Sentinel-5 P data usage

[JPPereira93]

Hi! I've been trying to use sentinel-5 data to map CH4 emissions over my area of interest.

I replicated pretty much the code that i previously had for sentinel 1 and sentinel 2 processing:

sentinel_search_url = "https://planetarycomputer.microsoft.com/api/stac/v1"
sentinel_stac_client = pystac_client.Client.open(sentinel_search_url)

items = sentinel_stac_client.search(
    bbox=bounds,
    collections=["sentinel-5p-l2-netcdf"],
    datetime=f"{start_date}/{end_date}",
    query={"s5p:processing_mode": {"eq": "OFFL"}, "s5p:product_name": {"eq": "ch4"}},
).item_collection()

print(f"Total number of items found: {len(items)}")

scene_dates = sorted([item.datetime for item in items])

selected_scenes = [scene_dates[0]]
for i in range(1, len(scene_dates)):
    if (scene_dates[i] - selected_scenes[-1]).days >= min_time_step:
        selected_scenes.append(scene_dates[i])

items = [
    item for item in items if item.datetime in selected_scenes
]

print(f"Number of items after minimum time step filtering: {len(items)}")

print("\nSelected scenes after filtering:")
for item in items:
    print(f"Scene date: {item.datetime}")


(i had to provide a proj:epsg field as this data doesn't have it)

for item in items:
    # Access the asset metadata
    asset = item.assets['ch4']
    
    # Add proj:epsg metadata if it doesn't exist
    if 'proj:epsg' not in asset.extra_fields:
        asset.extra_fields['proj:epsg'] = 4326

sentinel_stack = stackstac.stack(
    items,
    assets=["ch4"],
    gdal_env=stackstac.DEFAULT_GDAL_ENV.updated({
        'GDAL_HTTP_MAX_RETRY': 3,
        'GDAL_HTTP_RETRY_DELAY': 5,
        'AWS_NO_SIGN_REQUEST': 'YES',
    }),
    epsg=4326,
    resolution=0.0629, 
    chunksize=(1, 1, 1000, 1000),
).to_dataset(dim='band')

# This length number represents the number  of assets (bands) that are to be extracted
# len(sentinel_stack)

sentinel_stack

# Remove attributes that are not time, y or x 
sentinel_stack = sentinel_stack.drop_vars([c for c in sentinel_stack.coords if not (c in ['time', 'y', 'x',])])
sentinel_stack

sentinel_stack_float32 = sentinel_stack.astype('float32')
sentinel_stack_float32

crs = "EPSG:4326"
crs_number = crs[5:]
sentinel_stack_float32 = sentinel_stack_float32.rio.write_crs(fr"{crs}", inplace=True)
sentinel_stack_float32

sentinel_stack_clipped = sentinel_stack_float32.rio.clip(aoi.geometry, aoi.crs, all_touched=True, drop=True)
with ProgressBar():
    sentinel_stack_clipped = sentinel_stack_clipped.persist()

Here, i get:

