : 'lung_044.nii' + }, + { + 'image' : 'lung_045.nii', + 'boxes' : 'lung_045.nii', + 'label' : 'lung_045.nii' + }, + { + 'image' : 'lung_046.nii', + 'boxes' : 'lung_046.nii', + 'label' : 'lung_046.nii' + }, + { + 'image' : 'lung_047.nii', + 'boxes' : 'lung_047.nii', + 'label' : 'lung_047.nii' + }, + { + 'image' : 'lung_048.nii', + 'boxes' : 'lung_048.nii', + 'label' : 'lung_048.nii' + }, + { + 'image' : 'lung_049.nii', + 'boxes' : 'lung_049.nii', + 'label' : 'lung_049.nii' + }, + { + 'image' : 'lung_051.nii', + 'boxes' : 'lung_051.nii', + 'label' : 'lung_051.nii' + }, + { + 'image' : 'lung_053.nii', + 'boxes' : 'lung_053.nii', + 'label' : 'lung_053.nii' + }, + { + 'image' : 'lung_054.nii', + 'boxes' : 'lung_054.nii', + 'label' : 'lung_054.nii' + }, + { + 'image' : 'lung_055.nii', + 'boxes' : 'lung_055.nii', + 'label' : 'lung_055.nii' + }, + { + 'image' : 'lung_057.nii', + 'boxes' : 'lung_057.nii', + 'label' : 'lung_057.nii' + }, + { + 'image' : 'lung_058.nii', + 'boxes' : 'lung_058.nii', + 'label' : 'lung_058.nii' + }, + { + 'image' : 'lung_059.nii', + 'boxes' : 'lung_059.nii', + 'label' : 'lung_059.nii' + }, + { + 'image' : 'lung_061.nii', + 'boxes' : 'lung_061.nii', + 'label' : 'lung_061.nii' + }, + { + 'image' : 'lung_062.nii', + 'boxes' : 'lung_062.nii', + 'label' : 'lung_062.nii' + }, + { + 'image' : 'lung_064.nii', + 'boxes' : 'lung_064.nii', + 'label' : 'lung_064.nii' + }, + { + 'image' : 'lung_065.nii', + 'boxes' : 'lung_065.nii', + 'label' : 'lung_065.nii' + }, + { + 'image' : 'lung_066.nii', + 'boxes' : 'lung_066.nii', + 'label' : 'lung_066.nii' + }, + { + 'image' : 'lung_069.nii', + 'boxes' : 'lung_069.nii', + 'label' : 'lung_069.nii' + }, + { + 'image' : 'lung_070.nii', + 'boxes' : 'lung_070.nii', + 'label' : 'lung_070.nii' + }, + { + 'image' : 'lung_071.nii', + 'boxes' : 'lung_071.nii', + 'label' : 'lung_071.nii' + }, + { + 'image' : 'lung_073.nii', + 'boxes' : 'lung_073.nii', + 'label' : 'lung_073.nii' + }, + { + 'image' : 'lung_074.nii', + 'boxes' : 'lung_074.nii', + 'label' : 'lung_074.nii' + }, + { + 'image' : 'lung_075.nii', + 'boxes' : 'lung_075.nii', + 'label' : 'lung_075.nii' + }, + { + 'image' : 'lung_078.nii', + 'boxes' : 'lung_078.nii', + 'label' : 'lung_078.nii' + }, + { + 'image' : 'lung_079.nii', + 'boxes' : 'lung_079.nii', + 'label' : 'lung_079.nii' + }, + { + 'image' : 'lung_080.nii', + 'boxes' : 'lung_080.nii', + 'label' : 'lung_080.nii' + } +] + +val: [ + { + 'image' : 'lung_081.nii', + 'boxes' : 'lung_081.nii', + 'label' : 'lung_081.nii' + }, + { + 'image' : 'lung_083.nii', + 'boxes' : 'lung_083.nii', + 'label' : 'lung_083.nii' + }, + { + 'image' : 'lung_084.nii', + 'boxes' : 'lung_084.nii', + 'label' : 'lung_084.nii' + }, + { + 'image' : 'lung_086.nii', + 'boxes' : 'lung_086.nii', + 'label' : 'lung_086.nii' + }, + { + 'image' : 'lung_092.nii', + 'boxes' : 'lung_092.nii', + 'label' : 'lung_092.nii' + }, + { + 'image' : 'lung_093.nii', + 'boxes' : 'lung_093.nii', + 'label' : 'lung_093.nii' + }, + { + 'image' : 'lung_095.nii', + 'boxes' : 'lung_095.nii', + 'label' : 'lung_095.nii' + } +] \ No newline at end of file diff --git a/training/Resources/Idun_Train_1/full_size.yaml b/training/Resources/Idun_Train_1/full_size.yaml new file mode 100644 index 0000000000000000000000000000000000000000..83a1f8986a6131f5ad1818ee5bfb51f12500fa34 --- /dev/null +++ b/training/Resources/Idun_Train_1/full_size.yaml @@ -0,0 +1,320 @@ +image_prefix: "/cluster/work/sosevle/d1/imagesTr/" +boxes_prefix: "/cluster/work/sosevle/d1/boxes/" +label_prefix: "/cluster/work/sosevle/d1/labelsTr/" + +train: + [ + { + 'image' : 'lung_001.nii/lung_001.nii', + 'boxes' : 'lung_001.nii', + 'label': 'lung_001.nii/lung_001.nii' + }, + { + 'image' : 'lung_003.nii/lung_003.nii', + 'boxes' : 'lung_003.nii', + 'label': 'lung_003.nii/lung_003.nii' + }, + { + 'image' : 'lung_004.nii/lung_004.nii', + 'boxes' : 'lung_004.nii', + 'label': 'lung_004.nii/lung_004.nii' + }, + { + 'image' : 'lung_005.nii/lung_005.nii', + 'boxes' : 'lung_005.nii', + 'label': 'lung_005.nii/lung_005.nii' + }, + { + 'image' : 'lung_006.nii/lung_006.nii', + 'boxes' : 'lung_006.nii', + 'label': 'lung_006.nii/lung_006.nii' + }, + { + 'image' : 'lung_009.nii/lung_009.nii', + 'boxes' : 'lung_009.nii', + 'label': 'lung_009.nii/lung_009.nii' + }, + { + 'image' : 'lung_010.nii/lung_010.nii', + 'boxes' : 'lung_010.nii', + 'label': 'lung_010.nii/lung_010.nii' + }, + { + 'image' : 'lung_014.nii/lung_014.nii', + 'boxes' : 'lung_014.nii', + 'label': 'lung_014.nii/lung_014.nii' + }, + { + 'image' : 'lung_015.nii/lung_015.nii', + 'boxes' : 'lung_015.nii', + 'label': 'lung_015.nii/lung_015.nii' + }, + { + 'image' : 'lung_016.nii/lung_016.nii', + 'boxes' : 'lung_016.nii', + 'label': 'lung_016.nii/lung_016.nii' + }, + { + 'image' : 'lung_018.nii/lung_018.nii', + 'boxes' : 'lung_018.nii', + 'label': 'lung_018.nii/lung_018.nii' + }, + { + 'image' : 'lung_020.nii/lung_020.nii', + 'boxes' : 'lung_020.nii', + 'label': 'lung_020.nii/lung_020.nii' + }, + { + 'image' : 'lung_022.nii/lung_022.nii', + 'boxes' : 'lung_022.nii', + 'label': 'lung_022.nii/lung_022.nii' + }, + { + 'image' : 'lung_023.nii/lung_023.nii', + 'boxes' : 'lung_023.nii', + 'label': 'lung_023.nii/lung_023.nii' + }, + { + 'image' : 'lung_025.nii/lung_025.nii', + 'boxes' : 'lung_025.nii', + 'label': 'lung_025.nii/lung_025.nii' + }, + { + 'image' : 'lung_026.nii/lung_026.nii', + 'boxes' : 'lung_026.nii', + 'label': 'lung_026.nii/lung_026.nii' + }, + { + 'image' : 'lung_027.nii/lung_027.nii', + 'boxes' : 'lung_027.nii', + 'label': 'lung_027.nii/lung_027.nii' + }, + { + 'image' : 'lung_028.nii/lung_028.nii', + 'boxes' : 'lung_028.nii', + 'label': 'lung_028.nii/lung_028.nii' + }, + { + 'image' : 'lung_029.nii/lung_029.nii', + 'boxes' : 'lung_029.nii', + 'label': 'lung_029.nii/lung_029.nii' + }, + { + 'image' : 'lung_031.nii/lung_031.nii', + 'boxes' : 'lung_031.nii', + 'label': 'lung_031.nii/lung_031.nii' + }, + { + 'image' : 'lung_033.nii/lung_033.nii', + 'boxes' : 'lung_033.nii', + 'label': 'lung_033.nii/lung_033.nii' + }, + { + 'image' : 'lung_034.nii/lung_034.nii', + 'boxes' : 'lung_034.nii', + 'label': 'lung_034.nii/lung_034.nii' + }, + { + 'image' : 'lung_036.nii/lung_036.nii', + 'boxes' : 'lung_036.nii', + 'label': 'lung_036.nii/lung_036.nii' + }, + { + 'image' : 'lung_037.nii/lung_037.nii', + 'boxes' : 'lung_037.nii', + 'label': 'lung_037.nii/lung_037.nii' + }, + { + 'image' : 'lung_038.nii/lung_038.nii', + 'boxes' : 'lung_038.nii', + 'label': 'lung_038.nii/lung_038.nii' + }, + { + 'image' : 'lung_041.nii/lung_041.nii', + 'boxes' : 'lung_041.nii', + 'label': 'lung_041.nii/lung_041.nii' + }, + { + 'image' : 'lung_042.nii/lung_042.nii', + 'boxes' : 'lung_042.nii', + 'label': 'lung_042.nii/lung_042.nii' + }, + { + 'image' : 'lung_043.nii/lung_043.nii', + 'boxes' : 'lung_043.nii', + 'label': 'lung_043.nii/lung_043.nii' + }, + { + 'image' : 'lung_044.nii/lung_044.nii', + 'boxes' : 'lung_044.nii', + 'label': 'lung_044.nii/lung_044.nii' + }, + { + 'image' : 'lung_045.nii/lung_045.nii', + 'boxes' : 'lung_045.nii', + 'label': 'lung_045.nii/lung_045.nii' + }, + { + 'image' : 'lung_046.nii/lung_046.nii', + 'boxes' : 'lung_046.nii', + 'label': 'lung_046.nii/lung_046.nii' + }, + { + 'image' : 'lung_047.nii/lung_047.nii', + 'boxes' : 'lung_047.nii', + 'label': 'lung_047.nii/lung_047.nii' + }, + { + 'image' : 'lung_048.nii/lung_048.nii', + 'boxes' : 'lung_048.nii', + 'label': 'lung_048.nii/lung_048.nii' + }, + { + 'image' : 'lung_049.nii/lung_049.nii', + 'boxes' : 'lung_049.nii', + 'label': 'lung_049.nii/lung_049.nii' + }, + { + 'image' : 'lung_051.nii/lung_051.nii', + 'boxes' : 'lung_051.nii', + 'label': 'lung_051.nii/lung_051.nii' + }, + { + 'image' : 'lung_053.nii/lung_053.nii', + 'boxes' : 'lung_053.nii', + 'label': 'lung_053.nii/lung_053.nii' + }, + { + 'image' : 'lung_054.nii/lung_054.nii', + 'boxes' : 'lung_054.nii', + 'label': 'lung_054.nii/lung_054.nii' + }, + { + 'image' : 'lung_055.nii/lung_055.nii', + 'boxes' : 'lung_055.nii', + 'label': 'lung_055.nii/lung_055.nii' + }, + { + 'image' : 'lung_057.nii/lung_057.nii', + 'boxes' : 'lung_057.nii', + 'label': 'lung_057.nii/lung_057.nii' + }, + { + 'image' : 'lung_058.nii/lung_058.nii', + 'boxes' : 'lung_058.nii', + 'label': 'lung_058.nii/lung_058.nii' + }, + { + 'image' : 'lung_059.nii/lung_059.nii', + 'boxes' : 'lung_059.nii', + 'label': 'lung_059.nii/lung_059.nii' + }, + { + 'image' : 'lung_061.nii/lung_061.nii', + 'boxes' : 'lung_061.nii', + 'label': 'lung_061.nii/lung_061.nii' + }, + { + 'image' : 'lung_062.nii/lung_062.nii', + 'boxes' : 'lung_062.nii', + 'label': 'lung_062.nii/lung_062.nii' + }, + { + 'image' : 'lung_064.nii/lung_064.nii', + 'boxes' : 'lung_064.nii', + 'label': 'lung_064.nii/lung_064.nii' + }, + { + 'image' : 'lung_065.nii/lung_065.nii', + 'boxes' : 'lung_065.nii', + 'label': 'lung_065.nii/lung_065.nii' + }, + { + 'image' : 'lung_066.nii/lung_066.nii', + 'boxes' : 'lung_066.nii', + 'label': 'lung_066.nii/lung_066.nii' + }, + { + 'image' : 'lung_069.nii/lung_069.nii', + 'boxes' : 'lung_069.nii', + 'label': 'lung_069.nii/lung_069.nii' + }, + { + 'image' : 'lung_070.nii/lung_070.nii', + 'boxes' : 'lung_070.nii', + 'label': 'lung_070.nii/lung_070.nii' + }, + { + 'image' : 'lung_071.nii/lung_071.nii', + 'boxes' : 'lung_071.nii', + 'label': 'lung_071.nii/lung_071.nii' + }, + { + 'image' : 'lung_073.nii/lung_073.nii', + 'boxes' : 'lung_073.nii', + 'label': 'lung_073.nii/lung_073.nii' + }, + { + 'image' : 'lung_074.nii/lung_074.nii', + 'boxes' : 'lung_074.nii', + 'label': 'lung_074.nii/lung_074.nii' + }, + { + 'image' : 'lung_075.nii/lung_075.nii', + 'boxes' : 'lung_075.nii', + 'label': 'lung_075.nii/lung_075.nii' + }, + { + 'image' : 'lung_078.nii/lung_078.nii', + 'boxes' : 'lung_078.nii', + 'label': 'lung_078.nii/lung_078.nii' + }, + { + 'image' : 'lung_079.nii/lung_079.nii', + 'boxes' : 'lung_079.nii', + 'label': 'lung_079.nii/lung_079.nii' + }, + { + 'image' : 'lung_080.nii/lung_080.nii', + 'boxes' : 'lung_080.nii', + 'label': 'lung_080.nii/lung_080.nii' + } +] + +val: [ + { + 'image' : 'lung_081.nii/lung_081.nii', + 'boxes' : 'lung_081.nii', + 'label': 'lung_081.nii/lung_081.nii' + }, + { + 'image' : 'lung_083.nii/lung_083.nii', + 'boxes' : 'lung_083.nii', + 'label': 'lung_083.nii/lung_083.nii' + }, + { + 'image' : 'lung_084.nii/lung_084.nii', + 'boxes' : 'lung_084.nii', + 'label': 'lung_084.nii/lung_084.nii' + }, + { + 'image' : 'lung_086.nii/lung_086.nii', + 'boxes' : 'lung_086.nii', + 'label': 'lung_086.nii/lung_086.nii' + }, + { + 'image' : 'lung_092.nii/lung_092.nii', + 'boxes' : 'lung_092.nii', + 'label': 'lung_092.nii/lung_092.nii' + }, + { + 'image' : 'lung_093.nii/lung_093.nii', + 'boxes' : 'lung_093.nii', + 'label': 'lung_093.nii/lung_093.nii' + }, + { + 'image' : 'lung_095.nii/lung_095.nii', + 'boxes' : 'lung_095.nii', + 'label': 'lung_095.nii/lung_095.nii' + } +] \ No newline at end of file diff --git a/training/Resources/Idun_Train_1/train_25.yaml b/training/Resources/Idun_Train_1/train_25.yaml new file mode 100644 index 0000000000000000000000000000000000000000..8cd0d9616d85c5a728bb9df14e607b3ade7c3123 --- /dev/null +++ b/training/Resources/Idun_Train_1/train_25.yaml @@ -0,0 +1,27 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/cropped.yaml" + aug_prob: 0.25 + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet_filter + loss: DiceLoss + filter_base: 64 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.0002 + +train: + max_epochs: 500 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t25.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/25/" + steps_per_plot: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_1/train_50.yaml b/training/Resources/Idun_Train_1/train_50.yaml new file mode 100644 index 0000000000000000000000000000000000000000..6aceb91ae053b105f379359b56f00c968bde8a88 --- /dev/null +++ b/training/Resources/Idun_Train_1/train_50.yaml @@ -0,0 +1,28 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/cropped.yaml" + aug_prob: 0.5 + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet_filter + loss: DiceLoss + weights: /cluster/work/sosevle/models/50/model_500.pth + filter_base: 64 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.0002 + +train: + max_epochs: 500 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t50_2.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/50_2/" + batch_size: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_1/train_75.yaml b/training/Resources/Idun_Train_1/train_75.yaml new file mode 100644 index 0000000000000000000000000000000000000000..80f74abd36470d39c1e9b28e507fced1e6b439ac --- /dev/null +++ b/training/Resources/Idun_Train_1/train_75.yaml @@ -0,0 +1,27 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/cropped.yaml" + aug_prob: 0.75 + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet_filter + loss: DiceLoss + filter_base: 64 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.0002 + +train: + max_epochs: 500 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t75.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/75/" + steps_per_plot: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_1/train_full_filter_cropped.yaml b/training/Resources/Idun_Train_1/train_full_filter_cropped.yaml new file mode 100644 index 0000000000000000000000000000000000000000..0b3733a51f61fe49cc4ec4ae0a3bc0bdb320b412 --- /dev/null +++ b/training/Resources/Idun_Train_1/train_full_filter_cropped.yaml @@ -0,0 +1,27 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/cropped.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet_filter + loss: DiceLoss + filter_base: 64 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.0002 + +train: + max_epochs: 500 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/full_filter.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/full_filter/" + steps_per_plot: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_1/train_full_filter_full_image.yaml b/training/Resources/Idun_Train_1/train_full_filter_full_image.yaml new file mode 100644 index 0000000000000000000000000000000000000000..81032729700edee953713d229b17a2612ce23d87 --- /dev/null +++ b/training/Resources/Idun_Train_1/train_full_filter_full_image.yaml @@ -0,0 +1,27 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/full_size.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet_filter + loss: DiceLoss + filter_base: 64 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.0002 + +train: + max_epochs: 500 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/full_filter_fs.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/full_filter_fs/" + steps_per_plot: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_1/train_half_filter_cropped.yaml b/training/Resources/Idun_Train_1/train_half_filter_cropped.yaml new file mode 100644 index 0000000000000000000000000000000000000000..0a56e40438ac9efb829c7fb506092b99ae382050 --- /dev/null +++ b/training/Resources/Idun_Train_1/train_half_filter_cropped.yaml @@ -0,0 +1,27 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/cropped.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet_filter + loss: DiceLoss + filter_base: 32 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.0002 + +train: + max_epochs: 500 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/half_filter.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/half_filter/" + steps_per_plot: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_2/data.yaml b/training/Resources/Idun_Train_2/data.yaml new file mode 100644 index 0000000000000000000000000000000000000000..e238e92cdc15bab701feb60b647810a940459af6 --- /dev/null +++ b/training/Resources/Idun_Train_2/data.yaml @@ -0,0 +1,3123 @@ +image_prefix: "/cluster/work/sosevle/full_data/train_student/Images/" +label_prefix: "/cluster/work/sosevle/full_data/train_student/Labels/" +boxes_prefix: "/cluster/work/sosevle/full_data/train_student/Boxes/" + +train: + [ + { + 'image' : 'lung_001.nii.gz', + 'boxes' : 'lung_001.nii.gz', + 'label': 'lung_001.nii.gz', + }, + { + 'image' : 'lung_003.nii.gz', + 'boxes' : 'lung_003.nii.gz', + 'label': 'lung_003.nii.gz', + }, + { + 'image' : 'lung_004.nii.gz', + 'boxes' : 'lung_004.nii.gz', + 'label': 'lung_004.nii.gz', + }, + { + 'image' : 'lung_005.nii.gz', + 'boxes' : 'lung_005.nii.gz', + 'label': 'lung_005.nii.gz', + }, + { + 'image' : 'lung_006.nii.gz', + 'boxes' : 'lung_006.nii.gz', + 'label': 'lung_006.nii.gz', + }, + { + 'image' : 'lung_009.nii.gz', + 'boxes' : 'lung_009.nii.gz', + 'label': 'lung_009.nii.gz', + }, + { + 'image' : 'lung_010.nii.gz', + 'boxes' : 'lung_010.nii.gz', + 'label': 'lung_010.nii.gz', + }, + { + 'image' : 'lung_014.nii.gz', + 'boxes' : 'lung_014.nii.gz', + 'label': 'lung_014.nii.gz', + }, + { + 'image' : 'lung_015.nii.gz', + 'boxes' : 'lung_015.nii.gz', + 'label': 'lung_015.nii.gz', + }, + { + 'image' : 'lung_016.nii.gz', + 'boxes' : 'lung_016.nii.gz', + 'label': 'lung_016.nii.gz', + }, + { + 'image' : 'lung_018.nii.gz', + 'boxes' : 'lung_018.nii.gz', + 'label': 'lung_018.nii.gz', + }, + { + 'image' : 'lung_020.nii.gz', + 'boxes' : 'lung_020.nii.gz', + 'label': 'lung_020.nii.gz', + }, + { + 'image' : 'lung_022.nii.gz', + 'boxes' : 'lung_022.nii.gz', + 'label': 'lung_022.nii.gz', + }, + { + 'image' : 'lung_023.nii.gz', + 'boxes' : 'lung_023.nii.gz', + 'label': 'lung_023.nii.gz', + }, + { + 'image' : 'lung_025.nii.gz', + 'boxes' : 'lung_025.nii.gz', + 'label': 'lung_025.nii.gz', + }, + { + 'image' : 'lung_026.nii.gz', + 'boxes' : 'lung_026.nii.gz', + 'label': 'lung_026.nii.gz', + }, + { + 'image' : 'lung_027.nii.gz', + 'boxes' : 'lung_027.nii.gz', + 'label': 'lung_027.nii.gz', + }, + { + 'image' : 'lung_028.nii.gz', + 'boxes' : 'lung_028.nii.gz', + 'label': 'lung_028.nii.gz', + }, + { + 'image' : 'lung_029.nii.gz', + 'boxes' : 'lung_029.nii.gz', + 'label': 'lung_029.nii.gz', + }, + { + 'image' : 'lung_031.nii.gz', + 'boxes' : 'lung_031.nii.gz', + 'label': 'lung_031.nii.gz', + }, + { + 'image' : 'lung_033.nii.gz', + 'boxes' : 'lung_033.nii.gz', + 'label': 'lung_033.nii.gz', + }, + { + 'image' : 'lung_034.nii.gz', + 'boxes' : 'lung_034.nii.gz', + 'label': 'lung_034.nii.gz', + }, + { + 'image' : 'lung_036.nii.gz', + 'boxes' : 'lung_036.nii.gz', + 'label': 'lung_036.nii.gz', + }, + { + 'image' : 'lung_037.nii.gz', + 'boxes' : 'lung_037.nii.gz', + 'label': 'lung_037.nii.gz', + }, + { + 'image' : 'lung_038.nii.gz', + 'boxes' : 'lung_038.nii.gz', + 'label': 'lung_038.nii.gz', + }, + { + 'image' : 'lung_041.nii.gz', + 'boxes' : 'lung_041.nii.gz', + 'label': 'lung_041.nii.gz', + }, + { + 'image' : 'lung_042.nii.gz', + 'boxes' : 'lung_042.nii.gz', + 'label': 'lung_042.nii.gz', + }, + { + 'image' : 'lung_043.nii.gz', + 'boxes' : 'lung_043.nii.gz', + 'label': 'lung_043.nii.gz', + }, + { + 'image' : 'lung_044.nii.gz', + 'boxes' : 'lung_044.nii.gz', + 'label': 'lung_044.nii.gz', + }, + { + 'image' : 'lung_045.nii.gz', + 'boxes' : 'lung_045.nii.gz', + 'label': 'lung_045.nii.gz', + }, + { + 'image' : 'lung_046.nii.gz', + 'boxes' : 'lung_046.nii.gz', + 'label': 'lung_046.nii.gz', + }, + { + 'image' : 'lung_047.nii.gz', + 'boxes' : 'lung_047.nii.gz', + 'label': 