diff --git a/README.md b/README.md index b90bf52..1776125 100644 --- a/README.md +++ b/README.md @@ -44,7 +44,9 @@ poetry run python3 src/train.py The training script supports early stopping, model checkpoints, and tracks the loss function and evaluation metrics (IoU, Precision, Recall, DICE, Pixel accurracy). -4. Predict New Areas +4. Predictions + +**Note:** The predict script can predict on the test dataset (for which you have labels) or on the pictures without annotation. You need to change the parameter `MODE` from `configs/predict/default.yaml` to `predict` (if you want to predict on unnanotated pictures), or `test` if you want to predict on the test dataset. This difference occurs only because in the test dataset we have acces to the shapefile of the school, and we don't have to predict on the entire image. Once the model is trained, you can use it to generate predictions for new images. The following script takes an input image and outputs the corresponding segmentation mask: @@ -66,3 +68,5 @@ To evaluate the model’s performance on the test dataset, run the metrics scrip poetry run python3 src/metrics.py ``` + +6. 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a/src/predict.py b/src/predict.py index d09b19c..a7d205b 100755 --- a/src/predict.py +++ b/src/predict.py @@ -76,7 +76,10 @@ def apply_ignore_index(predicted_mask, ground_truth_mask, ignore_value=-1): return predicted_mask -def predict_image(image_path, mask_path, model, output_mask_path): +def predict_test_image(image_path, mask_path, model, output_mask_path): + if not os.path.exists(output_mask_path): + os.makedirs(output_mask_path) + input_tensor, original_size = preprocess_image(image_path) with torch.no_grad(): output = model(input_tensor)["out"] @@ -107,18 +110,145 @@ def predict_image(image_path, mask_path, model, output_mask_path): print(f"Predicted mask saved at {pred_mask_name}") +def patch_and_pad_image(image, patch_size=512, overlap=0): + """ + Divide an image into patches of the given size, with optional overlap. + + Args: + image (PIL.Image): The input image. + patch_size (int): The size of each square patch (default: 512). + overlap (int): The overlap between adjacent patches (default: 0). + + Returns: + patches (list): List of image patches as NumPy arrays and their top-left coordinates. + padded_size (tuple): Dimensions of the padded image (width, height). + original_size (tuple): Original dimensions of the image (width, height). + """ + original_width, original_height = image.size + + # Calculate padding + pad_width = (patch_size - (original_width % patch_size)) % patch_size + pad_height = (patch_size - (original_height % patch_size)) % patch_size + + padded_width = original_width + pad_width + padded_height = original_height + pad_height + + # Pad the image + padded_image = Image.new("RGB", (padded_width, padded_height)) + padded_image.paste(image, (0, 0)) + + # Divide into patches + patches = [] + step = patch_size - overlap # Adjust step size based on overlap + for y in range(0, padded_height, step): + for x in range(0, padded_width, step): + patch = padded_image.crop((x, y, x + patch_size, y + patch_size)) + patches.append((patch, (x, y))) + + return patches, (padded_width, padded_height), (original_width, original_height) + + +def stitch_patches(patches, padded_size, original_size, patch_size=512): + """ + Combine patches back into a single image, trimming any padding. + + Args: + patches (list): List of predicted patches as NumPy arrays. + padded_size (tuple): Dimensions of the padded image (width, height). + original_size (tuple): Original dimensions of the image (width, height). + patch_size (int): The size of each square patch (default: 512). + + Returns: + stitched_image (PIL.Image): The reconstructed image without padding. + """ + padded_width, padded_height = padded_size + original_width, original_height = original_size + + # Create a blank array for the full padded image + full_image = np.zeros((padded_height, padded_width), dtype=np.int16) + + # Place patches into the full image + idx = 0 + for y in range(0, padded_height, patch_size): + for x in range(0, padded_width, patch_size): + full_image[y : y + patch_size, x : x + patch_size] = patches[idx] + idx += 1 + + # Crop to the original size + stitched_image = Image.fromarray(full_image[:original_height, :original_width]) + + return stitched_image + + +def predict_non_annotated_image( + image_path, model, output_mask_path, patch_size=512, overlap=0 +): + if not os.path.exists(output_mask_path): + os.makedirs(output_mask_path) + + # Load and preprocess the image + image = Image.open(image_path).convert("RGB") + patches, padded_size, original_size = patch_and_pad_image( + image, patch_size, overlap + ) + + padded_width, padded_height = padded_size + num_classes = model.classifier[4].out_channels # Get the number of output classes + vote_map = np.zeros((padded_height, padded_width, num_classes), dtype=np.int32) + + # Predict each patch + with torch.no_grad(): + for patch, (x, y) in patches: + patch_tensor = T.ToTensor()(patch).unsqueeze(0) + output = model(patch_tensor)["out"] + predicted_patch = torch.argmax(output.squeeze(), dim=0).cpu().numpy() + + # Get the actual dimensions of the current patch (may differ for edge patches) + patch_height, patch_width = predicted_patch.shape + + # Dynamically slice the vote_map to match the patch size + vote_map[y : y + patch_height, x : x + patch_width] += np.eye( + num_classes, dtype=np.int32 + )[predicted_patch] + + # Take the class with the most votes + final_mask = np.argmax(vote_map, axis=2).astype(np.uint8) + + # Crop to the original size + final_mask = final_mask[: original_size[1], : original_size[0]] + + # Save the final mask + pred_mask_name = os.path.join( + output_mask_path, + "predmask_" + os.path.basename(image_path).split(".")[0] + ".tif", + ) + Image.fromarray(final_mask).save(pred_mask_name) + print(f"Predicted mask saved at {pred_mask_name}") + + @hydra.main(version_base=None, config_path="../configs", config_name="config") def main(cfg): - if not os.path.exists(cfg.paths.PRED_TEST_MASKS): - os.makedirs(cfg.paths.PRED_TEST_MASKS) + valid_modes = ["test", "predict"] + if cfg.predict.MODE not in valid_modes: + raise ValueError( + f"Invalid MODE: {cfg.predict.MODE}. Valid options are: {', '.join(valid_modes)}" + ) # Load the model model = load_model(cfg.paths.MODEL_PATH) - # Run prediction and save the mask - predict_image( - cfg.paths.INPUT_IMAGE, cfg.paths.GT_TEST_MASKS, model, cfg.paths.PRED_TEST_MASKS - ) + if cfg.predict.MODE == "test": + predict_test_image( + cfg.paths.INPUT_IMAGE, + cfg.paths.GT_TEST_MASKS, + model, + cfg.paths.PRED_TEST_MASKS, + ) + + elif cfg.predict.MODE == "predict": + predict_non_annotated_image( + cfg.paths.INPUT_IMAGE, model, cfg.paths.PREDICTED_MASKS, patch_size=512 + ) if __name__ == "__main__": diff --git a/src/predict_crop.py b/src/predict_crop.py deleted file mode 100644 index 55937c3..0000000 --- a/src/predict_crop.py +++ /dev/null @@ -1,190 +0,0 @@ -#!/usr/env/bin python3 - -import os -import sys - -import numpy as np -import torch -import torchvision.transforms as T -import yaml -from PIL import Image -from torchvision.models.segmentation import deeplabv3_resnet50 - - -def load_model(checkpoint_path, num_classes=8): - model = deeplabv3_resnet50(pretrained=False) - model.classifier[4] = torch.nn.Conv2d(256, num_classes, kernel_size=(1, 1)) - - # Load the saved state dict - checkpoint = torch.load( - checkpoint_path, - map_location=torch.device("cuda" if torch.cuda.is_available() else "cpu"), - ) - - # Remove the 'model.' prefix from the state_dict keys - state_dict = { - k.replace("model.", ""): v for k, v in checkpoint["state_dict"].items() - } - - # Filter out the auxiliary classifier keys - state_dict = {k: v for k, v in state_dict.items() if "aux_classifier" not in k} - - # Load the modified state_dict into the model - model.load_state_dict(state_dict, strict=False) - model.eval() # Set the model to evaluation mode - return model - - -def preprocess_image(image_path, patch_size=(512, 512)): - # Ensure patch_size is a tuple of integers - if isinstance(patch_size, tuple) and len(patch_size) == 2: - pass # Valid patch_size - else: - raise ValueError( - f"Invalid patch_size: {patch_size}. Expected a tuple (height, width)." - ) - - # Open the image file using PIL - image = Image.open(image_path).convert("RGB") - - # Save the original image size - original_size = image.size # (width, height) - - # Calculate padding required to make dimensions divisible by patch size - width, height = original_size - pad_width = (patch_size[0] - (width % patch_size[0])) % patch_size[0] - pad_height = (patch_size[1] - (height % patch_size[1])) % patch_size[1] - - # Apply padding - padded_image = Image.new("RGB", (width + pad_width, height + pad_height), (0, 0, 0)) - padded_image.paste(image, (0, 0)) - - # Convert to tensor - preprocess = T.Compose([T.ToTensor()]) - input_tensor = preprocess(padded_image).unsqueeze(0) - - return input_tensor, original_size, (width + pad_width, height + pad_height) - - -def get_corresponding_mask(image_path, mask_dir): - """ - Finds the corresponding ground truth mask for a given image. - - Args: - image_path (str): Path to the input image. - mask_dir (str): Directory containing ground truth masks. - - Returns: - str: Path to the corresponding ground truth mask. - """ - image_filename = os.path.basename(image_path) - identifier = image_filename.split("image_")[-1].replace(".png", "") - mask_filename = f"mask_{identifier}.tif" - - mask_path = os.path.join(mask_dir, mask_filename) - - if not os.path.exists(mask_path): - raise FileNotFoundError( - f"Mask file not found for {image_path}. Expected: {mask_path}" - ) - - return mask_path - - -def apply_ignore_index(predicted_mask, ground_truth_mask, ignore_value=-1): - # Ensure both predicted_mask and ground_truth_mask are numpy arrays - if isinstance(predicted_mask, Image.Image): - predicted_mask = np.array(predicted_mask) - - if isinstance(ground_truth_mask, Image.Image): - ground_truth_mask = np.array(ground_truth_mask) - - # Set the values in the predicted mask to -1 wherever the ground truth mask is -1 - predicted_mask[ground_truth_mask == ignore_value] = ignore_value - - return predicted_mask - - -def predict_image( - image_path, - mask_dir, - model, - output_mask_path, - patch_size=(512, 512), - ignore_value=-1, -): - """ - Predicts segmentation mask for a single image, applies ignore index based on ground truth, and saves the output. - - Args: - image_path (str): Path to the input image. - mask_dir (str): Directory containing the ground truth masks. - model (torch.nn.Module): Pretrained segmentation model. - output_mask_path (str): Directory to save the predicted mask. - patch_size (tuple): Size of the patch for padding (default: (512, 512)). - ignore_value (int): Value to ignore in the ground truth mask. - """ - # Preprocess the image (padding applied) - input_tensor, original_size, padded_size = preprocess_image(image_path, patch_size) - original_width, original_height = original_size - - with torch.no_grad(): - output = model(input_tensor)["out"] - - # Get predicted mask - predicted_mask = torch.argmax(output.squeeze(), dim=0).cpu().numpy() - - # Crop the predicted mask back to the original image size - predicted_mask_cropped = predicted_mask[:original_height, :original_width] - - # Find the corresponding ground truth mask - gt_mask_path = get_corresponding_mask(image_path, mask_dir) - if not os.path.exists(gt_mask_path): - raise FileNotFoundError(f"Ground truth mask not found: {gt_mask_path}") - ground_truth_mask = Image.open(gt_mask_path) - - # Apply ignore index to predicted mask - final_mask_with_ignore = apply_ignore_index( - predicted_mask_cropped, ground_truth_mask, ignore_value - ) - - # Ensure the output directory exists - os.makedirs(output_mask_path, exist_ok=True) - - # Save the final mask - pred_mask_name = os.path.join( - output_mask_path, - "predmask_" + os.path.basename(image_path).split(".")[0] + ".tif", - ) - final_mask = Image.fromarray(final_mask_with_ignore.astype(np.int16)) - final_mask.save(pred_mask_name) - print(f"Predicted mask saved at {pred_mask_name}") - - -if __name__ == "__main__": - with open("./config.yaml") as f: - cfg = yaml.load(f, Loader=yaml.FullLoader) - - if not os.path.exists(cfg["PRED_TEST_MASKS"]): - os.makedirs(cfg["PRED_TEST_MASKS"]) - - if len(sys.argv) != 2: - print("Usage: python predict.py ") - sys.exit(1) - - input_image_path = sys.argv[1] - - # Load the model - model = load_model(cfg["MODEL_PATH"]) - - # Run prediction and save the mask - predict_image( - image_path=input_image_path, - model=model, - mask_dir=cfg["GT_TEST_MASKS"], - output_mask_path=cfg["PRED_TEST_MASKS"], - patch_size=( - 512, - 512, - ), # Use the default explicitly or omit this if the default is fine - )