############ ] | 32% Completed | 1.75 sms
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/01/01/S5P_OFFL_L2__CH4____20240101T092629_20240101T110759_32220_03_020600_20240103T013302/S5P_OFFL_L2__CH4____20240101T092629_20240101T110759_32220_03_020600_20240103T013302.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/01/06/S5P_OFFL_L2__CH4____20240106T093259_20240106T111429_32291_03_020600_20240108T014844/S5P_OFFL_L2__CH4____20240106T093259_20240106T111429_32291_03_020600_20240108T014844.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/03/17/S5P_OFFL_L2__CH4____20240317T104914_20240317T123044_33299_03_020600_20240319T160340/S5P_OFFL_L2__CH4____20240317T104914_20240317T123044_33299_03_020600_20240319T160340.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/04/19/S5P_OFFL_L2__CH4____20240419T103414_20240419T121544_33767_03_020600_20240421T231632/S5P_OFFL_L2__CH4____20240419T103414_20240419T121544_33767_03_020600_20240421T231632.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/03/27/S5P_OFFL_L2__CH4____20240327T110315_20240327T124445_33441_03_020600_20240329T115341/S5P_OFFL_L2__CH4____20240327T110315_20240327T124445_33441_03_020600_20240329T115341.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/03/22/S5P_OFFL_L2__CH4____20240322T105615_20240322T123745_33370_03_020600_20240324T111434/S5P_OFFL_L2__CH4____20240322T105615_20240322T123745_33370_03_020600_20240324T111434.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/02/26/S5P_OFFL_L2__CH4____20240226T102115_20240226T120245_33015_03_020600_20240228T022449/S5P_OFFL_L2__CH4____20240226T102115_20240226T120245_33015_03_020600_20240228T022449.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/04/01/S5P_OFFL_L2__CH4____20240401T111013_20240401T125144_33512_03_020600_20240403T032212/S5P_OFFL_L2__CH4____20240401T111013_20240401T125144_33512_03_020600_20240403T032212.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/02/21/S5P_OFFL_L2__CH4____20240221T101417_20240221T115547_32944_03_020600_20240223T023451/S5P_OFFL_L2__CH4____20240221T101417_20240221T115547_32944_03_020600_20240223T023451.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/01/11/S5P_OFFL_L2__CH4____20240111T093933_20240111T112103_32362_03_020600_20240113T020813/S5P_OFFL_L2__CH4____20240111T093933_20240111T112103_32362_03_020600_20240113T020813.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/03/07/S5P_OFFL_L2__CH4____20240307T103513_20240307T121644_33157_03_020600_20240309T030532/S5P_OFFL_L2__CH4____20240307T103513_20240307T121644_33157_03_020600_20240309T030532.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/03/02/S5P_OFFL_L2__CH4____20240302T102814_20240302T120944_33086_03_020600_20240304T025010/S5P_OFFL_L2__CH4____20240302T102814_20240302T120944_33086_03_020600_20240304T025010.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/04/08/S5P_OFFL_L2__CH4____20240408T103921_20240408T122051_33611_03_020600_20240410T030005/S5P_OFFL_L2__CH4____20240408T103921_20240408T122051_33611_03_020600_20240410T030005.nc': RasterioIOError('HTTP response code: 404')
...
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/01/21/S5P_OFFL_L2__CH4____20240121T095247_20240121T113418_32504_03_020600_20240123T022011/S5P_OFFL_L2__CH4____20240121T095247_20240121T113418_32504_03_020600_20240123T022011.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/07/24/S5P_OFFL_L2__CH4____20240724T103609_20240724T121739_35129_03_020600_20240726T072607/S5P_OFFL_L2__CH4____20240724T103609_20240724T121739_35129_03_020600_20240726T072607.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...
[################################## ] | 85% Completed | 1.96 s