'lung_047.nii.gz', + }, + { + 'image' : 'lung_048.nii.gz', + 'boxes' : 'lung_048.nii.gz', + 'label': 'lung_048.nii.gz', + }, + { + 'image' : 'lung_049.nii.gz', + 'boxes' : 'lung_049.nii.gz', + 'label': 'lung_049.nii.gz', + }, + { + 'image' : 'lung_051.nii.gz', + 'boxes' : 'lung_051.nii.gz', + 'label': 'lung_051.nii.gz', + }, + { + 'image' : 'lung_053.nii.gz', + 'boxes' : 'lung_053.nii.gz', + 'label': 'lung_053.nii.gz', + }, + { + 'image' : 'lung_054.nii.gz', + 'boxes' : 'lung_054.nii.gz', + 'label': 'lung_054.nii.gz', + }, + { + 'image' : 'lung_055.nii.gz', + 'boxes' : 'lung_055.nii.gz', + 'label': 'lung_055.nii.gz', + }, + { + 'image' : 'lung_057.nii.gz', + 'boxes' : 'lung_057.nii.gz', + 'label': 'lung_057.nii.gz', + }, + { + 'image' : 'lung_058.nii.gz', + 'boxes' : 'lung_058.nii.gz', + 'label': 'lung_058.nii.gz', + }, + { + 'image' : 'lung_059.nii.gz', + 'boxes' : 'lung_059.nii.gz', + 'label': 'lung_059.nii.gz', + }, + { + 'image' : 'lung_061.nii.gz', + 'boxes' : 'lung_061.nii.gz', + 'label': 'lung_061.nii.gz', + }, + { + 'image' : 'lung_062.nii.gz', + 'boxes' : 'lung_062.nii.gz', + 'label': 'lung_062.nii.gz', + }, + { + 'image' : 'lung_064.nii.gz', + 'boxes' : 'lung_064.nii.gz', + 'label': 'lung_064.nii.gz', + }, + { + 'image' : 'lung_065.nii.gz', + 'boxes' : 'lung_065.nii.gz', + 'label': 'lung_065.nii.gz', + }, + { + 'image' : 'lung_066.nii.gz', + 'boxes' : 'lung_066.nii.gz', + 'label': 'lung_066.nii.gz', + }, + { + 'image' : 'lung_069.nii.gz', + 'boxes' : 'lung_069.nii.gz', + 'label': 'lung_069.nii.gz', + }, + { + 'image' : 'lung_070.nii.gz', + 'boxes' : 'lung_070.nii.gz', + 'label': 'lung_070.nii.gz', + }, + { + 'image' : 'lung_071.nii.gz', + 'boxes' : 'lung_071.nii.gz', + 'label': 'lung_071.nii.gz', + } +] + +train2: [ + { + 'image' : 'A0001_scan1.nii.gz', + 'boxes': 'A0001_scan1.nii.gz', + 'label': 'A0001_scan1.nii.gz' + }, + { + 'image' : 'A0001_scan2.nii.gz', + 'boxes': 'A0001_scan2.nii.gz', + 'label': 'A0001_scan2.nii.gz' + }, + { + 'image' : 'A0002_scan1.nii.gz', + 'boxes': 'A0002_scan1.nii.gz', + 'label': 'A0002_scan1.nii.gz' + }, + { + 'image' : 'A0003_scan1.nii.gz', + 'boxes': 'A0003_scan1.nii.gz', + 'label': 'A0003_scan1.nii.gz' + }, + { + 'image' : 'A0003_scan2.nii.gz', + 'boxes': 'A0003_scan2.nii.gz', + 'label': 'A0003_scan2.nii.gz' + }, + { + 'image' : 'A0004_scan1.nii.gz', + 'boxes': 'A0004_scan1.nii.gz', + 'label': 'A0004_scan1.nii.gz' + }, + { + 'image' : 'A0004_scan2.nii.gz', + 'boxes': 'A0004_scan2.nii.gz', + 'label': 'A0004_scan2.nii.gz' + }, + { + 'image' : 'A0006_scan1.nii.gz', + 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'G0056_scan1.nii.gz' + }, + { + 'image' : 'G0056_scan3.nii.gz', + 'boxes': 'G0056_scan3.nii.gz', + 'label': 'G0056_scan3.nii.gz' + }, + { + 'image' : 'G0057_scan1.nii.gz', + 'boxes': 'G0057_scan1.nii.gz', + 'label': 'G0057_scan1.nii.gz' + }, + { + 'image' : 'G0057_scan3.nii.gz', + 'boxes': 'G0057_scan3.nii.gz', + 'label': 'G0057_scan3.nii.gz' + }, + { + 'image' : 'G0058_scan1.nii.gz', + 'boxes': 'G0058_scan1.nii.gz', + 'label': 'G0058_scan1.nii.gz' + }, + { + 'image' : 'G0058_scan3.nii.gz', + 'boxes': 'G0058_scan3.nii.gz', + 'label': 'G0058_scan3.nii.gz' + }, + { + 'image' : 'G0059_scan1.nii.gz', + 'boxes': 'G0059_scan1.nii.gz', + 'label': 'G0059_scan1.nii.gz' + }, + { + 'image' : 'G0059_scan2.nii.gz', + 'boxes': 'G0059_scan2.nii.gz', + 'label': 'G0059_scan2.nii.gz' + }, + { + 'image' : 'G0060_scan1.nii.gz', + 'boxes': 'G0060_scan1.nii.gz', + 'label': 'G0060_scan1.nii.gz' + }, + { + 'image' : 'G0060_scan2.nii.gz', + 'boxes': 'G0060_scan2.nii.gz', + 'label': 'G0060_scan2.nii.gz' + }, + { + 'image' : 'G0062_scan1.nii.gz', + 'boxes': 'G0062_scan1.nii.gz', + 'label': 'G0062_scan1.nii.gz' + }, + { + 'image' : 'G0062_scan3.nii.gz', + 'boxes': 'G0062_scan3.nii.gz', + 'label': 'G0062_scan3.nii.gz' + }, + +] + +val: [ + { + 'image' : 'lung_073.nii.gz', + 'boxes' : 'lung_073.nii.gz', + 'label': 'lung_073.nii.gz', + }, + { + 'image' : 'lung_074.nii.gz', + 'boxes' : 'lung_074.nii.gz', + 'label': 'lung_074.nii.gz', + }, + { + 'image' : 'lung_075.nii.gz', + 'boxes' : 'lung_075.nii.gz', + 'label': 'lung_075.nii.gz', + }, + { + 'image' : 'lung_078.nii.gz', + 'boxes' : 'lung_078.nii.gz', + 'label': 'lung_078.nii.gz', + }, + { + 'image' : 'lung_079.nii.gz', + 'boxes' : 'lung_079.nii.gz', + 'label': 'lung_079.nii.gz', + } +] + + +val2: [ + { + 'image' : 'A0110_scan1.nii.gz', + 'boxes': 'A0110_scan1.nii.gz', + 'label': 'A0110_scan1.nii.gz' + }, + { + 'image' : 'A0110_scan2.nii.gz', + 'boxes': 'A0110_scan2.nii.gz', + 'label': 'A0110_scan2.nii.gz' + }, + { + 'image' : 'A0110_scan3.nii.gz', + 'boxes': 'A0110_scan3.nii.gz', + 'label': 'A0110_scan3.nii.gz' + }, + { + 'image' : 'A0111_scan1.nii.gz', + 'boxes': 'A0111_scan1.nii.gz', + 'label': 'A0111_scan1.nii.gz' + }, + { + 'image' : 'A0111_scan2.nii.gz', + 'boxes': 'A0111_scan2.nii.gz', + 'label': 'A0111_scan2.nii.gz' + }, + { + 'image' : 'A0111_scan3.nii.gz', + 'boxes': 'A0111_scan3.nii.gz', + 'label': 'A0111_scan3.nii.gz' + }, + { + 'image' : 'A0112_scan2.nii.gz', + 'boxes': 'A0112_scan2.nii.gz', + 'label': 'A0112_scan2.nii.gz' + }, + { + 'image' : 'A0112_scan3.nii.gz', + 'boxes': 'A0112_scan3.nii.gz', + 'label': 'A0112_scan3.nii.gz' + }, + { + 'image' : 'A0112_scan4.nii.gz', + 'boxes': 'A0112_scan4.nii.gz', + 'label': 'A0112_scan4.nii.gz' + }, + { + 'image' : 'A0113_scan1.nii.gz', + 'boxes': 'A0113_scan1.nii.gz', + 'label': 'A0113_scan1.nii.gz' + }, + { + 'image' : 'A0113_scan2.nii.gz', + 'boxes': 'A0113_scan2.nii.gz', + 'label': 'A0113_scan2.nii.gz' + }, + { + 'image' : 'A0113_scan3.nii.gz', + 'boxes': 'A0113_scan3.nii.gz', + 'label': 'A0113_scan3.nii.gz' + }, + { + 'image' : 'A0113_scan4.nii.gz', + 'boxes': 'A0113_scan4.nii.gz', + 'label': 'A0113_scan4.nii.gz' + }, + { + 'image' : 'A0113_scan5.nii.gz', + 'boxes': 'A0113_scan5.nii.gz', + 'label': 'A0113_scan5.nii.gz' + }, + { + 'image' : 'A0114_scan2.nii.gz', + 'boxes': 'A0114_scan2.nii.gz', + 'label': 'A0114_scan2.nii.gz' + }, + { + 'image' : 'A0115_scan2.nii.gz', + 'boxes': 'A0115_scan2.nii.gz', + 'label': 'A0115_scan2.nii.gz' + }, + { + 'image' : 'A0116_scan1.nii.gz', + 'boxes': 'A0116_scan1.nii.gz', + 'label': 'A0116_scan1.nii.gz' + }, + { + 'image' : 'A0116_scan2.nii.gz', + 'boxes': 'A0116_scan2.nii.gz', + 'label': 'A0116_scan2.nii.gz' + }, + { + 'image' : 'A0117_scan1.nii.gz', + 'boxes': 'A0117_scan1.nii.gz', + 'label': 'A0117_scan1.nii.gz' + }, + { + 'image' : 'A0117_scan2.nii.gz', + 'boxes': 'A0117_scan2.nii.gz', + 'label': 'A0117_scan2.nii.gz' + }, + { + 'image' : 'A0117_scan3.nii.gz', + 'boxes': 'A0117_scan3.nii.gz', + 'label': 'A0117_scan3.nii.gz' + }, + { + 'image' : 'A0117_scan4.nii.gz', + 'boxes': 'A0117_scan4.nii.gz', + 'label': 'A0117_scan4.nii.gz' + }, + { + 'image' : 'A0117_scan5.nii.gz', + 'boxes': 'A0117_scan5.nii.gz', + 'label': 'A0117_scan5.nii.gz' + }, + { + 'image' : 'A0117_scan6.nii.gz', + 'boxes': 'A0117_scan6.nii.gz', + 'label': 'A0117_scan6.nii.gz' + }, + { + 'image' : 'A0119_scan1.nii.gz', + 'boxes': 'A0119_scan1.nii.gz', + 'label': 'A0119_scan1.nii.gz' + }, + { + 'image' : 'A0119_scan2.nii.gz', + 'boxes': 'A0119_scan2.nii.gz', + 'label': 'A0119_scan2.nii.gz' + } +] diff --git a/training/Resources/Idun_Train_2/lungdx_data.yaml b/training/Resources/Idun_Train_2/lungdx_data.yaml new file mode 100644 index 0000000000000000000000000000000000000000..8075ec390ae54b6d28e5d7a8c202824e6226692d --- /dev/null +++ b/training/Resources/Idun_Train_2/lungdx_data.yaml @@ -0,0 +1,2571 @@ +image_prefix: "/cluster/work/sosevle/full_data/LungDx-Lung/Images/" +boxes_prefix: "/cluster/work/sosevle/full_data/LungDx-Lung/Boxes/" +label_prefix: "/cluster/work/sosevle/full_data/LungDx-Lung/Labels/" + +train: + [ + { + 'image' : 'A0001_scan1_left.nii.gz', + 'label': 'A0001_scan1_left.nii.gz' + }, + { + 'image' : 'A0001_scan1_right.nii.gz', + 'label': 'A0001_scan1_right.nii.gz' + }, + { + 'image' : 'A0001_scan2_left.nii.gz', + 'label': 'A0001_scan2_left.nii.gz' + }, + { + 'image' : 'A0002_scan1_right.nii.gz', + 'label': 'A0002_scan1_right.nii.gz' + }, + { + 'image' : 'A0002_scan2_left.nii.gz', + 'label': 'A0002_scan2_left.nii.gz' + }, + { + 'image' : 'A0002_scan2_right.nii.gz', + 'label': 'A0002_scan2_right.nii.gz' + }, + { + 'image' : 'A0003_scan1_left.nii.gz', + 'label': 'A0003_scan1_left.nii.gz' + }, + { + 'image' : 'A0003_scan2_left.nii.gz', + 'label': 'A0003_scan2_left.nii.gz' + }, + { + 'image' : 'A0004_scan1_right.nii.gz', + 'label': 'A0004_scan1_right.nii.gz' + }, + { + 'image' : 'A0004_scan2_right.nii.gz', + 'label': 'A0004_scan2_right.nii.gz' + }, + { + 'image' : 'A0005_scan1_right.nii.gz', + 'label': 'A0005_scan1_right.nii.gz' + }, + { + 'image' : 'A0005_scan2_right.nii.gz', + 'label': 'A0005_scan2_right.nii.gz' + }, + { + 'image' : 'A0006_scan1_right.nii.gz', + 'label': 'A0006_scan1_right.nii.gz' + }, + { + 'image' : 'A0006_scan4_right.nii.gz', + 'label': 'A0006_scan4_right.nii.gz' + }, + { + 'image' : 'A0007_scan1_left.nii.gz', + 'label': 'A0007_scan1_left.nii.gz' + }, + { + 'image' : 'A0007_scan2_left.nii.gz', + 'label': 'A0007_scan2_left.nii.gz' + }, + { + 'image' : 'A0008_scan1_right.nii.gz', + 'label': 'A0008_scan1_right.nii.gz' + }, + { + 'image' : 'A0008_scan2_right.nii.gz', + 'label': 'A0008_scan2_right.nii.gz' + }, + { + 'image' : 'A0009_scan1_right.nii.gz', + 'label': 'A0009_scan1_right.nii.gz' + }, + { + 'image' : 'A0009_scan2_right.nii.gz', + 'label': 'A0009_scan2_right.nii.gz' + }, + { + 'image' : 'A0010_scan1_right.nii.gz', + 'label': 'A0010_scan1_right.nii.gz' + }, + { + 'image' : 'A0010_scan2_right.nii.gz', + 'label': 'A0010_scan2_right.nii.gz' + }, + { + 'image' : 'A0011_scan1_left.nii.gz', + 'label': 'A0011_scan1_left.nii.gz' + }, + { + 'image' : 'A0011_scan2_left.nii.gz', + 'label': 'A0011_scan2_left.nii.gz' + }, + { + 'image' : 'A0013_scan1_right.nii.gz', + 'label': 'A0013_scan1_right.nii.gz' + }, + { + 'image' : 'A0014_scan1_right.nii.gz', + 'label': 'A0014_scan1_right.nii.gz' + }, + { + 'image' : 'A0015_scan1_left.nii.gz', + 'label': 'A0015_scan1_left.nii.gz' + }, + { + 'image' : 'A0015_scan2_left.nii.gz', + 'label': 'A0015_scan2_left.nii.gz' + }, + { + 'image' : 'A0018_scan1_right.nii.gz', + 'label': 'A0018_scan1_right.nii.gz' + }, + { + 'image' : 'A0019_scan1_left.nii.gz', + 'label': 'A0019_scan1_left.nii.gz' + }, + { + 'image' : 'A0019_scan2_left.nii.gz', + 'label': 'A0019_scan2_left.nii.gz' + }, + { + 'image' : 'A0019_scan3_left.nii.gz', + 'label': 'A0019_scan3_left.nii.gz' + }, + { + 'image' : 'A0022_scan1_right.nii.gz', + 'label': 'A0022_scan1_right.nii.gz' + }, + { + 'image' : 'A0022_scan2_right.nii.gz', + 'label': 'A0022_scan2_right.nii.gz' + }, + { + 'image' : 'A0022_scan3_right.nii.gz', + 'label': 'A0022_scan3_right.nii.gz' + }, + { + 'image' : 'A0022_scan4_right.nii.gz', + 'label': 'A0022_scan4_right.nii.gz' + }, + { + 'image' : 'A0023_scan1_left.nii.gz', + 'label': 'A0023_scan1_left.nii.gz' + }, + { + 'image' : 'A0026_scan1_left.nii.gz', + 'label': 'A0026_scan1_left.nii.gz' + }, + { + 'image' : 'A0026_scan2_left.nii.gz', + 'label': 'A0026_scan2_left.nii.gz' + }, + { + 'image' : 'A0028_scan1_right.nii.gz', + 'label': 'A0028_scan1_right.nii.gz' + }, + { + 'image' : 'A0028_scan2_right.nii.gz', + 'label': 'A0028_scan2_right.nii.gz' + }, + { + 'image' : 'A0029_scan1_right.nii.gz', + 'label': 'A0029_scan1_right.nii.gz' + }, + { + 'image' : 'A0029_scan2_right.nii.gz', + 'label': 'A0029_scan2_right.nii.gz' + }, + { + 'image' : 'A0029_scan3_right.nii.gz', + 'label': 'A0029_scan3_right.nii.gz' + }, + { + 'image' : 'A0029_scan4_right.nii.gz', + 'label': 'A0029_scan4_right.nii.gz' + }, + { + 'image' : 'A0031_scan1_right.nii.gz', + 'label': 'A0031_scan1_right.nii.gz' + }, + { + 'image' : 'A0032_scan1_left.nii.gz', + 'label': 'A0032_scan1_left.nii.gz' + }, + { + 'image' : 'A0033_scan1_right.nii.gz', + 'label': 'A0033_scan1_right.nii.gz' + }, + { + 'image' : 'A0034_scan1_left.nii.gz', + 'label': 'A0034_scan1_left.nii.gz' + }, + { + 'image' : 'A0034_scan2_left.nii.gz', + 'label': 'A0034_scan2_left.nii.gz' + }, + { + 'image' : 'A0035_scan1_right.nii.gz', + 'label': 'A0035_scan1_right.nii.gz' + }, + { + 'image' : 'A0035_scan2_right.nii.gz', + 'label': 'A0035_scan2_right.nii.gz' + }, + { + 'image' : 'A0036_scan1_left.nii.gz', + 'label': 'A0036_scan1_left.nii.gz' + }, + { + 'image' : 'A0037_scan1_left.nii.gz', + 'label': 'A0037_scan1_left.nii.gz' + }, + { + 'image' : 'A0039_scan1_left.nii.gz', + 'label': 'A0039_scan1_left.nii.gz' + }, + { + 'image' : 'A0040_scan1_left.nii.gz', + 'label': 'A0040_scan1_left.nii.gz' + }, + { + 'image' : 'A0041_scan1_left.nii.gz', + 'label': 'A0041_scan1_left.nii.gz' + }, + { + 'image' : 'A0041_scan2_left.nii.gz', + 'label': 'A0041_scan2_left.nii.gz' + }, + { + 'image' : 'A0041_scan3_left.nii.gz', + 'label': 'A0041_scan3_left.nii.gz' + }, + { + 'image' : 'A0041_scan4_left.nii.gz', + 'label': 'A0041_scan4_left.nii.gz' + }, + { + 'image' : 'A0042_scan1_right.nii.gz', + 'label': 'A0042_scan1_right.nii.gz' + }, + { + 'image' : 'A0043_scan1_left.nii.gz', + 'label': 'A0043_scan1_left.nii.gz' + }, + { + 'image' : 'A0043_scan2_left.nii.gz', + 'label': 'A0043_scan2_left.nii.gz' + }, + { + 'image' : 'A0044_scan1_right.nii.gz', + 'label': 'A0044_scan1_right.nii.gz' + }, + { + 'image' : 'A0044_scan2_right.nii.gz', + 'label': 'A0044_scan2_right.nii.gz' + }, + { + 'image' : 'A0046_scan1_right.nii.gz', + 'label': 'A0046_scan1_right.nii.gz' + }, + { + 'image' : 'A0047_scan1_right.nii.gz', + 'label': 'A0047_scan1_right.nii.gz' + }, + { + 'image' : 'A0048_scan1_right.nii.gz', + 'label': 'A0048_scan1_right.nii.gz' + }, + { + 'image' : 'A0048_scan2_right.nii.gz', + 'label': 'A0048_scan2_right.nii.gz' + }, + { + 'image' : 'A0049_scan1_left.nii.gz', + 'label': 'A0049_scan1_left.nii.gz' + }, + { + 'image' : 'A0051_scan1_left.nii.gz', + 'label': 'A0051_scan1_left.nii.gz' + }, + { + 'image' : 'A0051_scan2_left.nii.gz', + 'label': 'A0051_scan2_left.nii.gz' + }, + { + 'image' : 'A0052_scan1_left.nii.gz', + 'label': 'A0052_scan1_left.nii.gz' + }, + { + 'image' : 'A0052_scan2_left.nii.gz', + 'label': 'A0052_scan2_left.nii.gz' + }, + { + 'image' : 'A0053_scan1_right.nii.gz', + 'label': 'A0053_scan1_right.nii.gz' + }, + { + 'image' : 'A0054_scan1_left.nii.gz', + 'label': 'A0054_scan1_left.nii.gz' + }, + { + 'image' : 'A0054_scan1_right.nii.gz', + 'label': 'A0054_scan1_right.nii.gz' + }, + { + 'image' : 'A0056_scan1_right.nii.gz', + 'label': 'A0056_scan1_right.nii.gz' + }, + { + 'image' : 'A0056_scan2_right.nii.gz', + 'label': 'A0056_scan2_right.nii.gz' + }, + { + 'image' : 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'G0060_scan2_left.nii.gz', + 'label': 'G0060_scan2_left.nii.gz' + }, + { + 'image' : 'G0060_scan2_right.nii.gz', + 'label': 'G0060_scan2_right.nii.gz' + }, + { + 'image' : 'G0062_scan1_left.nii.gz', + 'label': 'G0062_scan1_left.nii.gz' + }, + { + 'image' : 'G0062_scan2_left.nii.gz', + 'label': 'G0062_scan2_left.nii.gz' + } + ] + +val : + [ + { + 'image' : 'G0055_scan1_right.nii.gz', + 'label': 'G0055_scan1_right.nii.gz' + }, + { + 'image' : 'G0055_scan2_right.nii.gz', + 'label': 'G0055_scan2_right.nii.gz' + }, + { + 'image' : 'G0056_scan1_right.nii.gz', + 'label': 'G0056_scan1_right.nii.gz' + }, + { + 'image' : 'G0056_scan2_right.nii.gz', + 'label': 'G0056_scan2_right.nii.gz' + }, + { + 'image' : 'A0141_scan1_left.nii.gz', + 'label': 'A0141_scan1_left.nii.gz' + }, + { + 'image' : 'A0141_scan2_left.nii.gz', + 'label': 'A0141_scan2_left.nii.gz' + }, + { + 'image' : 'A0142_scan1_left.nii.gz', + 'label': 'A0142_scan1_left.nii.gz' + }, + { + 'image' : 'A0143_scan1_right.nii.gz', + 'label': 'A0143_scan1_right.nii.gz' + }, + { + 'image' : 'A0144_scan1_right.nii.gz', + 'label': 'A0144_scan1_right.nii.gz' + }, + { + 'image' : 'A0144_scan2_right.nii.gz', + 'label': 'A0144_scan2_right.nii.gz' + }, + { + 'image' : 'A0145_scan1_left.nii.gz', + 'label': 'A0145_scan1_left.nii.gz' + }, + { + 'image' : 'A0145_scan2_left.nii.gz', + 'label': 'A0145_scan2_left.nii.gz' + }, + { + 'image' : 'A0146_scan1_right.nii.gz', + 'label': 'A0146_scan1_right.nii.gz' + }, + { + 'image' : 'A0146_scan2_right.nii.gz', + 'label': 'A0146_scan2_right.nii.gz' + }, + { + 'image' : 'A0147_scan1_right.nii.gz', + 'label': 'A0147_scan1_right.nii.gz' + }, + { + 'image' : 'A0147_scan2_right.nii.gz', + 'label': 'A0147_scan2_right.nii.gz' + }, + { + 'image' : 'A0148_scan1_right.nii.gz', + 'label': 'A0148_scan1_right.nii.gz' + }, + { + 'image' : 'A0148_scan2_right.nii.gz', + 'label': 'A0148_scan2_right.nii.gz' + }, + { + 'image' : 'B0033_scan2_left.nii.gz', + 'label': 'B0033_scan2_left.nii.gz' + }, + { + 'image' : 'B0034_scan1_left.nii.gz', + 'label': 'B0034_scan1_left.nii.gz' + }, + { + 'image' : 'B0034_scan2_left.nii.gz', + 'label': 'B0034_scan2_left.nii.gz' + }, + { + 'image' : 'B0036_scan1_left.nii.gz', + 'label': 'B0036_scan1_left.nii.gz' + }, + { + 'image' : 'B0036_scan2_left.nii.gz', + 'label': 'B0036_scan2_left.nii.gz' + } + ] + +test : + [ + { + 'image' : 'A0201_scan1_right.nii.gz', + 'label': 'A0201_scan1_right.nii.gz' + }, + { + 'image' : 'A0201_scan2_right.nii.gz', + 'label': 'A0201_scan2_right.nii.gz' + }, + { + 'image' : 'A0202_scan1_right.nii.gz', + 'label': 'A0202_scan1_right.nii.gz' + }, + { + 'image' : 'A0202_scan2_right.nii.gz', + 'label': 'A0202_scan2_right.nii.gz' + }, + { + 'image' : 'A0203_scan1_left.nii.gz', + 'label': 'A0203_scan1_left.nii.gz' + }, + { + 'image' : 'A0203_scan2_left.nii.gz', + 'label': 'A0203_scan2_left.nii.gz' + }, + { + 'image' : 'A0204_scan1_left.nii.gz', + 'label': 'A0204_scan1_left.nii.gz' + }, + { + 'image' : 'A0204_scan2_left.nii.gz', + 'label': 'A0204_scan2_left.nii.gz' + }, + { + 'image' : 'A0205_scan1_left.nii.gz', + 'label': 'A0205_scan1_left.nii.gz' + }, + { + 'image' : 'A0205_scan2_left.nii.gz', + 'label': 'A0205_scan2_left.nii.gz' + }, + { + 'image' : 'A0206_scan1_left.nii.gz', + 'label': 'A0206_scan1_left.nii.gz' + }, + { + 'image' : 'A0206_scan2_left.nii.gz', + 'label': 'A0206_scan2_left.nii.gz' + }, + { + 'image' : 'A0208_scan1_right.nii.gz', + 'label': 'A0208_scan1_right.nii.gz' + }, + { + 'image' : 'A0208_scan2_right.nii.gz', + 'label': 'A0208_scan2_right.nii.gz' + }, + { + 'image' : 'A0210_scan1_right.nii.gz', + 'label': 'A0210_scan1_right.nii.gz' + }, + { + 'image' : 'A0210_scan2_right.nii.gz', + 'label': 'A0210_scan2_right.nii.gz' + }, + { + 'image' : 'G0053_scan1_right.nii.gz', + 'label': 'G0053_scan1_right.nii.gz' + }, + { + 'image' : 'G0053_scan2_right.nii.gz', + 'label': 'G0053_scan2_right.nii.gz' + }, + { + 'image' : 'G0054_scan1_left.nii.gz', + 'label': 'G0054_scan1_left.nii.gz' + }, + { + 'image' : 'G0054_scan2_left.nii.gz', + 'label': 'G0054_scan2_left.nii.gz' + }, + { + 'image' : 'B0025_scan1_right.nii.gz', + 'label': 'B0025_scan1_right.nii.gz' + }, + { + 'image' : 'B0026_scan1_left.nii.gz', + 'label': 'B0026_scan1_left.nii.gz' + }, + { + 'image' : 'B0026_scan2_left.nii.gz', + 'label': 'B0026_scan2_left.nii.gz' + }, + { + 'image' : 'B0027_scan1_right.nii.gz', + 'label': 'B0027_scan1_right.nii.gz' + }, + { + 'image' : 'B0027_scan2_right.nii.gz', + 'label': 'B0027_scan2_right.nii.gz' + }, + { + 'image' : 'B0028_scan1_left.nii.gz', + 'label': 'B0028_scan1_left.nii.gz' + }, + { + 'image' : 'B0028_scan2_left.nii.gz', + 'label': 'B0028_scan2_left.nii.gz' + } + ] diff --git a/training/Resources/Idun_Train_2/msd_data.yaml b/training/Resources/Idun_Train_2/msd_data.