diff --git a/.gitignore b/.gitignore index d21a1872..38a71de2 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ +temporary_trashcan/ + # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] diff --git a/benchmarks/REPORT.MD b/benchmarks/REPORT.MD new file mode 100644 index 00000000..943fc6f3 --- /dev/null +++ b/benchmarks/REPORT.MD @@ -0,0 +1,287 @@ +# Aggregate Spatial Analysis + +## Disclaimer + +**A lot has changed in the testing setup so the documentation needs to be updated.** + +The latest scripts for `xvec` and `exactextract` can be found in: + +- `benchmarks/xvec/` +- `benchmarks/exactextract/` + +Data still remains in: + +- `benchmarks/data/` + +Although not maintained anymore `memory_profiler` is still working and was used. + +Profiling decorator has been added to the `aggregate_spatial` function to enable line by line profiling. + +`openeo-processes-dask/openeo_processes_dask/process_implementations/cubes/aggregate.py` + +Example to run the scripts with `memory_profiler`: + +```bash +mprof run xvec_small_sample.py +``` + +Dont forget to install all extras when installing with poetry to get the `benchmark` extras and all other requirements. + +```bash +poetry install --all-extras +``` + +## Table of Contents + +1. [Introduction](#10-introduction) +2. [Methodology](#20-methodology) +3. [Datasets](#30-datasets) +4. [Initial Results (OUTDATED)](#40-initial-results-outdated) + 1. [Small Dataset (2 polygons)](#41-small-dataset-2-polygons) + 1. [OpenEO xvec](#411-openeo-xvec) + 2. [OpenEO exactextract](#412-openeo-exactextract) + 2. [Large Dataset (116 polygons)](#42-large-dataset-116-polygons) + 1. [OpenEO xvec](#421-openeo-xvec) + 2. [OpenEO exactextract](#422-openeo-exactextract) +5. [Conclusion and Comments](#50-conclusion-and-comments) + +## 1.0 Introduction + +The purpose of this benchmark is to quantify the performance of the OpenEO aggregate_spatial process. Current implementation uses the `xvec` library. Issues arise if a large vector dataset is used. The kernel tends to crash, suggesting the current implementation is not efficient enough. The benchmark will test the performance of the current implementation and compare it to a new implementation using the `exactextract` library. + +## 2.0 Methodology + +TODO + +## 3.0 Datasets + +For the purpose of testing the performance we have obtained two datasets. The first is a very small dataset containing two polygons in the Bolzano area. The second dataset is a larger dataset containing the Alto Adige region. + +The first dataset: `sample_polygons.geojson` has been provided by @clausmichele + +- 2 polygons + +The second dataset: `alto_adige.geojson` comes from the Openpolis github repository: `https://github.com/openpolis/geojson-italy` + +- 116 polygons + +## 4.0 Initial Results (Outdated) + +The sections below provide some results for the `small` and `large` dataset. We are comparing the current OpenEO `xvec` implementation first, followed by utilizing `exactextract` to perform the same operation. + +Quick summary of the results: + +| Metric | Small Dataset (2 polygons) | Large Dataset (116 polygons) | +| --- | --- | --- | +|OpenEO xvec| 20-27 seconds | 1057 seconds / 17 minutes | +|OpenEO exactextract| 15-25 seconds | 1085 seconds / 18 minutes | + +### 4.1 Small Dataset (2 polygons) + +#### 4.1.1 OpenEO xvec + +```python +from profiler import Profiler + +import json +import fiona +import geopandas as gpd +from openeo.local import LocalConnection + +local_conn = LocalConnection("./") + +url = "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a" +spatial_extent = {"east": 11.40, "north": 46.52, "south": 46.46, "west": 11.25} +temporal_extent = ["2022-06-01", "2022-06-30"] +bands = ["red"] +properties = {"eo:cloud_cover": dict(lt=80)} + +s2_datacube = local_conn.load_stac( + url=url, + spatial_extent=spatial_extent, + temporal_extent=temporal_extent, + bands=bands, + properties=properties, +) + +s2_datacube = s2_datacube.resample_spatial( + projection="EPSG:4326", resolution=0.0001 +).drop_dimension("band") + +polys_path = "./data/sample_polygons.geojson" + +polys = gpd.read_file(polys_path) + +# Don't know why this is needed but it is. +# https://geopandas.org/en/stable/docs/reference/api/geopandas.GeoDataFrame.__geo_interface__.html +polys = polys.