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/07/29/S5P_OFFL_L2__CH4____20240729T104210_20240729T122340_35200_03_020600_20240804T092141/S5P_OFFL_L2__CH4____20240729T104210_20240729T122340_35200_03_020600_20240804T092141.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/08/03/S5P_OFFL_L2__CH4____20240803T104809_20240803T122938_35271_03_020600_20240809T130432/S5P_OFFL_L2__CH4____20240803T104809_20240803T122938_35271_03_020600_20240809T130432.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/08/08/S5P_OFFL_L2__CH4____20240808T105404_20240808T123534_35342_03_020600_20240812T214910/S5P_OFFL_L2__CH4____20240808T105404_20240808T123534_35342_03_020600_20240812T214910.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/08/18/S5P_OFFL_L2__CH4____20240818T110547_20240818T124717_35484_03_020600_20240820T031012/S5P_OFFL_L2__CH4____20240818T110547_20240818T124717_35484_03_020600_20240820T031012.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/08/23/S5P_OFFL_L2__CH4____20240823T111134_20240823T125304_35555_03_020600_20240825T033549/S5P_OFFL_L2__CH4____20240823T111134_20240823T125304_35555_03_020600_20240825T033549.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/08/28/S5P_OFFL_L2__CH4____20240828T111719_20240828T125848_35626_03_020600_20240830T032246/S5P_OFFL_L2__CH4____20240828T111719_20240828T125848_35626_03_020600_20240830T032246.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/09/02/S5P_OFFL_L2__CH4____20240902T112301_20240902T130431_35697_03_020600_20240904T034141/S5P_OFFL_L2__CH4____20240902T112301_20240902T130431_35697_03_020600_20240904T034141.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/09/07/S5P_OFFL_L2__CH4____20240907T112851_20240907T131021_35768_03_020600_20240909T040338/S5P_OFFL_L2__CH4____20240907T112851_20240907T131021_35768_03_020600_20240909T040338.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/09/17/S5P_OFFL_L2__CH4____20240917T114040_20240917T132210_35910_03_020701_20240919T063955/S5P_OFFL_L2__CH4____20240917T114040_20240917T132210_35910_03_020701_20240919T063955.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/08/13/S5P_OFFL_L2__CH4____20240813T105958_20240813T124127_35413_03_020600_20240815T215037/S5P_OFFL_L2__CH4____20240813T105958_20240813T124127_35413_03_020600_20240815T215037.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/09/22/S5P_OFFL_L2__CH4____20240922T114632_20240922T132801_35981_03_020701_20240924T071754/S5P_OFFL_L2__CH4____20240922T114632_20240922T132801_35981_03_020701_20240924T071754.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/09/12/S5P_OFFL_L2__CH4____20240912T113447_20240912T131617_35839_03_020701_20240914T201419/S5P_OFFL_L2__CH4____20240912T113447_20240912T131617_35839_03_020701_20240914T201419.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/01/26/S5P_OFFL_L2__CH4____20240126T114058_20240126T132228_32576_03_020600_20240128T051841/S5P_OFFL_L2__CH4____20240126T114058_20240126T132228_32576_03_020600_20240128T051841.nc': RasterioIOError('HTTP response code: 404')
...
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/11/12/S5P_OFFL_L2__CH4____20241112T104321_20241112T122450_36704_03_020701_20241115T183324/S5P_OFFL_L2__CH4____20241112T104321_20241112T122450_36704_03_020701_20241115T183324.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/12/17/S5P_OFFL_L2__CH4____20241217T094534_20241217T112704_37200_03_020800_20241219T020255/S5P_OFFL_L2__CH4____20241217T094534_20241217T112704_37200_03_020800_20241219T020255.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...
[########################################] | 100% Completed | 2.06 s
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/02/05/S5P_OFFL_L2__CH4____20240205T115424_20240205T133554_32718_03_020600_20240207T042306/S5P_OFFL_L2__CH4____20240205T115424_20240205T133554_32718_03_020600_20240207T042306.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/02/10/S5P_OFFL_L2__CH4____20240210T120110_20240210T134240_32789_03_020600_20240212T042117/S5P_OFFL_L2__CH4____20240210T120110_20240210T134240_32789_03_020600_20240212T042117.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)
c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:329: UserWarning: Error opening 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/02/16/S5P_OFFL_L2__CH4____20240216T100729_20240216T114900_32873_03_020600_20240218T023150/S5P_OFFL_L2__CH4____20240216T100729_20240216T114900_32873_03_020600_20240218T023150.nc': RasterioIOError('HTTP response code: 404')
warnings.warn(msg)

