Sentinel2 Class not behaving as expected

Hello!

I am working with the Sentinel2 class. I have updated the class to deal with a different data format when downloaded from google cloud. (.SAFE data format, with Geo-JPEG2000 for the bands)

when trying to plot the individual bands, they are all coming out as identical, I am trying to get the individual bands to use in NDVI indice

class Sentinel(RasterDataset):
    """Abstract base class for all Sentinel datasets.

    `Sentinel <https://sentinel.esa.int/web/sentinel/home>`_ is a family of
    satellites launched by the `European Space Agency (ESA) <https://www.esa.int/>`_
    under the `Copernicus Programme <https://www.copernicus.eu/en>`_.

    If you use this dataset in your research, please cite it using the following format:

    * https://asf.alaska.edu/data-sets/sar-data-sets/sentinel-1/sentinel-1-how-to-cite/
    """


class Sentinel2(Sentinel):
    """Sentinel-2 dataset.

    The `Copernicus Sentinel-2 mission
    <https://sentinel.esa.int/web/sentinel/missions/sentinel-2>`_ comprises a
    constellation of two polar-orbiting satellites placed in the same sun-synchronous
    orbit, phased at 180° to each other. It aims at monitoring variability in land
    surface conditions, and its wide swath width (290 km) and high revisit time (10 days
    at the equator with one satellite, and 5 days with 2 satellites under cloud-free
    conditions which results in 2-3 days at mid-latitudes) will support monitoring of
    Earth's surface changes.
    """

    # TODO: files downloaded from USGS Earth Explorer seem to have a different
    # filename format than the official documentation
    # https://sentinels.copernicus.eu/web/sentinel/user-guides/sentinel-2-msi/naming-convention
    # https://sentinel.esa.int/documents/247904/685211/Sentinel-2-MSI-L2A-Product-Format-Specifications.pdf
    filename_glob = "T*.jp2"
    # filename_regex = r"""
    #     ^T(?P<tile>\d{2}[A-Z]{3})
    #     _(?P<date>\d{8}T\d{6})
    #     _(?P<band>B[018][\dA])
    #     _(?P<resolution>\d{2}m)
    #     \..*$
    # """
    date_format = "%Y%m%dT%H%M%S"

    # https://gisgeography.com/sentinel-2-bands-combinations/
    all_bands = [
        "B01",
        "B02",
        "B03",
        "B04",
        "B05",
        "B06",
        "B07",
        "B08",
        "B8A",
        "B09",
        "B10",
        "B11",
        "B12",
    ]
    RGB_BANDS = ["B04", "B03", "B02"]

    separate_files = True
    def __init__(
        self,
        root: str = "data",
        crs: Optional[CRS] = None,
        res: Optional[float] = None,
        bands: Sequence[str] = [],
        transforms: Optional[Callable[[Dict[str, Any]], Dict[str, Any]]] = None,
        cache: bool = True,
    ) -> None:
        """Initialize a new Dataset instance.

        Args:
            root: root directory where dataset can be found
            crs: :term:`coordinate reference system (CRS)` to warp to
                (defaults to the CRS of the first file found)
            res: resolution of the dataset in units of CRS
                (defaults to the resolution of the first file found)
            bands: bands to return (defaults to all bands)
            transforms: a function/transform that takes an input sample
                and returns a transformed version
            cache: if True, cache file handle to speed up repeated sampling

        Raises:
            FileNotFoundError: if no files are found in ``root``
        """
        self.bands = bands if bands else self.all_bands

        super().__init__(root, crs, res, transforms, cache)


    def plot(  # type: ignore[override]
        self,
        sample: Dict[str, Tensor],
        show_titles: bool = True,
        suptitle: Optional[str] = None,
    ) -> plt.Figure:
            """Plot a sample from the dataset.

