feat: alpha support for major-tom-core

README.md

@@ -42,13 +42,14 @@ The docker image can be used to run it on other operating systems:
 ### Supported Remote Sensing Datasets
 
 Currently, `rico-hdl` supports:
-- [BigEarthNet-S1 v2.0][ben]
-- [BigEarthNet-S2 v2.0][ben]
-- [BigEarthNet-MM v2.0][ben]
-- [HySpecNet-11k][hyspecnet]
-- [UC Merced Land Use][ucmerced]
-- [EuroSAT][euro]
-- [SSL4EO-S12][ssl4eo-s12]
+- [BigEarthNet-S1 v2.0](#bigearthnet-example)
+- [BigEarthNet-S2 v2.0](#bigearthnet-example)
+- [BigEarthNet-MM v2.0](#bigearthnet-example)
+- [HySpecNet-11k](#hyspecnet-11k-example)
+- [UC Merced Land Use](#uc-merced-land-use-example)
+- [EuroSAT](#eurosat-example)
+- [SSL4EO-S12](#ssl4eo-s12-example)
+- [Major-Tom-Core](#major-tom-core-example)
 
 Additional datasets will be added in the near future.
 
@@ -683,6 +684,116 @@ rgb_tensor = np.stack([safetensor_dict[b] for b in rgb_bands])
 assert rgb_tensor.shape == (3, 264, 264)
 ```
 
+## [Major-TOM-Core][major-tom] Example
+
+First, [download the rico-hdl](#Download) binary and install
+the Python [lmdb][pyl] and [saftensors][pys] packages.
+Then, to convert the Sentinel-1 and Sentinel-2 patches from the [Major-TOM-Core][major-tom]
+dataset into the optimized format, call the application with:
+
+```bash
+rico-hdl major-tom-core --s1-dir <S1_ROOT_DIR> --s2-dir <S2_ROOT_DIR> --target-dir encoded-major-tom
+```
+
+In Major-TOM-Core, each band is stored as a separate file with the associate band as the name (`B01.tif`, `B12.tif`, `vv.tif`, ...).
+The directory that contains the bands is the associated product id/patch and
+is uniquely identifiable if it is combined with the associated grid cell id (parent directory).
+The encoder groups all unique patches (`<grid_cell>_<product_id>`) and stores the data as a [safetensors][s] dictionary,
+where the dictionary's key is the band name (`B01`, `B12`, `vv`, ...).
+
+> [!NOTE]
+> The encoder will _not_ encode the `thumbnail.png` nor the `cloud_mask.tif` band!
+
+<details>
+  <summary>Example Input</summary>
+
+```
+├── <S1_ROOT_DIR>
+│  └── 897U
+│     └── 897U_171R
+│        └── S1B_IW_GRDH_1SDV_20210827T012624_20210827T012653_028425_036437_rtc
+│           ├── thumbnail.png
+│           ├── vh.tif
+│           └── vv.tif
+└── <S2_ROOT_DIR>
+   └── 199U
+      └── 199U_1099R
+         └── S2B_MSIL2A_20200223T032739_N9999_R018_T48QUE_20230924T183543
+            ├── B01.tif
+            ├── B02.tif
+            ├── B03.tif
+            ├── B04.tif
+            ├── B05.tif
+            ├── B06.tif
+            ├── B07.tif
+            ├── B08.tif
+            ├── B09.tif
+            ├── B8A.tif
+            ├── B11.tif
+            ├── B12.tif
+            ├── cloud_mask.tif
+            └── thumbnail.png
+```
+
+</details>
+
+<details>
+  <summary>LMDB Result</summary>
+
+```
+'897U_171R_S1B_IW_GRDH_1SDV_20210827T012624_20210827T012653_028425_036437_rtc':
+  {
+    'vh': <1068x1068 float32 safetensors image data>
+    'vv': <1068x1068 float32 safetensors image data>
+  },
+'199U_1099R_S2A_MSIL2A_20170613T101031_N9999_R022_T33UUP':
+  {
+    'B01': <178x178   uint16 safetensors image data>,
+    'B02': <1068x1068 uint16 safetensors image data>,
+    'B03': <1068x1068 uint16 safetensors image data>,
+    'B04': <1068x1068 uint16 safetensors image data>,
+    'B05': <534x534   uint16 safetensors image data>,
+    'B06': <534x534   uint16 safetensors image data>,