__geo_interface__ + +aggregate = s2_datacube.aggregate_spatial(geometries=polys, reducer="mean") + +@Profiler(reruns=1, sample_interval=1, log_file="sm_xvec.csv") +def run_aggregate(): + aggregate.execute() + +run_aggregate() +``` + +| Metric | Value | +| --- | --- | +|Run_ID| X | +|Timestamp| X | +|Sample_Timestamp| X | +|CPU_Usage_%| 24% | +|Time_Taken| 20-27 seconds | +|Median_Memory_Usage_MB| 45 - 65 MB | + +#### 4.1.2 OpenEO exactextract + +```python +from profiler import Profiler + +import json +import geopandas as gpd +from openeo.local import LocalConnection +from exactextract import exact_extract + +local_conn = LocalConnection("./") + +url = "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a" +spatial_extent = {"east": 11.40, "north": 46.52, "south": 46.46, "west": 11.25} +temporal_extent = ["2022-06-01", "2022-06-30"] +bands = ["red"] +properties = {"eo:cloud_cover": dict(lt=80)} + +s2_datacube = local_conn.load_stac( + url=url, + spatial_extent=spatial_extent, + temporal_extent=temporal_extent, + bands=bands, + properties=properties, +) + +s2_datacube = s2_datacube.resample_spatial(projection="EPSG:4326",resolution=0.0001).drop_dimension("band") +data = s2_datacube.execute() + +polys = gpd.read_file("./data/sample_polygons.geojson") + +@Profiler(reruns=1, sample_interval=1) +def run_extract(): + exact_extract(data, polys, 'mean') + +run_extract() +``` + +| Metric | Value | +| --- | --- | +|Run_ID| X | +|Timestamp| X | +|Sample_Timestamp| X | +|CPU_Usage_%| 28% | +|Time_Taken| 15-25 seconds | +|Median_Memory_Usage_MB| 40 - 60 MB | + +### 4.2 Large Dataset (116 polygons) + +#### 4.2.1 OpenEO xvec + +```python +from profiler import Profiler + +import json +import geopandas as gpd +from openeo.local import LocalConnection + +local_conn = LocalConnection("./") + +URL = "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a" +SPATIAL_EXTENT = {"east": 11.8638, "north": 46.7135, "south": 46.3867, "west": 10.7817} +TEMPORAL_EXTENT = ["2022-06-01", "2022-06-30"] +BANDS = ["red"] +PROPERTIES = {"eo:cloud_cover": dict(lt=80)} + +s2_datacube = local_conn.load_stac( + url=URL, + spatial_extent=SPATIAL_EXTENT, + temporal_extent=TEMPORAL_EXTENT, + bands=BANDS, + properties=PROPERTIES, +) + +s2_datacube = s2_datacube.resample_spatial( + projection="EPSG:4326", resolution=0.0001).drop_dimension("band") + +polys = gpd.read_file("./data/alto_adige.geojson") +polys = polys.__geo_interface__ + +aggregate = s2_datacube.aggregate_spatial(geometries=polys, reducer="mean") + + +@Profiler(reruns=1, sample_interval=1) +def run_aggregate(): + aggregate.execute() + +run_aggregate() +``` + +| Metric | Value | +| --- | --- | +|Run_ID| X | +|Timestamp| X | +|Sample_Timestamp| X | +|CPU_Usage_%| 59% | +|Time_Taken| 1057 seconds / 17 minutes | +|Median_Memory_Usage_MB| 360 MB | + +#### 4.2.2 OpenEO exactextract + +```python +from profiler import Profiler + +import json +import geopandas as gpd +from openeo.local import LocalConnection +from exactextract import exact_extract + +local_conn = LocalConnection("./") + +URL = "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a" +SPATIAL_EXTENT = {"east": 11.8638, "north": 46.7135, "south": 46.3867, "west": 10.7817} +TEMPORAL_EXTENT = ["2022-06-01", "2022-06-30"] +BANDS = ["red"] +PROPERTIES = {"eo:cloud_cover": dict(lt=80)} + +s2_datacube = local_conn.load_stac( + url=URL, + spatial_extent=SPATIAL_EXTENT, + temporal_extent=TEMPORAL_EXTENT, + bands=BANDS, + properties=PROPERTIES, +) + +s2_datacube = s2_datacube.resample_spatial(projection="EPSG:4326",resolution=0.0001).drop_dimension("band") +data = s2_datacube.execute() + +polys = gpd.read_file("./data/alto_adige.geojson") + +@Profiler(reruns=1, sample_interval=1) +def run_extract(): + exact_extract(data, polys, 'mean') + +run_extract() +``` + +| Metric | Value | +| --- | --- | +|Run_ID| X | +|Timestamp| X | +|Sample_Timestamp| X | +|CPU_Usage_%| 63% | +|Time_Taken| 1085 seconds / 18 minutes | +|Median_Memory_Usage_MB| 360 MB | + +### 5.0 Conclusion and Comments + +So based on running the two comparisons, the efficiency is actually not that much +different. I am not exactly sure why yet, perhaps the OpenEO input cube causes it +to be slow even on exactextract. diff --git a/benchmarks/__init__.py b/benchmarks/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/benchmarks/data/alto_adige.geojson b/benchmarks/data/alto_adige.geojson new file mode 100644 index 00000000..2a471b33 --- /dev/null +++ b/benchmarks/data/alto_adige.geojson @@ -0,0 +1,118 @@ +{"type":"FeatureCollection","bbox":[10.386105190810296,46.219772403066244,12.477704031274008,47.09178374646217], "features": [ 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a/benchmarks/exactextract/ee_big_sample.py b/benchmarks/exactextract/ee_big_sample.py new file mode 100644 index 00000000..98c2c4ee --- /dev/null +++ b/benchmarks/exactextract/ee_big_sample.py @@ -0,0 +1,30 @@ +import geopandas as gpd +from openeo.local import LocalConnection +from exactextract import exact_extract + +local_conn = LocalConnection("./") + +URL = "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a" +SPATIAL_EXTENT = {"east": 11.8638, "north": 46.7135, "south": 46.3867, "west": 10.7817} +TEMPORAL_EXTENT = ["2022-06-01", "2022-06-30"] +BANDS = ["red"] +PROPERTIES = {"eo:cloud_cover": dict(lt=80)} + +s2_datacube = local_conn.load_stac( + url=URL, + spatial_extent=SPATIAL_EXTENT, + temporal_extent=TEMPORAL_EXTENT, + bands=BANDS, + properties=PROPERTIES, +) + +s2_datacube = s2_datacube.resample_spatial(projection="EPSG:4326",resolution=0.0001).drop_dimension("band") +data = s2_datacube.execute() + +polys = gpd.read_file("./data/alto_adige.geojson") + +def run_extract(): + exact_extract(data, polys, 'mean') + +if __name__ == "__main__": + run_extract() \ No newline at end of file diff --git a/benchmarks/exactextract/ee_fr_slo.py b/benchmarks/exactextract/ee_fr_slo.py new file mode 100644 index 00000000..9300a18f --- /dev/null +++ b/benchmarks/exactextract/ee_fr_slo.py @@ -0,0 +1,32 @@ +import geopandas as gpd +from openeo.local import LocalConnection +from exactextract import exact_extract + +local_conn = LocalConnection("./") + +url = "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a" +temporal_extent = ["2022-06-01", "2022-06-30"] +spatial_extent = {"west": 5.9139132444292954,"south": 45.0965802219263,"east": 13.829701504566117,"north": 46.954031232759576} +bands = ["red"] +properties = {"eo:cloud_cover": dict(lt=80)} + +s2_datacube = local_conn.load_stac( + url=url, + spatial_extent=spatial_extent, + temporal_extent=temporal_extent, + bands=bands, + properties=properties, +) + +s2_datacube = s2_datacube.resample_spatial( + projection="EPSG:4326", resolution=0.0001).drop_dimension("band") + +data = s2_datacube.execute() + +polys = gpd.read_file("../data/fr_slo.geojson") + +def run_extract(): + exact_extract(data, polys, 'mean') + +if __name__ == "__main__": + run_extract() \ No newline at end of file diff --git a/benchmarks/exactextract/ee_small_sample.py b/benchmarks/exactextract/ee_small_sample.py new file mode 100644 index 00000000..92171d67 --- /dev/null +++ b/benchmarks/exactextract/ee_small_sample.py @@ -0,0 +1,30 @@ +import geopandas as gpd +from openeo.local import LocalConnection +from exactextract import exact_extract + +local_conn = LocalConnection("./") + +url = "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a" +spatial_extent = {"east": 11.40, "north": 46.52, "south": 46.46, "west": 11.25} +temporal_extent = ["2022-06-01", "2022-06-30"] +bands = ["red"] +properties = {"eo:cloud_cover": dict(lt=80)} + +s2_datacube = local_conn.load_stac( + url=url, + spatial_extent=spatial_extent, + temporal_extent=temporal_extent, + bands=bands, + properties=properties, +) + +s2_datacube = s2_datacube.resample_spatial(projection="EPSG:4326",resolution=0.0001).drop_dimension("band") +data = s2_datacube.execute() + +polys = gpd.read_file("./data/sample_polygons.geojson") + +def run_extract(): + exact_extract(data, polys, 'mean') + +if __name__ == "__main__": + run_extract() \ No newline at end of file diff --git a/benchmarks/profiler.py b/benchmarks/profiler.py new file mode 100644 index 00000000..8ff3371b --- /dev/null +++ b/benchmarks/profiler.py @@ -0,0 +1,164 @@ +""" +Generic profiling class to support generating different statistics +and measure perfoamnce of the code. + +- Example usage as a decorator +@Profiler() +def some_function(): + # Your code here + pass + +- Example usage with a with statement +with Profiler(): + # Your code block here + pass + +NOTE: There is a lot of things broken with the CSV output reporting +due it taking only 1 timestamp etc. but I feel like it is unnecessary work +to extend the functionality as what we have now is good enough. + +""" +import cProfile +import functools +import gc +import os +import psutil +import statistics +import threading +import time +import timeit +import tracemalloc +import uuid +from datetime import datetime, timedelta +import csv + +class Profiler: + def __init__(self, reruns=1, log_file="profiler_log.csv", sample_interval=0.1): + self.reruns = reruns + self.times = [] + self.memory_usages = [] + self.cpu_usages = [] + self.disk_io_read = [] + self.disk_io_write = [] + self.net_io_sent = [] + self.net_io_recv = [] + self.profile = cProfile.Profile() + self.process = psutil.Process(os.getpid()) + self.log_file = log_file + self.memory_samples = [] + self.cpu_samples = [] + self.sample_interval = sample_interval + self.sampling_thread = None + self.sampling_stop_event = threading.Event() + + def start_sampling_thread(self): + def sample_memory_and_cpu(): + while not