diff --git a/annotations.json b/annotations.json index 2f86c42..4dad91f 100644 --- a/annotations.json +++ b/annotations.json @@ -5,11 +5,14 @@ "ring2.jpg": {"mask_path":"./dataset/train/masks/ring2.jpg", "bbox": [569, 239, 1286, 944]}, "ring3.jpg": {"mask_path":"./dataset/train/masks/ring3.jpg", "bbox": [135, 68, 466, 415]}, "ring4.jpg": {"mask_path":"./dataset/train/masks/ring4.jpg", "bbox": [133, 234, 1085, 718]}, -"ring5.jpg": {"mask_path":"./dataset/train/masks/ring5.jpg", "bbox": [163, 197, 477, 597]} +"ring5.jpg": {"mask_path":"./dataset/train/masks/ring5.jpg", "bbox": [163, 197, 477, 597]}, +"ring6.jpg": {"mask_path":"./dataset/train/masks/ring6.jpg", "bbox": [12, 30, 438, 288]}, +"ring7.jpg": {"mask_path":"./dataset/train/masks/ring7.jpg", "bbox": [4, 11, 789, 438]}, +"ring8.jpg": {"mask_path":"./dataset/train/masks/ring8.jpg", "bbox": [185, 83, 621, 639]} }, "test": -{"ring_test_1.jpg" : {"bbox": [74, 351, 936, 649]}, -"ring_test_2.jpg" : {"bbox": [138, 196, 508, 610]} +{"ring_test_1.jpg" : {"mask_path":"./dataset/test/masks/ring_test_1.jpg", "bbox": [74, 351, 936, 649]}, +"ring_test_2.jpg" : {"mask_path":"./dataset/test/masks/ring_test_2.jpg", "bbox": [138, 196, 508, 610]} } } \ No newline at end of file diff --git a/eval_inference.py b/eval_inference.py deleted file mode 100644 index 6bf40d8..0000000 --- a/eval_inference.py +++ /dev/null @@ -1,67 +0,0 @@ -import torch -import monai -from tqdm import tqdm -from statistics import mean -from torch.utils.data import Dataset, DataLoader -from torchvision import datasets, transforms -from torch.optim import Adam -from torch.nn.functional import threshold, normalize -from torchvision.utils import save_image -import src.utils as utils -from src.dataloader import DatasetSegmentation, collate_fn -from src.processor import Samprocessor -from src.segment_anything import build_sam_vit_b, SamPredictor -from src.lora import LoRA_sam -import matplotlib.pyplot as plt -import yaml -import torch.nn.functional as F - -def dice_loss(input, target): - smooth = 1. - - iflat = input.view(-1) - tflat = target.view(-1) - intersection = (iflat * tflat).sum() - - return 1 - ((2. * intersection + smooth) / (iflat.sum() + tflat.sum() + smooth)) - -device = "cuda" if torch.cuda.is_available() else "cpu" - -# Load the config file -with open("./config.yaml", "r") as ymlfile: - config_file = yaml.load(ymlfile, Loader=yaml.Loader) - -# Load SAM model -sam = build_sam_vit_b(checkpoint=config_file["SAM"]["CHECKPOINT"]) -#Create SAM LoRA -sam_lora = LoRA_sam(sam, config_file["SAM"]["RANK"]) -sam_lora.load_lora_parameters(f"./lora_weights/lora_rank{sam_lora.rank}.safetensors") -model = sam_lora.sam - -# Process the dataset -processor = Samprocessor(model) -dataset = DatasetSegmentation(config_file, processor, is_test=True) - -# Create a dataloader -test_dataloader = DataLoader(dataset, batch_size=1, collate_fn=collate_fn) - - -# Set model to train and into the device -model.eval() -model.to(device) - -with torch.no_grad(): - total_score = [] - for i, batch in enumerate(tqdm(test_dataloader)): - - outputs = model(batched_input=batch, - multimask_output=False) - - gt_mask_tensor = batch[0]["ground_truth_mask"].unsqueeze(0).unsqueeze(0) # We need to get the [B, C, H, W] starting from [H, W] - dice_score = dice_loss(outputs[0]["low_res_logits"], gt_mask_tensor.float().to(device)) - - total_score.append(dice_score.item()) - print("Dice score: ", total_score[-1]) - - - print(f'Mean loss: {mean(total_score)}') diff --git a/inference_baseline.py b/inference_baseline.py deleted file mode 100644 index 1e91729..0000000 --- a/inference_baseline.py +++ /dev/null @@ -1,78 +0,0 @@ -import torch -import numpy as np -import src.utils as utils -from src.segment_anything import build_sam_vit_b, SamPredictor, sam_model_registry -import torchvision.transforms.functional as F -import matplotlib.pyplot as plt -from PIL import Image, ImageDraw -import json - -device = "cuda" if torch.cuda.is_available() else "cpu" -model_type = "vit_b" -sam_checkpoint = "sam_vit_b_01ec64.pth" - -f = open('annotations.json') -annotations = json.load(f) - -def inference_standard_sam(image_path, filename, mask_path=None, bbox=None): - - image = Image.open(image_path) - if mask_path != None: - mask = Image.open(mask_path) - mask = mask.convert('1') - ground_truth_mask = np.array(mask) - box = utils.get_bounding_box(ground_truth_mask) - print(box) - - - else: - box = bbox - sam = sam_model_registry[model_type](checkpoint=sam_checkpoint) - sam.to(device=device) - predictor = SamPredictor(sam) - predictor.set_image(np.array(image)) - - masks, _, _ = predictor.predict( - box=np.array(box), - multimask_output=False, - ) - - if mask_path == None: - fig, (ax1, ax2) = plt.subplots(1, 2, sharex=True, sharey=True, figsize=(15, 15)) - draw = ImageDraw.Draw(image) - draw.rectangle(box, outline ="red") - ax1.imshow(image) - ax1.set_title(f"Original image + Bounding box: {filename}") - - ax2.imshow(masks[0]) - ax2.set_title(f"Baseline SAM prediction: {filename}") - plt.savefig("./plots/baseline/" + filename) - - else: - fig, (ax1, ax2, ax3) = plt.subplots(1, 3, sharex=True, sharey=True, figsize=(15, 15)) - draw = ImageDraw.Draw(image) - draw.rectangle(box, outline ="red") - ax1.imshow(image) - ax1.set_title(f"Original image + Bounding box: {filename}") - - ax2.imshow(ground_truth_mask) - ax2.set_title(f"Ground truth mask: {filename}") - - ax3.imshow(masks[0]) - ax3.set_title(f"Baseline SAM prediction: {filename}") - plt.savefig("./plots/baseline/" + filename) - - -train_set = annotations["train"] -test_set = annotations["test"] -inference_train = False - -if inference_train: - for image_name, dict_annot in train_set.items(): - image_path = f"./dataset/train/images/{image_name}" - inference_standard_sam(image_path, filename=image_name, mask_path=dict_annot["mask_path"], bbox=dict_annot["bbox"]) - -else: - for image_name, dict_annot in test_set.items(): - image_path = f"./dataset/test/{image_name}" - inference_standard_sam(image_path, filename=image_name, bbox=dict_annot["bbox"]) diff --git a/inference_eval.py b/inference_eval.py new file mode 100644 index 0000000..3a0d159 --- /dev/null +++ b/inference_eval.py @@ -0,0 +1,99 @@ +import torch +import monai +from tqdm import tqdm +from statistics import mean +from torch.utils.data import Dataset, DataLoader +from torchvision import datasets, transforms +from torch.optim import Adam +from torch.nn.functional import threshold, normalize +from torchvision.utils import save_image +import src.utils as utils +from src.dataloader import DatasetSegmentation, collate_fn +from src.processor import Samprocessor +from src.segment_anything import build_sam_vit_b, SamPredictor +from src.lora import LoRA_sam +import matplotlib.pyplot as plt +import yaml +import torch.nn.functional as F +import monai +import numpy as np + +device = "cuda" if torch.cuda.is_available() else "cpu" +seg_loss = monai.losses.DiceCELoss(sigmoid=True, squared_pred=True, reduction='mean') +# Load the config file +with open("./config.yaml", "r") as ymlfile: + config_file = yaml.load(ymlfile, Loader=yaml.Loader) +rank_list = [2, 4, 6, 8, 16, 32, 64, 128, 256, 512] +rank_loss = [] +# Load SAM model +seg_loss = monai.losses.DiceCELoss(sigmoid=True, squared_pred=True, reduction='mean') +with torch.no_grad(): + for rank in rank_list: + sam = build_sam_vit_b(checkpoint=config_file["SAM"]["CHECKPOINT"]) + #Create SAM LoRA + sam_lora = LoRA_sam(sam, rank) + sam_lora.load_lora_parameters(f"./lora_weights/lora_rank{rank}.safetensors") + model = sam_lora.sam + + # Process the dataset + processor = Samprocessor(model) + dataset = DatasetSegmentation(config_file, processor, mode="test") + + # Create a dataloader + test_dataloader = DataLoader(dataset, batch_size=1, collate_fn=collate_fn) + + + # Set model to train and into the device + model.eval() + model.to(device) + + + total_score = [] + for i, batch in enumerate(tqdm(test_dataloader)): + + outputs = model(batched_input=batch, + multimask_output=False) + + gt_mask_tensor = batch[0]["ground_truth_mask"].unsqueeze(0).unsqueeze(0) # We need to get the [B, C, H, W] starting from [H, W] + loss = seg_loss(outputs[0]["low_res_logits"], gt_mask_tensor.float().to(device)) + + total_score.append(loss.item()) + + + print(f'Mean dice score: {mean(total_score)}') + rank_loss.append(mean(total_score)) + + +print("RANK