Problem with dowloading EOPatches with eo-learn

Hi @Nagama.TY ,

Could you please point me the notebook you’re running that has the error? It would be even better if you could provide the parameters you used in the code that can reproduce the error.

Thank you.

Thank you for your reply. I share the link of my notebook. I deleted the connection settings for security reasons.

https://colab.research.google.com/drive/12rwB3NquzYlxKi660yAcnL5qmR096-6G?authuser=3#scrollTo=XEpAKS0uX3D3

It seems that I don’t have the permission.

I just gave everyone access to the code. You can also see the code below

# Jupyter notebook related
%reload_ext autoreload
%autoreload 2
%matplotlib inline

# Built-in modules
import os
import datetime
import itertools
from aenum import MultiValueEnum
from enum import Enum

# Basics of Python data handling and visualization
import numpy as np

#np.random.seed(42)
import geopandas as gpd
import matplotlib.pyplot as plt
import matplotlib as mpl
from matplotlib.colors import ListedColormap, BoundaryNorm
from shapely.geometry import Polygon
from tqdm.auto import tqdm

# Machine learning
import lightgbm as lgb
import joblib
from sklearn import metrics
from sklearn import preprocessing

from eolearn.core import(
    EOTask,
    EOPatch,
    EOWorkflow,
    linearly_connect_tasks,
    FeatureType,
    OverwritePermission,
    LoadTask,
    SaveTask,
    EOExecutor,
    MergeFeatureTask,
)
from eolearn.io import SentinelHubInputTask, VectorImportTask, ExportToTiffTask
from eolearn.geometry import VectorToRasterTask, ErosionTask
from eolearn.features import LinearInterpolationTask, SimpleFilterTask, NormalizedDifferenceIndexTask
from eolearn.features import LinearInterpolationTask
from eolearn.ml_tools import FractionSamplingTask
from sentinelhub import UtmZoneSplitter, DataCollection, SHConfig, CRS


# Folder where data for running the notebook is stored
DATA_FOLDER = os.path.join(".", "example_data")
# Locations for collected data and intermediate results
EOPATCH_FOLDER = os.path.join(".", "eopatches")
EOPATCH_SAMPLES_FOLDER = os.path.join(".", "eopatches_sampled")
RESULTS_FOLDER = os.path.join(".", "results")
for folder in (DATA_FOLDER, EOPATCH_FOLDER, EOPATCH_SAMPLES_FOLDER, RESULTS_FOLDER):
    os.makedirs(folder, exist_ok=True)


# Load geojson file
aoi = gpd.read_file(os.path.join(DATA_FOLDER, 'new_coordonates', 'EO_Browser_2480_36','Kossou_2480_36_km2.geojson'))

# Plot country
aoi.plot()
plt.axis('off');

#config crs
aoi_crs = CRS.UTM_30N
aoi = aoi.to_crs(epsg=aoi_crs.epsg)
aoi.plot()
plt.axis('off')

aoi = gpd.read_file(os.path.join(DATA_FOLDER, 'new_coordonates', 'EO_Browser_2480_36','Kossou_2480_36_km2.geojson'))
aoi = aoi.to_crs(epsg=aoi_crs.epsg)



# Create a splitter to obtain a list of bboxes with 5km sides
bbox_splitter = UtmZoneSplitter([aoi_shape], aoi.crs, 5000)
bbox_list = np.array(bbox_splitter.get_bbox_list())
info_list = np.array(bbox_splitter.get_info_list())

len(bbox_list)


# Prepare info of selected EOPatches
geometry = [Polygon(bbox.get_polygon()) for bbox in bbox_list]
idxs = [info["index"] for info in info_list]
idxs_x = [info["index_x"] for info in info_list]
idxs_y = [info["index_y"] for info in info_list]

bbox_gdf = gpd.GeoDataFrame({"index": idxs, "index_x": idxs_x, "index_y": idxs_y}, crs=aoi.crs, geometry=geometry)

# select a 5x5 area (id of center patch)
ID = 58

# Obtain surrounding 5x5 patches
patchIDs = []
for idx, (bbox, info) in enumerate(zip(bbox_list, info_list)):
    if abs(info["index_x"] - info_list[ID]["index_x"]) <= 2 and abs(info["index_y"] - info_list[ID]["index_y"]) <= 2:
        patchIDs.append(idx)

# Check if final size is 5x5
if len(patchIDs) != 5 * 5:
    print("Warning! Use a different central patch ID, this one is on the border.")