self.sampling_stop_event.is_set(): + self.sample_memory_usage() + self.sample_cpu_usage() + time.sleep(self.sample_interval) + + self.sampling_thread = threading.Thread(target=sample_memory_and_cpu) + self.sampling_thread.start() + + def stop_sampling_thread(self): + self.sampling_stop_event.set() + if self.sampling_thread: + self.sampling_thread.join() + + def sample_cpu_usage(self): + cpu_usage = self.process.cpu_percent(interval=None) + self.cpu_samples.append(cpu_usage) + + def start_profiling(self): + tracemalloc.start() + self.start_time = timeit.default_timer() + self.start_memory_info = self.process.memory_info() + self.start_disk_io = psutil.disk_io_counters() + self.start_net_io = psutil.net_io_counters() + self.memory_samples = [] + self.cpu_samples = [] + self.profile.enable() + + def sample_memory_usage(self): + gc.collect() + current, peak = tracemalloc.get_traced_memory() + self.memory_samples.append(peak / (1024 ** 2)) + + def stop_profiling(self): + tracemalloc.stop() + self.profile.disable() + self.end_time = timeit.default_timer() + self.end_memory_info = self.process.memory_info() + self.end_disk_io = psutil.disk_io_counters() + self.end_net_io = psutil.net_io_counters() + + time_taken = self.end_time - self.start_time + median_memory_usage = statistics.median(self.memory_samples) if self.memory_samples else 0 + median_cpu_usage = statistics.median(self.cpu_samples) if self.cpu_samples else 0 + + disk_io_read = (self.end_disk_io.read_bytes - self.start_disk_io.read_bytes) / (1024**2) + disk_io_write = (self.end_disk_io.write_bytes - self.start_disk_io.write_bytes) / (1024**2) + net_io_sent = (self.end_net_io.bytes_sent - self.start_net_io.bytes_sent) / (1024**2) + net_io_recv = (self.end_net_io.bytes_recv - self.start_net_io.bytes_recv) / (1024**2) + + self.times.append(time_taken) + self.memory_usages.append(median_memory_usage) + self.cpu_usages.append(median_cpu_usage) + self.disk_io_read.append(disk_io_read) + self.disk_io_write.append(disk_io_write) + self.net_io_sent.append(net_io_sent) + self.net_io_recv.append(net_io_recv) + + self.log_results(time_taken, median_memory_usage, median_cpu_usage, disk_io_read, disk_io_write, net_io_sent, net_io_recv) + + def report(self): + median_time = statistics.median(self.times) if self.times else 0 + median_memory_usage = statistics.median(self.memory_usages) if self.memory_usages else 0 + median_cpu_usage = statistics.median(self.cpu_usages) if self.cpu_usages else 0 + + print(f"Median Time: {median_time:.2f} seconds") + print(f"Median Memory Usage: {median_memory_usage:.2f} MB") + print(f"Median CPU Usage: {median_cpu_usage:.2f}%") + + self.profile.print_stats() + + def log_results(self, time_taken, median_memory_usage, median_cpu_usage, disk_io_read, disk_io_write, net_io_sent, net_io_recv): + run_id = uuid.uuid4() + timestamp = datetime.now() + headers = ['Run_ID', 'Timestamp', 'Sample_Timestamp', 'Memory_Sample_MB', 'CPU_Usage_%', 'Time_Taken', 'Median_Memory_Usage_MB', 'Median_CPU_Usage_%', 'Disk_IO_Read_MB', 'Disk_IO_Write_MB', 'Network_IO_Sent_MB', 'Network_IO_Received_MB'] + + file_exists = os.path.isfile(self.log_file) + with open(self.log_file, 'a', newline='') as csvfile: + writer = csv.writer(csvfile) + if not file_exists: + writer.writerow(headers) + for i, (memory_sample, cpu_sample) in enumerate(zip(self.memory_samples, self.cpu_samples)): + sample_time = timestamp + timedelta(seconds=i * self.sample_interval) + sample_timestamp = sample_time.strftime("%Y-%m-%d %H:%M:%S") + data = [str(run_id), timestamp.strftime("%Y-%m-%d %H:%M:%S"), sample_timestamp, memory_sample, cpu_sample, time_taken, median_memory_usage, median_cpu_usage, disk_io_read, disk_io_write, net_io_sent, net_io_recv] + writer.writerow(data) + + def __call__(self, func): + @functools.wraps(func) + def wrapper(*args, **kwargs): + for _ in range(self.reruns): + if hasattr(func, 'cache_clear'): + func.cache_clear() + self.start_profiling() + self.start_sampling_thread() + result = func(*args, **kwargs) + self.stop_sampling_thread() + self.stop_profiling() + self.report() + return result + return wrapper + + def __enter__(self): + self.start_profiling() + return self + + def __exit__(self, *args): + self.stop_profiling() + self.report() + diff --git a/benchmarks/report_tests.ipynb b/benchmarks/report_tests.ipynb new file mode 100644 index 00000000..ae0098e1 --- /dev/null +++ b/benchmarks/report_tests.ipynb @@ -0,0 +1,1796 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# OUTDATED: This script is outdated and will be updated soon\n", + "# THANK YOU FOR YOUR PATIENCE\n", + "# SEE REPORT.MD FOR LATEST SCRIPTS\n", + "\n", + "from profiler import Profiler\n", + "\n", + "import json\n", + "import