+    'B07': <534x534   uint16 safetensors image data>,
+    'B08': <1068x1068 uint16 safetensors image data>,
+    'B8A': <534x534   uint16 safetensors image data>,
+    'B09': <178x178   uint16 safetensors image data>,
+    'B11': <534x534   uint16 safetensors image data>,
+    'B12': <534x534   uint16 safetensors image data>,
+  }
+```
+
+</details>
+
+The following code shows how to access the converted database:
+
+```python
+import lmdb
+# import desired deep-learning library:
+# numpy, torch, tensorflow, paddle, flax, mlx
+from safetensors.numpy import load
+from pathlib import Path
+
+# path to the encoded dataset/output of rico-hdl
+encoded_path = Path("./encoded-major-tom")
+
+# Make sure to only open the environment once
+# and not everytime an item is accessed.
+env = lmdb.open(str(encoded_path), readonly=True)
+
+with env.begin() as txn:
+  # string encoding is required to map the string to an LMDB key
+  safetensor_dict = load(txn.get("199U_1099R_S2A_MSIL2A_20170613T101031_N9999_R022_T33UUP".encode()))
+
+rgb_bands = ["B04", "B03", "B02"]
+rgb_tensor = np.stack([safetensor_dict[b] for b in rgb_bands])
+assert rgb_tensor.shape == (3, 1068, 1068)
+```
+
+
+> [!TIP]
+> Remember to use the appropriate `load` function for a given deep-learning library.
+
 
 ## Design
 
@@ -747,3 +858,4 @@ If you use this work, please cite:
 [ucmerced]: http://weegee.vision.ucmerced.edu/datasets/landuse.html
 [euro]: https://zenodo.org/records/7711810
 [ssl4eo-s12]: https://github.com/zhu-xlab/SSL4EO-S12
+[major-tom]: https://github.com/ESA-PhiLab/Major-TOM

flake.nix

@@ -67,6 +67,8 @@
           export PATH="$out/bin:$PATH"
           export RICO_HDL_S1_PATH=${./integration_tests/tiffs/BigEarthNet/BigEarthNet-S1}
           export RICO_HDL_S2_PATH=${./integration_tests/tiffs/BigEarthNet/BigEarthNet-S2}
+          export RICO_HDL_MAJOR_TOM_CORE_S1_PATH=${./integration_tests/tiffs/Major-TOM-Core/S1RTC}
+          export RICO_HDL_MAJOR_TOM_CORE_S2_PATH=${./integration_tests/tiffs/Major-TOM-Core/S2L2A}
           export RICO_HDL_SSL4EO_S12_S1_PATH=${./integration_tests/tiffs/SSL4EO-S12}/s1
           export RICO_HDL_SSL4EO_S12_S2_L1C_PATH=${./integration_tests/tiffs/SSL4EO-S12}/s2c
           export RICO_HDL_SSL4EO_S12_S2_L2A_PATH=${./integration_tests/tiffs/SSL4EO-S12}/s2a
@@ -142,6 +144,8 @@
             env.RICO_HDL_SSL4EO_S12_S1_PATH = "${config.env.DEVENV_ROOT}/integration_tests/tiffs/SSL4EO-S12/s1";
             env.RICO_HDL_SSL4EO_S12_S2_L1C_PATH = "${config.env.DEVENV_ROOT}/integration_tests/tiffs/SSL4EO-S12/s2c";
             env.RICO_HDL_SSL4EO_S12_S2_L2A_PATH = "${config.env.DEVENV_ROOT}/integration_tests/tiffs/SSL4EO-S12/s2a";
+            env.RICO_HDL_MAJOR_TOM_CORE_S1_PATH = "${config.env.DEVENV_ROOT}/integration_tests/tiffs/Major-TOM-Core/S1RTC/";
+            env.RICO_HDL_MAJOR_TOM_CORE_S2_PATH = "${config.env.DEVENV_ROOT}/integration_tests/tiffs/Major-TOM-Core/S2L2A/";
             packages =
               [
                 (mkPoetryEnv

integration_tests/test_python_integration.py

@@ -105,6 +105,48 @@ def eurosat_ms_root() -> Path:
     return p
 
 
+@pytest.fixture(scope="session")
+def major_tom_core_s1_root() -> Path:
+    str_p = (
+        os.environ.get("RICO_HDL_MAJOR_TOM_CORE_S1_PATH")
+        or "./tiffs/Major-TOM-Core/S1RTC/"
+    )
+    p = Path(str_p)
+    assert p.exists()
+    assert p.is_dir()
+    return p
+
+
+@pytest.fixture(scope="session")