            Args:
                sample: a sample returned by :meth:`RasterDataset.__getitem__`
                show_titles: flag indicating whether to show titles above each panel
                suptitle: optional string to use as a suptitle

            Returns:
                a matplotlib Figure with the rendered sample

            Raises:
                ValueError: if the RGB bands are not included in ``self.bands``

            .. versionadded:: 0.3
            """
            rgb_indices = []
            for band in self.RGB_BANDS:
                if band in self.bands:
                    rgb_indices.append(self.bands.index(band))
                else:
                    raise ValueError("Dataset doesn't contain some of the RGB bands")

            image = sample["image"][rgb_indices].permute(1, 2, 0)
            image = torch.clamp(image / 3000, min=0, max=1)  # type: ignore[attr-defined]

            fig, ax = plt.subplots(1, 1, figsize=(4, 4))

            ax.imshow(image)
            ax.axis("off")

            if show_titles:
                ax.set_title("Image")

            if suptitle is not None:
                plt.suptitle(suptitle)

            return fig

I have two folders with jp2 band data

#path contains four .jp2 files for the four bands, path8 only contains band8
path = '/Users/gracecolverd/Documents/Fire_Proj/sentinel2/S2A_MSIL1C_20160911T092032_N0204_R093_T35UNU_20160911T092026.SAFE/GRANULE/L1C_T35UNU_A006382_20160911T092026/IMG_DATA'
path8 = '/Users/gracecolverd/Documents/Fire_Proj/sentinel2/S2A_MSIL1C_20160911T092032_N0204_R093_T35UNU_20160911T092026.SAFE/GRANULE/L1C_T35UNU_A006382_20160911T092026/IMG_DATA/b8'

when I try to look at individual bands they are all coming back the same

ds = Sentinel2(path, bands=['B02', 'B03' , 'B04', 'B08'])

sampler = RandomGeoSampler(ds, size=1024, length=1)
dl = DataLoader(ds, sampler=sampler, collate_fn=stack_samples)

fig, ax = plt.subplots(3, figsize = (10,10) )

for sample in dl:
      print('count')
      image = sample['image']
      print(image.shape)
      image = torch.squeeze(image)
      print(image)
      ax[0].imshow(image[0])
      ax[1].imshow(image[1])
      ax[2].imshow(image[2])

The image is tensor 4 deep as expected with the four bands, but all the tensors are the same

torch.Size([1, 4, 102, 102])
tensor([[[2473, 2428, 2356,  ..., 2941, 2987, 2998],
         [2337, 2431, 2436,  ..., 2873, 2901, 2962],
         [2364, 2485, 2395,  ..., 2831, 2910, 2945],
         ...,
         [2353, 2389, 2388,  ..., 2799, 2784, 2449],
         [2582, 2600, 2580,  ..., 2687, 2499, 1956],
         [2795, 2802, 2711,  ..., 2195, 1849, 1642]],

        [[2473, 2428, 2356,  ..., 2941, 2987, 2998],
         [2337, 2431, 2436,  ..., 2873, 2901, 2962],
         [2364, 2485, 2395,  ..., 2831, 2910, 2945],
         ...,
         [2353, 2389, 2388,  ..., 2799, 2784, 2449],
         [2582, 2600, 2580,  ..., 2687, 2499, 1956],
         [2795, 2802, 2711,  ..., 2195, 1849, 1642]],

        [[2473, 2428, 2356,  ..., 2941, 2987, 2998],
         [2337, 2431, 2436,  ..., 2873, 2901, 2962],
         [2364, 2485, 2395,  ..., 2831, 2910, 2945],
         ...,
         [2353, 2389, 2388,  ..., 2799, 2784, 2449],
         [2582, 2600, 2580,  ..., 2687, 2499, 1956],
         [2795, 2802, 2711,  ..., 2195, 1849, 1642]],

        [[2473, 2428, 2356,  ..., 2941, 2987, 2998],
         [2337, 2431, 2436,  ..., 2873, 2901, 2962],
         [2364, 2485, 2395,  ..., 2831, 2910, 2945],
         ...,
         [2353, 2389, 2388,  ..., 2799, 2784, 2449],
         [2582, 2600, 2580,  ..., 2687, 2499, 1956],
         [2795, 2802, 2711,  ..., 2195, 1849, 1642]]], dtype=torch.int32)

The image that is returned is

I can’t attach the JP2 files but the files I used were B2, B3, B4, B8 from

S2A_MSIL1C_20160911T092032_N0204_R093_T35UNU_20160911T092026.SAFE

[graceebc9]

thanks! confirmed that the bands work in the order as expected -the issue was normalising. thanks also for the insights re. the indices - we’ve taken those onbord

[graceebc9]

Thanks Adam!

all of the files are in the same directory - the filename_glob : filename_glob = “T*.jp2” catches them all