from huggingface_hub import hf_hub_download import os import functools from typing import List import numpy as np import torch import yaml from einops import rearrange from Prithvi import MaskedAutoencoderViT from functools import partial import rasterio from rasterio.merge import merge from rasterio import Affine from rasterio.warp import calculate_default_transform, reproject, Resampling import streamlit as st from streamlit_image_comparison import image_comparison NO_DATA = -9999 NO_DATA_FLOAT = 0.0001 PERCENTILES = (0.1, 99.9) TOKEN = "JONATHAN_TOKEN" yaml_file_path=hf_hub_download(repo_id="ibm-nasa-geospatial/Prithvi-100M", filename="Prithvi_100M_config.yaml", token=TOKEN) checkpoint=hf_hub_download(repo_id="ibm-nasa-geospatial/Prithvi-100M", filename='Prithvi_100M.pt', token=TOKEN) model_def=hf_hub_download(repo_id="ibm-nasa-geospatial/Prithvi-100M", filename='Prithvi.py', token=TOKEN) def process_channel_group(orig_img, new_img, channels, data_mean, data_std): """ Process *orig_img* and *new_img* for RGB visualization. Each band is rescaled back to the original range using *data_mean* and *data_std* and then lowest and highest percentiles are removed to enhance contrast. Data is rescaled to (0, 1) range and stacked channels_first. Args: orig_img: torch.Tensor representing original image (reference) with shape = (bands, H, W). new_img: torch.Tensor representing image with shape = (bands, H, W). channels: list of indices representing RGB channels. data_mean: list of mean values for each band. data_std: list of std values for each band. Returns: torch.Tensor with shape (num_channels, height, width) for original image torch.Tensor with shape (num_channels, height, width) for the other image """ stack_c = [], [] for c in channels: orig_ch = orig_img[c, ...] valid_mask = torch.ones_like(orig_ch, dtype=torch.bool) valid_mask[orig_ch == NO_DATA_FLOAT] = False # Back to original data range orig_ch = (orig_ch * data_std[c]) + data_mean[c] new_ch = (new_img[c, ...] * data_std[c]) + data_mean[c] # Rescale (enhancing contrast) min_value, max_value = np.percentile(orig_ch[valid_mask], PERCENTILES) orig_ch = torch.clamp((orig_ch - min_value) / (max_value - min_value), 0, 1) new_ch = torch.clamp((new_ch - min_value) / (max_value - min_value), 0, 1) # No data as zeros orig_ch[~valid_mask] = 0 new_ch[~valid_mask] = 0 stack_c[0].append(orig_ch) stack_c[1].append(new_ch) # Channels first stack_orig = torch.stack(stack_c[0], dim=0) stack_rec = torch.stack(stack_c[1], dim=0) return stack_orig, stack_rec def read_geotiff(file_path: str): """ Read all bands from *file_path* and returns image + meta info. Args: file_path: path to image file. Returns: np.ndarray with shape (bands, height, width) meta info dict """ with rasterio.open(file_path) as src: img = src.read() meta = src.meta return img, meta def save_geotiff(image, output_path: str, meta: dict): """ Save multi-band image in Geotiff file. Args: image: np.ndarray with shape (bands, height, width) output_path: path where to save the image meta: dict with meta info. """ with rasterio.open(output_path, "w", **meta) as dest: for i in range(image.shape[0]): dest.write(image[i, :, :], i + 1) return def _convert_np_uint8(float_image: torch.Tensor): image = float_image.numpy() * 255.0 image = image.astype(dtype=np.uint8) image = image.transpose((1, 2, 0)) return image def load_example(file_paths: List[str], mean: List[float], std: List[float]): """ Build an input example by loading images in *file_paths*. Args: file_paths: list of file paths . mean: list containing mean values for each band in the images in *file_paths*. std: list containing std values for each band in the images in *file_paths*. Returns: np.array containing created example list of meta info for each image in *file_paths* """ imgs = [] metas = [] for file in file_paths: img, meta = read_geotiff(file) img = img[:6]*10000 if img[:6].mean() <= 2 else img[:6] # Rescaling (don't normalize on nodata) img = np.moveaxis(img, 0, -1) # channels last for rescaling img = np.where(img == NO_DATA, NO_DATA_FLOAT, (img - mean) / std) imgs.append(img) metas.append(meta) imgs = np.stack(imgs, axis=0) # num_frames, H, W, C imgs = np.moveaxis(imgs, -1, 0).astype('float32') # C, num_frames, H, W imgs = np.expand_dims(imgs, axis=0) # add batch dim return imgs, metas def run_model(model: torch.nn.Module, input_data: torch.Tensor, mask_ratio: float, device: torch.device): """ Run *model* with *input_data* and create images from output tokens (mask, reconstructed + visible). Args: model: MAE model to run. input_data: torch.Tensor with shape (B, C, T, H, W). mask_ratio: mask ratio to use. device: device where model