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4b780696e0c05ee88c28f79cd831591f5f33b27e --- /dev/null +++ b/training/Resources/Idun_Train_2/msd_data.yaml @@ -0,0 +1,243 @@ +image_prefix: "/cluster/work/sosevle/full_data/MSD-Lung/Images/" +boxes_prefix: "/cluster/work/sosevle/full_data/MSD-Lung/Boxes/" +label_prefix: "/cluster/work/sosevle/full_data/MSD-Lung/Labels/" + +train: + [ + { + 'image' : 'lung_001_right.nii.gz', + 'label': 'lung_001_right.nii.gz' + }, + { + 'image' : 'lung_003_left.nii.gz', + 'label': 'lung_003_left.nii.gz' + }, + { + 'image' : 'lung_004_left.nii.gz', + 'label': 'lung_004_left.nii.gz' + }, + { + 'image' : 'lung_005_right.nii.gz', + 'label': 'lung_005_right.nii.gz' + }, + { + 'image' : 'lung_006_left.nii.gz', + 'label': 'lung_006_left.nii.gz' + }, + { + 'image' : 'lung_009_right.nii.gz', + 'label': 'lung_009_right.nii.gz' + }, + { + 'image' : 'lung_010_left.nii.gz', + 'label': 'lung_010_left.nii.gz' + }, + { + 'image' : 'lung_014_right.nii.gz', + 'label': 'lung_014_right.nii.gz' + }, + { + 'image' : 'lung_015_right.nii.gz', + 'label': 'lung_015_right.nii.gz' + }, + { + 'image' : 'lung_016_left.nii.gz', + 'label': 'lung_016_left.nii.gz' + }, + { + 'image' : 'lung_018_right.nii.gz', + 'label': 'lung_018_right.nii.gz' + }, + { + 'image' : 'lung_020_right.nii.gz', + 'label': 'lung_020_right.nii.gz' + }, + { + 'image' : 'lung_022_right.nii.gz', + 'label': 'lung_022_right.nii.gz' + }, + { + 'image' : 'lung_023_left.nii.gz', + 'label': 'lung_023_left.nii.gz' + }, + { + 'image' : 'lung_023_right.nii.gz', + 'label': 'lung_023_right.nii.gz' + }, + { + 'image' : 'lung_025_left.nii.gz', + 'label': 'lung_025_left.nii.gz' + }, + { + 'image' : 'lung_026_right.nii.gz', + 'label': 'lung_026_right.nii.gz' + }, + { + 'image' : 'lung_027_right.nii.gz', + 'label': 'lung_027_right.nii.gz' + }, + { + 'image' : 'lung_028_left.nii.gz', + 'label': 'lung_028_left.nii.gz' + }, + { + 'image' : 'lung_029_left.nii.gz', + 'label': 'lung_029_left.nii.gz' + }, + { + 'image' : 'lung_031_right.nii.gz', + 'label': 'lung_031_right.nii.gz' + }, + { + 'image' : 'lung_033_left.nii.gz', + 'label': 'lung_033_left.nii.gz' + }, + { + 'image' : 'lung_034_right.nii.gz', + 'label': 'lung_034_right.nii.gz' + }, + { + 'image' : 'lung_036_left.nii.gz', + 'label': 'lung_036_left.nii.gz' + }, + { + 'image' : 'lung_037_right.nii.gz', + 'label': 'lung_037_right.nii.gz' + }, + { + 'image' : 'lung_038_right.nii.gz', + 'label': 'lung_038_right.nii.gz' + }, + { + 'image' : 'lung_041_right.nii.gz', + 'label': 'lung_041_right.nii.gz' + }, + { + 'image' : 'lung_042_right.nii.gz', + 'label': 'lung_042_right.nii.gz' + }, + { + 'image' : 'lung_043_right.nii.gz', + 'label': 'lung_043_right.nii.gz' + }, + { + 'image' : 'lung_044_left.nii.gz', + 'label': 'lung_044_left.nii.gz' + }, + { + 'image' : 'lung_045_left.nii.gz', + 'label': 'lung_045_left.nii.gz' + }, + { + 'image' : 'lung_046_left.nii.gz', + 'label': 'lung_046_left.nii.gz' + }, + { + 'image' : 'lung_047_right.nii.gz', + 'label': 'lung_047_right.nii.gz' + }, + { + 'image' : 'lung_048_right.nii.gz', + 'label': 'lung_048_right.nii.gz' + }, + { + 'image' : 'lung_049_right.nii.gz', + 'label': 'lung_049_right.nii.gz' + }, + { + 'image' : 'lung_051_left.nii.gz', + 'label': 'lung_051_left.nii.gz' + }, + { + 'image' : 'lung_053_right.nii.gz', + 'label': 'lung_053_right.nii.gz' + }, + { + 'image' : 'lung_054_right.nii.gz', + 'label': 'lung_054_right.nii.gz' + }, + { + 'image' : 'lung_055_left.nii.gz', + 'label': 'lung_055_left.nii.gz' + }, + { + 'image' : 'lung_057_left.nii.gz', + 'label': 'lung_057_left.nii.gz' + }, + { + 'image' : 'lung_058_right.nii.gz', + 'label': 'lung_058_right.nii.gz' + }, + { + 'image' : 'lung_059_left.nii.gz', + 'label': 'lung_059_left.nii.gz' + }, + { + 'image' : 'lung_061_left.nii.gz', + 'label': 'lung_061_left.nii.gz' + }, + { + 'image' : 'lung_062_left.nii.gz', + 'label': 'lung_062_left.nii.gz' + }, + { + 'image' : 'lung_064_left.nii.gz', + 'label': 'lung_064_left.nii.gz' + }, + { + 'image' : 'lung_065_left.nii.gz', + 'label': 'lung_065_left.nii.gz' + }, + { + 'image' : 'lung_066_left.nii.gz', + 'label': 'lung_066_left.nii.gz' + }, + { + 'image' : 'lung_066_right.nii.gz', + 'label': 'lung_066_right.nii.gz' + }, + { + 'image' : 'lung_069_right.nii.gz', + 'label': 'lung_069_right.nii.gz' + }, + { + 'image' : 'lung_070_left.nii.gz', + 'label': 'lung_070_left.nii.gz' + }, + { + 'image' : 'lung_071_right.nii.gz', + 'label': 'lung_071_right.nii.gz' + }, + { + 'image' : 'lung_073_left.nii.gz', + 'label': 'lung_073_left.nii.gz' + }, + { + 'image' : 'lung_074_left.nii.gz', + 'label': 'lung_074_left.nii.gz' + }, + ] + +val : + [ + { + 'image' : 'lung_075_left.nii.gz', + 'label': 'lung_075_left.nii.gz' + }, + { + 'image' : 'lung_078_left.nii.gz', + 'label': 'lung_078_left.nii.gz' + }, + { + 'image' : 'lung_079_right.nii.gz', + 'label': 'lung_079_right.nii.gz' + }, + { + 'image' : 'lung_080_left.nii.gz', + 'label': 'lung_080_left.nii.gz' + }, + { + 'image' : 'lung_081_right.nii.gz', + 'label': 'lung_081_right.nii.gz' + } + ] \ No newline at end of file diff --git a/training/Resources/Idun_Train_2/train_16.yaml b/training/Resources/Idun_Train_2/train_16.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5daf60ba96ab460018a027a1f8a2ecfc44558b37 --- /dev/null +++ b/training/Resources/Idun_Train_2/train_16.yaml @@ -0,0 +1,28 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/data.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet4 + loss: DiceLoss + weights: + filter_base: 32 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.001 + +train: + max_epochs: 5000 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t16.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/16/" + batch_size: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_2/train_32.yaml b/training/Resources/Idun_Train_2/train_32.yaml new file mode 100644 index 0000000000000000000000000000000000000000..53e2f3ea79b6f43bc86b13d7188d802aeb3139fa --- /dev/null +++ b/training/Resources/Idun_Train_2/train_32.yaml @@ -0,0 +1,28 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/data.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet4 + loss: DiceLoss + weights: + filter_base: 32 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.0001 + +train: + max_epochs: 5000 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t32.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/32/" + batch_size: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_2/train_48.yaml b/training/Resources/Idun_Train_2/train_48.yaml new file mode 100644 index 0000000000000000000000000000000000000000..cdb55cdc4cb4d9a9df1c2453ddc7b7d1e1b35e8f --- /dev/null +++ b/training/Resources/Idun_Train_2/train_48.yaml @@ -0,0 +1,28 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/data.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet4 + loss: DiceLoss + weights: + filter_base: 32 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.00001 + +train: + max_epochs: 5000 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t48.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/48/" + batch_size: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_2/train_64.yaml b/training/Resources/Idun_Train_2/train_64.yaml new file mode 100644 index 0000000000000000000000000000000000000000..61f8eb73c240f8677bb92914b933cd907cdc4127 --- /dev/null +++ b/training/Resources/Idun_Train_2/train_64.yaml @@ -0,0 +1,28 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/data.yaml" + aug_prob: 0.5 + scale_dim: + d_0: 176 + d_1: 176 + d_2: 96 + +model: + architecture: UNet4 + loss: DiceLoss + weights: + filter_base: 64 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.00012 + +train: + max_epochs: 5000 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t64.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/64/" + batch_size: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_2/train_focal.yaml b/training/Resources/Idun_Train_2/train_focal.yaml new file mode 100644 index 0000000000000000000000000000000000000000..83e81071cc6a92382de6424c88bf6159fca26c5a --- /dev/null +++ b/training/Resources/Idun_Train_2/train_focal.yaml @@ -0,0 +1,28 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/full_size.yaml" + aug_prob: 0.15 + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet_test + loss: DiceLoss + weights: + filter_base: 32 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.00025 + +train: + max_epochs: 5000 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t_test2.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/t_test2/" + batch_size: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_2/train_tversky.yaml b/training/Resources/Idun_Train_2/train_tversky.yaml new file mode 100644 index 0000000000000000000000000000000000000000..adb4d897572ea407a81a8cf2282e7e945a5f5971 --- /dev/null +++ b/training/Resources/Idun_Train_2/train_tversky.yaml @@ -0,0 +1,28 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/data.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet4 + loss: Tversky + weights: + filter_base: 32 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.0004 + +train: + max_epochs: 5000 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t_tver.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/t_tver/" + batch_size: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_2/train_ud.yaml b/training/Resources/Idun_Train_2/train_ud.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2bbbb650a6d552039411ea318ed5a8f1b66e6e6d --- /dev/null +++ b/training/Resources/Idun_Train_2/train_ud.yaml @@ -0,0 +1,29 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/data.yaml" + aug_prob: 0.2 + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet_monai_double + loss: DiceLoss + weights: + filter_base: 32 + filter_expansion: 2 + filters: [64, 128, 256, 512] + optimizer: + name: 'Adam' + lr: 0.00005 + +train: + max_epochs: 5000 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t_ud.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/ud/" + batch_size: 10 \ No newline at end of file diff --git a/training/Resources/Idun_Train_2/train_us.yaml b/training/Resources/Idun_Train_2/train_us.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f629790be0b024f542fa95eee1e335651f8e88b9 --- /dev/null +++ b/training/Resources/Idun_Train_2/train_us.yaml @@ -0,0 +1,29 @@ +device: 'cuda' + +data: + train_dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/data.yaml" + aug_prob: 0.2 + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet_monai + loss: DiceLoss + weights: + filter_base: 32 + filter_expansion: 2 + filters: [64, 128, 256, 512] + optimizer: + name: 'Adam' + lr: 0.00005 + +train: + max_epochs: 5000 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/cluster/work/sosevle/metrics/t_us.csv" + save_frequency: 5 + model_directory: "/cluster/work/sosevle/models/us/" + batch_size: 10 \ No newline at end of file diff --git a/training/Resources/Inference/inference.yaml b/training/Resources/Inference/inference.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9d8e7098ed2680a0913a820cb255c86e44c74605 --- /dev/null +++ b/training/Resources/Inference/inference.yaml @@ -0,0 +1,18 @@ +device: 'cuda' + +data: + dataset: "/cluster/work/sosevle/LungTumorSegmentation/Resources/Inference/teacher_inference_data.yaml" + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet_test + weights: "/cluster/work/sosevle/model_last_128.pth" + loss: DiceLoss + filter_base: 128 + filter_expansion: 2 + +inference: + save_directory: '/cluster/work/sosevle/Lung-Dx_Cropped/Cropped/Labels/' \ No newline at end of file diff --git a/training/Resources/Inference/malvik.yaml b/training/Resources/Inference/malvik.yaml new file mode 100644 index 0000000000000000000000000000000000000000..3197628fcfe84ede213dd3daafe263ab9de1196a --- /dev/null +++ b/training/Resources/Inference/malvik.yaml @@ -0,0 +1,18 @@ +device: 'cuda' + +data: + dataset: "/home/tumor/LungTumorSegmentation/Resources/Inference/malvik_inference_data2.yaml" + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet_test + weights: "/home/tumor/model_last_128.pth" + loss: DiceLoss + filter_base: 128 + filter_expansion: 2 + +inference: + save_directory: '/home/tumor/data/SoftLabels/' diff --git a/training/Resources/Inference/malvik_inference_data.yaml b/training/Resources/Inference/malvik_inference_data.yaml new file mode 100644 index 0000000000000000000000000000000000000000..6741853750959c910cd91c25c5a6b5e68712efa1 --- /dev/null +++ b/training/Resources/Inference/malvik_inference_data.yaml @@ -0,0 +1,2379 @@ +image_prefix: "/home/tumor/data/for_annotation/Images/" +label_prefix: "" +boxes_prefix: "/home/tumor/data/for_annotation//Boxes/" +data: + [ + { + 'image' : 'A0001_scan1.nii', + 'boxes': 'A0001_scan1.nii' + }, + { + 'image' : 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{ + 'image' : 'G0056_scan1.nii', + 'boxes': 'G0056_scan1.nii' + }, + { + 'image' : 'G0056_scan3.nii', + 'boxes': 'G0056_scan3.nii' + }, + { + 'image' : 'G0057_scan1.nii', + 'boxes': 'G0057_scan1.nii' + }, + { + 'image' : 'G0057_scan3.nii', + 'boxes': 'G0057_scan3.nii' + }, + { + 'image' : 'G0058_scan1.nii', + 'boxes': 'G0058_scan1.nii' + }, + { + 'image' : 'G0058_scan3.nii', + 'boxes': 'G0058_scan3.nii' + }, + { + 'image' : 'G0059_scan1.nii', + 'boxes': 'G0059_scan1.nii' + }, + { + 'image' : 'G0059_scan2.nii', + 'boxes': 'G0059_scan2.nii' + }, + { + 'image' : 'G0060_scan1.nii', + 'boxes': 'G0060_scan1.nii' + }, + { + 'image' : 'G0060_scan2.nii', + 'boxes': 'G0060_scan2.nii' + }, + { + 'image' : 'G0062_scan1.nii', + 'boxes': 'G0062_scan1.nii' + }, + { + 'image' : 'G0062_scan3.nii', + 'boxes': 'G0062_scan3.nii' + }, + +] diff --git a/training/Resources/Inference/malvik_inference_data2.yaml b/training/Resources/Inference/malvik_inference_data2.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d32ceb2c39ac9d4bc5ca7d97c68f981c58578688 --- /dev/null +++ b/training/Resources/Inference/malvik_inference_data2.yaml @@ -0,0 +1,42 @@ +image_prefix: "/home/tumor/data/for_annotation/Images/" +label_prefix: "" +boxes_prefix: "/home/tumor/data/for_annotation//Boxes/" +data: + [ + { + 'image' : 'lung_092.nii', + 'boxes' : 'lung_092.nii', + 'label' : 'lung_092.nii' + }, + { + 'image' : 'lung_093.nii', + 'boxes' : 'lung_093.nii', + 'label' : 'lung_093.nii' + }, + { + 'image' : 'lung_095.nii', + 'boxes' : 'lung_095.nii', + 'label' : 'lung_095.nii' + }, + { + 'image' : 'lung_081.nii', + 'boxes' : 'lung_081.nii', + 'label' : 'lung_081.nii' + }, + { + 'image' : 'lung_083.nii', + 'boxes' : 'lung_083.nii', + 'label' : 'lung_083.nii' + }, + { + 'image' : 'lung_084.nii', + 'boxes' : 'lung_084.nii', + 'label' : 'lung_084.nii' + }, + { + 'image' : 'lung_086.nii', + 'boxes' : 'lung_086.nii', + 'label' : 'lung_086.nii' + } + +] diff --git a/training/Resources/Inference/teacher_inference_data.yaml b/training/Resources/Inference/teacher_inference_data.yaml new file mode 100644 index 0000000000000000000000000000000000000000..0f89325d8fae43caf20604dc674012336098d14b --- /dev/null +++ b/training/Resources/Inference/teacher_inference_data.yaml @@ -0,0 +1,2379 @@ +image_prefix: "/cluster/work/sosevle/Lung-Dx_Cropped/Cropped/Images/" +label_prefix: "" +boxes_prefix: "/cluster/work/sosevle/Lung-Dx_Cropped/Cropped/Boxes/" +data: + [ + { + 'image' : 'A0001_scan1.nii', + 'boxes': 'A0001_scan1.nii' + }, + { + 'image' : 'A0001_scan2.nii', + 'boxes': 'A0001_scan2.nii' + }, + { + 'image' : 'A0002_scan1.nii', + 'boxes': 'A0002_scan1.nii' + }, + { + 'image' : 'A0002_scan2.nii', + 'boxes': 'A0002_scan2.nii' + }, + { + 'image' : 'A0003_scan1.nii', + 'boxes': 'A0003_scan1.nii' + }, + { + 'image' : 'A0003_scan2.nii', + 'boxes': 'A0003_scan2.nii' + }, + { + 'image' : 'A0004_scan1.nii', + 'boxes': 'A0004_scan1.nii' + }, + { + 'image' : 'A0004_scan2.nii', + 'boxes': 'A0004_scan2.nii' + }, + { + 'image' : 'A0006_scan1.nii', + 'boxes': 'A0006_scan1.nii' + }, + { + 'image' : 'A0006_scan4.nii', + 'boxes': 'A0006_scan4.nii' + }, + { + 'image' : 'A0007_scan1.nii', + 'boxes': 'A0007_scan1.nii' + }, + { + 'image' : 'A0007_scan2.nii', + 'boxes': 'A0007_scan2.nii' + }, + { + 'image' : 'A0008_scan1.nii', + 'boxes': 'A0008_scan1.nii' + }, + { + 'image' : 'A0008_scan2.nii', + 'boxes': 'A0008_scan2.nii' + }, + { + 'image' : 'A0009_scan1.nii', + 'boxes': 'A0009_scan1.nii' + }, + { + 'image' : 'A0009_scan2.nii', + 'boxes': 'A0009_scan2.nii' + }, + { + 'image' : 'A0010_scan1.nii', + 'boxes': 'A0010_scan1.nii' + }, + { + 'image' : 'A0010_scan2.nii', + 'boxes': 'A0010_scan2.nii' + }, + { + 'image' : 'A0011_scan2.nii', + 'boxes': 'A0011_scan2.nii' + }, + { + 'image' : 'A0011_scan4.nii', + 'boxes': 'A0011_scan4.nii' + }, + { + 'image' : 'A0013_scan3.nii', + 'boxes': 'A0013_scan3.nii' + }, + { + 'image' : 'A0014_scan2.nii', + 'boxes': 'A0014_scan2.nii' + }, + { + 'image' : 'A0015_scan1.nii', + 'boxes': 'A0015_scan1.nii' + }, + { + 'image' : 'A0015_scan2.nii', + 'boxes': 'A0015_scan2.nii' + }, + { + 'image' : 'A0018_scan3.nii', + 'boxes': 'A0018_scan3.nii' + }, + { + 'image' : 'A0018_scan4.nii', + 'boxes': 'A0018_scan4.nii' + }, + { + 'image' : 'A0019_scan3.nii', + 'boxes': 'A0019_scan3.nii' + }, + { + 'image' : 'A0019_scan4.nii', + 'boxes': 'A0019_scan4.nii' + }, + { + 'image' : 'A0019_scan5.nii', + 'boxes': 'A0019_scan5.nii' + }, + { + 'image' : 'A0022_scan2.nii', + 'boxes': 'A0022_scan2.nii' + }, + { + 'image' : 'A0022_scan3.nii', + 'boxes': 'A0022_scan3.nii' + }, + { + 'image' : 'A0022_scan4.nii', + 'boxes': 'A0022_scan4.nii' + }, + { + 'image' : 'A0022_scan5.nii', + 'boxes': 'A0022_scan5.nii' + }, + { + 'image' : 'A0023_scan2.nii', + 'boxes': 'A0023_scan2.nii' + }, + { + 'image' : 'A0026_scan1.nii', + 'boxes': 'A0026_scan1.nii' + }, + { + 'image' : 'A0026_scan2.nii', + 'boxes': 'A0026_scan2.nii' + }, + { + 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{ + 'image' : 'G0059_scan1.nii', + 'boxes': 'G0059_scan1.nii' + }, + { + 'image' : 'G0059_scan2.nii', + 'boxes': 'G0059_scan2.nii' + }, + { + 'image' : 'G0060_scan1.nii', + 'boxes': 'G0060_scan1.nii' + }, + { + 'image' : 'G0060_scan2.nii', + 'boxes': 'G0060_scan2.nii' + }, + { + 'image' : 'G0062_scan1.nii', + 'boxes': 'G0062_scan1.nii' + }, + { + 'image' : 'G0062_scan3.nii', + 'boxes': 'G0062_scan3.nii' + }, + +] \ No newline at end of file diff --git a/training/Resources/Malvik/inference.yaml b/training/Resources/Malvik/inference.yaml new file mode 100644 index 0000000000000000000000000000000000000000..8d06ab24fb08b93c881e84e7e0adf2ff30b55fe1 --- /dev/null +++ b/training/Resources/Malvik/inference.yaml @@ -0,0 +1,23 @@ +device: 'cuda' + +data: + dataset: "/home/tumor/LungTumorSegmentation/Resources/Malvik/msd_dataset.