fiona\n", + "import geopandas as gpd\n", + "from openeo.local import LocalConnection\n", + "\n", + "local_conn = LocalConnection(\"./\")\n", + "\n", + "url = \"https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a\"\n", + "spatial_extent = {\"east\": 11.40, \"north\": 46.52, \"south\": 46.46, \"west\": 11.25}\n", + "temporal_extent = [\"2022-06-01\", \"2022-06-30\"]\n", + "bands = [\"red\"]\n", + "properties = {\"eo:cloud_cover\": dict(lt=80)}\n", + "\n", + "s2_datacube = local_conn.load_stac(\n", + " url=url,\n", + " spatial_extent=spatial_extent,\n", + " temporal_extent=temporal_extent,\n", + " bands=bands,\n", + " properties=properties,\n", + ")\n", + "\n", + "s2_datacube = s2_datacube.resample_spatial(\n", + " projection=\"EPSG:4326\", resolution=0.0001\n", + ").drop_dimension(\"band\")\n", + "\n", + "polys_path = \"./data/sample_polygons.geojson\"\n", + "\n", + "polys = gpd.read_file(polys_path)\n", + "polys = polys.__geo_interface__\n", + "\n", + "aggregate = s2_datacube.aggregate_spatial(geometries=polys, reducer=\"mean\")\n", + "\n", + "@Profiler(reruns=1, sample_interval=1, log_file=\"sm_xvec.csv\")\n", + "def run_aggregate():\n", + " aggregate.execute()\n", + "\n", + "run_aggregate()" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/jzvolensky/eurac/projects/openeo-processes-dask/.venv/lib/python3.10/site-packages/stackstac/prepare.py:408: UserWarning: The argument 'infer_datetime_format' is deprecated and will be removed in a future version. A strict version of it is now the default, see https://pandas.pydata.org/pdeps/0004-consistent-to-datetime-parsing.html. You can safely remove this argument.\n", + " times = pd.to_datetime(\n", + "/home/jzvolensky/eurac/projects/openeo-processes-dask/.venv/lib/python3.10/site-packages/stackstac/prepare.py:408: UserWarning: The argument 'infer_datetime_format' is deprecated and will be removed in a future version. A strict version of it is now the default, see https://pandas.pydata.org/pdeps/0004-consistent-to-datetime-parsing.html. You can safely remove this argument.\n", + " times = pd.to_datetime(\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Median Time: 17.69 seconds\n", + "Median Memory Usage: 52.53 MB\n", + "Median CPU Usage: 28.55%\n", + " 1226398 function calls (1210236 primitive calls) in 17.688 seconds\n", + "\n", + " Ordered by: standard name\n", + "\n", + " ncalls tottime percall cumtime percall filename:lineno(function)\n", + " 1 0.000 0.000 16.677 16.677 1088549347.py:29(run_extract)\n", + " 15 0.000 0.000 0.000 0.000 :100(acquire)\n", + " 14/6 0.000 0.000 0.058 0.010 :1022(_find_and_load)\n", + " 5 0.000 0.000 0.033 0.007 :1038(_gcd_import)\n", + " 155/147 0.000 0.000 0.022 0.000 :1053(_handle_fromlist)\n", + " 15 0.000 0.000 0.000 0.000 :125(release)\n", + " 14 0.000 0.000 0.000 0.000 :165(__init__)\n", + " 14 0.000 0.000 0.000 0.000 :169(__enter__)\n", + " 14 0.000 0.000 0.000 0.000 :173(__exit__)\n", + " 15 0.000 0.000 0.000 0.000 :179(_get_module_lock)\n", + " 15 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0.000 {method 'update' of 'set' objects}\n", + " 2722 0.002 0.000 0.002 0.000 {method 'values' of 'dict' objects}\n", + " 48 0.000 0.000 0.000 0.000 {method 'view' of 'numpy.generic' objects}\n", + " 1 0.000 0.000 0.000 0.000 {method 'view' of 'numpy.ndarray' objects}\n", + "\n", + "\n" + ] + } + ], + "source": [ + "from profiler import Profiler\n", + "\n", + "import json\n", + "import geopandas as gpd\n", + "from openeo.local import LocalConnection\n", + "from exactextract import exact_extract\n", + "\n", + "local_conn = LocalConnection(\"./\")\n", + "\n", + "url = \"https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a\"\n", + "spatial_extent = {\"east\": 11.40, \"north\": 46.52, \"south\": 46.46, \"west\": 11.25}\n", + "temporal_extent = [\"2022-06-01\", \"2022-06-30\"]\n", + "bands = [\"red\"]\n", + "properties = {\"eo:cloud_cover\": dict(lt=80)}\n", + "\n", + "s2_datacube = local_conn.load_stac(\n", + " url=url,\n", + " spatial_extent=spatial_extent,\n", + " temporal_extent=temporal_extent,\n", + " bands=bands,\n", + " properties=properties,\n", + ")\n", + "\n", + "s2_datacube = s2_datacube.resample_spatial(projection=\"EPSG:4326\",resolution=0.0001).drop_dimension(\"band\")\n", + "data = s2_datacube.execute()\n", + "\n", + "polys = gpd.read_file(\"./data/sample_polygons.geojson\")\n", + "\n", + "@Profiler(reruns=1, sample_interval=1)\n", + "def run_extract():\n", + " exact_extract(data, polys, 'mean')\n", + "\n", + "run_extract()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from profiler import Profiler\n", + "\n", + "import json\n", + "import geopandas as gpd\n", + "from