And when i try to save the datarray by computing the mean over this clipped area, i get a tiff file with no results

[JPPereira93]

update:

I forget to sign in to get access to STAC items

I added:

for item in items:
    for asset_key, asset in item.assets.items():
        asset.href = pc_sign(asset.href)

but now i got this error:

RuntimeError: Assets must have exactly 1 band, but file 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/01/06/S5P_OFFL_L2__CH4____20240106T093259_20240106T111429_32291_03_020600_20240108T014844/S5P_OFFL_L2__CH4____20240106T093259_20240106T111429_32291_03_020600_20240108T014844.nc?st=2025-03-19T16%3A57%3A48Z&se=2025-03-20T17%3A42%3A48Z&sp=rl&sv=2024-05-04&sr=c&skoid=9c8ff44a-6a2c-4dfb-b298-1c9212f64d9a&sktid=72f988bf-86f1-41af-91ab-2d7cd011db47&skt=2025-03-17T09%3A00%3A07Z&ske=2025-03-24T09%3A00%3A07Z&sks=b&skv=2024-05-04&sig=twF3L4zjzRxfoNWUJPXqZWXHLL4w%2BLeor3fYlDkWQ2E%3D' has 0. We can't currently handle multi-band rasters (each band has to be a separate STAC asset), so you'll need to exclude this asset from your analysis.

[777arc]

Mind sharing the full code up until the point of error? Thanks!

[JPPereira93]

start_date = "2024-01-01" 
end_date = "2024-12-30"
time_range = f"{start_date}/{end_date}"

aoi_path = "aoi_1_4326_part_1.geojson"
aoi = gpd.read_file(aoi_path)
min_time_step = 30

output_directory = r"C:\Users\fuji_\methane-mapping"

bounds = aoi.total_bounds
geometry = box(bounds[0], bounds[1], bounds[2], bounds[3])  
wkt_aoi = geometry.wkt 
geojson_aoi = mapping(geometry)  

print(wkt_aoi)

# Search for Sentinel-5p L2 data using the Planetary Computer STAC API

sentinel_search_url = "https://planetarycomputer.microsoft.com/api/stac/v1"
sentinel_stac_client = pystac_client.Client.open(sentinel_search_url)

items = sentinel_stac_client.search(
    bbox=bounds,
    collections=["sentinel-5p-l2-netcdf"],
    datetime=f"{start_date}/{end_date}",
    query={"s5p:processing_mode": {"eq": "OFFL"}, "s5p:product_name": {"eq": "ch4"}},
).item_collection()

print(f"Total number of items found: {len(items)}")

scene_dates = sorted([item.datetime for item in items])

selected_scenes = [scene_dates[0]]
for i in range(1, len(scene_dates)):
    if (scene_dates[i] - selected_scenes[-1]).days >= min_time_step:
        selected_scenes.append(scene_dates[i])

items = [
    item for item in items if item.datetime in selected_scenes
]

print(f"Number of items after minimum time step filtering: {len(items)}")

print("\nSelected scenes after filtering:")
for item in items:
    print(f"Scene date: {item.datetime}")

# Print available assets in the first item

first_item = items[0]

# Check available assets
print("Available assets:", list(first_item.assets.keys()))

## Must sign to the PC STAC assets to get access 

for item in items:
    for asset_key, asset in item.assets.items():
        asset.href = pc_sign(asset.href)


sentinel_stack = stackstac.stack(
    items,
    assets=["ch4"],
    gdal_env=stackstac.DEFAULT_GDAL_ENV.updated({
        'GDAL_HTTP_MAX_RETRY': 3,
        'GDAL_HTTP_RETRY_DELAY': 5,
        'AWS_NO_SIGN_REQUEST': 'YES',
    }),
    epsg=4326,
    resolution=0.0629, 
    chunksize=(1, 1, 1000, 1000),
).to_dataset(dim='band')

