diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000000000000000000000000000000000000..ef67f6bacaa062992d968bcb9f122cc16904e0dc --- /dev/null +++ b/.gitattributes @@ -0,0 +1,3 @@ +*.npy filter=lfs diff=lfs merge=lfs -text +*.npz filter=lfs diff=lfs merge=lfs -text +*.ipynb filter=lfs diff=lfs merge=lfs -text diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..83fd68414d9d64d40fb263ff8ed6878768079474 --- /dev/null +++ b/.gitignore @@ -0,0 +1,11 @@ +*.PNG +*.png +*.csv +archives/ +neo_1month/ +*.npz +*.npy +__pycache__ +*.pyc +dataset/ + diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..948d126f427c45f4a9629eb5e5db539f66bdd0c1 --- /dev/null +++ b/README.md @@ -0,0 +1,29 @@ +

NEO dataset

 + +Preprocessing and loading scripts for NEO datasets: 1 week and 1 month variants. Go in either [1 week](neo_1week) or +[1 month](neo_1month) directories. + +Steps: +1. **Download raw data** + + Use the `./download_raw_data.py -o raw_data` script. + + 1.1 **For weekly data only**. Use the `preprocess_raw_1week_data.py raw_data -o raw_data_fixed` script. + + - NDVI is only sampled at 16 days, we make an average of two consecutive samples to create an 8 day average. + + - We rename the data from YYYY-MM-DD to YYYY-MM-E (E=1,2,3,4 depending on which week bucket). This is needed because + different sensors sample data at different weeks + + +2. **Convert from PNG to NPY files** + - Converts from raw PNG to [0:1] normalied, 540x1080 npy files, and adds NaNs to invalid regions in the NEO data. + + `./convert_png_to_npy.py raw_data -o npy_data [--resolution 540 1080]` + + - If `--resolution` is not set, it will default to `540 x 1080`. + +3. Run the [neo_viewer](neo_viewer.ipynb) and [data analysis](neo_data_analysis.ipynb) notebook + - Set the path to `neo_1week/npy_data` or `neo_1month/npy_data`. + +4. Use in ML python scripts via the [neo reader](neo_reader/neo_reader.py). You can also run it with the `npy_data`. diff --git a/neo_1month/data/AOD/2000-03.npz b/neo_1month/data/AOD/2000-03.npz new file mode 100644 index 0000000000000000000000000000000000000000..9c1d0cb8f459d54494bace8726aaacef99432b7f --- /dev/null +++ b/neo_1month/data/AOD/2000-03.npz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ba90af78b1fa2d450e802720fcebc8cb3c0f7fccfab2338c33c51d644e86283f +size 1166664 diff --git a/neo_1month/data/AOD/2000-04.npz b/neo_1month/data/AOD/2000-04.npz new file mode 100644 index 0000000000000000000000000000000000000000..3494ab537fe7eba8dad7ea97f4bd20ca71b8fae6 --- /dev/null +++ b/neo_1month/data/AOD/2000-04.npz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:922bf63969790f7e3d6190aa0df629d4fc1fe6f7cc5be9cbf0191f8e17f2542d +size 1166664 diff --git a/neo_1month/data/AOD/2000-05.npz b/neo_1month/data/AOD/2000-05.npz new file mode 100644 index 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-0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2a97c0ceab14137d6e47be8a1d5fb2d1678fe6b9bdfb791169058833d561d00f +size 1166664 diff --git a/neo_1month/data_split/train/WV/2014-08.npz b/neo_1month/data_split/train/WV/2014-08.npz new file mode 100644 index 0000000000000000000000000000000000000000..5cfcf472127d55021428e616102464046d015e16 --- /dev/null +++ b/neo_1month/data_split/train/WV/2014-08.npz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e9d6c242ee878acf5630e3034e5223e8d1187d4ae18ca9d6b68ec2ccd757d3f0 +size 1166664 diff --git a/neo_reader/__init__.py b/neo_reader/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..32cb2f3f762fa05d144ffa9412be634fc802aa1b --- /dev/null +++ b/neo_reader/__init__.py @@ -0,0 +1,3 @@ +"""init file""" +from .neo_reader import NEOReader +from .neo_node import NEONode diff --git a/neo_reader/cmaps/AerosolOpticalDepth.act b/neo_reader/cmaps/AerosolOpticalDepth.act new file mode 100644 index 0000000000000000000000000000000000000000..70e5dd766f4c94c06fb98d2d0bfd32de54001cd6 Binary files /dev/null and