+def major_tom_core_s2_root() -> Path:
+    str_p = (
+        os.environ.get("RICO_HDL_MAJOR_TOM_CORE_S2_PATH")
+        or "./tiffs/Major-TOM-Core/S2L2A/"
+    )
+    p = Path(str_p)
+    assert p.exists()
+    assert p.is_dir()
+    return p
+
+
+@pytest.fixture
+def encoded_major_tom_core_path(
+    major_tom_core_s1_root, major_tom_core_s2_root, tmpdir_factory
+) -> Path:
+    tmp_path = tmpdir_factory.mktemp("lmdb")
+    subprocess.run(
+        [
+            "rico-hdl",
+            "major-tom-core",
+            f"--s1-dir={major_tom_core_s1_root}",
+            f"--s2-dir={major_tom_core_s2_root}",
+            f"--target-dir={tmp_path}",
+        ],
+        check=True,
+    )
+    return Path(tmp_path)
+
+
 # https://docs.pytest.org/en/6.2.x/tmpdir.html#[email protected](scope="session")
 @pytest.fixture
 def encoded_bigearthnet_s1_s2_path(
@@ -306,6 +348,78 @@ def test_bigearthnet_integration(
     )
 
 
+def test_major_tom_core_integration(
+    major_tom_core_s1_root, major_tom_core_s2_root, encoded_major_tom_core_path
+):
+    env = lmdb.open(str(encoded_major_tom_core_path), readonly=True)
+
+    with env.begin(write=False) as txn:
+        cur = txn.cursor()
+        decoded_lmdb_data = {k.decode("utf-8"): load(v) for (k, v) in cur}
+
+    assert decoded_lmdb_data.keys() == set(
+        [
+            "0U_199R_S1A_IW_GRDH_1SDV_20220703T043413_20220703T043438_043931_053E87_rtc",
+            "897U_171R_S1B_IW_GRDH_1SDV_20210827T012624_20210827T012653_028425_036437_rtc",
+            "0U_199R_S2A_MSIL2A_20220706T085611_N0400_R007_T33NZA_20220706T153419",
+            "199U_1099R_S2B_MSIL2A_20200223T032739_N9999_R018_T48QUE_20230924T183543",
+        ]
+    )
+
+    sample_s1_safetensors_dict = decoded_lmdb_data.get(
+        "0U_199R_S1A_IW_GRDH_1SDV_20220703T043413_20220703T043438_043931_053E87_rtc",
+    )
+    sample_s2_safetensors_dict = decoded_lmdb_data.get(
+        "0U_199R_S2A_MSIL2A_20220706T085611_N0400_R007_T33NZA_20220706T153419"
+    )
+    safetensors_s1_keys = sample_s1_safetensors_dict.keys()
+    safetensors_s2_keys = sample_s2_safetensors_dict.keys()
+    assert (
+        set(
+            [
+                "B01",
+                "B02",
+                "B03",
+                "B04",
+                "B05",
+                "B06",
+                "B07",
+                "B08",
+                "B8A",
+                "B09",
+                "B11",
+                "B12",
+            ]
+        )
+        == safetensors_s2_keys
+    )
+    assert (
+        set(
+            [
+                "vv",
+                "vh",
+            ]
+        )
+        == safetensors_s1_keys
+    )
+
+    assert all(arr.shape == (1068, 1068) for arr in sample_s1_safetensors_dict.values())
+    assert all(arr.dtype == "float32" for arr in sample_s1_safetensors_dict.values())
+
+    assert all(arr.dtype == "uint16" for arr in sample_s2_safetensors_dict.values())
+    assert all(
+        sample_s2_safetensors_dict[key].shape == (1068, 1068)
+        for key in ["B02", "B03", "B04", "B08"]
+    )
+    assert all(
+        sample_s2_safetensors_dict[key].shape == (534, 534)
+        for key in ["B05", "B06", "B07", "B8A", "B11", "B12"]
+    )
+    assert all(
+        sample_s2_safetensors_dict[key].shape == (178, 178) for key in ["B01", "B09"]
+    )
+
+
 def test_ssl4eo_s12_integration(
     ssl4eo_s12_s1_root,
     ssl4eo_s12_s2_l1c_root,