# This length number represents the number  of assets (bands) that are to be extracted
# len(sentinel_stack)

# Remove attributes that are not time, y or x 
sentinel_stack = sentinel_stack.drop_vars([c for c in sentinel_stack.coords if not (c in ['time', 'y', 'x',])])
sentinel_stack_float32 = sentinel_stack.astype('float32')

crs = "EPSG:4326"
crs_number = crs[5:]
sentinel_stack_float32 = sentinel_stack_float32.rio.write_crs(fr"{crs}", inplace=True)

sentinel_stack_clipped = sentinel_stack_float32.rio.clip(aoi.geometry, aoi.crs, all_touched=True, drop=True)
with ProgressBar():
    sentinel_stack_clipped = sentinel_stack_clipped.persist()

[#                                       ] | 4% Completed | 16.44 sms
[c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:325](file:///C:/Users/fuji_/anaconda3/envs/geo/Lib/site-packages/stackstac/rio_reader.py:325): NotGeoreferencedWarning: Dataset has no geotransform, gcps, or rpcs. The identity matrix will be returned.
  ds = SelfCleaningDatasetReader(self.url, sharing=False)
[#                                       ] | 4% Completed | 16.60 s

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[25], line 3
      1 sentinel_stack_clipped = sentinel_stack_float32.rio.clip(aoi.geometry, aoi.crs, all_touched=True, drop=True)
      2 with ProgressBar():
----> 3     sentinel_stack_clipped = sentinel_stack_clipped.persist()

File c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\xarray\core\dataset.py:1117, in Dataset.persist(self, **kwargs)
   1093 """Trigger computation, keeping data as chunked arrays.
   1094 
   1095 This operation can be used to trigger computation on underlying dask
   (...)
   1114 dask.persist
   1115 """
   1116 new = self.copy(deep=False)
-> 1117 return new._persist_inplace(**kwargs)

File c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\xarray\core\dataset.py:1085, in Dataset._persist_inplace(self, **kwargs)
   1082 chunkmanager = get_chunked_array_type(*lazy_data.values())
   1084 # evaluate all the dask arrays simultaneously
-> 1085 evaluated_data = chunkmanager.persist(*lazy_data.values(), **kwargs)
   1087 for k, data in zip(lazy_data, evaluated_data, strict=False):
   1088     self.variables[k].data = data

File c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\xarray\namedarray\daskmanager.py:90, in DaskManager.persist(self, *data, **kwargs)
     87 def persist(self, *data: Any, **kwargs: Any) -> tuple[DaskArray | Any, ...]:
     88     from dask import persist
---> 90     return persist(*data, **kwargs)

File c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\dask\base.py:1001, in persist(traverse, optimize_graph, scheduler, *args, **kwargs)
    998     postpersists.append((rebuild, a_keys, state))
   1000 with shorten_traceback():
-> 1001     results = schedule(dsk, keys, **kwargs)
   1003 d = dict(zip(keys, results))
   1004 results2 = [r({k: d[k] for k in ks}, *s) for r, ks, s in postpersists]

File c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\to_dask.py:189, in fetch_raster_window(reader_table, slices, dtype, fill_value)
    182 # Only read if the window we're fetching actually overlaps with the asset
    183 if windows.intersect(current_window, asset_window):
    184     # NOTE: when there are multiple assets, we _could_ parallelize these reads with our own threadpool.
    185     # However, that would probably increase memory usage, since the internal, thread-local GDAL datasets
    186     # would end up copied to even more threads.
    187 
    188     # TODO when the Reader won't be rescaling, support passing `output` to avoid the copy?
--> 189     data = reader.read(current_window)
    191     if all_empty:
    192         # Turn `output` from a broadcast-trick array to a real array, so it's writeable
    193         if (
    194             np.isnan(data)
    195             if np.isnan(fill_value)
    196             else np.equal(data, fill_value)
    197         ).all():
    198             # Unless the data we just read is all empty anyway

File c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:383, in AutoParallelRioReader.read(self, window, **kwargs)
    382 def read(self, window: Window, **kwargs) -> np.ndarray:
--> 383     reader = self.dataset
    384     try:
    385         result = reader.read(
    386             window=window,
    387             out_dtype=self.dtype,
   (...)
    391             **kwargs,
    392         )