LOSS :", rank_loss) + +width = 0.25 # the width of the bars +multiplier = 0 +models_results= {"Rank 2": rank_loss[0], + "Rank 4": rank_loss[1], + "Rank 6": rank_loss[2], + "Rank 8": rank_loss[3], + "Rank 16": rank_loss[4], + "Rank 32": rank_loss[5], + "Rank 64": rank_loss[6], + "Rank 128": rank_loss[7], + "Rank 256": rank_loss[8], + "Rank 512": rank_loss[9] + } +eval_scores_name = ["Rank"] +x = np.arange(len(eval_scores_name)) +fig, ax = plt.subplots(layout='constrained') + +for model_name, score in models_results.items(): + offset = width * multiplier + rects = ax.bar(x + offset, score, width, label=model_name) + ax.bar_label(rects, padding=3) + multiplier += 1 + +# Add some text for labels, title and custom x-axis tick labels, etc. +ax.set_ylabel('Dice Loss') +ax.set_title('LoRA trained on 50 epochs - Rank comparison on test set') +ax.set_xticks(x + width, eval_scores_name) +ax.legend(loc=3, ncols=2) +ax.set_ylim(0, 0.15) + +plt.savefig("./plots/rank_comparison.jpg") \ No newline at end of file diff --git a/inference.py b/inference_plots.py similarity index 88% rename from inference.py rename to inference_plots.py index 2e1e8e3..3957c52 100644 --- a/inference.py +++ b/inference_plots.py @@ -14,7 +14,7 @@ sam_checkpoint = "sam_vit_b_01ec64.pth" device = "cuda" if torch.cuda.is_available() else "cpu" sam = build_sam_vit_b(checkpoint=sam_checkpoint) -rank = 64 +rank = 512 sam_lora = LoRA_sam(sam, rank) sam_lora.load_lora_parameters(f"./lora_weights/lora_rank{rank}.safetensors") model = sam_lora.sam @@ -25,7 +25,7 @@ def inference_model(sam_model, image_path, filename, mask_path=None, bbox=None, model = sam_model.sam rank = sam_model.rank else: - model = sam_model + model = build_sam_vit_b(checkpoint=sam_checkpoint) model.eval() model.to(device) @@ -55,9 +55,10 @@ def inference_model(sam_model, image_path, filename, mask_path=None, bbox=None, ax2.imshow(masks[0]) if is_baseline: ax2.set_title(f"Baseline SAM prediction: {filename}") + plt.savefig(f"./plots/{filename}_baseline.jpg") else: ax2.set_title(f"SAM LoRA rank {rank} prediction: {filename}") - plt.savefig("./plots/" + filename) + plt.savefig(f"./plots/{filename[:-4]}_rank{rank}.jpg") else: fig, (ax1, ax2, ax3) = plt.subplots(1, 3, sharex=True, sharey=True, figsize=(15, 15)) @@ -72,9 +73,10 @@ def inference_model(sam_model, image_path, filename, mask_path=None, bbox=None, ax3.imshow(masks[0]) if is_baseline: ax3.set_title(f"Baseline SAM prediction: {filename}") + plt.savefig(f"./plots/{filename}_baseline.jpg") else: ax3.set_title(f"SAM LoRA rank {rank} prediction: {filename}") - plt.savefig("./plots/" + filename) + plt.savefig(f"./plots/{filename[:-4]}_rank{rank}.jpg") # Open configuration file @@ -91,16 +93,16 @@ def inference_model(sam_model, image_path, filename, mask_path=None, bbox=None, inference_train = False if inference_train: - total_loss = [] + for image_name, dict_annot in train_set.items(): image_path = f"./dataset/train/images/{image_name}" - inference_model(sam_lora, image_path, filename=image_name, mask_path=dict_annot["mask_path"], bbox=dict_annot["bbox"], is_baseline=False) + inference_model(sam_lora, image_path, filename=image_name, mask_path=dict_annot["mask_path"], bbox=dict_annot["bbox"], is_baseline=True) else: - total_loss = [] + for image_name, dict_annot in test_set.items(): image_path = f"./dataset/test/images/{image_name}" - inference_model(sam_lora, image_path, filename=image_name, bbox=dict_annot["bbox"], is_baseline=False) + inference_model(sam_lora, image_path, filename=image_name, 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self.mask_files.append(os.path.join(config_file["DATASET"]["TRAIN_PATH"],'masks', os.path.basename(img_path)[:-4] + ".jpg")) - elif mode == "valid": - - self.img_files = glob.glob(os.path.join(config_file["DATASET"]["VALID_PATH"],'images','*.jpg')) - self.mask_files = [] - for img_path in self.img_files: - self.mask_files.append(os.path.join(config_file["DATASET"]["VALID_PATH"],'masks', os.path.basename(img_path)[:-4] + ".jpg")) - else: self.img_files = glob.glob(os.path.join(config_file["DATASET"]["TEST_PATH"],'images','*.jpg')) self.mask_files = []