b/neo_reader/cmaps/AerosolOpticalDepth.act differ diff --git a/neo_reader/cmaps/Albedo.act b/neo_reader/cmaps/Albedo.act new file mode 100644 index 0000000000000000000000000000000000000000..c2a38714df757bd6503609bf96c8e097fbb66d83 Binary files /dev/null and b/neo_reader/cmaps/Albedo.act differ diff --git a/neo_reader/cmaps/CarbonMonoxide.act b/neo_reader/cmaps/CarbonMonoxide.act new file mode 100644 index 0000000000000000000000000000000000000000..04fe989698fcec3572b9382401dbd9189e22b980 Binary files /dev/null and b/neo_reader/cmaps/CarbonMonoxide.act differ diff --git a/neo_reader/cmaps/Chlorophyll.act b/neo_reader/cmaps/Chlorophyll.act new file mode 100644 index 0000000000000000000000000000000000000000..e4a691a8f57b9fced398cc647f6462a97bd6ff0f Binary files /dev/null and b/neo_reader/cmaps/Chlorophyll.act differ diff --git a/neo_reader/cmaps/CloudFraction.act b/neo_reader/cmaps/CloudFraction.act new file mode 100644 index 0000000000000000000000000000000000000000..fbe7e475247c066936340c65795900f7c2e20220 Binary files /dev/null and b/neo_reader/cmaps/CloudFraction.act differ diff --git a/neo_reader/cmaps/CloudOpticalThickness.act b/neo_reader/cmaps/CloudOpticalThickness.act new file mode 100644 index 0000000000000000000000000000000000000000..33a6d15d3403b208900b18a92a1bcede072c6c34 Binary files /dev/null and b/neo_reader/cmaps/CloudOpticalThickness.act differ diff --git a/neo_reader/cmaps/CloudParticleRadius.act b/neo_reader/cmaps/CloudParticleRadius.act new file mode 100644 index 0000000000000000000000000000000000000000..a266a464d79d10fbefe555a79e09b7b351f8b155 Binary files /dev/null and b/neo_reader/cmaps/CloudParticleRadius.act differ diff --git a/neo_reader/cmaps/CloudWaterContent.act b/neo_reader/cmaps/CloudWaterContent.act new file mode 100644 index 0000000000000000000000000000000000000000..773738bc970ca11356a4da7dee837b5850b53e8a 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0000000000000000000000000000000000000000..f0c21db45e53c94789f2fab06f6e4cf8aebf1861 Binary files /dev/null and b/neo_reader/cmaps/NitrogenDioxide.act differ diff --git a/neo_reader/cmaps/OutgoingLongwaveRadiation.act b/neo_reader/cmaps/OutgoingLongwaveRadiation.act new file mode 100644 index 0000000000000000000000000000000000000000..8804dc9027bb9fa4fc3dec516fbd69ce10e508fa Binary files /dev/null and b/neo_reader/cmaps/OutgoingLongwaveRadiation.act differ diff --git a/neo_reader/cmaps/Ozone.act b/neo_reader/cmaps/Ozone.act new file mode 100644 index 0000000000000000000000000000000000000000..297aae5a555f45c2d3518846295487f7d173e03d Binary files /dev/null and b/neo_reader/cmaps/Ozone.act differ diff --git a/neo_reader/cmaps/ReflectedShortwaveRadiation.act b/neo_reader/cmaps/ReflectedShortwaveRadiation.act new file mode 100644 index 0000000000000000000000000000000000000000..b55e84952c96f532dd41c9fb856b71e83b5fa3c4 Binary files /dev/null and b/neo_reader/cmaps/ReflectedShortwaveRadiation.act differ diff --git a/neo_reader/cmaps/SeaSurfaceTemperature.act b/neo_reader/cmaps/SeaSurfaceTemperature.act new file mode 100644 index 0000000000000000000000000000000000000000..b2c43549ff2edda9f3bf722e588175532feeae85 Binary files /dev/null and b/neo_reader/cmaps/SeaSurfaceTemperature.act differ diff --git a/neo_reader/cmaps/SnowCover.act b/neo_reader/cmaps/SnowCover.act new file mode 100644 index 0000000000000000000000000000000000000000..4760e0fc8433ccb63e26782a9bf457241546b861 Binary files /dev/null and b/neo_reader/cmaps/SnowCover.act differ diff --git a/neo_reader/cmaps/SolarInsolation.act b/neo_reader/cmaps/SolarInsolation.act new file mode 100644 index 0000000000000000000000000000000000000000..7ea58a82ba76d778fabded6231639b685082fb97 Binary files /dev/null and b/neo_reader/cmaps/SolarInsolation.act differ diff --git a/neo_reader/cmaps/Temperature.act b/neo_reader/cmaps/Temperature.act new file mode 100644 index 0000000000000000000000000000000000000000..de034ee73ace1b3bebf459213c9d17e21f688bb5 