Renamed examples. Updated root Readme accordingly. Updated .gitignore…

… accordingly. - Added Readme to GLC24_pre_extracted example
plantnet · Jul 5, 2024 · be98661 · be98661
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diff --git a/.gitignore b/.gitignore
@@ -16,15 +16,16 @@ examples/custom_train/micro_geolifeclef*/outputs/*
 examples/custom_train/sentinel-2a-rgbnir/dataset/*.tif
 examples/custom_train/sentinel-2a-rgbnir/outputs/*
 examples/custom_train/sentinel-2a-rgbnir_bioclim/outputs/*
+examples/custom_train/Irokube
 
 examples/inference/micro_geolifeclef*/dataset/patches
 examples/inference/micro_geolifeclef*/dataset/rasters
 examples/inference/micro_geolifeclef*/outputs/*
 examples/inference/sentinel-2a-rgbnir/outputs/*
 
-examples/benchmarks/kaggle/geolifeclef2022/dataset
-examples/benchmarks/kaggle/geolifeclef2024/dataset
-examples/benchmarks/kaggle/geolifeclef2024_pre_extracted/dataset
+examples/benchmarks/geolifeclef/geolifeclef2022/dataset
+examples/benchmarks/geolifeclef/geolifeclef2024/dataset
+examples/benchmarks/geolifeclef/geolifeclef2024_pre_extracted/dataset
 
 examples/benchmarks/cifar-10/dataset/*
 examples/benchmarks/cifar-10/outputs/*

diff --git a/README.md b/README.md
@@ -30,14 +30,15 @@ Malpolon is destined to be used by various user profiles, some more experimented
 
 Here is a list of the currently available scenarios:
 
-- [**Kaggle**](examples/kaggle/) : I am a potential kaggle participant on the GeoLifeClef challenge. I want to train a model on the provided datasets without having to worry about the data loading, starting from a plug-and-play example.
-  - [<u>GeoLifeClef2022</u>](examples/kaggle/geolifeclef2022/) : contains a fully functionnal example of a model training on the GeoLifeClef2022 dataset, from data download, to training and prediction.
-  - [<u>GeoLifeClef2023</u>](examples/kaggle/geolifeclef2023/) : contains dataloaders for the GeoLifeClef2023 dataset (different from the GLC2022 dataloaders). The training and prediction scripts are not provided.
-- [**Ecologists**](examples/ecologists/) : I have a dataset of my own and I want to train a model on it. I want to be able to easily customize the training process and the model architecture.
+- [**Benchmarks**](examples/benchmarks/) : I want to compare the performance of different models on a given known dataset;\
+  or I am a potential kaggle participant on the GeoLifeClef challenge. I want to train a model on the provided datasets without having to worry about the data loading, starting from a plug-and-play example.
+  - [<u>GeoLifeClef2022</u>](examples/benchmarks/geolifeclef2022/) : contains a fully functionnal example of a model training on the GeoLifeClef2022 dataset, from data download, to training and prediction.
+  - [<u>GeoLifeClef2023</u>](examples/benchmarks/geolifeclef2023/) : contains dataloaders for the GeoLifeClef2023 dataset (different from the GLC2022 dataloaders). The training and prediction scripts are not provided.
+  - [<u>GeoLifeClef2024 (pre-extracted)</u>](examples/benchmarks/geolifeclef2024_pre_extracted/) : contains a fully functional example of a multimodal ensemble model used to provide a strong baseline for the [GeoLifeClef2024 kaggle competition](https://www.kaggle.com/competitions/geolifeclef-2024). The example uses unique dataloaders and models to handle pre-extracted values from satellite patches, satellite time series and bioclimatic time series.
+- [**Train (custom datasets)**](examples/custom_train/) : I have a dataset of my own and I want to train a model on it. I want to be able to easily customize the training process and the model architecture.
   - <u>Drop and play</u> : I have an observations file (.csv) and I want to train a model on different environmental variables (rasters, satellite imagery) without having to worry about the data loading.
   - <u>Custom dataset</u> : I have my own dataset consisting of pre-extracted image patches and/or rasters and I want to train a model on it.
 - [**Inference**](examples/inference/) : I have an observations file (.csv) and I want to predict the presence of species on a given area using a model I trained previously and a selected dataset or a shapefile I would provide.
-- [**Benchmark**](examples/benchmark/) : I want to compare the performance of different models on a given known dataset, or validate the framework's backbone (every module apart from the datasets and datamodule) on a specific hardware.
 