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet4 + loss: DiceLoss + weights: "/home/tumor/out/models/model_best.pth" + filter_base: 16 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.0001 + +inference: + save_directory: "/home/tumor/segs/" + diff --git a/training/Resources/Malvik/inference_data.yaml b/training/Resources/Malvik/inference_data.yaml new file mode 100644 index 0000000000000000000000000000000000000000..df4ae9cc8ec93e7608a82cf5bfd6355c07532a00 --- /dev/null +++ b/training/Resources/Malvik/inference_data.yaml @@ -0,0 +1,2533 @@ +image_prefix: "/home/tumor/data/LungDx-Tumor/Images/" +boxes_prefix: "/home/tumor/data/LungDx-Tumor/Boxes/" +test: + [ + { + 'image' : 'A0028_scan2.nii.gz', + 'boxes': 'A0028_scan2.nii.gz' + }, + { + 'image' : 'A0222_scan2.nii.gz', + 'boxes': 'A0222_scan2.nii.gz' + }, + { + 'image' : 'A0231_scan1.nii.gz', + 'boxes': 'A0231_scan1.nii.gz' + }, + { + 'image' : 'A0155_scan1.nii.gz', + 'boxes': 'A0155_scan1.nii.gz' + }, + { + 'image' : 'A0113_scan2.nii.gz', + 'boxes': 'A0113_scan2.nii.gz' + }, + { + 'image' : 'A0134_scan5.nii.gz', + 'boxes': 'A0134_scan5.nii.gz' 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'G0036_scan1_right.nii.gz', + 'label': 'G0036_scan1_right.nii.gz' + }, + { + 'image' : 'G0036_scan2_right.nii.gz', + 'label': 'G0036_scan2_right.nii.gz' + }, + { + 'image' : 'G0037_scan1_left.nii.gz', + 'label': 'G0037_scan1_left.nii.gz' + }, + { + 'image' : 'G0037_scan2_left.nii.gz', + 'label': 'G0037_scan2_left.nii.gz' + }, + { + 'image' : 'G0038_scan1_right.nii.gz', + 'label': 'G0038_scan1_right.nii.gz' + }, + { + 'image' : 'G0038_scan2_right.nii.gz', + 'label': 'G0038_scan2_right.nii.gz' + }, + { + 'image' : 'G0039_scan1_right.nii.gz', + 'label': 'G0039_scan1_right.nii.gz' + }, + { + 'image' : 'G0039_scan2_right.nii.gz', + 'label': 'G0039_scan2_right.nii.gz' + }, + { + 'image' : 'G0040_scan1_left.nii.gz', + 'label': 'G0040_scan1_left.nii.gz' + }, + { + 'image' : 'G0040_scan2_left.nii.gz', + 'label': 'G0040_scan2_left.nii.gz' + }, + { + 'image' : 'G0041_scan1_right.nii.gz', + 'label': 'G0041_scan1_right.nii.gz' + }, + { + 'image' : 'G0041_scan2_right.nii.gz', + 'label': 'G0041_scan2_right.nii.gz' + }, + { + 'image' : 'G0042_scan1_right.nii.gz', + 'label': 'G0042_scan1_right.nii.gz' + }, + { + 'image' : 'G0042_scan2_right.nii.gz', + 'label': 'G0042_scan2_right.nii.gz' + }, + { + 'image' : 'G0043_scan1_left.nii.gz', + 'label': 'G0043_scan1_left.nii.gz' + }, + { + 'image' : 'G0043_scan2_left.nii.gz', + 'label': 'G0043_scan2_left.nii.gz' + }, + { + 'image' : 'G0044_scan1_left.nii.gz', + 'label': 'G0044_scan1_left.nii.gz' + }, + { + 'image' : 'G0044_scan2_left.nii.gz', + 'label': 'G0044_scan2_left.nii.gz' + }, + { + 'image' : 'G0045_scan1_right.nii.gz', + 'label': 'G0045_scan1_right.nii.gz' + }, + { + 'image' : 'G0045_scan2_right.nii.gz', + 'label': 'G0045_scan2_right.nii.gz' + }, + { + 'image' : 'G0046_scan1_left.nii.gz', + 'label': 'G0046_scan1_left.nii.gz' + }, + { + 'image' : 'G0046_scan2_left.nii.gz', + 'label': 'G0046_scan2_left.nii.gz' + }, + { + 'image' : 'G0047_scan1_left.nii.gz', + 'label': 'G0047_scan1_left.nii.gz' + }, + { + 'image' : 'G0048_scan1_right.nii.gz', + 'label': 'G0048_scan1_right.nii.gz' + }, + { + 'image' : 'G0049_scan1_left.nii.gz', + 'label': 'G0049_scan1_left.nii.gz' + }, + { + 'image' : 'G0049_scan1_right.nii.gz', + 'label': 'G0049_scan1_right.nii.gz' + }, + { + 'image' : 'G0049_scan2_left.nii.gz', + 'label': 'G0049_scan2_left.nii.gz' + }, + { + 'image' : 'G0049_scan2_right.nii.gz', + 'label': 'G0049_scan2_right.nii.gz' + }, + { + 'image' : 'G0050_scan1_right.nii.gz', + 'label': 'G0050_scan1_right.nii.gz' + }, + { + 'image' : 'G0050_scan2_right.nii.gz', + 'label': 'G0050_scan2_right.nii.gz' + }, + { + 'image' : 'G0051_scan1_right.nii.gz', + 'label': 'G0051_scan1_right.nii.gz' + }, + { + 'image' : 'G0051_scan2_right.nii.gz', + 'label': 'G0051_scan2_right.nii.gz' + }, + { + 'image' : 'G0052_scan1_left.nii.gz', + 'label': 'G0052_scan1_left.nii.gz' + }, + { + 'image' : 'G0052_scan2_left.nii.gz', + 'label': 'G0052_scan2_left.nii.gz' + }, + { + 'image' : 'G0057_scan1_right.nii.gz', + 'label': 'G0057_scan1_right.nii.gz' + }, + { + 'image' : 'G0057_scan2_right.nii.gz', + 'label': 'G0057_scan2_right.nii.gz' + }, + { + 'image' : 'G0058_scan1_left.nii.gz', + 'label': 'G0058_scan1_left.nii.gz' + }, + { + 'image' : 'G0058_scan2_left.nii.gz', + 'label': 'G0058_scan2_left.nii.gz' + }, + { + 'image' : 'G0059_scan1_right.nii.gz', + 'label': 'G0059_scan1_right.nii.gz' + }, + { + 'image' : 'G0059_scan2_right.nii.gz', + 'label': 'G0059_scan2_right.nii.gz' + }, + { + 'image' : 'G0060_scan1_left.nii.gz', + 'label': 'G0060_scan1_left.nii.gz' + }, + { + 'image' : 'G0060_scan2_left.nii.gz', + 'label': 'G0060_scan2_left.nii.gz' + }, + { + 'image' : 'G0060_scan2_right.nii.gz', + 'label': 'G0060_scan2_right.nii.gz' + }, + { + 'image' : 'G0062_scan1_left.nii.gz', + 'label': 'G0062_scan1_left.nii.gz' + }, + { + 'image' : 'G0062_scan2_left.nii.gz', + 'label': 'G0062_scan2_left.nii.gz' + } + ] + +val : + [ + { + 'image' : 'G0055_scan1_right.nii.gz', + 'label': 'G0055_scan1_right.nii.gz' + }, + { + 'image' : 'G0055_scan2_right.nii.gz', + 'label': 'G0055_scan2_right.nii.gz' + }, + { + 'image' : 'G0056_scan1_right.nii.gz', + 'label': 'G0056_scan1_right.nii.gz' + }, + { + 'image' : 'G0056_scan2_right.nii.gz', + 'label': 'G0056_scan2_right.nii.gz' + }, + { + 'image' : 'A0141_scan1_left.nii.gz', + 'label': 'A0141_scan1_left.nii.gz' + }, + { + 'image' : 'A0141_scan2_left.nii.gz', + 'label': 'A0141_scan2_left.nii.gz' + }, + { + 'image' : 'A0142_scan1_left.nii.gz', + 'label': 'A0142_scan1_left.nii.gz' + }, + { + 'image' : 'A0143_scan1_right.nii.gz', + 'label': 'A0143_scan1_right.nii.gz' + }, + { + 'image' : 'A0144_scan1_right.nii.gz', + 'label': 'A0144_scan1_right.nii.gz' + }, + { + 'image' : 'A0144_scan2_right.nii.gz', + 'label': 'A0144_scan2_right.nii.gz' + }, + { + 'image' : 'A0145_scan1_left.nii.gz', + 'label': 'A0145_scan1_left.nii.gz' + }, + { + 'image' : 'A0145_scan2_left.nii.gz', + 'label': 'A0145_scan2_left.nii.gz' + }, + { + 'image' : 'A0146_scan1_right.nii.gz', + 'label': 'A0146_scan1_right.nii.gz' + }, + { + 'image' : 'A0146_scan2_right.nii.gz', + 'label': 'A0146_scan2_right.nii.gz' + }, + { + 'image' : 'A0147_scan1_right.nii.gz', + 'label': 'A0147_scan1_right.nii.gz' + }, + { + 'image' : 'A0147_scan2_right.nii.gz', + 'label': 'A0147_scan2_right.nii.gz' + }, + { + 'image' : 'A0148_scan1_right.nii.gz', + 'label': 'A0148_scan1_right.nii.gz' + }, + { + 'image' : 'A0148_scan2_right.nii.gz', + 'label': 'A0148_scan2_right.nii.gz' + }, + { + 'image' : 'B0033_scan2_left.nii.gz', + 'label': 'B0033_scan2_left.nii.gz' + }, + { + 'image' : 'B0034_scan1_left.nii.gz', + 'label': 'B0034_scan1_left.nii.gz' + }, + { + 'image' : 'B0034_scan2_left.nii.gz', + 'label': 'B0034_scan2_left.nii.gz' + }, + { + 'image' : 'B0036_scan1_left.nii.gz', + 'label': 'B0036_scan1_left.nii.gz' + }, + { + 'image' : 'B0036_scan2_left.nii.gz', + 'label': 'B0036_scan2_left.nii.gz' + } + ] + +test : + [ + { + 'image' : 'A0201_scan1_right.nii.gz', + 'label': 'A0201_scan1_right.nii.gz' + }, + { + 'image' : 'A0201_scan2_right.nii.gz', + 'label': 'A0201_scan2_right.nii.gz' + }, + { + 'image' : 'A0202_scan1_right.nii.gz', + 'label': 'A0202_scan1_right.nii.gz' + }, + { + 'image' : 'A0202_scan2_right.nii.gz', + 'label': 'A0202_scan2_right.nii.gz' + }, + { + 'image' : 'A0203_scan1_left.nii.gz', + 'label': 'A0203_scan1_left.nii.gz' + }, + { + 'image' : 'A0203_scan2_left.nii.gz', + 'label': 'A0203_scan2_left.nii.gz' + }, + { + 'image' : 'A0204_scan1_left.nii.gz', + 'label': 'A0204_scan1_left.nii.gz' + }, + { + 'image' : 'A0204_scan2_left.nii.gz', + 'label': 'A0204_scan2_left.nii.gz' + }, + { + 'image' : 'A0205_scan1_left.nii.gz', + 'label': 'A0205_scan1_left.nii.gz' + }, + { + 'image' : 'A0205_scan2_left.nii.gz', + 'label': 'A0205_scan2_left.nii.gz' + }, + { + 'image' : 'A0206_scan1_left.nii.gz', + 'label': 'A0206_scan1_left.nii.gz' + }, + { + 'image' : 'A0206_scan2_left.nii.gz', + 'label': 'A0206_scan2_left.nii.gz' + }, + { + 'image' : 'A0208_scan1_right.nii.gz', + 'label': 'A0208_scan1_right.nii.gz' + }, + { + 'image' : 'A0208_scan2_right.nii.gz', + 'label': 'A0208_scan2_right.nii.gz' + }, + { + 'image' : 'A0210_scan1_right.nii.gz', + 'label': 'A0210_scan1_right.nii.gz' + }, + { + 'image' : 'A0210_scan2_right.nii.gz', + 'label': 'A0210_scan2_right.nii.gz' + }, + { + 'image' : 'G0053_scan1_right.nii.gz', + 'label': 'G0053_scan1_right.nii.gz' + }, + { + 'image' : 'G0053_scan2_right.nii.gz', + 'label': 'G0053_scan2_right.nii.gz' + }, + { + 'image' : 'G0054_scan1_left.nii.gz', + 'label': 'G0054_scan1_left.nii.gz' + }, + { + 'image' : 'G0054_scan2_left.nii.gz', + 'label': 'G0054_scan2_left.nii.gz' + }, + { + 'image' : 'B0025_scan1_right.nii.gz', + 'label': 'B0025_scan1_right.nii.gz' + }, + { + 'image' : 'B0026_scan1_left.nii.gz', + 'label': 'B0026_scan1_left.nii.gz' + }, + { + 'image' : 'B0026_scan2_left.nii.gz', + 'label': 'B0026_scan2_left.nii.gz' + }, + { + 'image' : 'B0027_scan1_right.nii.gz', + 'label': 'B0027_scan1_right.nii.gz' + }, + { + 'image' : 'B0027_scan2_right.nii.gz', + 'label': 'B0027_scan2_right.nii.gz' + }, + { + 'image' : 'B0028_scan1_left.nii.gz', + 'label': 'B0028_scan1_left.nii.gz' + }, + { + 'image' : 'B0028_scan2_left.nii.gz', + 'label': 'B0028_scan2_left.nii.gz' + } + ] diff --git a/training/Resources/Malvik/msd_dataset.yaml b/training/Resources/Malvik/msd_dataset.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a204fe510c8cafc64fa2b591381812ba9b615f7f --- /dev/null +++ b/training/Resources/Malvik/msd_dataset.yaml @@ -0,0 +1,274 @@ +image_prefix: "/home/tumor/data/MSD-Lung/Images/" +label_prefix: "/home/tumor/data/MSD-Lung/Labels/" + +train: + [ + { + 'image' : 'lung_001_right.nii.gz', + 'label': 'lung_001_right.nii.gz' + }, + { + 'image' : 'lung_003_left.nii.gz', + 'label': 'lung_003_left.nii.gz' + }, + { + 'image' : 'lung_004_left.nii.gz', + 'label': 'lung_004_left.nii.gz' + }, + { + 'image' : 'lung_005_right.nii.gz', + 'label': 'lung_005_right.nii.gz' + }, + { + 'image' : 'lung_006_left.nii.gz', + 'label': 'lung_006_left.nii.gz' + }, + { + 'image' : 'lung_009_right.nii.gz', + 'label': 'lung_009_right.nii.gz' + }, + { + 'image' : 'lung_010_left.nii.gz', + 'label': 'lung_010_left.nii.gz' + }, + { + 'image' : 'lung_014_right.nii.gz', + 'label': 'lung_014_right.nii.gz' + }, + { + 'image' : 'lung_015_right.nii.gz', + 'label': 'lung_015_right.nii.gz' + }, + { + 'image' : 'lung_016_left.nii.gz', + 'label': 'lung_016_left.nii.gz' + }, + { + 'image' : 'lung_018_right.nii.gz', + 'label': 'lung_018_right.nii.gz' + }, + { + 'image' : 'lung_020_right.nii.gz', + 'label': 'lung_020_right.nii.gz' + }, + { + 'image' : 'lung_022_right.nii.gz', + 'label': 'lung_022_right.nii.gz' + }, + { + 'image' : 'lung_023_left.nii.gz', + 'label': 'lung_023_left.nii.gz' + }, + { + 'image' : 'lung_023_right.nii.gz', + 'label': 'lung_023_right.nii.gz' + }, + { + 'image' : 'lung_025_left.nii.gz', + 'label': 'lung_025_left.nii.gz' + }, + { + 'image' : 'lung_026_right.nii.gz', + 'label': 'lung_026_right.nii.gz' + }, + { + 'image' : 'lung_027_right.nii.gz', + 'label': 'lung_027_right.nii.gz' + }, + { + 'image' : 'lung_028_left.nii.gz', + 'label': 'lung_028_left.nii.gz' + }, + { + 'image' : 'lung_029_left.nii.gz', + 'label': 'lung_029_left.nii.gz' + }, + { + 'image' : 'lung_031_right.nii.gz', + 'label': 'lung_031_right.nii.gz' + }, + { + 'image' : 'lung_033_left.nii.gz', + 'label': 'lung_033_left.nii.gz' + }, + { + 'image' : 'lung_034_right.nii.gz', + 'label': 'lung_034_right.nii.gz' + }, + { + 'image' : 'lung_036_left.nii.gz', + 'label': 'lung_036_left.nii.gz' + }, + { + 'image' : 'lung_037_right.nii.gz', + 'label': 'lung_037_right.nii.gz' + }, + { + 'image' : 'lung_038_right.nii.gz', + 'label': 'lung_038_right.nii.gz' + }, + { + 'image' : 'lung_041_right.nii.gz', + 'label': 'lung_041_right.nii.gz' + }, + { + 'image' : 'lung_042_right.nii.gz', + 'label': 'lung_042_right.nii.gz' + }, + { + 'image' : 'lung_043_right.nii.gz', + 'label': 'lung_043_right.nii.gz' + }, + { + 'image' : 'lung_044_left.nii.gz', + 'label': 'lung_044_left.nii.gz' + }, + { + 'image' : 'lung_045_left.nii.gz', + 'label': 'lung_045_left.nii.gz' + }, + { + 'image' : 'lung_046_left.nii.gz', + 'label': 'lung_046_left.nii.gz' + }, + { + 'image' : 'lung_047_right.nii.gz', + 'label': 'lung_047_right.nii.gz' + }, + { + 'image' : 'lung_048_right.nii.gz', + 'label': 'lung_048_right.nii.gz' + }, + { + 'image' : 'lung_049_right.nii.gz', + 'label': 'lung_049_right.nii.gz' + }, + { + 'image' : 'lung_051_left.nii.gz', + 'label': 'lung_051_left.nii.gz' + }, + { + 'image' : 'lung_053_right.nii.gz', + 'label': 'lung_053_right.nii.gz' + }, + { + 'image' : 'lung_054_right.nii.gz', + 'label': 'lung_054_right.nii.gz' + }, + { + 'image' : 'lung_055_left.nii.gz', + 'label': 'lung_055_left.nii.gz' + }, + { + 'image' : 'lung_057_left.nii.gz', + 'label': 'lung_057_left.nii.gz' + }, + { + 'image' : 'lung_058_right.nii.gz', + 'label': 'lung_058_right.nii.gz' + }, + { + 'image' : 'lung_059_left.nii.gz', + 'label': 'lung_059_left.nii.gz' + }, + { + 'image' : 'lung_061_left.nii.gz', + 'label': 'lung_061_left.nii.gz' + }, + { + 'image' : 'lung_062_left.nii.gz', + 'label': 'lung_062_left.nii.gz' + }, + { + 'image' : 'lung_064_left.nii.gz', + 'label': 'lung_064_left.nii.gz' + }, + { + 'image' : 'lung_065_left.nii.gz', + 'label': 'lung_065_left.nii.gz' + }, + { + 'image' : 'lung_066_left.nii.gz', + 'label': 'lung_066_left.nii.gz' + }, + { + 'image' : 'lung_066_right.nii.gz', + 'label': 'lung_066_right.nii.gz' + }, + { + 'image' : 'lung_069_right.nii.gz', + 'label': 'lung_069_right.nii.gz' + }, + { + 'image' : 'lung_070_left.nii.gz', + 'label': 'lung_070_left.nii.gz' + }, + { + 'image' : 'lung_071_right.nii.gz', + 'label': 'lung_071_right.nii.gz' + }, + { + 'image' : 'lung_073_left.nii.gz', + 'label': 'lung_073_left.nii.gz' + }, + { + 'image' : 'lung_074_left.nii.gz', + 'label': 'lung_074_left.nii.gz' + }, + +] +val : + [ + { + 'image' : 'lung_075_left.nii.gz', + 'label': 'lung_075_left.nii.gz' + }, + { + 'image' : 'lung_078_left.nii.gz', + 'label': 'lung_078_left.nii.gz' + }, + { + 'image' : 'lung_079_right.nii.gz', + 'label': 'lung_079_right.nii.gz' + }, + { + 'image' : 'lung_080_left.nii.gz', + 'label': 'lung_080_left.nii.gz' + }, + { + 'image' : 'lung_081_right.nii.gz', + 'label': 'lung_081_right.nii.gz' + } + ] + +test : + [ + { + 'image' : 'lung_083_right.nii.gz', + 'label': 'lung_083_right.nii.gz' + }, + { + 'image' : 'lung_084_left.nii.gz', + 'label': 'lung_084_left.nii.gz' + }, + { + 'image' : 'lung_086_right.nii.gz', + 'label': 'lung_086_right.nii.gz' + }, + { + 'image' : 'lung_092_right.nii.gz', + 'label': 'lung_092_right.nii.gz' + }, + { + 'image' : 'lung_093_right.nii.gz', + 'label': 'lung_093_right.nii.gz' + }, + { + 'image' : 'lung_095_right.nii.gz', + 'label': 'lung_095_right.nii.gz' + }, + { + 'image' : 'lung_096_right.nii.gz', + 'label': 'lung_096_right.nii.gz' + } + ] diff --git a/training/Resources/Malvik/student.yaml b/training/Resources/Malvik/student.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9642f5be22cd79a4ec24ce3712e12151a228563a --- /dev/null +++ b/training/Resources/Malvik/student.yaml @@ -0,0 +1,28 @@ +device: 'cuda' + +data: + train_dataset: "" + aug_prob: 0.1 + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet4 + loss: DiceLoss + filter_base: 16 + filter_expansion: 2 + weights: + optimizer: + name: 'Adam' + lr: 0.000025 + +train: + max_epochs: 500 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/home/tumor/out/metric.csv" + save_frequency: 50 + model_directory: "/home/tumor/out/models/" + batch_size: 10 diff --git a/training/Resources/Malvik/teacher.yaml b/training/Resources/Malvik/teacher.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4eb538fc146d323c46a48b6dbaba547c3df12648 --- /dev/null +++ b/training/Resources/Malvik/teacher.yaml @@ -0,0 +1,29 @@ +device: 'cuda' + +data: + train_dataset: "/home/tumor/LungTumorSegmentation/Resources/Malvik/teacher_data.yaml" + aug_prob: 0.25 + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet5_Teacher + loss: DiceLoss + filter_base: 64 + filter_expansion: 2 + weights: + optimizer: + name: 'Adam' + lr: 0.000025 + +train: + max_epochs: 500 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/home/tumor/out/metric.csv" + save_frequency: 50 + model_directory: "/home/tumor/out/models/" + batch_size: 10 + diff --git a/training/Resources/Malvik/teacher_data.yaml b/training/Resources/Malvik/teacher_data.yaml new file mode 100644 index 0000000000000000000000000000000000000000..06ea64d2f36f74f492a320dda57704d734907ff6 --- /dev/null +++ b/training/Resources/Malvik/teacher_data.yaml @@ -0,0 +1,325 @@ +image_prefix: "/home/tumor/data/MSD-Tumor/Images/" +boxes_prefix: "/home/tumor/data/MSD-Tumor/Boxes/" +label_prefix: "/home/tumor/data/MSD-Tumor/Labels/" + +train: + [ + { + 'image' : 'lung_001.nii.gz', + 'boxes' : 'lung_001.nii.gz', + 'label' : 'lung_001.nii.gz' + }, + { + 'image' : 'lung_003.nii.gz', + 'boxes' : 'lung_003.nii.gz', + 'label' : 'lung_003.nii.gz' + }, + { + 'image' : 'lung_004.nii.gz', + 'boxes' : 'lung_004.nii.gz', + 'label' : 'lung_004.nii.gz' + }, + { + 'image' : 'lung_005.nii.gz', + 'boxes' : 'lung_005.nii.gz', + 'label' : 'lung_005.nii.gz' + }, + { + 'image' : 'lung_006.nii.gz', + 'boxes' : 'lung_006.nii.gz', + 'label' : 'lung_006.nii.gz' + }, + { + 'image' : 'lung_009.nii.gz', + 'boxes' : 'lung_009.nii.gz', + 'label' : 'lung_009.nii.gz' + }, + { + 'image' : 'lung_010.nii.gz', + 'boxes' : 'lung_010.nii.gz', + 'label' : 'lung_010.nii.gz' + }, + { + 'image' : 'lung_014.nii.gz', + 'boxes' : 'lung_014.nii.gz', + 'label' : 'lung_014.nii.gz' + }, + { + 'image' : 'lung_015.nii.gz', + 'boxes' : 'lung_015.nii.gz', + 'label' : 'lung_015.nii.gz' + }, + { + 'image' : 'lung_016.nii.gz', + 'boxes' : 'lung_016.nii.gz', + 'label' : 'lung_016.nii.gz' + }, + { + 'image' : 'lung_018.nii.gz', + 'boxes' : 'lung_018.nii.gz', + 'label' : 'lung_018.nii.gz' + }, + { + 'image' : 'lung_020.nii.gz', + 'boxes' : 'lung_020.nii.gz', + 'label' : 'lung_020.nii.gz' + }, + { + 'image' : 'lung_022.nii.gz', + 'boxes' : 'lung_022.nii.gz', + 'label' : 'lung_022.nii.gz' + }, + { + 'image' : 'lung_023.nii.gz', + 'boxes' : 'lung_023.nii.gz', + 'label' : 'lung_023.nii.gz' + }, + { + 'image' : 'lung_025.nii.gz', + 'boxes' : 'lung_025.nii.gz', + 'label' : 'lung_025.nii.gz' + }, + { + 'image' : 'lung_026.nii.gz', + 'boxes' : 'lung_026.nii.gz', + 'label' : 'lung_026.nii.gz' + }, + { + 'image' : 'lung_027.nii.gz', + 'boxes' : 'lung_027.nii.gz', + 'label' : 'lung_027.nii.gz' + }, + { + 'image' : 'lung_028.nii.gz', + 'boxes' : 'lung_028.nii.gz', + 'label' : 'lung_028.nii.gz' + }, + { + 'image' : 'lung_029.nii.gz', + 'boxes' : 'lung_029.nii.gz', + 'label' : 'lung_029.nii.gz' + }, + { + 'image' : 'lung_031.nii.gz', + 'boxes' : 'lung_031.nii.gz', + 'label' : 'lung_031.nii.gz' + }, + { + 'image' : 'lung_033.nii.gz', + 'boxes' : 'lung_033.nii.gz', + 'label' : 'lung_033.nii.gz' + }, + { + 'image' : 'lung_034.nii.gz', + 'boxes' : 'lung_034.nii.gz', + 'label' : 'lung_034.nii.gz' + }, + { + 'image' : 'lung_036.nii.gz', + 'boxes' : 'lung_036.nii.gz', + 'label' : 'lung_036.nii.gz' + }, + { + 'image' : 'lung_037.nii.gz', + 