should run. Returns: 3 torch.Tensor with shape (B, C, T, H, W). """ with torch.no_grad(): x = input_data.to(device) _, pred, mask = model(x, mask_ratio) # Create mask and prediction images (un-patchify) mask_img = model.unpatchify(mask.unsqueeze(-1).repeat(1, 1, pred.shape[-1])).detach().cpu() pred_img = model.unpatchify(pred).detach().cpu() # Mix visible and predicted patches rec_img = input_data.clone() rec_img[mask_img == 1] = pred_img[mask_img == 1] # binary mask: 0 is keep, 1 is remove # Switch zeros/ones in mask images so masked patches appear darker in plots (better visualization) mask_img = (~(mask_img.to(torch.bool))).to(torch.float) return rec_img, mask_img def save_rgb_imgs(input_img, rec_img, mask_img, channels, mean, std, output_dir, meta_data): """ Wrapper function to save Geotiff images (original, reconstructed, masked) per timestamp. Args: input_img: input torch.Tensor with shape (C, T, H, W). rec_img: reconstructed torch.Tensor with shape (C, T, H, W). mask_img: mask torch.Tensor with shape (C, T, H, W). channels: list of indices representing RGB channels. mean: list of mean values for each band. std: list of std values for each band. output_dir: directory where to save outputs. meta_data: list of dicts with geotiff meta info. """ for t in range(input_img.shape[1]): rgb_orig, rgb_pred = process_channel_group(orig_img=input_img[:, t, :, :], new_img=rec_img[:, t, :, :], channels=channels, data_mean=mean, data_std=std) rgb_mask = mask_img[channels, t, :, :] * rgb_orig # Saving images save_geotiff(image=_convert_np_uint8(rgb_orig), output_path=os.path.join(output_dir, f"original_rgb_t{t}.tiff"), meta=meta_data[t]) save_geotiff(image=_convert_np_uint8(rgb_pred), output_path=os.path.join(output_dir, f"predicted_rgb_t{t}.tiff"), meta=meta_data[t]) save_geotiff(image=_convert_np_uint8(rgb_mask), output_path=os.path.join(output_dir, f"masked_rgb_t{t}.tiff"), meta=meta_data[t]) def extract_rgb_imgs(input_img, rec_img, mask_img, channels, mean, std): """ Wrapper function to save Geotiff images (original, reconstructed, masked) per timestamp. Args: input_img: input torch.Tensor with shape (C, T, H, W). rec_img: reconstructed torch.Tensor with shape (C, T, H, W). mask_img: mask torch.Tensor with shape (C, T, H, W). channels: list of indices representing RGB channels. mean: list of mean values for each band. std: list of std values for each band. output_dir: directory where to save outputs. meta_data: list of dicts with geotiff meta info. """ rgb_orig_list = [] rgb_mask_list = [] rgb_pred_list = [] for t in range(input_img.shape[1]): rgb_orig, rgb_pred = process_channel_group(orig_img=input_img[:, t, :, :], new_img=rec_img[:, t, :, :], channels=channels, data_mean=mean, data_std=std) rgb_mask = mask_img[channels, t, :, :] * rgb_orig # extract images rgb_orig_list.append(_convert_np_uint8(rgb_orig)) rgb_mask_list.append(_convert_np_uint8(rgb_mask)) rgb_pred_list.append(_convert_np_uint8(rgb_pred)) outputs = rgb_orig_list + rgb_mask_list + rgb_pred_list return outputs def predict_on_images(data_files: list, mask_ratio: float, yaml_file_path: str, checkpoint: str): try: data_files = [x.name for x in data_files] print('Path extracted from example') except: print('Files submitted through UI') # Get parameters -------- print('This is the printout', data_files) with open(yaml_file_path, 'r') as f: params = yaml.safe_load(f) # data related num_frames = params['num_frames'] img_size = params['img_size'] bands = params['bands'] mean = params['data_mean'] std = params['data_std'] # model related depth = params['depth'] patch_size = params['patch_size'] embed_dim = params['embed_dim'] num_heads = params['num_heads'] tubelet_size = params['tubelet_size'] decoder_embed_dim = params['decoder_embed_dim'] decoder_num_heads = params['decoder_num_heads'] decoder_depth = params['decoder_depth'] batch_size = params['batch_size'] mask_ratio = params['mask_ratio'] if mask_ratio is None else mask_ratio # We must have *num_frames* files to build one example! assert len(data_files) == num_frames, "File list must be equal to expected number of frames." if torch.cuda.is_available(): device = torch.device('cuda') else: device = torch.device('cpu') print(f"Using {device} device.\n") # Loading data --------------------------------------------------------------------------------- input_data, meta_data = load_example(file_paths=data_files, mean=mean, std=std) # Create model and load checkpoint ------------------------------------------------------------- model = MaskedAutoencoderViT( img_size=img_size, patch_size=patch_size, num_frames=num_frames, tubelet_size=tubelet_size, in_chans=len(bands), embed_dim=embed_dim, depth=depth, num_heads=num_heads, decoder_embed_dim=decoder_embed_dim, decoder_depth=decoder_depth, decoder_num_heads=decoder_num_heads, mlp_ratio=4., norm_layer=functools.partial(torch.nn.LayerNorm, eps=1e-6), norm_pix_loss=False) total_params = sum(p.numel() for p in model.parameters() if p.requires_grad) print(f"\n--> Model has {total_params:,} parameters.