# Change the order of the patches (useful for plotting)
patchIDs = np.transpose(np.fliplr(np.array(patchIDs).reshape(5, 5))).ravel()

# Save to shapefile
shapefile_name = "grid_kossou_983_29_500x500.gpkg"
bbox_gdf.to_file(os.path.join(RESULTS_FOLDER, shapefile_name), driver="GPKG")

# Display bboxes over area
fig, ax = plt.subplots(figsize=(30, 30))
ax.set_title("Selected 5x5 tiles from kossou", fontsize=25)
aoi.plot(ax=ax, facecolor="w", edgecolor="b", alpha=0.5)
bbox_gdf.plot(ax=ax, facecolor="w", edgecolor="r", alpha=0.5)

for bbox, info in zip(bbox_list, info_list):
    geo = bbox.geometry
    ax.text(geo.centroid.x, geo.centroid.y, info["index"], ha="center", va="center")

# Mark bboxes of selected area
bbox_gdf[bbox_gdf.index.isin(patchIDs)].plot(ax=ax, facecolor="g", edgecolor="r", alpha=0.5)
plt.axis("off");


#Download Data

class SentinelHubValidDataTask(EOTask):
    """
    Combine Sen2Cor's classification map with `IS_DATA` to define a `VALID_DATA_SH` mask
    The SentinelHub's cloud mask is asumed to be found in eopatch.mask['CLM']
    """

    def __init__(self, output_feature):
        self.output_feature = output_feature

    def execute(self, eopatch):
        eopatch[self.output_feature] = eopatch.mask["IS_DATA"].astype(bool) & (~eopatch.mask["CLM"].astype(bool))
        return eopatch


class AddValidCountTask(EOTask):
    """
    The task counts number of valid observations in time-series and stores the results in the timeless mask.
    """
    def __init__(self, count_what, feature_name):
        self.what = count_what
        self.name = feature_name

    def execute(self, eopatch):
        eopatch[FeatureType.MASK_TIMELESS, self.name] = np.count_nonzero(eopatch.mask[self.what], axis=0)
        return eopatch


# BAND DATA
# Add a request for S2 bands.
# Here we also do a simple filter of cloudy scenes (on tile level).
# The s2cloudless masks and probabilities are requested via additional data.

band_names = ["B01", "B02", "B03", "B04", "B05", "B06", "B07", "B08", "B8A", "B09", "B11", "B12"]
add_data = SentinelHubInputTask(
    bands_feature=(FeatureType.DATA, "BANDS"),
    bands=band_names,
    resolution=20,
    maxcc=0.8,
    time_difference=datetime.timedelta(minutes=120),
    data_collection=DataCollection.SENTINEL2_L1C,
    additional_data=[(FeatureType.MASK, "dataMask", "IS_DATA"), (FeatureType.MASK, "CLM"), (FeatureType.DATA, "CLP")],
    config=config,
    max_threads=5,
)

scl = SentinelHubInputTask(
    data_collection=DataCollection.SENTINEL2_L2A,
    bands=["B01", "B02", "B03", "B04", "B05", "B06", "B07", "B08", "B8A", "B09", "B11", "B12"],
    bands_feature=(FeatureType.DATA, "L2A_data"),
    additional_data=[(FeatureType.MASK, "SCL")],
    resolution=20,
    maxcc=0.8,
    time_difference=datetime.timedelta(minutes=120),
    config=config,
    max_threads=3,
)