'boxes' : 'lung_037.nii.gz', + 'label' : 'lung_037.nii.gz' + }, + { + 'image' : 'lung_038.nii.gz', + 'boxes' : 'lung_038.nii.gz', + 'label' : 'lung_038.nii.gz' + }, + { + 'image' : 'lung_041.nii.gz', + 'boxes' : 'lung_041.nii.gz', + 'label' : 'lung_041.nii.gz' + }, + { + 'image' : 'lung_042.nii.gz', + 'boxes' : 'lung_042.nii.gz', + 'label' : 'lung_042.nii.gz' + }, + { + 'image' : 'lung_043.nii.gz', + 'boxes' : 'lung_043.nii.gz', + 'label' : 'lung_043.nii.gz' + }, + { + 'image' : 'lung_044.nii.gz', + 'boxes' : 'lung_044.nii.gz', + 'label' : 'lung_044.nii.gz' + }, + { + 'image' : 'lung_045.nii.gz', + 'boxes' : 'lung_045.nii.gz', + 'label' : 'lung_045.nii.gz' + }, + { + 'image' : 'lung_046.nii.gz', + 'boxes' : 'lung_046.nii.gz', + 'label' : 'lung_046.nii.gz' + }, + { + 'image' : 'lung_047.nii.gz', + 'boxes' : 'lung_047.nii.gz', + 'label' : 'lung_047.nii.gz' + }, + { + 'image' : 'lung_048.nii.gz', + 'boxes' : 'lung_048.nii.gz', + 'label' : 'lung_048.nii.gz' + }, + { + 'image' : 'lung_049.nii.gz', + 'boxes' : 'lung_049.nii.gz', + 'label' : 'lung_049.nii.gz' + }, + { + 'image' : 'lung_051.nii.gz', + 'boxes' : 'lung_051.nii.gz', + 'label' : 'lung_051.nii.gz' + }, + { + 'image' : 'lung_053.nii.gz', + 'boxes' : 'lung_053.nii.gz', + 'label' : 'lung_053.nii.gz' + }, + { + 'image' : 'lung_054.nii.gz', + 'boxes' : 'lung_054.nii.gz', + 'label' : 'lung_054.nii.gz' + }, + { + 'image' : 'lung_055.nii.gz', + 'boxes' : 'lung_055.nii.gz', + 'label' : 'lung_055.nii.gz' + }, + { + 'image' : 'lung_057.nii.gz', + 'boxes' : 'lung_057.nii.gz', + 'label' : 'lung_057.nii.gz' + }, + { + 'image' : 'lung_058.nii.gz', + 'boxes' : 'lung_058.nii.gz', + 'label' : 'lung_058.nii.gz' + }, + { + 'image' : 'lung_059.nii.gz', + 'boxes' : 'lung_059.nii.gz', + 'label' : 'lung_059.nii.gz' + }, + { + 'image' : 'lung_061.nii.gz', + 'boxes' : 'lung_061.nii.gz', + 'label' : 'lung_061.nii.gz' + }, + { + 'image' : 'lung_062.nii.gz', + 'boxes' : 'lung_062.nii.gz', + 'label' : 'lung_062.nii.gz' + }, + { + 'image' : 'lung_064.nii.gz', + 'boxes' : 'lung_064.nii.gz', + 'label' : 'lung_064.nii.gz' + }, + { + 'image' : 'lung_065.nii.gz', + 'boxes' : 'lung_065.nii.gz', + 'label' : 'lung_065.nii.gz' + }, + { + 'image' : 'lung_066.nii.gz', + 'boxes' : 'lung_066.nii.gz', + 'label' : 'lung_066.nii.gz' + }, + { + 'image' : 'lung_069.nii.gz', + 'boxes' : 'lung_069.nii.gz', + 'label' : 'lung_069.nii.gz' + }, + { + 'image' : 'lung_070.nii.gz', + 'boxes' : 'lung_070.nii.gz', + 'label' : 'lung_070.nii.gz' + }, + { + 'image' : 'lung_071.nii.gz', + 'boxes' : 'lung_071.nii.gz', + 'label' : 'lung_071.nii.gz' + }, + { + 'image' : 'lung_073.nii.gz', + 'boxes' : 'lung_073.nii.gz', + 'label' : 'lung_073.nii.gz' + } +] + +val: + [ + { + 'image' : 'lung_074.nii.gz', + 'boxes' : 'lung_074.nii.gz', + 'label' : 'lung_074.nii.gz' + }, + { + 'image' : 'lung_075.nii.gz', + 'boxes' : 'lung_075.nii.gz', + 'label' : 'lung_075.nii.gz' + }, + { + 'image' : 'lung_078.nii.gz', + 'boxes' : 'lung_078.nii.gz', + 'label' : 'lung_078.nii.gz' + }, + { + 'image' : 'lung_079.nii.gz', + 'boxes' : 'lung_079.nii.gz', + 'label' : 'lung_079.nii.gz' + }, + { + 'image' : 'lung_080.nii.gz', + 'boxes' : 'lung_080.nii.gz', + 'label' : 'lung_080.nii.gz' + } + ] + +test: [ + { + 'image' : 'lung_081.nii.gz', + 'boxes' : 'lung_081.nii.gz', + 'label' : 'lung_081.nii.gz' + }, + { + 'image' : 'lung_083.nii.gz', + 'boxes' : 'lung_083.nii.gz', + 'label' : 'lung_083.nii.gz' + }, + { + 'image' : 'lung_084.nii.gz', + 'boxes' : 'lung_084.nii.gz', + 'label' : 'lung_084.nii.gz' + }, + { + 'image' : 'lung_086.nii.gz', + 'boxes' : 'lung_086.nii.gz', + 'label' : 'lung_086.nii.gz' + }, + { + 'image' : 'lung_092.nii.gz', + 'boxes' : 'lung_092.nii.gz', + 'label' : 'lung_092.nii.gz' + }, + { + 'image' : 'lung_093.nii.gz', + 'boxes' : 'lung_093.nii.gz', + 'label' : 'lung_093.nii.gz' + }, + { + 'image' : 'lung_095.nii.gz', + 'boxes' : 'lung_095.nii.gz', + 'label' : 'lung_095.nii.gz' + } +] + diff --git a/training/Resources/Malvik_train_1/config_fullfeature_cropped.yaml b/training/Resources/Malvik_train_1/config_fullfeature_cropped.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5248bbd2e7b32a334a9f1cfeec2aae7aa4500bba --- /dev/null +++ b/training/Resources/Malvik_train_1/config_fullfeature_cropped.yaml @@ -0,0 +1,27 @@ +device: 'cuda' + +data: + train_dataset: "/home/tumor/LungTumorSegmentation/Resources/Malvik_train_1/standard.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet_test + loss: DiceLoss + filter_base: 64 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.00001 + +train: + max_epochs: 500 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/home/tumor/out/full_filter.csv" + save_frequency: 15 + model_directory: "/home/tumor/out/models/" + batch_size: 10 diff --git a/training/Resources/Malvik_train_1/cropped.yaml b/training/Resources/Malvik_train_1/cropped.yaml new file mode 100644 index 0000000000000000000000000000000000000000..669a8594d67381a477ae04d11dc592a708009656 --- /dev/null +++ b/training/Resources/Malvik_train_1/cropped.yaml @@ -0,0 +1,320 @@ +image_prefix: "/home/tumor/data/Cropped/Images/" +boxes_prefix: "/home/tumor/data/Cropped/Boxes/" +label_prefix: "/home/tumor/data/Cropped/Labels/" + +train: + [ + { + 'image' : 'lung_001.nii', + 'boxes' : 'lung_001.nii', + 'label' : 'lung_001.nii' + }, + { + 'image' : 'lung_003.nii', + 'boxes' : 'lung_003.nii', + 'label' : 'lung_003.nii' + }, + { + 'image' : 'lung_004.nii', + 'boxes' : 'lung_004.nii', + 'label' : 'lung_004.nii' + }, + { + 'image' : 'lung_005.nii', + 'boxes' : 'lung_005.nii', + 'label' : 'lung_005.nii' + }, + { + 'image' : 'lung_006.nii', + 'boxes' : 'lung_006.nii', + 'label' : 'lung_006.nii' + }, + { + 'image' : 'lung_009.nii', + 'boxes' : 'lung_009.nii', + 'label' : 'lung_009.nii' + }, + { + 'image' : 'lung_010.nii', + 'boxes' : 'lung_010.nii', + 'label' : 'lung_010.nii' + }, + { + 'image' : 'lung_014.nii', + 'boxes' : 'lung_014.nii', + 'label' : 'lung_014.nii' + }, + { + 'image' : 'lung_015.nii', + 'boxes' : 'lung_015.nii', + 'label' : 'lung_015.nii' + }, + { + 'image' : 'lung_016.nii', + 'boxes' : 'lung_016.nii', + 'label' : 'lung_016.nii' + }, + { + 'image' : 'lung_018.nii', + 'boxes' : 'lung_018.nii', + 'label' : 'lung_018.nii' + }, + { + 'image' : 'lung_020.nii', + 'boxes' : 'lung_020.nii', + 'label' : 'lung_020.nii' + }, + { + 'image' : 'lung_022.nii', + 'boxes' : 'lung_022.nii', + 'label' : 'lung_022.nii' + }, + { + 'image' : 'lung_023.nii', + 'boxes' : 'lung_023.nii', + 'label' : 'lung_023.nii' + }, + { + 'image' : 'lung_025.nii', + 'boxes' : 'lung_025.nii', + 'label' : 'lung_025.nii' + }, + { + 'image' : 'lung_026.nii', + 'boxes' : 'lung_026.nii', + 'label' : 'lung_026.nii' + }, + { + 'image' : 'lung_027.nii', + 'boxes' : 'lung_027.nii', + 'label' : 'lung_027.nii' + }, + { + 'image' : 'lung_028.nii', + 'boxes' : 'lung_028.nii', + 'label' : 'lung_028.nii' + }, + { + 'image' : 'lung_029.nii', + 'boxes' : 'lung_029.nii', + 'label' : 'lung_029.nii' + }, + { + 'image' : 'lung_031.nii', + 'boxes' : 'lung_031.nii', + 'label' : 'lung_031.nii' + }, + { + 'image' : 'lung_033.nii', + 'boxes' : 'lung_033.nii', + 'label' : 'lung_033.nii' + }, + { + 'image' : 'lung_034.nii', + 'boxes' : 'lung_034.nii', + 'label' : 'lung_034.nii' + }, + { + 'image' : 'lung_036.nii', + 'boxes' : 'lung_036.nii', + 'label' : 'lung_036.nii' + }, + { + 'image' : 'lung_037.nii', + 'boxes' : 'lung_037.nii', + 'label' : 'lung_037.nii' + }, + { + 'image' : 'lung_038.nii', + 'boxes' : 'lung_038.nii', + 'label' : 'lung_038.nii' + }, + { + 'image' : 'lung_041.nii', + 'boxes' : 'lung_041.nii', + 'label' : 'lung_041.nii' + }, + { + 'image' : 'lung_042.nii', + 'boxes' : 'lung_042.nii', + 'label' : 'lung_042.nii' + }, + { + 'image' : 'lung_043.nii', + 'boxes' : 'lung_043.nii', + 'label' : 'lung_043.nii' + }, + { + 'image' : 'lung_044.nii', + 'boxes' : 'lung_044.nii', + 'label' : 'lung_044.nii' + }, + { + 'image' : 'lung_045.nii', + 'boxes' : 'lung_045.nii', + 'label' : 'lung_045.nii' + }, + { + 'image' : 'lung_046.nii', + 'boxes' : 'lung_046.nii', + 'label' : 'lung_046.nii' + }, + { + 'image' : 'lung_047.nii', + 'boxes' : 'lung_047.nii', + 'label' : 'lung_047.nii' + }, + { + 'image' : 'lung_048.nii', + 'boxes' : 'lung_048.nii', + 'label' : 'lung_048.nii' + }, + { + 'image' : 'lung_049.nii', + 'boxes' : 'lung_049.nii', + 'label' : 'lung_049.nii' + }, + { + 'image' : 'lung_051.nii', + 'boxes' : 'lung_051.nii', + 'label' : 'lung_051.nii' + }, + { + 'image' : 'lung_053.nii', + 'boxes' : 'lung_053.nii', + 'label' : 'lung_053.nii' + }, + { + 'image' : 'lung_054.nii', + 'boxes' : 'lung_054.nii', + 'label' : 'lung_054.nii' + }, + { + 'image' : 'lung_055.nii', + 'boxes' : 'lung_055.nii', + 'label' : 'lung_055.nii' + }, + { + 'image' : 'lung_057.nii', + 'boxes' : 'lung_057.nii', + 'label' : 'lung_057.nii' + }, + { + 'image' : 'lung_058.nii', + 'boxes' : 'lung_058.nii', + 'label' : 'lung_058.nii' + }, + { + 'image' : 'lung_059.nii', + 'boxes' : 'lung_059.nii', + 'label' : 'lung_059.nii' + }, + { + 'image' : 'lung_061.nii', + 'boxes' : 'lung_061.nii', + 'label' : 'lung_061.nii' + }, + { + 'image' : 'lung_062.nii', + 'boxes' : 'lung_062.nii', + 'label' : 'lung_062.nii' + }, + { + 'image' : 'lung_064.nii', + 'boxes' : 'lung_064.nii', + 'label' : 'lung_064.nii' + }, + { + 'image' : 'lung_065.nii', + 'boxes' : 'lung_065.nii', + 'label' : 'lung_065.nii' + }, + { + 'image' : 'lung_066.nii', + 'boxes' : 'lung_066.nii', + 'label' : 'lung_066.nii' + }, + { + 'image' : 'lung_069.nii', + 'boxes' : 'lung_069.nii', + 'label' : 'lung_069.nii' + }, + { + 'image' : 'lung_070.nii', + 'boxes' : 'lung_070.nii', + 'label' : 'lung_070.nii' + }, + { + 'image' : 'lung_071.nii', + 'boxes' : 'lung_071.nii', + 'label' : 'lung_071.nii' + }, + { + 'image' : 'lung_073.nii', + 'boxes' : 'lung_073.nii', + 'label' : 'lung_073.nii' + }, + { + 'image' : 'lung_074.nii', + 'boxes' : 'lung_074.nii', + 'label' : 'lung_074.nii' + }, + { + 'image' : 'lung_075.nii', + 'boxes' : 'lung_075.nii', + 'label' : 'lung_075.nii' + }, + { + 'image' : 'lung_078.nii', + 'boxes' : 'lung_078.nii', + 'label' : 'lung_078.nii' + }, + { + 'image' : 'lung_079.nii', + 'boxes' : 'lung_079.nii', + 'label' : 'lung_079.nii' + }, + { + 'image' : 'lung_080.nii', + 'boxes' : 'lung_080.nii', + 'label' : 'lung_080.nii' + } +] + +val: [ + { + 'image' : 'lung_081.nii', + 'boxes' : 'lung_081.nii', + 'label' : 'lung_081.nii' + }, + { + 'image' : 'lung_083.nii', + 'boxes' : 'lung_083.nii', + 'label' : 'lung_083.nii' + }, + { + 'image' : 'lung_084.nii', + 'boxes' : 'lung_084.nii', + 'label' : 'lung_084.nii' + }, + { + 'image' : 'lung_086.nii', + 'boxes' : 'lung_086.nii', + 'label' : 'lung_086.nii' + }, + { + 'image' : 'lung_092.nii', + 'boxes' : 'lung_092.nii', + 'label' : 'lung_092.nii' + }, + { + 'image' : 'lung_093.nii', + 'boxes' : 'lung_093.nii', + 'label' : 'lung_093.nii' + }, + { + 'image' : 'lung_095.nii', + 'boxes' : 'lung_095.nii', + 'label' : 'lung_095.nii' + } +] diff --git a/training/Resources/Malvik_train_1/standard.yaml b/training/Resources/Malvik_train_1/standard.yaml new file mode 100644 index 0000000000000000000000000000000000000000..c3901c0dc4383eb05efa3f9ab51c33ddef912793 --- /dev/null +++ b/training/Resources/Malvik_train_1/standard.yaml @@ -0,0 +1,320 @@ +image_prefix: "/home/tumor/data/Task06_Lung/Images/" +boxes_prefix: "/home/tumor/data/Task06_Lung/Boxes/" +label_prefix: "/home/tumor/data/Task06_Lung/Label/" + +train: + [ + { + 'image' : 'lung_001.nii', + 'boxes' : 'lung_001.nii', + 'label' : 'lung_001.nii' + }, + { + 'image' : 'lung_003.nii', + 'boxes' : 'lung_003.nii', + 'label' : 'lung_003.nii' + }, + { + 'image' : 'lung_004.nii', + 'boxes' : 'lung_004.nii', + 'label' : 'lung_004.nii' + }, + { + 'image' : 'lung_005.nii', + 'boxes' : 'lung_005.nii', + 'label' : 'lung_005.nii' + }, + { + 'image' : 'lung_006.nii', + 'boxes' : 'lung_006.nii', + 'label' : 'lung_006.nii' + }, + { + 'image' : 'lung_009.nii', + 'boxes' : 'lung_009.nii', + 'label' : 'lung_009.nii' + }, + { + 'image' : 'lung_010.nii', + 'boxes' : 'lung_010.nii', + 'label' : 'lung_010.nii' + }, + { + 'image' : 'lung_014.nii', + 'boxes' : 'lung_014.nii', + 'label' : 'lung_014.nii' + }, + { + 'image' : 'lung_015.nii', + 'boxes' : 'lung_015.nii', + 'label' : 'lung_015.nii' + }, + { + 'image' : 'lung_016.nii', + 'boxes' : 'lung_016.nii', + 'label' : 'lung_016.nii' + }, + { + 'image' : 'lung_018.nii', + 'boxes' : 'lung_018.nii', + 'label' : 'lung_018.nii' + }, + { + 'image' : 'lung_020.nii', + 'boxes' : 'lung_020.nii', + 'label' : 'lung_020.nii' + }, + { + 'image' : 'lung_022.nii', + 'boxes' : 'lung_022.nii', + 'label' : 'lung_022.nii' + }, + { + 'image' : 'lung_023.nii', + 'boxes' : 'lung_023.nii', + 'label' : 'lung_023.nii' + }, + { + 'image' : 'lung_025.nii', + 'boxes' : 'lung_025.nii', + 'label' : 'lung_025.nii' + }, + { + 'image' : 'lung_026.nii', + 'boxes' : 'lung_026.nii', + 'label' : 'lung_026.nii' + }, + { + 'image' : 'lung_027.nii', + 'boxes' : 'lung_027.nii', + 'label' : 'lung_027.nii' + }, + { + 'image' : 'lung_028.nii', + 'boxes' : 'lung_028.nii', + 'label' : 'lung_028.nii' + }, + { + 'image' : 'lung_029.nii', + 'boxes' : 'lung_029.nii', + 'label' : 'lung_029.nii' + }, + { + 'image' : 'lung_031.nii', + 'boxes' : 'lung_031.nii', + 'label' : 'lung_031.nii' + }, + { + 'image' : 'lung_033.nii', + 'boxes' : 'lung_033.nii', + 'label' : 'lung_033.nii' + }, + { + 'image' : 'lung_034.nii', + 'boxes' : 'lung_034.nii', + 'label' : 'lung_034.nii' + }, + { + 'image' : 'lung_036.nii', + 'boxes' : 'lung_036.nii', + 'label' : 'lung_036.nii' + }, + { + 'image' : 'lung_037.nii', + 'boxes' : 'lung_037.nii', + 'label' : 'lung_037.nii' + }, + { + 'image' : 'lung_038.nii', + 'boxes' : 'lung_038.nii', + 'label' : 'lung_038.nii' + }, + { + 'image' : 'lung_041.nii', + 'boxes' : 'lung_041.nii', + 'label' : 'lung_041.nii' + }, + { + 'image' : 'lung_042.nii', + 'boxes' : 'lung_042.nii', + 'label' : 'lung_042.nii' + }, + { + 'image' : 'lung_043.nii', + 'boxes' : 'lung_043.nii', + 'label' : 'lung_043.nii' + }, + { + 'image' : 'lung_044.nii', + 'boxes' : 'lung_044.nii', + 'label' : 'lung_044.nii' + }, + { + 'image' : 'lung_045.nii', + 'boxes' : 'lung_045.nii', + 'label' : 'lung_045.nii' + }, + { + 'image' : 'lung_046.nii', + 'boxes' : 'lung_046.nii', + 'label' : 'lung_046.nii' + }, + { + 'image' : 'lung_047.nii', + 'boxes' : 'lung_047.nii', + 'label' : 'lung_047.nii' + }, + { + 'image' : 'lung_048.nii', + 'boxes' : 'lung_048.nii', + 'label' : 'lung_048.nii' + }, + { + 'image' : 'lung_049.nii', + 'boxes' : 'lung_049.nii', + 'label' : 'lung_049.nii' + }, + { + 'image' : 'lung_051.nii', + 'boxes' : 'lung_051.nii', + 'label' : 'lung_051.nii' + }, + { + 'image' : 'lung_053.nii', + 'boxes' : 'lung_053.nii', + 'label' : 'lung_053.nii' + }, + { + 'image' : 'lung_054.nii', + 'boxes' : 'lung_054.nii', + 'label' : 'lung_054.nii' + }, + { + 'image' : 'lung_055.nii', + 'boxes' : 'lung_055.nii', + 'label' : 'lung_055.nii' + }, + { + 'image' : 'lung_057.nii', + 'boxes' : 'lung_057.nii', + 'label' : 'lung_057.nii' + }, + { + 'image' : 'lung_058.nii', + 'boxes' : 'lung_058.nii', + 'label' : 'lung_058.nii' + }, + { + 'image' : 'lung_059.nii', + 'boxes' : 'lung_059.nii', + 'label' : 'lung_059.nii' + }, + { + 'image' : 'lung_061.nii', + 'boxes' : 'lung_061.nii', + 'label' : 'lung_061.nii' + }, + { + 'image' : 'lung_062.nii', + 'boxes' : 'lung_062.nii', + 'label' : 'lung_062.nii' + }, + { + 'image' : 'lung_064.nii', + 'boxes' : 'lung_064.nii', + 'label' : 'lung_064.nii' + }, + { + 'image' : 'lung_065.nii', + 'boxes' : 'lung_065.nii', + 'label' : 'lung_065.nii' + }, + { + 'image' : 'lung_066.nii', + 'boxes' : 'lung_066.nii', + 'label' : 'lung_066.nii' + }, + { + 'image' : 'lung_069.nii', + 'boxes' : 'lung_069.nii', + 'label' : 'lung_069.nii' + }, + { + 'image' : 'lung_070.nii', + 'boxes' : 'lung_070.nii', + 'label' : 'lung_070.nii' + }, + { + 'image' : 'lung_071.nii', + 'boxes' : 'lung_071.nii', + 'label' : 'lung_071.nii' + }, + { + 'image' : 'lung_073.nii', + 'boxes' : 'lung_073.nii', + 'label' : 'lung_073.nii' + }, + { + 'image' : 'lung_074.nii', + 'boxes' : 'lung_074.nii', + 'label' : 'lung_074.nii' + }, + { + 'image' : 'lung_075.nii', + 'boxes' : 'lung_075.nii', + 'label' : 'lung_075.nii' + }, + { + 'image' : 'lung_078.nii', + 'boxes' : 'lung_078.nii', + 'label' : 'lung_078.nii' + }, + { + 'image' : 'lung_079.nii', + 'boxes' : 'lung_079.nii', + 'label' : 'lung_079.nii' + }, + { + 'image' : 'lung_080.nii', + 'boxes' : 'lung_080.nii', + 'label' : 'lung_080.nii' + } +] + +val: [ + { + 'image' : 'lung_081.nii', + 'boxes' : 'lung_081.nii', + 'label' : 'lung_081.nii' + }, + { + 'image' : 'lung_083.nii', + 'boxes' : 'lung_083.nii', + 'label' : 'lung_083.nii' + }, + { + 'image' : 'lung_084.nii', + 'boxes' : 'lung_084.nii', + 'label' : 'lung_084.nii' + }, + { + 'image' : 'lung_086.nii', + 'boxes' : 'lung_086.nii', + 'label' : 'lung_086.nii' + }, + { + 'image' : 'lung_092.nii', + 'boxes' : 'lung_092.nii', + 'label' : 'lung_092.nii' + }, + { + 'image' : 'lung_093.nii', + 'boxes' : 'lung_093.nii', + 'label' : 'lung_093.nii' + }, + { + 'image' : 'lung_095.nii', + 'boxes' : 'lung_095.nii', + 'label' : 'lung_095.nii' + } +] diff --git a/training/Resources/Malvik_train_1/test.yaml b/training/Resources/Malvik_train_1/test.yaml new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/training/Resources/Malvik_train_1/test_data.yaml b/training/Resources/Malvik_train_1/test_data.yaml new file mode 100644 index 0000000000000000000000000000000000000000..46b66104879ecfc7c3d1ab7aee59d6139001b1d8 --- /dev/null +++ b/training/Resources/Malvik_train_1/test_data.yaml @@ -0,0 +1,66 @@ +image_prefix: "/home/tumor/data/LungDx-Lung/Images/" +label_prefix: "/home/tumor/data/LungDx-Lung/Labels/" +boxes_prefix: "/home/tumor/data/LungDx-Lung/Boxes/" + +train: + [ + { + 'image' : 'A0250_scan1_right.nii.gz', + 'label' : 'A0250_scan1_right.nii.gz', + 'boxes' : 'A0250_scan1_right.nii.gz' + }, + { + 'image' : 'G0049_scan1_right.nii.gz', + 'label' : 'G0049_scan1_right.nii.gz', + 'boxes' : 'G0049_scan1_right.nii.gz' + }, + { + 'image' : 'A0250_scan2_right.nii.gz', + 'label' : 'A0250_scan2_right.nii.gz', + 'boxes' : 'A0250_scan2_right.nii.gz' + }, + { + 'image' : 'G0049_scan2_right.nii.gz', + 'label' : 'G0049_scan2_right.nii.gz', + 'boxes' : 'G0049_scan2_right.nii.gz' + }, + { + 'image' : 'A0184_scan1_right.nii.gz', + 'label' : 'A0184_scan1_right.nii.gz', + 'boxes' : 'A0184_scan1_right.nii.gz' + }, + { + 'image' : 'A0263_scan1_left.nii.gz', + 'label' : 'A0263_scan1_left.nii.gz', + 'boxes' : 'A0263_scan1_left.nii.gz' + }, + { + 'image' : 'A0184_scan2_right.nii.gz', + 'label' : 'A0184_scan2_right.nii.gz', + 'boxes' : 'A0184_scan2_right.nii.gz' + }, + { + 'image' : 'B0041_scan2_right.nii.gz', + 'label' : 'B0041_scan2_right.nii.gz', + 'boxes' : 'B0041_scan2_right.nii.gz' + } + ] + +val: + [ + { + 'image' : 'A0263_scan1_left.nii.gz', + 'label' : 'A0263_scan1_left.nii.gz', + 'boxes' : 'A0263_scan1_left.nii.gz' + }, + { + 'image' : 'A0184_scan2_right.nii.gz', + 'label' : 'A0184_scan2_right.nii.gz', + 'boxes' : 'A0184_scan2_right.nii.gz' + }, + { + 'image' : 'B0041_scan2_right.nii.gz', + 'label' : 'B0041_scan2_right.nii.gz', + 'boxes' : 'B0041_scan2_right.nii.gz' + } + ] diff --git a/training/Resources/Student_Train/data.yaml b/training/Resources/Student_Train/data.