openeo.local import LocalConnection\n", + "\n", + "local_conn = LocalConnection(\"./\")\n", + "\n", + "URL = \"https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a\"\n", + "SPATIAL_EXTENT = {\"east\": 11.8638, \"north\": 46.7135, \"south\": 46.3867, \"west\": 10.7817}\n", + "TEMPORAL_EXTENT = [\"2022-06-01\", \"2022-06-30\"]\n", + "BANDS = [\"red\"]\n", + "PROPERTIES = {\"eo:cloud_cover\": dict(lt=80)}\n", + "\n", + "s2_datacube = local_conn.load_stac(\n", + " url=URL,\n", + " spatial_extent=SPATIAL_EXTENT,\n", + " temporal_extent=TEMPORAL_EXTENT,\n", + " bands=BANDS,\n", + " properties=PROPERTIES,\n", + ")\n", + "\n", + "s2_datacube = s2_datacube.resample_spatial(\n", + " projection=\"EPSG:4326\", resolution=0.0001\n", + ").drop_dimension(\"band\")\n", + "\n", + "polys = gpd.read_file(\"./data/alto_adige.geojson\")\n", + "polys = polys.__geo_interface__\n", + "\n", + "aggregate = s2_datacube.aggregate_spatial(geometries=polys, reducer=\"mean\")\n", + "\n", + "\n", + "@Profiler(reruns=1, sample_interval=1)\n", + "def run_aggregate():\n", + " aggregate.execute()\n", + "\n", + "run_aggregate()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from profiler import Profiler\n", + "\n", + "import json\n", + "import geopandas as gpd\n", + "from openeo.local import LocalConnection\n", + "from exactextract import exact_extract\n", + "\n", + "local_conn = LocalConnection(\"./\")\n", + "\n", + "URL = \"https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a\"\n", + "SPATIAL_EXTENT = {\"east\": 11.8638, \"north\": 46.7135, \"south\": 46.3867, \"west\": 10.7817}\n", + "TEMPORAL_EXTENT = [\"2022-06-01\", \"2022-06-30\"]\n", + "BANDS = [\"red\"]\n", + "PROPERTIES = {\"eo:cloud_cover\": dict(lt=80)}\n", + "\n", + "s2_datacube = local_conn.load_stac(\n", + " url=URL,\n", + " spatial_extent=SPATIAL_EXTENT,\n", + " temporal_extent=TEMPORAL_EXTENT,\n", + " bands=BANDS,\n", + " properties=PROPERTIES,\n", + ")\n", + "\n", + "s2_datacube = s2_datacube.resample_spatial(projection=\"EPSG:4326\",resolution=0.0001).drop_dimension(\"band\")\n", + "data = s2_datacube.execute()\n", + "\n", + "#polys = fiona.open('./data/alto_adige.geojson')\n", + "\n", + "polys = gpd.read_file(\"./data/alto_adige.geojson\")\n", + "#polys = polys.__geo_interface__\n", + "\n", + "@Profiler(reruns=1, sample_interval=1)\n", + "def run_extract():\n", + " exact_extract(data, polys, 'mean')\n", + "\n", + "run_extract()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.12" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/benchmarks/xvec/xvec_big_sample.py b/benchmarks/xvec/xvec_big_sample.py new file mode 100644 index 00000000..8b42ea86 --- /dev/null +++ b/benchmarks/xvec/xvec_big_sample.py @@ -0,0 +1,40 @@ +""" +OpenEO xvec example using 116 polygons of the +Alto Adige region in Italy. +""" + +import geopandas as gpd +from openeo.local import LocalConnection + +local_conn = LocalConnection("./") + +url = "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a" +spatial_extent = {"east": 11.8638, "north": 46.7135, "south": 46.3867, "west": 10.7817} +temporal_extent = ["2022-06-01", "2022-06-30"] +bands = ["red"] +properties = {"eo:cloud_cover": dict(lt=80)} + +s2_datacube = local_conn.load_stac( + url=url, + spatial_extent=spatial_extent, + temporal_extent=temporal_extent, + bands=bands, + properties=properties, +) + +s2_datacube = s2_datacube.resample_spatial( + projection="EPSG:4326", resolution=0.0001 +).drop_dimension("band") + +polys = gpd.read_file("./data/alto_adige.geojson") +polys = polys.__geo_interface__ + +aggregate = s2_datacube.aggregate_spatial(geometries=polys, reducer="mean") + +def run_aggregate(): + aggregate.execute().compute() + +run_aggregate() + +if __name__ == "__main__": + run_aggregate() \ No newline at end of file diff --git a/benchmarks/xvec/xvec_fr_slo_sample.py b/benchmarks/xvec/xvec_fr_slo_sample.py new file mode 100644 index 00000000..2203abc5 --- /dev/null +++ b/benchmarks/xvec/xvec_fr_slo_sample.py @@ -0,0 +1,43 @@ +""" +OpenEO xvec example using a large area with 2 polygons +on the french side of alps and 2 polygons on the slovenian side. +""" +import geopandas as gpd +from openeo.local import LocalConnection +from memory_profiler import profile + +local_conn = LocalConnection("./") + +polys_path = "../data/fr_slo.geojson" + +polys = gpd.read_file(polys_path) +polys = polys.