# CALCULATING NEW FEATURES
# NDVI: (B08 - B04)/(B08 + B04)
# NDWI: (B03 - B08)/(B03 + B08)
# NDBI: (B11 - B08)/(B11 + B08)
ndvi = NormalizedDifferenceIndexTask(
    (FeatureType.DATA, "BANDS"), (FeatureType.DATA, "NDVI"), [band_names.index("B08"), band_names.index("B04")]
)
ndwi = NormalizedDifferenceIndexTask(
    (FeatureType.DATA, "BANDS"), (FeatureType.DATA, "NDWI"), [band_names.index("B03"), band_names.index("B08")]
)
ndbi = NormalizedDifferenceIndexTask(
    (FeatureType.DATA, "BANDS"), (FeatureType.DATA, "NDBI"), [band_names.index("B11"), band_names.index("B08")]
)


# VALIDITY MASK
# Validate pixels using SentinelHub's cloud detection mask and region of acquisition
add_sh_validmask = SentinelHubValidDataTask((FeatureType.MASK, "IS_VALID"))

# COUNTING VALID PIXELS
# Count the number of valid observations per pixel using valid data mask
add_valid_count = AddValidCountTask("IS_VALID", "VALID_COUNT")

# SAVING TO OUTPUT (if needed)
save = SaveTask(EOPATCH_FOLDER, overwrite_permission=OverwritePermission.OVERWRITE_PATCH)


class LULC(MultiValueEnum):
    """Enum class containing basic LULC types"""

    NO_DATA = "No Data", 0, "#ffffff"
    WATER = "Water", 1, "#069af3"
    FOREST = "Forest", 2, "#054907"
    BUILDUP = "BuildUp", 3, "#dc143c"
    BARRENLAND = "BarrenLand", 4, "#a6a6a6"
    SAVANNA = "Savanna", 5, "#564234"

    @property
    def id(self):
        return self.values[1]

    @property
    def color(self):
        return self.values[2]


# Reference colormap things
lulc_cmap = ListedColormap([x.color for x in LULC], name="lulc_cmap")
lulc_norm = BoundaryNorm([x - 0.5 for x in range(len(LULC) + 1)], lulc_cmap.N)

# VALIDITY MASK
# Validate pixels using SentinelHub's cloud detection mask and region of acquisition
add_sh_validmask = SentinelHubValidDataTask((FeatureType.MASK, "IS_VALID"))

# COUNTING VALID PIXELS
# Count the number of valid observations per pixel using valid data mask
add_valid_count = AddValidCountTask("IS_VALID", "VALID_COUNT")

# SAVING TO OUTPUT (if needed)
save = SaveTask(EOPATCH_FOLDER, overwrite_permission=OverwritePermission.OVERWRITE_PATCH)

#Importing reference data

fg = os.path.join(DATA_FOLDER, 'new_coordonates', 'EO_Browser_2480_36', 'kossou_classification_2480_36_sec.gpkg')

data = gpd.read_file(fg)
outfg = os.path.join(DATA_FOLDER, "Kossou_final_classification_ref_map_5_788_02.gpkg")
data.to_file(outfg, driver="GPKG")
outfg = os.path.join(DATA_FOLDER, "Kossou_final_classification_ref_map_5_788_02.gpkg")
vector_feature = FeatureType.VECTOR_TIMELESS, "LULC_REFERENCE"

vector_import_task = VectorImportTask(vector_feature, outfg)

rasterization_task = VectorToRasterTask(
    vector_feature,
    (FeatureType.MASK_TIMELESS, "LULC"),
    values_column="DN",
    raster_shape=(FeatureType.MASK, "IS_DATA"),
    raster_dtype=np.uint8,
)