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9a7f1da4d203dbf609cead3c8f2887b35ed7715a --- /dev/null +++ b/training/Resources/Student_Train/data.yaml @@ -0,0 +1,3123 @@ +image_prefix: "/home/tumor/data/train_student/Images/" +label_prefix: "/home/tumor/data/train_student/Labels/" +boxes_prefix: "/home/tumor/data/train_student/Boxes/" + +train: + [ + { + 'image' : 'lung_001.nii.gz', + 'boxes' : 'lung_001.nii.gz', + 'label': 'lung_001.nii.gz', + }, + { + 'image' : 'lung_003.nii.gz', + 'boxes' : 'lung_003.nii.gz', + 'label': 'lung_003.nii.gz', + }, + { + 'image' : 'lung_004.nii.gz', + 'boxes' : 'lung_004.nii.gz', + 'label': 'lung_004.nii.gz', + }, + { + 'image' : 'lung_005.nii.gz', + 'boxes' : 'lung_005.nii.gz', + 'label': 'lung_005.nii.gz', + }, + { + 'image' : 'lung_006.nii.gz', + 'boxes' : 'lung_006.nii.gz', + 'label': 'lung_006.nii.gz', + }, + { + 'image' : 'lung_009.nii.gz', + 'boxes' : 'lung_009.nii.gz', + 'label': 'lung_009.nii.gz', + }, + { + 'image' : 'lung_010.nii.gz', + 'boxes' : 'lung_010.nii.gz', + 'label': 'lung_010.nii.gz', + }, + { + 'image' : 'lung_014.nii.gz', + 'boxes' : 'lung_014.nii.gz', + 'label': 'lung_014.nii.gz', + }, + { + 'image' : 'lung_015.nii.gz', + 'boxes' : 'lung_015.nii.gz', + 'label': 'lung_015.nii.gz', + }, + { + 'image' : 'lung_016.nii.gz', + 'boxes' : 'lung_016.nii.gz', + 'label': 'lung_016.nii.gz', + }, + { + 'image' : 'lung_018.nii.gz', + 'boxes' : 'lung_018.nii.gz', + 'label': 'lung_018.nii.gz', + }, + { + 'image' : 'lung_020.nii.gz', + 'boxes' : 'lung_020.nii.gz', + 'label': 'lung_020.nii.gz', + }, + { + 'image' : 'lung_022.nii.gz', + 'boxes' : 'lung_022.nii.gz', + 'label': 'lung_022.nii.gz', + }, + { + 'image' : 'lung_023.nii.gz', + 'boxes' : 'lung_023.nii.gz', + 'label': 'lung_023.nii.gz', + }, + { + 'image' : 'lung_025.nii.gz', + 'boxes' : 'lung_025.nii.gz', + 'label': 'lung_025.nii.gz', + }, + { + 'image' : 'lung_026.nii.gz', + 'boxes' : 'lung_026.nii.gz', + 'label': 'lung_026.nii.gz', + }, + { + 'image' : 'lung_027.nii.gz', + 'boxes' : 'lung_027.nii.gz', + 'label': 'lung_027.nii.gz', + }, + { + 'image' : 'lung_028.nii.gz', + 'boxes' : 'lung_028.nii.gz', + 'label': 'lung_028.nii.gz', + }, + { + 'image' : 'lung_029.nii.gz', + 'boxes' : 'lung_029.nii.gz', + 'label': 'lung_029.nii.gz', + }, + { + 'image' : 'lung_031.nii.gz', + 'boxes' : 'lung_031.nii.gz', + 'label': 'lung_031.nii.gz', + }, + { + 'image' : 'lung_033.nii.gz', + 'boxes' : 'lung_033.nii.gz', + 'label': 'lung_033.nii.gz', + }, + { + 'image' : 'lung_034.nii.gz', + 'boxes' : 'lung_034.nii.gz', + 'label': 'lung_034.nii.gz', + }, + { + 'image' : 'lung_036.nii.gz', + 'boxes' : 'lung_036.nii.gz', + 'label': 'lung_036.nii.gz', + }, + { + 'image' : 'lung_037.nii.gz', + 'boxes' : 'lung_037.nii.gz', + 'label': 'lung_037.nii.gz', + }, + { + 'image' : 'lung_038.nii.gz', + 'boxes' : 'lung_038.nii.gz', + 'label': 'lung_038.nii.gz', + }, + { + 'image' : 'lung_041.nii.gz', + 'boxes' : 'lung_041.nii.gz', + 'label': 'lung_041.nii.gz', + }, + { + 'image' : 'lung_042.nii.gz', + 'boxes' : 'lung_042.nii.gz', + 'label': 'lung_042.nii.gz', + }, + { + 'image' : 'lung_043.nii.gz', + 'boxes' : 'lung_043.nii.gz', + 'label': 'lung_043.nii.gz', + }, + { + 'image' : 'lung_044.nii.gz', + 'boxes' : 'lung_044.nii.gz', + 'label': 'lung_044.nii.gz', + }, + { + 'image' : 'lung_045.nii.gz', + 'boxes' : 'lung_045.nii.gz', + 'label': 'lung_045.nii.gz', + }, + { + 'image' : 'lung_046.nii.gz', + 'boxes' : 'lung_046.nii.gz', + 'label': 'lung_046.nii.gz', + }, + { + 'image' : 'lung_047.nii.gz', + 'boxes' : 'lung_047.nii.gz', + 'label': 'lung_047.nii.gz', + }, + { + 'image' : 'lung_048.nii.gz', + 'boxes' : 'lung_048.nii.gz', + 'label': 'lung_048.nii.gz', + }, + { + 'image' : 'lung_049.nii.gz', + 'boxes' : 'lung_049.nii.gz', + 'label': 'lung_049.nii.gz', + }, + { + 'image' : 'lung_051.nii.gz', + 'boxes' : 'lung_051.nii.gz', + 'label': 'lung_051.nii.gz', + }, + { + 'image' : 'lung_053.nii.gz', + 'boxes' : 'lung_053.nii.gz', + 'label': 'lung_053.nii.gz', + }, + { + 'image' : 'lung_054.nii.gz', + 'boxes' : 'lung_054.nii.gz', + 'label': 'lung_054.nii.gz', + }, + { + 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+ 'boxes': 'A0109_scan2.nii.gz' + 'label': 'A0109_scan2.nii.gz' + }, + { + 'image' : 'A0109_scan3.nii.gz', + 'boxes': 'A0109_scan3.nii.gz' + 'label': 'A0109_scan3.nii.gz' + }, +] \ No newline at end of file diff --git a/training/Resources/Student_Train/train.yaml b/training/Resources/Student_Train/train.yaml new file mode 100644 index 0000000000000000000000000000000000000000..cd3bc4997ef56396fe92000d8e3d713e2e36f3b0 --- /dev/null +++ b/training/Resources/Student_Train/train.yaml @@ -0,0 +1,28 @@ +device: 'cuda' + +data: + train_dataset: "/home/tumor/LungTumorSegmentation/Resources/Student_Train/data.yaml" + aug_prob: 0.1 + scale_dim: + d_0: 256 + d_1: 256 + d_2: 128 + +model: + architecture: UNet4 + loss: DiceLoss + weights: + filter_base: 32 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.000025 + +train: + max_epochs: 500 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "/home/tumor/out/metric.csv" + save_frequency: 50 + model_directory: "/home/tumor/out/models/" + steps_per_plot: 10 diff --git a/training/Resources/Test/data_inference.yaml b/training/Resources/Test/data_inference.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1dfff12158ed18724eb34d58bd3c97386e01508b --- /dev/null +++ b/training/Resources/Test/data_inference.yaml @@ -0,0 +1,15 @@ +image_prefix: "D:\\Datasets\\Task06_Lung\\imagesTr\\" +boxes_prefix: "D:\\Datasets\\Task06_Lung\\boxes\\" +label_prefix: "" + +data: + [ + { + 'image' : 'lung_001.nii\\lung_001.nii', + 'boxes' : 'lung_001.nii', + }, + { + 'image' : 'lung_003.nii\\lung_003.nii', + 'boxes' : 'lung_003.nii', + } +] diff --git a/training/Resources/Test/data_test_train.yaml b/training/Resources/Test/data_test_train.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d407562935f425d192df636b3d233af63b701748 --- /dev/null +++ b/training/Resources/Test/data_test_train.yaml @@ -0,0 +1,60 @@ +image_prefix: "D:\\Datasets\\Task06_Lung\\imagesTr\\" +boxes_prefix: "D:\\Datasets\\Task06_Lung\\boxes\\" +label_prefix: "D:\\Datasets\\Task06_Lung\\labelsTr\\" + +train: + [ + { + 'image' : 'lung_001.nii\\lung_001.nii', + 'boxes' : 'lung_001.nii', + 'label': 'lung_001.nii\\lung_001.nii' + }, + { + 'image' : 'lung_003.nii\\lung_003.nii', + 'boxes' : 'lung_003.nii', + 'label': 'lung_003.nii\\lung_003.nii' + }, + { + 'image' : 'lung_001.nii\\lung_001.nii', + 'boxes' : 'lung_001.nii', + 'label': 'lung_001.nii\\lung_001.nii' + }, + { + 'image' : 'lung_003.nii\\lung_003.nii', + 'boxes' : 'lung_003.nii', + 'label': 'lung_003.nii\\lung_003.nii' + }, + { + 'image' : 'lung_001.nii\\lung_001.nii', + 'boxes' : 'lung_001.nii', + 'label': 'lung_001.nii\\lung_001.nii' + }, + { + 'image' : 'lung_003.nii\\lung_003.nii', + 'boxes' : 'lung_003.nii', + 'label': 'lung_003.nii\\lung_003.nii' + }, + { + 'image' : 'lung_001.nii\\lung_001.nii', + 'boxes' : 'lung_001.nii', + 'label': 'lung_001.nii\\lung_001.nii' + }, + { + 'image' : 'lung_003.nii\\lung_003.nii', + 'boxes' : 'lung_003.nii', + 'label': 'lung_003.nii\\lung_003.nii' + } +] + +val: [ + { + 'image' : 'lung_081.nii\\lung_081.nii', + 'boxes' : 'lung_081.nii', + 'label': 'lung_081.nii\\lung_081.nii' + }, + { + 'image' : 'lung_003.nii\\lung_003.nii', + 'boxes' : 'lung_003.nii', + 'label': 'lung_003.nii\\lung_003.nii' + } +] \ No newline at end of file diff --git a/training/Resources/Test/test_inference.yaml b/training/Resources/Test/test_inference.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4a13951436113bb301086209f484129671a7b494 --- /dev/null +++ b/training/Resources/Test/test_inference.yaml @@ -0,0 +1,18 @@ +device: 'cuda' + +data: + dataset: "D:\\Repos\\LungTumorSegmentation\\Resources\\Test\\data_inference.yaml" + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet_filter + weights: "D:\\idun_models\\1\\model_last_128.pth" + loss: DiceLoss + filter_base: 128 + filter_expansion: 2 + +inference: + save_directory: 'D:\\Repos\\LungTumorSegmentation\\models\\' \ No newline at end of file diff --git a/training/Resources/Test/test_train.yaml b/training/Resources/Test/test_train.yaml new file mode 100644 index 0000000000000000000000000000000000000000..129b2c1a180c993703ba58c03cc513d7d8539027 --- /dev/null +++ b/training/Resources/Test/test_train.yaml @@ -0,0 +1,31 @@ +device: 'cuda' + +data: + train_dataset: ["D:\\Repos\\LungTumorSegmentation\\Resources\\Test\\data_test_train.yaml", + "D:\\Repos\\LungTumorSegmentation\\Resources\\Test\\data_test_train.yaml", + "D:\\Repos\\LungTumorSegmentation\\Resources\\Test\\data_test_train.yaml"] + aug_prob: 0.0 + scale_dim: + d_0: 64 + d_1: 64 + d_2: 64 + +model: + architecture: UNet_monai + loss: DiceLoss + weights: + filter_base: 32 + filter_expansion: 2 + filters: [2, 3, 4, 5] + optimizer: + name: 'Adam' + lr: 0.001 + +train: + max_epochs: 3 + val_frequency: 1 + output_threshold: 0.5 + metric_path: "D:\\Repos\\LungTumorSegmentation\\metrics.csv" + save_frequency: 5 + model_directory: "D:\\Repos\\LungTumorSegmentation\\models\\" + batch_size: 3 \ No newline at end of file diff --git a/training/Resources/Windows_Files/evaluate_data.yaml b/training/Resources/Windows_Files/evaluate_data.yaml new file mode 100644 index 0000000000000000000000000000000000000000..e41ecf9245cab0b626c961386e908aedcc2220b1 --- /dev/null +++ b/training/Resources/Windows_Files/evaluate_data.yaml @@ -0,0 +1,41 @@ +image_prefix: "D:\\Datasets\\Task06_Lung\\imagesTr\\" +boxes_prefix: "D:\\Datasets\\Task06_Lung\\boxes\\" +label_prefix: "D:\\Datasets\\Task06_Lung\\labelsTr\\" + +data: [ + { + 'image' : 'lung_092.nii\\lung_092.nii', + 'boxes' : 'lung_092.nii', + 'label' : 'lung_092.nii\\lung_092.nii' + }, + { + 'image' : 'lung_093.nii\\lung_093.nii', + 'boxes' : 'lung_093.nii', + 'label' : 'lung_093.nii\\lung_093.nii' + }, + { + 'image' : 'lung_095.nii\\lung_095.nii', + 'boxes' : 'lung_095.nii', + 'label' : 'lung_095.nii\\lung_095.nii' + }, + { + 'image' : 'lung_081.nii\\lung_081.nii', + 'boxes' : 'lung_081.nii', + 'label' : 'lung_081.nii\\lung_081.nii' + }, + { + 'image' : 'lung_083.nii\\lung_083.nii', + 'boxes' : 'lung_083.nii', + 'label' : 'lung_083.nii\\lung_083.nii' + }, + { + 'image' : 'lung_084.nii\\lung_084.nii', + 'boxes' : 'lung_084.nii', + 'label' : 'lung_084.nii\\lung_084.nii' + }, + { + 'image' : 'lung_086.nii\\lung_086.nii', + 'boxes' : 'lung_086.nii', + 'label' : 'lung_086.nii\\lung_086.nii' + } +] \ No newline at end of file diff --git a/training/Resources/Windows_Files/evaluate_data_msd.yaml b/training/Resources/Windows_Files/evaluate_data_msd.yaml new file mode 100644 index 0000000000000000000000000000000000000000..680bee472179eb26643bca4991df478602dd2f75 --- /dev/null +++ b/training/Resources/Windows_Files/evaluate_data_msd.yaml @@ -0,0 +1,41 @@ +image_prefix: "D:\\Datasets\\MSD_Cropped\\MSD_Cropped\\Images\\" +boxes_prefix: "D:\\Datasets\\MSD_Cropped\\MSD_Cropped\\Boxes\\" +label_prefix: "D:\\Datasets\\MSD_Cropped\\MSD_Cropped\\Labels\\" + +data: [ + { + 'image' : 'lung_092.nii', + 'boxes' : 'lung_092.nii', + 'label' : 'lung_092.nii' + }, + { + 'image' : 'lung_093.nii', + 'boxes' : 'lung_093.nii', + 'label' : 'lung_093.nii' + }, + { + 'image' : 'lung_095.nii', + 'boxes' : 'lung_095.nii', + 'label' : 'lung_095.nii' + }, + { + 'image' : 'lung_081.nii', + 'boxes' : 'lung_081.nii', + 'label' : 'lung_081.nii' + }, + { + 'image' : 'lung_083.nii', + 'boxes' : 'lung_083.nii', + 'label' : 'lung_083.nii' + }, + { + 'image' : 'lung_084.nii', + 'boxes' : 'lung_084.nii', + 'label' : 'lung_084.nii' + }, + { + 'image' : 'lung_086.nii', + 'boxes' : 'lung_086.nii', + 'label' : 'lung_086.nii' + } +] \ No newline at end of file diff --git a/training/Resources/Windows_Files/win_eval.yaml b/training/Resources/Windows_Files/win_eval.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7ffd4bc3ff87c8807c87a3cc348e6b1c324cd39a --- /dev/null +++ b/training/Resources/Windows_Files/win_eval.yaml @@ -0,0 +1,23 @@ +device: 'cuda' + +data: + train_dataset: "D:\\Repos\\LungTumorSegmentation\\Resources\\Windows_Files\\evaluate_data.yaml" + scale_dim: + d_0: 128 + d_1: 128 + d_2: 128 + +model: + architecture: UNet_test + weights: "D:\\idun_models\\3\\m_test.pth" + loss: DiceLoss + filter_base: 32 + filter_expansion: 2 + optimizer: + name: 'Adam' + lr: 0.01 + +evaluate: + save_segmentations: True + save_directory: 'D:\\Repos\\LungTumorSegmentation\\m_128\\' + output_threshold: 0.5 \ No newline at end of file diff --git a/training/Resources/requirements.txt b/training/Resources/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..632b686f2a684a04e645a5f171174589b47a2505 --- /dev/null +++ b/training/Resources/requirements.txt @@ -0,0 +1,10 @@ +numpy +SimpleITK +argparse +glob2 +monai +torch +pyyaml +python-csv +matplotlib +nibabel diff --git a/training/Runable/Evaluate/eval.py b/training/Runable/Evaluate/eval.py new file mode 100644 index 0000000000000000000000000000000000000000..de9bbe949eedd7bcf9cd7953ab88c7916ab29ab7 --- /dev/null +++ b/training/Runable/Evaluate/eval.py @@ -0,0 +1,4 @@ +from Engine.evaluate import initiate + +if __name__ == "__main__": + initiate("D:\\Repos\\LungTumorSegmentation\\Resources\\Windows_Files\\win_eval.yaml") \ No newline at end of file diff --git a/training/Runable/Evaluate/eval_malvik.py b/training/Runable/Evaluate/eval_malvik.py new file mode 100644 index 0000000000000000000000000000000000000000..ddcdd76d8dcc371a4a7ade97887df1f20708c37a --- /dev/null +++ b/training/Runable/Evaluate/eval_malvik.py @@ -0,0 +1,4 @@ +from Engine.inference import initiate + +if __name__ == "__main__": + initiate("/home/tumor/LungTumorSegmentation/Resources/Evaluate/malvik.yaml") diff --git a/training/Runable/Inference/inference.py b/training/Runable/Inference/inference.py new file mode 100644 index 0000000000000000000000000000000000000000..7a9b28398e068d86eb83d30bde70bc5a180ee316 --- /dev/null +++ b/training/Runable/Inference/inference.py @@ -0,0 +1,4 @@ +from Engine.inference import initiate + +if __name__ == "__main__": + initiate("/home/tumor/LungTumorSegmentation/Resources/Inference/malvik.yaml") diff --git a/training/Runable/Test/inf_test.py b/training/Runable/Test/inf_test.py new file mode 100644 index 0000000000000000000000000000000000000000..555ade1762b5a048e6cc08a442e80d8a8b2d569c --- /dev/null +++ b/training/Runable/Test/inf_test.py @@ -0,0 +1,4 @@ +from Engine.inference import initiate + +if __name__ == "__main__": + initiate("D:\\Repos\\LungTumorSegmentation\\Resources\\Test\\test_inference.yaml") \ No newline at end of file diff --git a/training/Runable/Test/test_sevlus.py b/training/Runable/Test/test_sevlus.py new file mode 100644 index 0000000000000000000000000000000000000000..2f1ef7a0d2d20d1bce5ece48f49970c1e2651c8d --- /dev/null +++ b/training/Runable/Test/test_sevlus.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("D:\\Repos\\LungTumorSegmentation\\Resources\\Test\\test_train.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_16.py b/training/Runable/Train/train_16.py new file mode 100644 index 0000000000000000000000000000000000000000..69a416825befb494e38a40f93fc8598ac735d458 --- /dev/null +++ b/training/Runable/Train/train_16.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_16.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_25.py b/training/Runable/Train/train_25.py new file mode 100644 index 0000000000000000000000000000000000000000..8f19f02d3222bfbccaf193f13d1523bbb6aebab3 --- /dev/null +++ b/training/Runable/Train/train_25.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/train_25.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_32.py b/training/Runable/Train/train_32.py new file mode 100644 index 0000000000000000000000000000000000000000..8e5133c98a4aeb8c4df3e72e5f7a5b083a0f4336 --- /dev/null +++ b/training/Runable/Train/train_32.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_32.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_48.py b/training/Runable/Train/train_48.py new file mode 100644 index 0000000000000000000000000000000000000000..8a39bbd78faf8e8040fe8d97961f719c16c971e7 --- /dev/null +++ b/training/Runable/Train/train_48.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_48.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_50.py b/training/Runable/Train/train_50.py new file mode 100644 index 0000000000000000000000000000000000000000..9cd8ddc825feff13099acd39a9faa13a17b9c9d2 --- /dev/null +++ b/training/Runable/Train/train_50.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/train_50.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_64.py b/training/Runable/Train/train_64.py new file mode 100644 index 0000000000000000000000000000000000000000..851208b74f7672b9e1cb50baf5d8cd75607887a6 --- /dev/null +++ b/training/Runable/Train/train_64.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_64.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_75.py b/training/Runable/Train/train_75.py new file mode 100644 index 0000000000000000000000000000000000000000..97eb6d690311dcde3538a490119a2da5f00a0b19 --- /dev/null +++ b/training/Runable/Train/train_75.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/train_75.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_focal.py b/training/Runable/Train/train_focal.py new file mode 100644 index 0000000000000000000000000000000000000000..5db800baa03febea51195b43325fb1d4b2381098 --- /dev/null +++ b/training/Runable/Train/train_focal.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_focal.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_full_images.py b/training/Runable/Train/train_full_images.py new file mode 100644 index 0000000000000000000000000000000000000000..98ae4417f3e5a4efc6aa3d6d512632628c3e4352 --- /dev/null +++ b/training/Runable/Train/train_full_images.py @@ -0,0 +1,4 @@ +from Engine.train_teacher import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/train_full_filter_full_image.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_half_filter.py b/training/Runable/Train/train_half_filter.py new file mode 100644 index 0000000000000000000000000000000000000000..58e954491a8447fea6ad1c8977e514e4583fcd9f --- /dev/null +++ b/training/Runable/Train/train_half_filter.py @@ -0,0 +1,4 @@ +from Engine.train_teacher import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/train_half_filter_cropped.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_student.py b/training/Runable/Train/train_student.py new file mode 100644 index 0000000000000000000000000000000000000000..20fd34621e88d2a933d75fe3ea7df98b5484acb9 --- /dev/null +++ b/training/Runable/Train/train_student.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/home/tumor/LungTumorSegmentation/Resources/Student_Train/train.yaml") diff --git a/training/Runable/Train/train_tver.py b/training/Runable/Train/train_tver.py new file mode 100644 index 0000000000000000000000000000000000000000..754c2538b13136a7f19d402b96c4d35204e33f96 --- /dev/null +++ b/training/Runable/Train/train_tver.