__geo_interface__ + +url = "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a" +temporal_extent = ["2022-06-01", "2022-06-30"] +spatial_extent = {"west": 5.9139132444292954,"south": 45.0965802219263,"east": 13.829701504566117,"north": 46.954031232759576} +bands = ["red"] +properties = {"eo:cloud_cover": dict(lt=80)} + +s2_datacube = local_conn.load_stac( + url=url, + spatial_extent=spatial_extent, + temporal_extent=temporal_extent, + bands=bands, + properties=properties, +) + +s2_datacube = s2_datacube.resample_spatial( + projection="EPSG:4326", resolution=0.0001 +).drop_dimension("band") + +aggregate = s2_datacube.aggregate_spatial(geometries=polys, reducer="mean") + +def execute(): + aggregate.execute().compute() + + +if __name__ == "__main__": + execute() + + \ No newline at end of file diff --git a/benchmarks/xvec/xvec_small_sample.py b/benchmarks/xvec/xvec_small_sample.py new file mode 100644 index 00000000..a79dc79c --- /dev/null +++ b/benchmarks/xvec/xvec_small_sample.py @@ -0,0 +1,37 @@ +""" +OpenEO xvec example on a small dataset around Bolzano +""" + +import geopandas as gpd +from openeo.local import LocalConnection + +local_conn = LocalConnection("./") + +url = "https://earth-search.aws.element84.com/v1/collections/sentinel-2-l2a" +spatial_extent = {"east": 11.40, "north": 46.52, "south": 46.46, "west": 11.25} +temporal_extent = ["2022-06-01", "2022-06-30"] +bands = ["red"] +properties = {"eo:cloud_cover": dict(lt=80)} + +s2_datacube = local_conn.load_stac( + url=url, + spatial_extent=spatial_extent, + temporal_extent=temporal_extent, + bands=bands, + properties=properties, +) + +s2_datacube = s2_datacube.resample_spatial( + projection="EPSG:4326", resolution=0.0001).drop_dimension("band") + +polys_path = "../data/sample_polygons.geojson" +polys = gpd.read_file(polys_path) +polys = polys.__geo_interface__ + +aggregate = s2_datacube.aggregate_spatial(geometries=polys, reducer="mean") + +def run_aggregate(): + aggregate.execute().compute() + +if __name__ == "__main__": + run_aggregate() \ No newline at end of file diff --git a/openeo_processes_dask/process_implementations/cubes/aggregate.py b/openeo_processes_dask/process_implementations/cubes/aggregate.py index 3af1d0d0..68cc729c 100644 --- a/openeo_processes_dask/process_implementations/cubes/aggregate.py +++ b/openeo_processes_dask/process_implementations/cubes/aggregate.py @@ -22,6 +22,8 @@ TooManyDimensions, ) +from memory_profiler import profile + __all__ = ["aggregate_temporal", "aggregate_temporal_period", "aggregate_spatial"] logger = logging.getLogger(__name__) @@ -110,7 +112,7 @@ def aggregate_temporal_period( reducer, keep_attrs=True, positional_parameters=positional_parameters ) - +@profile def aggregate_spatial( data: RasterCube, geometries, @@ -172,4 +174,4 @@ def aggregate_spatial( stats=reducer, positional_parameters=positional_parameters, ) - return vec_cube + return vec_cube \ No newline at end of file diff --git a/openeo_processes_dask/process_implementations/cubes/load.py b/openeo_processes_dask/process_implementations/cubes/load.py index c9a20587..fe03ac17 100644 --- a/openeo_processes_dask/process_implementations/cubes/load.py +++ b/openeo_processes_dask/process_implementations/cubes/load.py @@ -6,10 +6,11 @@ from typing import Any, Callable, Dict, List, Optional, Tuple, Union from urllib.parse import unquote, urljoin, urlparse +import numpy as np +import odc.stac import planetary_computer as pc import pyproj import pystac_client -import stackstac import xarray as xr from openeo_pg_parser_networkx.pg_schema import BoundingBox, TemporalInterval from stac_validator import stac_validator @@ -23,6 +24,7 @@ from openeo_processes_dask.process_implementations.data_model import RasterCube from openeo_processes_dask.process_implementations.exceptions import ( NoDataAvailable, + OpenEOException, TemporalExtentEmpty, ) @@ -89,6 +91,14 @@ def load_stac( ) -> RasterCube: asset_type = _validate_stac(url) + # TODO: load_stac should have a parameter to enable scale and offset + # apply_offset = False + # apply_scale = False + + # If the user provide the bands list as a single string, wrap it in a list: + if isinstance(bands, str): + bands = [bands] + if asset_type == "COLLECTION": # If query parameters are passed, try to get the parent Catalog if possible/exists, to use the /search endpoint if spatial_extent or temporal_extent or bands or properties: @@ -139,21 +149,61 @@ def load_stac( raise Exception( f"No parameters for filtering provided. Loading the whole STAC Collection is not supported yet." ) - elif asset_type == "ITEM": stac_api = pystac_client.stac_api_io.StacApiIO() stac_dict = json.loads(stac_api.read_text(url)) - items = stac_api.stac_object_from_dict(stac_dict) - + items = [stac_api.stac_object_from_dict(stac_dict)] else: raise Exception( f"The provided URL is a STAC {asset_type}, which is not yet supported. Please provide a valid URL to a STAC Collection or Item." ) + available_assets = list(items[0].assets.keys()) + if len(set(available_assets) & set(bands)) == 0: + raise OpenEOException( + f"The provided bands: {bands} can't be found in the STAC assets: {available_assets}" + ) + + asset_scale_offset = {} + for asset in items[0].assets: + if asset in bands: + asset_scale = 1 + asset_offset = 0 + asset_nodata = None + asset_dtype = None + asset_dict = items[0].assets[asset].to_dict() + if "raster:bands" in asset_dict: + asset_scale = asset_dict["raster:bands"][0].get("scale", 1) + asset_offset = asset_dict["raster:bands"][0].get("offset", 0) + asset_nodata = asset_dict["raster:bands"][0].get("nodata", None) + asset_dtype = asset_dict["raster:bands"][0].get("data_type", None) + asset_scale_offset[asset] = { + "scale": asset_scale, + "offset": asset_offset, + "nodata": asset_nodata, + "data_type": asset_dtype, + } + + # If at least one band has the nodata field set, we have to apply it at loading time + apply_nodata = True + nodata_set = {asset_scale_offset[k]["nodata"] for k in asset_scale_offset} + dtype_set = {asset_scale_offset[k]["data_type"] for k in asset_scale_offset} + kwargs = {} + if len(nodata_set) == 1 and list(nodata_set)[0] == None: + apply_nodata = False + if apply_nodata: + # We can pass only a single nodata value for all the assets/variables/bands https://github.com/opendatacube/odc-stac/issues/147#issuecomment-2005315438 + # Therefore, if we load multiple assets having different nodata values, the first one will be used + kwargs["nodata"] = list(nodata_set)[0] + dtype = list(dtype_set)[0] + if dtype is not None: + kwargs["nodata"] = np.dtype(dtype).type(kwargs["nodata"]) if bands is not None: - stack = stackstac.stack(items, assets=bands) + stack = odc.stac.load(items, bands=bands, chunks={}, **kwargs).to_dataarray( + dim="band" + ) else: - stack = stackstac.stack(items) + stack = odc.stac.load(items, chunks={}, **kwargs).to_dataarray(dim="band") if spatial_extent is not None: stack = filter_bbox(stack, spatial_extent) @@ -161,6 +211,29 @@ def load_stac( if temporal_extent is not None and asset_type == "ITEM": stack = filter_temporal(stack, temporal_extent) + # If at least one band requires to apply scale and/or offset, the datatype of the whole DataArray must be cast to float + # apply_scale = True + # scale_set = set([asset_scale_offset[k]["scale"] for k in asset_scale_offset]) + # if len(scale_set) == 1 and list(scale_set)[0] == 1: + # apply_scale = False + + # apply_offset = True + # offset_set = set([asset_scale_offset[k]["offset"] for k in asset_scale_offset]) + # if len(offset_set) == 1 and list(offset_set)[0] == 0: + # apply_offset = False + + # if apply_offset or apply_scale: + # stack = stack.astype(float) + + b_dim = stack.openeo.band_dims[0] + for b in stack[b_dim]: + scale = asset_scale_offset[b.item(0)]["scale"] + offset = asset_scale_offset[b.item(0)]["offset"] + if scale != 1: + stack.loc[{b_dim: b.item(0)}] *= scale + if offset != 0: + stack.loc[{b_dim: b.item(0)}] += offset + return stack diff --git a/pyproject.toml b/pyproject.toml index b4ee8c2c..a397897c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -35,7 +35,7 @@ rioxarray = { version = ">=0.12.0,<1", optional = true } openeo-pg-parser-networkx = { version = ">=2024.7", optional = true } odc-geo = { version = ">=0.4.1,<1", optional = true } stac_validator = { version = ">=3.3.1", optional = true } -stackstac = { version = ">=0.4.3", optional = true } +odc-stac = { version = ">=0.3.9", optional = true } pystac_client = { version = ">=0.6.1", optional = true } planetary_computer = { version = ">=0.5.1", optional = true } scipy = "^1.11.3" @@ -43,6 +43,7 @@ xvec = { version = ">=0.1.0", optional = true } joblib = { version = ">=1.3.2", optional = true } geoparquet = "^0.0.3" pyarrow = "^15.0.2" +memory-profiler = "^0.61.0" [tool.poetry.group.dev.dependencies] pytest = "^7.2.0" @@ -53,8 +54,16 @@ mapclassify = "^2.4.3" pre-commit = "^2.20.0" pytest-cov = "^4.0.0" +[tool.poetry.group.benchmark.dependencies] +psutil = "^6.0.0" +codecarbon = "^2.5.0" +openeo = { version = "^0.30.0", extras = ["localprocessing"] } +exactextract = "^0.2.0.dev0" +gdal = "3.8.4" +memory_profiler = "^0.61.0" + [tool.poetry.extras] -implementations = ["geopandas", "xarray", "dask", "rasterio", "dask-geopandas", "rioxarray", "openeo-pg-parser-networkx", "odc-geo", "stackstac", "planetary_computer", "pystac_client", "stac_validator", "xvec", "joblib"] +implementations = ["geopandas", "xarray", "dask", "rasterio", "dask-geopandas", "rioxarray", "openeo-pg-parser-networkx", "odc-geo", "odc-stac", "planetary_computer", "pystac_client", "stac_validator", "xvec", "joblib"] ml = ["xgboost"] [tool.pytest.ini_options]