File c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:379, in AutoParallelRioReader.dataset(self)
    377 with self._dataset_lock:
    378     if self._dataset is None:
--> 379         self._dataset = self._open()
    380     return self._dataset

File c:\Users\fuji_\anaconda3\envs\geo\Lib\site-packages\stackstac\rio_reader.py:338, in AutoParallelRioReader._open(self)
    336     nr_of_bands = ds.count
    337     ds.close()
--> 338     raise RuntimeError(
    339         f"Assets must have exactly 1 band, but file {self.url!r} has {nr_of_bands}. "
    340         "We can't currently handle multi-band rasters (each band has to be "
    341         "a separate STAC asset), so you'll need to exclude this asset from your analysis."
    342     )
    344 # Only make a VRT if the dataset doesn't match the spatial spec we want
    345 if self.spec.vrt_params != {
    346     "crs": ds.crs.to_epsg(),
    347     "transform": ds.transform,
    348     "height": ds.height,
    349     "width": ds.width,
    350 }:

RuntimeError: Assets must have exactly 1 band, but file 'https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__HCHO__/2024/03/01/S5P_OFFL_L2__HCHO___20240301T104708_20240301T122838_33072_03_020601_20240303T031309/S5P_OFFL_L2__HCHO___20240301T104708_20240301T122838_33072_03_020601_20240303T031309.nc?st=2025-03-19T17%3A09%3A51Z&se=2025-03-20T17%3A54%3A51Z&sp=rl&sv=2024-05-04&sr=c&skoid=9c8ff44a-6a2c-4dfb-b298-1c9212f64d9a&sktid=72f988bf-86f1-41af-91ab-2d7cd011db47&skt=2025-03-20T00%3A01%3A16Z&ske=2025-03-27T00%3A01%3A16Z&sks=b&skv=2024-05-04&sig=Lffz9KetmMI4xjoy%2BB7hhsD9wfIxOn5PVS/BYm72G4Q%3D' has 0. We can't currently handle multi-band rasters (each band has to be a separate STAC asset), so you'll need to exclude this asset from your analysis.

[JPPereira93]

Maybe stackstac doesnt work with these kind of files, im trying with this:

datasets = []
for item in items:
    f = fsspec.open(item.assets["ch4"].href).open()
    ds = xr.open_dataset(f, group="PRODUCT", engine="h5netcdf")
    datasets.append(ds)

# Merge datasets along the time dimension
ds_combined = xr.concat(datasets, dim="time")

# Extract methane data
ch4_data = ds_combined["methane_mixing_ratio"]
ch4_data

which is an adaptation of the code provided in the Example notebook, however it takes a long time to load a dataset (40 mins running with 12 items in the search list)

[777arc]

One reason it might be taking so long is because Sentinel-5 is in the form of NetCDF files which are not cloud optimized, so xarray is downloading the whole thing, regardless of your area of interest, and they are 50MB each for CH4. As far as the stacstack error, you're probably best opening an issue here https://github.com/gjoseph92/stackstac and reference one of the .nc files from MPC you're having trouble with so folks can easily download it. So for example, file

https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/01/06/S5P_OFFL_L2__CH4____20240106T093259_20240106T111429_32291_03_020600_20240108T014844/S5P_OFFL_L2__CH4____20240106T093259_20240106T111429_32291_03_020600_20240108T014844.nc

Can be downloaded easily by going to the url
https://planetarycomputer.microsoft.com/api/sas/v1/sign?href=https://sentinel5euwest.blob.core.windows.net/sentinel-5p/TROPOMI/L2__CH4___/2024/01/06/S5P_OFFL_L2__CH4____20240106T093259_20240106T111429_32291_03_020600_20240108T014844/S5P_OFFL_L2__CH4____20240106T093259_20240106T111429_32291_03_020600_20240108T014844.nc

then copy the part in "href" and paste in browser to download the file