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_tversky.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_ud.py b/training/Runable/Train/train_ud.py new file mode 100644 index 0000000000000000000000000000000000000000..9105e383bc14e75e940ff32432c7c47dd0d28d85 --- /dev/null +++ b/training/Runable/Train/train_ud.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_ud.yaml") \ No newline at end of file diff --git a/training/Runable/Train/train_us.py b/training/Runable/Train/train_us.py new file mode 100644 index 0000000000000000000000000000000000000000..d50190c127c637b08b33fb42802f0edf32797a41 --- /dev/null +++ b/training/Runable/Train/train_us.py @@ -0,0 +1,4 @@ +from Engine.train import initiate + +if __name__ == "__main__": + initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_us.yaml") \ No newline at end of file diff --git a/training/Runable/__init__.py b/training/Runable/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/training/Utils/MSD_utilities.py b/training/Utils/MSD_utilities.py new file mode 100644 index 0000000000000000000000000000000000000000..1c51afeb2251d1bec0017ac7d238db1ff4d2e014 --- /dev/null +++ b/training/Utils/MSD_utilities.py @@ -0,0 +1,28 @@ +import glob +import platform + +directory_split = "\\" if platform.system() == "Windows" else "/" + + +def generate_training_data(save_location, msd_directory, target_platform): + target_split = "\\\\" if target_platform.lower() == "windows" else "/" + with open(save_location, 'w+') as f: + print(msd_directory) + str = "image_prefix: \"\"\nlabel_prefix: \"\"\ntrain:\n\t[\n".replace("\t", " ") + f.write(str) + for file in sorted(glob.glob(msd_directory+f"{directory_split}Images{directory_split}*")): + print(file) + name = file.split('\\')[-1] + f.write("\t\t{\n".replace("\t", " ") + f"\t\t\t'image' : '{file.split(directory_split)[-1]}', \n\t\t\t'label': '{file.split(directory_split)[-1]}', \n\t\t\t'boxes': '{file.split(directory_split)[-1]}'".replace("\t", " ") + "\n\t\t},\n".replace("\t", " ")) + + f.write('\n]') + + f.write("\nval : []") + + + + +if __name__ == "__main__": + path = "/home/tumor/data/LungDx-Lung/" + + generate_training_data(path + "/lungdx_dataset.yaml", path, "linux") diff --git a/training/Utils/PETCT_LungDx_utilities.py b/training/Utils/PETCT_LungDx_utilities.py new file mode 100644 index 0000000000000000000000000000000000000000..02524381286107d969568fcd05a909cecc197833 --- /dev/null +++ b/training/Utils/PETCT_LungDx_utilities.py @@ -0,0 +1,147 @@ +import pydicom as dicomio +import SimpleITK as sitk +import glob +import xml.etree.ElementTree as ET +import platform +import numpy as np +import nibabel + +directory_split = "\\" if platform.system() == "Windows" else "/" + +def get_length(number_of_slices, thickness): + return (number_of_slices * thickness) / 10 + +def convert_to_nifti(dicom_folder, save_path): + image = [] + voxel_spacing = None + origin = None + + for dcm_f in glob.glob(dicom_folder + f"{directory_split}*.dcm"): + dicom = dicomio.read_file(dcm_f, force=True) + + if(dicom.Modality != 'CT' or hasattr(dicom, 'SecondaryCaptureDeviceID')): + return False + + layer = dicom.pixel_array + + layer = layer.astype('float32') + layer *= dicom.RescaleSlope + layer += dicom.RescaleIntercept + + origin = dicom.ImagePositionPatient + if(type(dicom) == dicomio.FileDataset): + voxel_spacing = [dicom.PixelSpacing[0], dicom.PixelSpacing[1], dicom.SliceThickness] + else: + voxel_spacing = [dicom.PixelSpacing[0], dicom.PixelSpacing[1], dicom.SpacingBetweenSlices] + + image.append(layer) + + affine = np.zeros((4,4)) + affine[0][0] = voxel_spacing[0] * origin[0]/np.abs(origin[0]) + affine[0][-1] = origin[0] * origin[0]/np.abs(origin[0]) + + affine[1][1] = voxel_spacing[1] * origin[1]/np.abs(origin[1]) + affine[1][-1] = origin[1] * origin[1]/np.abs(origin[1]) + + affine[2][2] = voxel_spacing[2] + affine[2][-1] = origin[2] + affine[-1][-1] = 1 + + image.reverse() + nifti = nibabel.Nifti1Image(np.swapaxes(np.array(image),0,2), affine) + + nifti.update_header() + if(get_length(len(image), voxel_spacing[-1]) > 16 and get_length(len(image), voxel_spacing[-1]) < 60): + nibabel.save(nifti, save_path) + + return True + return False + +def generate_segbox(annotations, dicom_folder, save_path): + image = [] + keys = annotations.keys() + + voxel_spacing = None + origin = None + + for dcm_f in glob.glob(dicom_folder + f"{directory_split}*.dcm"): + + dicom = dicomio.read_file(dcm_f, force=True) + origin = dicom.ImagePositionPatient + if(type(dicom) == dicomio.FileDataset): + voxel_spacing = [dicom.PixelSpacing[0], dicom.PixelSpacing[1], dicom.SliceThickness] + else: + voxel_spacing = [dicom.PixelSpacing[0], dicom.PixelSpacing[1], dicom.SpacingBetweenSlices] + uid = dicom.SOPInstanceUID + layer = np.zeros(dicom.pixel_array.shape) + if(uid in keys): + bndbox = annotations[uid] + layer[bndbox[1] - 1:bndbox[3], bndbox[0] - 1:bndbox[2]] = 1 + image.append(layer) + + affine = np.zeros((4,4)) + affine[0][0] = voxel_spacing[0] * origin[0]/np.abs(origin[0]) + affine[0][-1] = origin[0] * origin[0]/np.abs(origin[0]) + + affine[1][1] = voxel_spacing[1] * origin[1]/np.abs(origin[1]) + affine[1][-1] = origin[1] * origin[1]/np.abs(origin[1]) + + affine[2][2] = voxel_spacing[2] + affine[2][-1] = origin[2] + affine[-1][-1] = 1 + + image.reverse() + nifti = nibabel.Nifti1Image(np.swapaxes(np.array(image),0,2), affine) + + nifti.update_header() + if(get_length(len(image), voxel_spacing[-1]) > 20 and get_length(len(image), voxel_spacing[-1]) < 60): + nibabel.save(nifti, save_path) + +def load_annotations(folder): + annotations = {} + for file in glob.glob(folder + f"{directory_split}*.xml"): + annotations[file.replace('.xml', '').split(directory_split)[-1]] = extract_boundingbox(file) + + return annotations + +def extract_boundingbox(file_path): + try: + tree = ET.parse(file_path) + root = tree.getroot() + bndbox_xml = tree.findall('*/bndbox')[0] + + xmin = float(bndbox_xml.find('xmin').text) + ymin = float(bndbox_xml.find('ymin').text) + xmax = float(bndbox_xml.find('xmax').text) + ymax = float(bndbox_xml.find('ymax').text) + + return (int(xmin), int(ymin), int(xmax), int(ymax)) + except: + return (0, 0, 0, 0) + + +def convert_nsclc_petct(annotations_folder, nsclc_folder, label_folder, input_folder): + patient_folders = glob.glob(nsclc_folder + f"{directory_split}*") + for annotation_folder in glob.glob(annotations_folder + f"{directory_split}*"): + patient = annotation_folder.split(directory_split)[-1] + patient_folder = [p for p in patient_folders if patient in p][0] + annotations = load_annotations(annotation_folder) + + scan_number = 1 + for examination_folder in glob.glob(patient_folder + f"{directory_split}*"): + for scan_folder in glob.glob(examination_folder + f"{directory_split}*"): + print(f"Converting {scan_folder}") + if(convert_to_nifti(scan_folder, f"{input_folder}{directory_split}{patient}_scan{scan_number}.nii.gz")): + generate_segbox(annotations, scan_folder, f"{label_folder}{directory_split}{patient}_scan{scan_number}.nii.gz") + print(f"Saved {patient}_scan{scan_number}.nii.gz") + scan_number += 1 + + + +if __name__ == "__main__": + #pass + annotations = "D:\\Datasets\\NSCLC-Lung-PET-CT\\Temp\\Annotations\\" + nsclcs_folder = "D:\\Datasets\\NSCLC-Lung-PET-CT\\Temp\Patients\\" + labels = "D:\\Datasets\\NSCLC-Lung-PET-CT\\Temp\\Boxes\\" + inputs = "D:\\Datasets\\NSCLC-Lung-PET-CT\\Temp\\Images\\" + convert_nsclc_petct(annotations, nsclcs_folder, labels, inputs) \ No newline at end of file diff --git a/training/Utils/__init__.py b/training/Utils/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/training/Utils/conv_to_win.py b/training/Utils/conv_to_win.py new file mode 100644 index 0000000000000000000000000000000000000000..52a8745db6864bd620175ff2913b341bfb618a2e --- /dev/null +++ b/training/Utils/conv_to_win.py @@ -0,0 +1,35 @@ +def win_ops(): + data = "" + + with open("D:\\Repos\\LungTumorSegmentation\\Resources\\train_data_win.yaml", "r") as f: + data = f.read() + + data_split = data.split("label") + new_data = "" + ds = [] + for i in data_split[3:]: + ds.append(i.split(",")[0].split("\\")[2].split("'")[0]) + + for n, i in enumerate(data_split[2:]): + new_data += i + if (n < 63): + new_data += f"boxes' : '{ds[n]}',\n 'label" + + with open("D:\\Repos\\LungTumorSegmentation\\Resources\\train_data_win_with_boxes.yaml", "w+") as f: + f.write(new_data) + +def ub_ops(): + data = "" + + with open("D:\\Repos\\LungTumorSegmentation\\Resources\\train_data_win_with_boxes.yaml", "r") as f: + data = f.read() + + data = data.replace("\\" + "\\", "/") + + with open("D:\\Repos\\LungTumorSegmentation\\Resources\\train_data_with_boxes.yaml", "w+") as f: + f.write(data) + + +if __name__ == "__main__": + ub_ops() + diff --git a/training/Utils/crop.py b/training/Utils/crop.py new file mode 100644 index 0000000000000000000000000000000000000000..3aebcf9285dfe8b6225e4b648df38bad4e594b91 --- /dev/null +++ b/training/Utils/crop.py @@ -0,0 +1,211 @@ +import glob +import platform +import nibabel +import os +import numpy as np +import torch +from monai.transforms import Compose, Spacingd, ToTensord, LoadImaged, AddChanneld, ThresholdIntensityd, LoadImage, ScaleIntensityRanged, NormalizeIntensityd +from monai.data import NiftiSaver +from segment_to_segmentbox import generate_segmentbox +import pickle +from Logger.loggingservice import Logger + +logger = Logger("http://82.194.207.154:5000/api/log", "XqnJHdalUd") + +directory_split = "\\" if platform.system() == "Windows" else "/" + +voxel_normalizer = Compose( + [ + LoadImaged(keys=['image', 'boxes', 'label']), + ThresholdIntensityd(keys=['image'], above = False, threshold = 1000, cval = 1000), + ThresholdIntensityd(keys=['image'], above = True, threshold = -1024, cval = -1024), + AddChanneld(keys=['image', 'boxes', 'label']), + Spacingd(keys=['image', 'boxes', 'label'], pixdim=(0.7, 0.7, 0.7)), + #ScaleIntensityRanged(keys=['image'], a_min=-1024, a_max=400, b_min=-1, b_max=1), + NormalizeIntensityd(keys=['image']), + ThresholdIntensityd(keys=['boxes'], above = False, threshold = 0.5, cval = 1), + ThresholdIntensityd(keys=['boxes'], above = True, threshold = 0.5, cval = 0), + ToTensord(keys=['image', 'boxes', 'label']) + ] + ) + +# voxel_normalizer = Compose( +# [ +# LoadImaged(keys=['label']), +# AddChanneld(keys=['label']), +# Spacingd(keys=['label'], pixdim=(0.7, 0.7, 0.7)), +# ToTensord(keys=['label']) +# ] +# ) + + +def crop(image, center, dimensions): + #holder = np.zeros(shape=dimensions) + holder = np.full(dimensions, -1).astype(np.float32) + + crop = image[(center[0]-int(dimensions[0]/2)):center[0]+int(dimensions[0]/2), + (center[1]-int(dimensions[1]/2)):center[1]+int(dimensions[1]/2), + (center[2]-int(dimensions[2]/2)):center[2]+int(dimensions[2]/2)] + + #return crop + holder[:crop.shape[0], :crop.shape[1], : crop.shape[2]] = crop + return holder + +def find_center(box_array): + + z_min = -1 + z_max = 0 + y_min = float('inf') + y_max = 0 + x_min = float('inf') + x_max = 0 + + + box_array = box_array.swapaxes(0, 2) + for i, layer in enumerate(box_array): + if(np.amax(layer) < 1): + continue + if(z_min == -1): + z_min = i + z_max = i + + y = np.any(layer, axis = 1) + x = np.any(layer, axis = 0) + y_minl, y_maxl = np.argmax(y) + 1, layer.shape[0] - np.argmax(np.flipud(y)) + x_minl, x_maxl = np.argmax(x) + 1, layer.shape[1] - np.argmax(np.flipud(x)) + + if(y_minl < y_min): + y_min = y_minl + if(x_minl < x_min): + x_min = x_minl + if(y_maxl > y_max): + y_max = y_maxl + if(x_maxl > x_max): + x_max = x_maxl + + return x_min + int((x_max - x_min)/2), y_min + int((y_max - y_min)/2), z_min + int((z_max - z_min)/2) + +def crop_and_store(root_folder, save_folder): + #os.mkdir(f"{save_folder}{directory_split}Images") + #os.mkdir(f"{save_folder}{directory_split}Boxes") + #os.mkdir(f"{save_folder}{directory_split}Labels") + + image_directory = f'{root_folder}{directory_split}Images{directory_split}' + box_directory = f'{root_folder}{directory_split}Boxes{directory_split}' + label_directory = f'{root_folder}{directory_split}Labels{directory_split}' + + crop_corner_dict = {} + + for box_file in glob.glob(f'{box_directory}*'): + file_name = box_file.split(directory_split)[-1] + print(f"Processing {file_name}") + + data = [{'image' : f"{image_directory}{file_name}", 'boxes' : f"{box_directory}{file_name}", 'label': f"{label_directory}{file_name}"}] + + #imloader = LoadImage() + #org_box_shape = imloader(data[0]['boxes'])[0].shape + + data = voxel_normalizer(data) + + + box = nibabel.load(f"{box_directory}{file_name}") + new_box_arr = torch.nn.functional.interpolate(torch.Tensor(box.get_fdata()).unsqueeze(0).unsqueeze(0), + data[0]['image'].numpy().shape[1:], mode='trilinear', align_corners = False).squeeze(0).squeeze(0) + new_box_arr[new_box_arr < 0.5] = 0 + new_box_arr[new_box_arr >= 0.5] = 1 + #new_box_arr = + + #new_box_arr = data[0]['boxes'].squeeze() + try: + center = find_center(np.copy(new_box_arr.numpy())) + except: + print(f"Couldnt calculate center of {file_name}") + continue + + + centered_image = crop(data[0]['image'].squeeze(0).numpy(), center, (128, 128, 128)) + #centered_box = crop(data[0]['boxes'].squeeze(0).numpy(), center, (128, 128, 128)) + centered_box = crop(new_box_arr, center, (128, 128, 128)) + centered_label = crop(data[0]['label'].squeeze(0).numpy(), center, (128, 128, 128)) + centered_label[centered_label >= 0.5] = 1 + centered_label[centered_label < 0.5] = 0 + #centered_box = generate_segmentbox(np.copy(centered_label)) + #centered_box[centered_box < 0.5] = 0 + #centered_box[centered_box > 0.5] = 1 + + + affine = data[0]['image_meta_dict']['affine'] + + box_nifti = nibabel.Nifti1Image(centered_box, affine) + image_nifti = nibabel.Nifti1Image(centered_image, affine) + label_nifti = nibabel.Nifti1Image(centered_label, affine) + + nibabel.save(box_nifti, f"{save_folder}{directory_split}Boxes{directory_split}{file_name}") + nibabel.save(image_nifti, f"{save_folder}{directory_split}Images{directory_split}{file_name}") + nibabel.save(label_nifti, f"{save_folder}{directory_split}Labels{directory_split}{file_name}") + + org_box_shape = box.get_fdata().shape + crop_corner_dict[file_name] = (center, data[0]['image'].squeeze(0).numpy().shape, org_box_shape) + print(f"Saving {file_name}") + + + pickle.dump(crop_corner_dict, open( f"{save_folder}{directory_split}crop_reference.bin", "wb" )) + +def inject_image(holder, image, corner): + + x_max = min(corner[0]+image.shape[0], holder.shape[0]) + y_max = min(corner[1]+image.shape[1], holder.shape[1]) + z_max = min(corner[2]+image.shape[2], holder.shape[2]) + + x_imslice = corner[0]+image.shape[0] - x_max + y_imslice = corner[1]+image.shape[1] - y_max + z_imslice = corner[2]+image.shape[2] - z_max + + holder[corner[0]:x_max, corner[1]:y_max, corner[2]: z_max] = image[:image.shape[0] - x_imslice, :image.shape[1] - y_imslice, :image.shape[2] - z_imslice] + return holder + +def calculate_corner(imputation_shape, center_in_holder): + x = center_in_holder[0] - imputation_shape[0]/2 + y = center_in_holder[1] - imputation_shape[1]/2 + z = center_in_holder[2] - imputation_shape[2]/2 + return (int(x), int(y), int(z)) + +def load_and_relocate(reference_file, segment_folder, store_folder): + + ref_dict = pickle.load(open(reference_file, 'rb')) + + logger.LogInfo("Starting load and relocate", []) + for image_file in glob.glob(f"{segment_folder}{directory_split}*.nii.gz"): + try: + file_name = image_file.split(directory_split)[-1] + references = ref_dict[file_name[4:]] + + holder = np.zeros(shape=references[1]) + nib = nibabel.load(image_file) + image = nib.get_fdata() + corner = calculate_corner(image.shape, references[0]) + injected = inject_image(holder, image, corner) + + injected = torch.nn.functional.interpolate(torch.Tensor(injected).unsqueeze(0).unsqueeze(0), size=references[-1], mode='trilinear').squeeze(0).squeeze(0) + injected[injected >= 0.5] = 1 + injected[injected < 0.5] = 0 + injected = injected.numpy() + nifti = nibabel.Nifti1Image(injected, nib.affine) + nibabel.save(nifti, f"{save_folder}{directory_split}{file_name}") + + print(file_name) + except: + logger.LogWarning(f"Failed relocate", [image_file]) + + + +if __name__ == "__main__": + + crop_and_store("D:\\Datasets\\Temp\\", "D:\\Datasets\\Temp\\Save\\") + + #ref = "/home/tumor/data/LungDx-Tumor/crop_reference.bin" + #segment_folder = "/home/tumor/data/LungDx-Tumor/Labels/" + #save_folder = "/home/tumor/data/LungDx-Full/Labels/" + + #load_and_relocate(ref, segment_folder, save_folder) + #logger.LogMilestone("Finished relocating", []) diff --git a/training/Utils/crop_lungs.py b/training/Utils/crop_lungs.py new file mode 100644 index 0000000000000000000000000000000000000000..9eea4f23651a5e24c9349cdf342a4f1542dacd44 --- /dev/null +++ b/training/Utils/crop_lungs.py @@ -0,0 +1,196 @@ +from lungmask import mask +import lungmask +import SimpleITK as sitk +import numpy as np +import nibabel +import platform +import glob +import torch +import skimage +from tqdm import tqdm +from monai.transforms import Compose, LoadImaged, ToTensord, Spacingd, DivisiblePadd, SpatialCropd, ToNumpyd, AddChanneld, SqueezeDimd, Resized, Flipd, Rotate90d, NormalizeIntensityd, ThresholdIntensityd +from Logger.loggingservice import Logger + +logger = Logger("http://82.194.207.154:5000/api/log", "XqnJHdalUd") +directory_split = "\\" if platform.system() == "Windows" else "/" + + +def find_probable_air_value(image): + holder = np.copy(image) + min_val = np.amin(holder) + holder[holder == min_val] = float('inf') + return np.amin(holder), min_val + +def mask_lung(scan_dict, batch_size=20): + model = lungmask.mask.get_model('unet', 'R231') + device = torch.device('cuda') + model.to(device) + + transformer = Compose( + [ + LoadImaged(keys=['image']), + ToNumpyd(keys=['image']), + ] + ) + + scan_read = transformer(scan_dict) + inimg_raw = scan_read['image'].swapaxes(0,2) + + tvolslices, xnew_box = lungmask.utils.preprocess(inimg_raw, resolution=[256, 256]) + tvolslices[tvolslices > 600] = 600 + tvolslices = np.divide((tvolslices + 1024), 1624) + + torch_ds_val = lungmask.utils.LungLabelsDS_inf(tvolslices) + dataloader_val = torch.utils.data.DataLoader(torch_ds_val, batch_size=batch_size, shuffle=False, num_workers=1, + pin_memory=False) + + timage_res = np.empty((np.append(0, tvolslices[0].shape)), dtype=np.uint8) + + with torch.no_grad(): + for X in tqdm(dataloader_val): + X = X.float().to(device) + prediction = model(X) + pls = torch.max(prediction, 1)[1].detach().cpu().numpy().astype(np.uint8) + timage_res = np.vstack((timage_res, pls)) + + outmask = lungmask.utils.postrocessing(timage_res) + + + outmask = np.asarray( + [lungmask.utils.reshape_mask(outmask[i], xnew_box[i], inimg_raw.shape[1:]) for i in range(outmask.shape[0])], + dtype=np.uint8) + + outmask = np.swapaxes(outmask, 0, 2) + #outmask = np.flip(outmask, 0) + + + return outmask.astype(np.uint8), scan_read['image_meta_dict']['affine'] + +def segment_lung(image_path): + sitk_image = sitk.ReadImage(image_path) + segmentation = mask.apply(sitk_image, batch_size = 5, model = mask.get_model('unet', 'R231')) + return segmentation + +def calculate_extremes(image, annotation_value): + + holder = np.copy(image) + + x_min = float('inf') + x_max = 0 + y_min = float('inf') + y_max = 0 + z_min = -1 + z_max = 0 + + holder[holder != annotation_value] = 0 + + holder = np.swapaxes(holder, 0, 2) + for i, layer in enumerate(holder): + if(np.amax(layer) < 1): + continue + if(z_min == -1): + z_min = i + z_max = i + + y = np.any(layer, axis = 1) + x = np.any(layer, axis = 0) + y_minl, y_maxl = np.argmax(y) + 1, layer.shape[0] - np.argmax(np.flipud(y)) + x_minl, x_maxl = np.argmax(x) + 1, layer.shape[1] - np.argmax(np.flipud(x)) + + if(y_minl < y_min): + y_min = y_minl + if(x_minl < x_min): + x_min = x_minl + if(y_maxl > y_max): + y_max = y_maxl + if(x_maxl > x_max): + x_max = x_maxl + + return ((x_min, x_max), (y_min, y_max), (z_min, z_max)) + +def process_lung_scan(scan_dict, save_directory, extremes, lung): + + load_transformer = Compose( + [ + LoadImaged(keys=["image", "label", "boxes"]), + ThresholdIntensityd(keys=['image'], above = False, threshold = 1000, cval = 1000), + ThresholdIntensityd(keys=['image'], above = True, threshold = -1024, cval = -1024), + AddChanneld(keys=["image", "label", "boxes"]), + NormalizeIntensityd(keys=["image"]), + SpatialCropd(keys=["image", "label", "boxes"], roi_start=(extremes[0][0], extremes[1][0], extremes[2][0]), roi_end=(extremes[0][1], extremes[1][1], extremes[2][1])), + Spacingd(keys=["image"], pixdim=(1, 1, 1.5)), + ] + ) + + processed_1 = load_transformer(scan_dict) + if(np.amax(processed_1['label'][0]) == 0): + return + + transformer_1 = Compose( + [ + Resized(keys=["label", "boxes"], spatial_size=processed_1['image'].shape[1:]), + ThresholdIntensityd(keys=['boxes', 'label'], above = False, threshold = 0.5, cval = 1), + ThresholdIntensityd(keys=['boxes', 'label'], above = True, threshold = 0.5, cval = 0), + DivisiblePadd(keys=["image", "label", "boxes"], k=16, mode='symmetric'), + SqueezeDimd(keys=["image", "label", "boxes"], dim = 0), + ToNumpyd(keys=["image", "label", "boxes"]), + ] + ) + + processed_2 = transformer_1(processed_1) + + affine = processed_1['image_meta_dict']['affine'] + filename = scan_dict['image'].split(directory_split)[-1].split('.')