 ## 🔧 Installation
 

diff --git a/examples/benchmark/cifar-10/README.md → examples/benchmarks/cifar-10/README.md b/examples/benchmark/cifar-10/README.md → examples/benchmarks/cifar-10/README.md
diff --git a/examples/benchmark/cifar-10/cnn_cifar10.py → examples/benchmarks/cifar-10/cnn_cifar10.py b/examples/benchmark/cifar-10/cnn_cifar10.py → examples/benchmarks/cifar-10/cnn_cifar10.py
diff --git a/...enchmark/cifar-10/config/cnn_cifar10.yaml → ...nchmarks/cifar-10/config/cnn_cifar10.yaml b/...enchmark/cifar-10/config/cnn_cifar10.yaml → ...nchmarks/cifar-10/config/cnn_cifar10.yaml
diff --git a/examples/benchmark/cifar-10/transforms.py → examples/benchmarks/cifar-10/transforms.py b/examples/benchmark/cifar-10/transforms.py → examples/benchmarks/cifar-10/transforms.py
diff --git a/examples/kaggle/geolifeclef2022/README.md → ...rks/geolifeclef/geolifeclef2022/README.md b/examples/kaggle/geolifeclef2022/README.md → ...rks/geolifeclef/geolifeclef2022/README.md
@@ -1,7 +1,7 @@
 # GeoLifeCLEF 2022
 
 <div align="center">
-  <a href="https://www.kaggle.com/competitions/geolifeclef-2022-lifeclef-2022-fgvc9"><img src="../../../docs/resources/GLC2022_thumbnail.jpg" alt="glc22_thumbnail" style="width: 200px;  margin-top: 15px; margin-right: 50px;"></a>
+  <a href="https://www.kaggle.com/competitions/geolifeclef-2022-lifeclef-2022-fgvc9"><img src="../../../../docs/resources/GLC2022_thumbnail.jpg" alt="glc22_thumbnail" style="width: 200px;  margin-top: 15px; margin-right: 50px;"></a>
 </div>
 
 This repository is related to the GeoLifeCLEF challenge.

diff --git a/...gle/geolifeclef2022/cnn_on_rgb_patches.py → ...lef/geolifeclef2022/cnn_on_rgb_patches.py b/...gle/geolifeclef2022/cnn_on_rgb_patches.py → ...lef/geolifeclef2022/cnn_on_rgb_patches.py
diff --git a/...lef2022/cnn_on_rgb_temperature_patches.py → ...lef2022/cnn_on_rgb_temperature_patches.py b/...lef2022/cnn_on_rgb_temperature_patches.py → ...lef2022/cnn_on_rgb_temperature_patches.py
diff --git a/...ifeclef2022/cnn_on_temperature_patches.py → ...ifeclef2022/cnn_on_temperature_patches.py b/...ifeclef2022/cnn_on_temperature_patches.py → ...ifeclef2022/cnn_on_temperature_patches.py
diff --git a/...config/homogeneous_multi_modal_model.yaml → ...config/homogeneous_multi_modal_model.yaml b/...config/homogeneous_multi_modal_model.yaml → ...config/homogeneous_multi_modal_model.yaml
diff --git a/...2/config/mono_modal_3_channels_model.yaml → ...2/config/mono_modal_3_channels_model.yaml b/...2/config/mono_modal_3_channels_model.yaml → ...2/config/mono_modal_3_channels_model.yaml
diff --git a/...ples/kaggle/geolifeclef2022/transforms.py → ...geolifeclef/geolifeclef2022/transforms.py b/...ples/kaggle/geolifeclef2022/transforms.py → ...geolifeclef/geolifeclef2022/transforms.py
diff --git a/examples/kaggle/geolifeclef2023/README.md → ...rks/geolifeclef/geolifeclef2023/README.md b/examples/kaggle/geolifeclef2023/README.md → ...rks/geolifeclef/geolifeclef2023/README.md
@@ -1,7 +1,7 @@
 # GeoLifeCLEF 2023
 
 <div align="center">
-  <a href="https://www.kaggle.com/competitions/geolifeclef-2023-lifeclef-2023-x-fgvc10?rvi=1"><img src="../../../docs/resources/GLC2023_thumbnail.jpg" alt="glc23_thumbnail" style="width: 200px;  margin-top: 15px; margin-right: 50px;"></a>
+  <a href="https://www.kaggle.com/competitions/geolifeclef-2023-lifeclef-2023-x-fgvc10?rvi=1"><img src="../../../../docs/resources/GLC2023_thumbnail.jpg" alt="glc23_thumbnail" style="width: 200px;  margin-top: 15px; margin-right: 50px;"></a>
 </div>
 
 This repository is related to the GeoLifeCLEF challenge.