# Define the workflow
workflow_nodes = linearly_connect_tasks(
    add_data, ndvi, ndwi, ndbi, add_sh_validmask, add_valid_count, scl, vector_import_task, rasterization_task, save
)
workflow = EOWorkflow(workflow_nodes)

# Let's visualize it
workflow.dependency_graph()


%%time

# Time interval for the SH request
time_interval = ["2022-01-01", "2022-03-31"]


# Define additional parameters of the workflow
input_node = workflow_nodes[0]
save_node = workflow_nodes[-1]
execution_args = []
for idx, bbox in enumerate(bbox_list[patchIDs]):
    execution_args.append(
        {
            input_node: {"bbox": bbox, "time_interval": time_interval},
            save_node: {"eopatch_folder": f"eopatch_{idx}"},
        }
    )

# Execute the workflow
executor = EOExecutor(workflow, execution_args, save_logs=True)
executor.run(workers=4)

executor.make_report()

failed_ids = executor.get_failed_executions()
if failed_ids:
    raise RuntimeError(
        f"Execution failed EOPatches with IDs:\n{failed_ids}\n"
        f"For more info check report at {executor.get_report_path()}"
    )

Hi @Nagama.TY ,

I executed the notebook and got the error BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending. which looks like the usual issue of “jupyter notebooks and multiprocessing don’t play nicely outside of Linux”.

If this is the error you had and you’re using Mac, you could try this. Otherwise one can generally set the number of workers to 1, it will be slow but should work.

I work on Linux. I tried the workers at 1. I get a long message that starts with:

DEBUG:fiona.ogrext:Setting field 0, type 'int64', to value 2
DEBUG:fiona.ogrext:Set field DN: 2
DEBUG:fiona.ogrext:Creating feature in layer: {'id': '285', 'type': 'Feature', 'properties': {'DN': 2}, 'geometry': {'type': 'Polygon', 'coordinates': (((214627.6881537891, 783158.8817835766), (214665.49466143537, 783158.6716159518), (214665.28583181952, 783121.1024123096), (214703.0923572732, 783120.8922824796), (214702.2572494616, 782970.6155117612), (214588.83731039264, 782971.2458665003), (214588.62847514445, 782933.6766452814), (214626.4351591771, 782933.4665089982), (214626.22636163695, 782895.8972980912), (214588.41964986757, 782896.1074244973), (214588.00202922802, 782820.9689842344), (214550.19525204902, 782821.1791187947), (214549.9864289536, 782783.6098894373), (214512.17961410008, 782783.8200420266), (214513.01507725683, 782934.0970015855), (214550.8217811713, 782933.8868094772), (214551.23951711645, 783009.0252721071), (214589.04615561216, 783008.8150881545), (214589.2550108031, 783046.3843102437), (214551.44840004796, 783046.5945040747), (214551.65729295224, 783084.1637364773), (214589.46387596527, 783083.9535327681), (214589.67275109893, 783121.5227557274), (214627.47929642873, 783121.3125700589), (214627.6881537891, 783158.8817835766)),)}}
DEBUG:fiona.ogrext:Looking up DN in {'DN': 'DN'}
DEBUG:fiona.ogrext:Normalizing schema type for key 'DN' in schema OrderedDict([('DN', 'int')]) to 'int64'
DEBUG:fiona.ogrext:Setting field 0, type 'int64', to value 2
DEBUG:fiona.ogrext:Set field DN: 2

and ends with :

DEBUG:sentinelhub.download.sentinelhub_client:Sending POST request to https://services.sentinel-hub.com/api/v1/process. Hash of sent request is af823da65f9b52cf7eaaf178307cbfc0
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): services.sentinel-hub.com:443
DEBUG:urllib3.connectionpool:https://services.sentinel-hub.com:443 "POST /api/v1/process HTTP/1.1" 200 None

And when I visualize with the following code:

EOPatch.load('./eopatches/eopatch_0/')

I get this:

DEBUG:fiona.env:Entering env context: <fiona.env.Env object at 0x7f83fc244490>
DEBUG:fiona.env:Starting outermost env
DEBUG:fiona.env:No GDAL environment exists
DEBUG:fiona.env:New GDAL environment <fiona._env.GDALEnv object at 0x7f83fc70ddd0> created
DEBUG:fiona._env:GDAL data found in package: path='/usr/local/lib/python3.7/dist-packages/fiona/gdal_data'.
DEBUG:fiona._env:PROJ data found in package: path='/usr/local/lib/python3.7/dist-packages/fiona/proj_data'.
DEBUG:fiona._env:Started GDALEnv: self=<fiona._env.GDALEnv object at 0x7f83fc70ddd0>.
DEBUG:fiona.env:Updated existing <fiona._env.GDALEnv object at 0x7f83fc70ddd0> with options {}
DEBUG:fiona.env:Entered env context: <fiona.env.Env object at 0x7f83fc244490>
WARNING:fiona._env:File /vsimem/1e7531905b294a89bfd239c2fb7fff1a has GPKG application_id, but non conformant file extension
DEBUG:fiona.ogrext:Got coordinate system
DEBUG:fiona.ogrext:OLC_FASTSETNEXTBYINDEX: 0
DEBUG:fiona.ogrext:OLC_FASTFEATURECOUNT: 1
DEBUG:fiona.ogrext:Next index: 0
....
DEBUG:fiona.ogrext:Next index: 283
DEBUG:fiona.collection:Flushed buffer
DEBUG:fiona.collection:Stopped session
DEBUG:fiona.env:Exiting env context: <fiona.env.Env object at 0x7f83fc244490>
DEBUG:fiona.env:Cleared existing <fiona._env.GDALEnv object at 0x7f83fc70ddd0> options
DEBUG:fiona._env:Stopping GDALEnv <fiona._env.GDALEnv object at 0x7f83fc70ddd0>.
DEBUG:fiona._env:Error handler popped.
DEBUG:fiona._env:Stopped GDALEnv <fiona._env.GDALEnv object at 0x7f83fc70ddd0>.
DEBUG:fiona.env:Exiting outermost env
DEBUG:fiona.env:Exited env context: <fiona.env.Env object at 0x7f83fc244490>

Is this normal ? Thank you very much for your availability.

I am also having trouble downloading eopatches. I followed @Nagama.TY’s code above and receives this error:

eolearn.core.eoworkflow ERROR Task ‘VectorImportTask’ with id VectorImportTask-6843dc13ad7411ed868b-bb6fe1bb5745 failed

and

TypeError: to_epsg() got an unexpected keyword argument ‘min_confidence’

Please help me find a solution. Thank you

Hi @elcahapin ,

We have an example for eo-learn in the documentation. Could you pleas make sure you have the latest version of eo-learn and sentinelhub and try to follow the example noteobook?

Thank you.

You must use the latest versions of sentinelhub and eo-learn. This is how I then solved the problem effectively.

But however at the level of the preparation of the training data, I encounter problems at this level. The execution of the workflow runs without being able to generate the files even using the example of Slovenia. How can I resolve this ?

I have followed closely the installation guide and updated to the latest version of eo-learn and sentinel hub, but received this error:

eolearn.core.eoworkflow ERROR Task 'VectorImportTask
ValueError: {} is not a valid CRS

At this level I don’t know what the problem is due to. Is this a problem with the file you embedded in the VectorImportTask class? Otherwise with the update I was able to solve the problem.

Hi @elcahapin ,

From the error message it seems to me that the info of CRS is missing in your input. Could you try something along the lines:

print(geo_data_frame.crs)

to see if the geopandas data frame has valid CRS?

If I am (completely) off, please provide more info (where this happens etc).

Hi @Nagama.TY ,

May I ask what problems did you encounter? Could you please provide more information about it (what is the error, where does it happen, etc)?

Yes. Thank you. I have already solved it by using a different vector file.