[0] + filename_extension = '.' + '.'.join(scan_dict['image'].split(directory_split)[-1].split('.')[1:]) + + normalized_image = processed_2['image'] + image_save = nibabel.Nifti1Image(normalized_image, affine) + boxes_save = nibabel.Nifti1Image(processed_2['boxes'], affine) + label_save = nibabel.Nifti1Image(processed_2['label'], affine) + nibabel.save(image_save, f"{save_directory}{directory_split}Images{directory_split}{filename}_{lung}{filename_extension}") + nibabel.save(boxes_save, f"{save_directory}{directory_split}Boxes{directory_split}{filename}_{lung}{filename_extension}") + nibabel.save(label_save, f"{save_directory}{directory_split}Labels{directory_split}{filename}_{lung}{filename_extension}") + +passed = 0 +def process_scan(scan_dict, save_directory): + global passed + try: + masked, affine = mask_lung(scan_dict, batch_size=5) + #s = nibabel.Nifti1Image(masked, affine) + #nibabel.save(s, "D:\\Datasets\\Temp\\Images\\test4.nii.gz") + extremes = calculate_extremes(np.copy(masked), 1) + process_lung_scan(scan_dict, save_directory, extremes, "right") + extremes = calculate_extremes(masked, 2) + process_lung_scan(scan_dict, save_directory, extremes, "left") + except: + passed += 1 + logger.LogWarning("Skipped scan", [str(scan_dict)]) + print(f"passed {passed}") + + + + +def process_directory(directory, save_directory): + for image_file in glob.glob(f"{directory}{directory_split}Images{directory_split}*.nii.gz"): + filename = image_file.split(directory_split)[-1] + + scan_dict = { + 'image' : image_file, + 'label' : f"{directory}{directory_split}Labels{directory_split}{filename}", + 'boxes' : f"{directory}{directory_split}Boxes{directory_split}{filename}" + } + + print(f"Processing {filename}") + process_scan(scan_dict, save_directory) + +if __name__ == "__main__": + load_folder = "/home/tumor/data/MSD/" + store_folder = "/home/tumor/data/MSD-Lung/" + #load_folder = "D:\\Datasets\\Temp\\" + #store_folder = "D:\\Datasets\\Temp\\Save\\" + logger.LogInfo("Started cropping lungs", []) + process_directory(load_folder, store_folder) + logger.LogMilestone("Finished cropping lungs!", []) + + + diff --git a/training/Utils/fileconverter.py b/training/Utils/fileconverter.py new file mode 100644 index 0000000000000000000000000000000000000000..cd2b96767c832bbf9efd8cf05a3a35aa513adef9 --- /dev/null +++ b/training/Utils/fileconverter.py @@ -0,0 +1,33 @@ +import SimpleITK as sitk +import glob +import os +import platform + +directory_split = "\\" if platform.system() == "Windows" else '/' + +def read_itk(filename): + return sitk.ReadImage(filename) + +def read_dicoms(dicom_folder): + reader = sitk.ImageSeriesReader() + dicoms = reader.GetGDCMSeriesFileNames(dicom_folder) + reader.SetFileNames(dicoms) + + return reader.Execute() + +def write_nrrd(nrrd, filename): + writer = sitk.ImageFileWriter() + writer.SetFileName(filename) + writer.Execute(nrrd) + +def itk_to_nrrd(source, destination): + queue = glob.glob(source) + for f in queue: + if(os.path.isdir(f)): + os.mkdir(destination + f.split(directory_split)[-1]) + itk_to_nrrd(f + "\\*", destination + f.split(directory_split)[-1] + "\\") + elif(os.path.isfile(f)): + itk = read_itk(f) + dst = destination + "\\" + f.split(directory_split)[-1] + dst = dst[:dst.rfind('.')] + ".nrrd" + write_nrrd(itk, dst) \ No newline at end of file diff --git a/training/Utils/plot.py b/training/Utils/plot.py new file mode 100644 index 0000000000000000000000000000000000000000..94c1bad7bd3c9f11ced35854939c29a259eecc23 --- /dev/null +++ b/training/Utils/plot.py @@ -0,0 +1,61 @@ +import csv +import matplotlib.pyplot as plt +import numpy as np + +def _decode_train_csv(csv_path): + + epochs = [] + train_loss = [] + val_loss = [] + dice = [] + + with open(csv_path) as csv_file: + csv_reader = csv.DictReader(csv_file) + for row in csv_reader: + epochs.append(row['step']) + train_loss.append(row['train_loss']) + val_loss.append(row['val_loss']) + dice.append(row['dice_score']) + + return (np.array(epochs, dtype=np.uint), np.array(train_loss, dtype=np.float32), + np.array(val_loss, dtype=np.float32), np.array(dice, dtype=np.float32)) + +def plot_train_data(csv_path, store = None, show=True, steps_in_epoch = -1): + data = _decode_train_csv(csv_path) + + plt.plot(data[0], data[1], label = 'Training Loss') + plt.plot(data[0], data[2], label = 'Validation loss') + plt.plot(data[0], data[3], label = 'Dice Score') + + + if(steps_in_epoch > 0): + vlines = [x for x in range(0, data[0][-1]) if x % steps_in_epoch == 0] + plt.vlines(vlines, ymin = -0.2, ymax = -0.05) + + plt.ylim(-0.1, 1.1) + plt.ylabel('Training loss') + plt.xlabel('Train Step') + plt.legend(loc="upper left") + if(store): + plt.savefig(store) + if(show): + plt.show() + +def plot_multiple_val_losses(names, csvs): + for name, csv in zip(names, csvs): + data = _decode_train_csv(csv) + plt.plot(data[0], data[2], label = name) + + plt.ylim(-0.1, 1.1) + plt.xlim(0, 7000) + plt.ylabel('Validation Loss') + plt.xlabel('Train Step') + plt.legend(loc="upper left") + plt.show() + +if __name__ == "__main__": + #path = "D:\\Repos\\LungTumorSegmentation\\models\\metrics.csv" + #plot_train_data(path) + names = ['Base 16: Multiplier: 2x', 'Base 64: Multiplier: 2x', 'Base 128: Multiplier: 2x', 'Base 64: Multiplier: 3.5x', 'Base 192: Multiplier: 1.5x'] + csvs = ["C:\\Users\\vemun\\Desktop\\Plots\\16_2.csv", "C:\\Users\\vemun\\Desktop\\Plots\\64_2.csv", "C:\\Users\\vemun\\Desktop\\Plots\\128_2.csv", "C:\\Users\\vemun\\Desktop\\Plots\\64_3_5.csv", "C:\\Users\\vemun\\Desktop\\Plots\\192_1_5.csv"] + plot_multiple_val_losses(names, csvs) \ No newline at end of file diff --git a/training/Utils/radiomics_formatting.py b/training/Utils/radiomics_formatting.py new file mode 100644 index 0000000000000000000000000000000000000000..f2ddc1a700222a5ec4e71a3e0190b5915143b391 --- /dev/null +++ b/training/Utils/radiomics_formatting.py @@ -0,0 +1,52 @@ +from dcmrtstruct2nii import dcmrtstruct2nii, list_rt_structs +from glob import glob +import os +import platform + +directory_split = "\\" if platform.system() == "Windows" else "/" + +def format_scan(dicom_path, rstruct_path, savepath): + dcmrtstruct2nii(rstruct_path, dicom_path, savepath, mask_foreground_value=1, structures=['GTV-1']) + +def move_temporary_file(save_directory, file_name): + try: + os.rename(f"{save_directory}{directory_split}temp{directory_split}mask_GTV-1.nii.gz", f"{save_directory}{directory_split}Labels{directory_split}{file_name}") + os.rename(f"{save_directory}{directory_split}temp{directory_split}image.nii.gz", f"{save_directory}{directory_split}Images{directory_split}{file_name}") + except: + print("Segmentation or raw image not found\nmoving on...") + +def format_radiomics(load_directory, save_directory): + + os.mkdir(f"{save_directory}{directory_split}temp") + os.mkdir(f"{save_directory}{directory_split}Images") + os.mkdir(f"{save_directory}{directory_split}Labels") + temp_dir = f"{save_directory}{directory_split}temp" + + for scan in sorted(glob(f"{load_directory}{directory_split}*")): + file_name = "radiomics_" + scan.split(directory_split)[-1].split("-")[-1] + scan_folder = glob(f"{scan}{directory_split}*")[0] + components = glob(f"{scan_folder}{directory_split}*") + + dcm = components[0] + rstruct = components[0] + + for component in components: + if(len(glob(f"{component}{directory_split}*")) > 1): + dcm = component + break + + for component in components: + rs = glob(f"{component}{directory_split}*")[0] + try: + list_rt_structs(rs) + rstruct = rs + except: + pass + + format_scan(dcm, rstruct, temp_dir) + move_temporary_file(save_directory, f"{file_name}.nii.gz") + + + +if __name__ == "__main__": + format_radiomics("D:\\Datasets\\NSCLC-Radiomics\\NSCLC-Radiomics\\", "D:\\Datasets\\Temp\\") \ No newline at end of file diff --git a/training/Utils/segment_to_segmentbox.py b/training/Utils/segment_to_segmentbox.py new file mode 100644 index 0000000000000000000000000000000000000000..71e0abf31d61d838dab774db0b0f4df6c2d679ed --- /dev/null +++ b/training/Utils/segment_to_segmentbox.py @@ -0,0 +1,46 @@ +import nibabel +import numpy as np +import glob +import platform + +directory_split = "\\" if platform.system() == "Windows" else "/" + +def convert_folder(source_folder, destination_folder): + for seg in glob.glob(source_folder + "*.nii*"): + name = seg.split(directory_split)[-1] + convert_file(seg, destination_folder + name) + +def convert_file(source_file, destination_file): + nifti = read_nifti(source_file) + img = nifti.get_fdata() + segbox = generate_segmentbox(np.array(img)) + store_nifti(nifti, segbox, destination_file) + +def read_nifti(nifti_file): + return nibabel.load(nifti_file) + +def store_nifti(original, new_img, destination): + headers = original.header + save = nibabel.Nifti1Image(new_img, np.eye(4), headers) + + nibabel.save(save, destination) + +def generate_segmentbox(image): + image = np.swapaxes(image, 0, 2) + for i, layer in enumerate(image): + if(np.amax(layer) < 1): + continue + + y = np.any(layer, axis = 1) + x = np.any(layer, axis = 0) + y_min, y_max = np.argmax(y) + 1, layer.shape[0] - np.argmax(np.flipud(y)) + x_min, x_max = np.argmax(x) + 1, layer.shape[1] - np.argmax(np.flipud(x)) + + layer[y_min - 1:y_max, x_min - 1:x_max] = 1 + + image = np.swapaxes(image, 0, 2) + return image + +if __name__ == "__main__": + path = "D:\\Datasets\\Temp\\Labels\\" + convert_folder(path, "D:\\Datasets\\Temp\\Boxes\\") \ No newline at end of file diff --git a/training/Utils/volume_histogram.py b/training/Utils/volume_histogram.py new file mode 100644 index 0000000000000000000000000000000000000000..d43e33531710660b474b43efd37f27caf9000fdf --- /dev/null +++ b/training/Utils/volume_histogram.py @@ -0,0 +1,88 @@ +import numpy as np +import nibabel +import glob +import platform +import matplotlib.pyplot as plt + +directory_split = "\\" if platform.system() == "Windows" else "/" + +def calculate_scan(image_path, label_path): + + voxel_spacing = nibabel.load(image_path).header.get_zooms() + label_volume = nibabel.load(label_path).get_fdata() + + return calculate_volume(label_volume, voxel_spacing) + +def calculate_volume(label, voxel_spacing): + voxels = np.count_nonzero(label) + volume = voxels * (voxel_spacing[0]/10) * (voxel_spacing[1]/10) * (voxel_spacing[2]/10) + + return volume + +def calculate_all(image_directory, label_directory): + volumes = [] + for file in glob.glob(f"{image_directory}{directory_split}*"): + filename = file.split(directory_split)[-1] + + volumes.append(calculate_scan(file, f"{label_directory}{directory_split}{filename}")) + + return volumes + +def save_volumes(volumes, save_file): + with open(save_file, "w+") as file: + for volume in volumes: + file.write(f"{volume}\n") + +def read_volumes(volume_file): + file = open(volume_file, "r") + volumes = [] + lines = file.readlines() + for line in lines: + volumes.append(float(line)) + + return volumes + +def plot_histogram(volumes): + bins = [0, 5, 10, 15, 25, 50, 100, 150, 200, 300, 400, 1000] + + hist, bin_edges = np.histogram(volumes, bins) + fig, ax = plt.subplots() + + ax.set_xticks([0.5+i for i,j in enumerate(hist)]) + ax.bar(range(len(hist)),hist,width=1,color="#15497d",edgecolor='#0b2947',align='center',tick_label= + ['{} - {}'.format(bins[i],bins[i+1]) for i,j in enumerate(hist)]) + + + hist, bin_edges = np.histogram(volumes, bins) + ax.bar(range(len(hist)),hist,width=1,color="#15497d",edgecolor='#0b2947',align='center',tick_label= + ['{} - {}'.format(bins[i],bins[i+1]) for i,j in enumerate(hist)]) + + plt.xticks(rotation = 45) + plt.xlabel('Volume, cm\u00b3') + plt.ylabel('Number of Tumors') + plt.xlim(-0.5, 10.5) + plt.show() + +def plot_histograms(volumes): + #plt.figure(figsize=(8,6)) + plt.hist(volumes[2], bins=20, alpha=0.5, label="LungDx") + plt.hist(volumes[1], bins=20, alpha=0.5, label="Radiomics") + plt.hist(volumes[0], bins=20, alpha=1, label="MSD") + + plt.xlabel("Volume, cm\u00b3", size=14) + plt.ylabel("Count", size=14) + plt.title("Tumor Volumes") + plt.legend(loc='upper right') + + plt.show() + +if __name__ == "__main__": + #vol =calculate_scan("D:\\Datasets\\Temp\\Images\\radiomics_010.nii.gz", "D:\\Datasets\\Temp\\Labels\\radiomics_010.nii.gz") + #print(vol) + #volumes = calculate_all("D:\\Datasets\\Temp\\Images\\", "D:\\Datasets\\Temp\\Labels\\") + #save_volumes(volumes, "D:\\Datasets\\radiomics.txt") + volumes = [] + volumes.append(read_volumes("C:\\Users\\vemun\\Desktop\\msd_volumes.txt")) + volumes.append(read_volumes("C:\\Users\\vemun\\Desktop\\radiomics_volumes.txt")) + volumes.append(read_volumes("C:\\Users\\vemun\\Desktop\\lungdx_volumes.txt")) + plot_histograms(volumes) \ No newline at end of file diff --git a/training/interface.py b/training/interface.py new file mode 100644 index 0000000000000000000000000000000000000000..549eb7eac922357dd84f0e6ffed5632dfe91a8da --- /dev/null +++ b/training/interface.py @@ -0,0 +1,93 @@ +import argparse +import sys + +from Utils.fileconverter import itk_to_nrrd +from Engine.train import initiate as train_initiate +from Engine.evaluate import initiate as evaluate_initiate +from Utils.MSD_utilities import generate_training_data +from Utils.plot import plot_train_data +from Utils.PETCT_LungDx_utilities import convert_nsclc_petct + + +class Parser(object): + + def __init__(self): + parser = argparse.ArgumentParser( + description='Interface for utilities', + usage='''interface [] + + Available commands: + itk_to_nrrd Converts files in folder from other ITK formats to .nrrd format + train Initiates training + evaluate Initiates evaluation + plot Generates and shows plot based on specified metric file + msd_generate_data_file Generates a datafile for training on MSD dataset + format_petct_dataset Converts the the LUNGPTCT dataset to nifti files and generates segboxes for each scan + + ''') + parser.add_argument('command', help='Subcommand to run') + + args = parser.parse_args(sys.argv[1:2]) + if(not hasattr(self, args.command)): + print('Unrecognized command') + parser.print_help() + exit(1) + + getattr(self, args.command)() + + def itk_to_nrrd(self): + parser = argparse.ArgumentParser( + description='Converts files in folder from other ITK formats to .nrrd format') + + parser.add_argument("source") + parser.add_argument("destination") + + args = parser.parse_args(sys.argv[2:]) + itk_to_nrrd(args.source, args.destination) + + def train(self): + parser = argparse.ArgumentParser( + description='Initiates training of model based on specified config file') + parser.add_argument("config") + args = parser.parse_args(sys.argv[2:]) + train_initiate(args.config) + + def evaluate(self): + parser = argparse.ArgumentParser( + description='Initiates evaluation of model based on specified config file') + parser.add_argument("config") + args = parser.parse_args(sys.argv[2:]) + evaluate_initiate(args.config) + + def plot(self): + parser = argparse.ArgumentParser( + description='Generates and shows plot based on specified metric file') + parser.add_argument("metric_file") + parser.add_argument("-store_file") + parser.add_argument("--dont_show", "-d", default=False) + parser.add_argument("-steps_per_epoch", default=-1) + args = parser.parse_args(sys.argv[2:]) + + plot_train_data(args.metric_file, args.store_file, not args.dont_show, steps_in_epoch=int(args.steps_per_epoch)) + + def msd_generate_data_file(self): + parser = argparse.ArgumentParser( + description='Generates a datafile for training on MSD dataset') + parser.add_argument("datafile_save_path") + parser.add_argument("msd_directory") + parser.add_argument("target_platform") + args = parser.parse_args(sys.argv[2:]) + generate_training_data(args.datafile_save_path, args.msd_directory, args.target_platform) + + def format_petct_dataset(self): + parser = argparse.ArgumentParser( + description='Converts the the LUNGPTCT dataset to nifti files and generates segboxes for each scan') + parser.add_argument("annotation_folder") + parser.add_argument("dataset_folder") + parser.add_argument("label_folder") + parser.add_argument("input_folder") + args = parser.parse_args(sys.argv[2:]) + convert_nsclc_petct(args.annotation_folder, args.dataset_folder, args.label_folder, args.input_folder) + +if __name__ == '__main__': + Parser() \ No newline at end of file diff --git a/training/setup.py b/training/setup.py new file mode 100644 index 0000000000000000000000000000000000000000..ddd465ace55c5abd26164788da9e3b46660bb683 --- /dev/null +++ b/training/setup.py @@ -0,0 +1,11 @@ +from setuptools import setup, find_packages + +setup( + name="LungTumorSegmentation", + packages=find_packages(), + version='1.0.1', + author="Svein Ole M Sevle, Vemund Fredriksen", + url="https://github.com/VemundFredriksen/LungTumorSegmentation", + license="MIT", + python_requires='>=3.6' +)