diff --git a/...feclef2023/cnn_on_rgbnir_glc23_patches.py → ...feclef2023/cnn_on_rgbnir_glc23_patches.py b/...feclef2023/cnn_on_rgbnir_glc23_patches.py → ...feclef2023/cnn_on_rgbnir_glc23_patches.py
diff --git a/...rgbnir_glc23_patches_test_multiclass.yaml → ...rgbnir_glc23_patches_test_multiclass.yaml b/...rgbnir_glc23_patches_test_multiclass.yaml → ...rgbnir_glc23_patches_test_multiclass.yaml
diff --git a/...rgbnir_glc23_patches_test_multilabel.yaml → ...rgbnir_glc23_patches_test_multilabel.yaml b/...rgbnir_glc23_patches_test_multilabel.yaml → ...rgbnir_glc23_patches_test_multilabel.yaml
diff --git a/...gbnir_glc23_patches_train_multiclass.yaml → ...gbnir_glc23_patches_train_multiclass.yaml b/...gbnir_glc23_patches_train_multiclass.yaml → ...gbnir_glc23_patches_train_multiclass.yaml
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diff --git a/...ta/SatelliteImages/rgb/75/20/4032075.jpeg → ...ta/SatelliteImages/rgb/75/20/4032075.jpeg b/...ta/SatelliteImages/rgb/75/20/4032075.jpeg → ...ta/SatelliteImages/rgb/75/20/4032075.jpeg
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diff --git a/...ta/SatelliteImages/rgb/94/71/5547194.jpeg → ...ta/SatelliteImages/rgb/94/71/5547194.jpeg b/...ta/SatelliteImages/rgb/94/71/5547194.jpeg → ...ta/SatelliteImages/rgb/94/71/5547194.jpeg
diff --git a/...ta/SatelliteImages/rgb/94/76/5757694.jpeg → ...ta/SatelliteImages/rgb/94/76/5757694.jpeg b/...ta/SatelliteImages/rgb/94/76/5757694.jpeg → ...ta/SatelliteImages/rgb/94/76/5757694.jpeg
diff --git a/...ta/SatelliteImages/rgb/95/18/3441895.jpeg → ...ta/SatelliteImages/rgb/95/18/3441895.jpeg b/...ta/SatelliteImages/rgb/95/18/3441895.jpeg → ...ta/SatelliteImages/rgb/95/18/3441895.jpeg
diff --git a/...ta/SatelliteImages/rgb/95/55/4875595.jpeg → ...ta/SatelliteImages/rgb/95/55/4875595.jpeg b/...ta/SatelliteImages/rgb/95/55/4875595.jpeg → ...ta/SatelliteImages/rgb/95/55/4875595.jpeg
diff --git a/...ta/SatelliteImages/rgb/95/60/3746095.jpeg → ...ta/SatelliteImages/rgb/95/60/3746095.jpeg b/...ta/SatelliteImages/rgb/95/60/3746095.jpeg → ...ta/SatelliteImages/rgb/95/60/3746095.jpeg
diff --git a/...ta/SatelliteImages/rgb/96/21/5362196.jpeg → ...ta/SatelliteImages/rgb/96/21/5362196.jpeg b/...ta/SatelliteImages/rgb/96/21/5362196.jpeg → ...ta/SatelliteImages/rgb/96/21/5362196.jpeg
diff --git a/...ta/SatelliteImages/rgb/97/32/5863297.jpeg → ...ta/SatelliteImages/rgb/97/32/5863297.jpeg b/...ta/SatelliteImages/rgb/97/32/5863297.jpeg → ...ta/SatelliteImages/rgb/97/32/5863297.jpeg
diff --git a/...ta/SatelliteImages/rgb/98/67/6386798.jpeg → ...ta/SatelliteImages/rgb/98/67/6386798.jpeg b/...ta/SatelliteImages/rgb/98/67/6386798.jpeg → ...ta/SatelliteImages/rgb/98/67/6386798.jpeg
diff --git a/.../SatelliteTimeSeries/time_series_blue.csv → .../SatelliteTimeSeries/time_series_blue.csv b/.../SatelliteTimeSeries/time_series_blue.csv → .../SatelliteTimeSeries/time_series_blue.csv
diff --git a/...SatelliteTimeSeries/time_series_green.csv → ...SatelliteTimeSeries/time_series_green.csv b/...SatelliteTimeSeries/time_series_green.csv → ...SatelliteTimeSeries/time_series_green.csv
diff --git a/...a/SatelliteTimeSeries/time_series_nir.csv → ...a/SatelliteTimeSeries/time_series_nir.csv b/...a/SatelliteTimeSeries/time_series_nir.csv → ...a/SatelliteTimeSeries/time_series_nir.csv
diff --git a/...a/SatelliteTimeSeries/time_series_red.csv → ...a/SatelliteTimeSeries/time_series_red.csv b/...a/SatelliteTimeSeries/time_series_red.csv → ...a/SatelliteTimeSeries/time_series_red.csv
diff --git a/...SatelliteTimeSeries/time_series_swir1.csv → ...SatelliteTimeSeries/time_series_swir1.csv b/...SatelliteTimeSeries/time_series_swir1.csv → ...SatelliteTimeSeries/time_series_swir1.csv
diff --git a/...SatelliteTimeSeries/time_series_swir2.csv → ...SatelliteTimeSeries/time_series_swir2.csv b/...SatelliteTimeSeries/time_series_swir2.csv → ...SatelliteTimeSeries/time_series_swir2.csv
diff --git a/...ple_data_SatelliteImages_rgb_mean_std.csv → ...ple_data_SatelliteImages_rgb_mean_std.csv b/...ple_data_SatelliteImages_rgb_mean_std.csv → ...ple_data_SatelliteImages_rgb_mean_std.csv
diff --git a/.../geolifeclef2023/example_patch_loading.py → .../geolifeclef2023/example_patch_loading.py b/.../geolifeclef2023/example_patch_loading.py → .../geolifeclef2023/example_patch_loading.py
diff --git a/...feclef2023/example_time_series_loading.py → ...feclef2023/example_time_series_loading.py b/...feclef2023/example_time_series_loading.py → ...feclef2023/example_time_series_loading.py