A Rasterio dataset's index() method gives you the row, col index of the pixel containing the point x, y (in the dataset's CRS units).
Define a 1x1 pixel read window starting at that index (see the tiny_window() function below) and use it to read an ndarray. The one in this case has shape (3, 1, 1): 3 bands, 1 row, and 1 column. The values of the 3 bands at the point x, y for this case are 28, 29, and 27.
| $ rio insp ~/code/rasterio/tests/data/RGB.byte.tif | |
| Rasterio 0.17 Interactive Inspector (Python 2.7.9) | |
| Type "src.meta", "src.read_band(1)", or "help(src)" for more information. | |
| >>> x = (src.bounds.left + src.bounds.right)/2.0 | |
| >>> y = (src.bounds.bottom + src.bounds.top)/2.0 | |
| >>> src.index(x, y) | |
| (359, 396) | |
| >>> def tiny_window(dataset, x, y): | |
| ... r, c = dataset.index(x, y) | |
| ... return ((r, r+1), (c, c+1)) | |
| ... | |
| >>> data = src.read(window=tiny_window(src, x, y)) | |
| >>> list(data[:,0,0]) | |
| [28, 29, 27] |