\n") model.to(device) state_dict = torch.load(checkpoint, map_location=device) model.load_state_dict(state_dict) print(f"Loaded checkpoint from {checkpoint}") # Running model -------------------------------------------------------------------------------- model.eval() channels = [bands.index(b) for b in ['B04', 'B03', 'B02']] # BGR -> RGB # Reflect pad if not divisible by img_size original_h, original_w = input_data.shape[-2:] pad_h = img_size - (original_h % img_size) pad_w = img_size - (original_w % img_size) input_data = np.pad(input_data, ((0, 0), (0, 0), (0, 0), (0, pad_h), (0, pad_w)), mode='reflect') # Build sliding window batch = torch.tensor(input_data, device='cpu') windows = batch.unfold(3, img_size, img_size).unfold(4, img_size, img_size) h1, w1 = windows.shape[3:5] windows = rearrange(windows, 'b c t h1 w1 h w -> (b h1 w1) c t h w', h=img_size, w=img_size) # Split into batches if number of windows > batch_size num_batches = windows.shape[0] // batch_size if windows.shape[0] > batch_size else 1 windows = torch.tensor_split(windows, num_batches, dim=0) # Run model rec_imgs = [] mask_imgs = [] for x in windows: rec_img, mask_img = run_model(model, x, mask_ratio, device) rec_imgs.append(rec_img) mask_imgs.append(mask_img) rec_imgs = torch.concat(rec_imgs, dim=0) mask_imgs = torch.concat(mask_imgs, dim=0) # Build images from patches rec_imgs = rearrange(rec_imgs, '(b h1 w1) c t h w -> b c t (h1 h) (w1 w)', h=img_size, w=img_size, b=1, c=len(bands), t=num_frames, h1=h1, w1=w1) mask_imgs = rearrange(mask_imgs, '(b h1 w1) c t h w -> b c t (h1 h) (w1 w)', h=img_size, w=img_size, b=1, c=len(bands), t=num_frames, h1=h1, w1=w1) # Cut padded images back to original size rec_imgs_full = rec_imgs[..., :original_h, :original_w] mask_imgs_full = mask_imgs[..., :original_h, :original_w] batch_full = batch[..., :original_h, :original_w] # Build RGB images for d in meta_data: d.update(count=3, dtype='uint8', compress='lzw', nodata=0) # save_rgb_imgs(batch[0, ...], rec_imgs_full[0, ...], mask_imgs_full[0, ...], # channels, mean, std, output_dir, meta_data) outputs = extract_rgb_imgs(batch_full[0, ...], rec_imgs_full[0, ...], mask_imgs_full[0, ...], channels, mean, std) print("Done!") return outputs # partial function prep func = partial(predict_on_images, yaml_file_path=yaml_file_path,checkpoint=checkpoint,mask_ratio=0.75) ## South Korea rural area HSL landset merger (from B02 channel to B07 channel) def raw_NASA_tif_file_merger(PSD_NAME,tif_files): src_files_to_mosaic = [] for tif_file in tif_files: src = rasterio.open(tif_file) src_files_to_mosaic.append(src) mosaic, out_trans = merge(src_files_to_mosaic) out_meta = src.meta.copy() out_meta.update({"driver": "GTiff", "height": mosaic.shape[1], "width": mosaic.shape[2], "transform": out_trans}) with rasterio.open(PSD_NAME, "w", **out_meta) as dest: dest.write(mosaic) # raw_NASA_tif_file_merger("third.tif","./1/*.tif") # streamlit area def main_loop(): st.title("HuggingFace Inference Demo") st.subheader("Be sure to set the parameter") [out1_orig_t1,out2_orig_t2,out3_orig_t3,out4_masked_t1,out5_masked_t2,out6_masked_t3,out7_pred_t1,out8_pred_t2,out9_pred_t3]=func(["first.tif","second.tif","third.tif"]) st.markdown("### first original image and masked image comparison") image_comparison( img1=out1_orig_t1, img2=out4_masked_t1, label1="original-1", label2="masked-1", width=1024, ) st.markdown("### second original image and masked image comparison") image_comparison( img1=out2_orig_t2, img2=out5_masked_t2, label1="original-2", label2="masked-2", width=1024, ) st.markdown("### thrid original image and masked image comparison") image_comparison( img1=out3_orig_t3, img2=out6_masked_t3, label1="original-1", label2="masked-1", width=1024, ) st.markdown("### first original image and encoded image comparison") image_comparison( img1=out1_orig_t1, img2=out7_pred_t1, label1="original-1", label2="masked-1", width=1024, ) st.markdown("### second original image and encoded image comparison") image_comparison( img1=out2_orig_t2, img2=out8_pred_t2, label1="original-2", label2="masked-2", width=1024, ) st.markdown("### thrid original image and encoded image comparison") image_comparison( img1=out3_orig_t3, img2=out9_pred_t3, label1="original-1", label2="masked-1", width=1024, ) if __name__ == '__main__': main_loop()