Binary files /dev/null and b/neo_reader/cmaps/Temperature.act differ diff --git a/neo_reader/cmaps/TemperatureAnomaly.act b/neo_reader/cmaps/TemperatureAnomaly.act new file mode 100644 index 0000000000000000000000000000000000000000..828f3f7d8de4d9b5b28f3ebd6e5c10e2292fe214 Binary files /dev/null and b/neo_reader/cmaps/TemperatureAnomaly.act differ diff --git a/neo_reader/cmaps/Vegetation.act b/neo_reader/cmaps/Vegetation.act new file mode 100644 index 0000000000000000000000000000000000000000..b7ae1aa4e1e2ccbe428cba6ae324845fff3f806b Binary files /dev/null and b/neo_reader/cmaps/Vegetation.act differ diff --git a/neo_reader/cmaps/WaterVapor.act b/neo_reader/cmaps/WaterVapor.act new file mode 100644 index 0000000000000000000000000000000000000000..eb9fe2a96348ecf5f1500cf2dfec5ccdd5c44dbc Binary files /dev/null and b/neo_reader/cmaps/WaterVapor.act differ diff --git a/neo_reader/neo_node.py b/neo_reader/neo_node.py new file mode 100644 index 0000000000000000000000000000000000000000..5ef8e9eacb59c38e9df5452de307d0d65645f8c2 --- /dev/null +++ b/neo_reader/neo_node.py @@ -0,0 +1,71 @@ +"""NEO nodes implementation in ngclib repository""" +from pathlib import Path +import numpy as np +from codecs import encode + +def _cmap_hex_to_rgb(hex_list): + res = [] + for hex_data in hex_list: + r = int(hex_data[1: 3], 16) + g = int(hex_data[3: 5], 16) + b = int(hex_data[5: 7], 16) + res.append([r, g, b]) + return np.array(res) + +def _act_to_cmap(act_file: Path) -> np.ndarray: + """converts the .act file to a matplotlib cmap representation""" + with open(act_file, "rb") as act: + raw_data = act.read() # Read binary data + hex_data = encode(raw_data, "hex") # Convert it to hexadecimal values + total_colors_count = int(hex_data[-7:-4], 16) # Get last 3 digits to get number of colors total + total_colors_count = 256 + + # Decode colors from hex to string and split it by 6 (because colors are #1c1c1c) + colors = [hex_data[i: i + 6].decode() for i in range(0, total_colors_count * 6, 6)] + + # Add # to each item and filter empty items if there is a corrupted total_colors_count bit + hex_colors = [f"#{i}" for i in colors if len(i)] + rgb_colors = _cmap_hex_to_rgb(hex_colors) + return rgb_colors + +class NEONode: + """NEO nodes implementation in ngclib repository""" + def __init__(self, node_type: str, name: str): + # all neo nodes have 1 dimension. + valid_node_types = ["AerosolOpticalDepth", "Albedo", "CarbonMonoxide", "Chlorophyll", "CloudFraction", + "CloudOpticalThickness", "CloudParticleRadius", "CloudWaterContent", "Fire", + "LeafAreaIndex", "NetRadiation", "NitrogenDioxide", "OutgoingLongwaveRadiation", "Ozone", + "ReflectedShortwaveRadiation", "SeaSurfaceTemperature", "SnowCover", "SolarInsolation", + "Temperature", "TemperatureAnomaly", "Vegetation", "WaterVapor"] + assert node_type in valid_node_types, f"Node type '{node_type}' not in {valid_node_types}" + self.node_type = node_type + self.name = name + self.cmap = _act_to_cmap(Path(__file__).absolute().parent / "cmaps" / f"{self.node_type}.act") + + def load_from_disk(self, x: np.ndarray) -> np.ndarray: + y: np.ndarray = np.float32(x) + if y.shape[0] == 1: # pylint: disable=unsubscriptable-object + y = y[0] # pylint: disable=unsubscriptable-object + if len(y.shape) == 2: + y = np.expand_dims(y, axis=-1) + y[np.isnan(y)] = 0 + return y.astype(np.float32) + + def save_to_disk(self, x: np.ndarray) -> np.ndarray: + return x.clip(0, 1) + + def plot_fn(self, x: np.ndarray | None) -> np.ndarray | None: + if x is None: + return x + y = np.clip(x, 0, 1) + y = y * 255 + y[y == 0] = 255 + y = y.astype(np.uint).squeeze() + y_rgb = self.cmap[y].astype(np.uint8) + return y_rgb + + def __repr__(self): + return self.name + + def __str__(self): + return f"NEONode({self.name})" diff --git a/neo_reader/neo_reader.py b/neo_reader/neo_reader.py new file mode 100755 index 0000000000000000000000000000000000000000..92f69d6f0474891e3e2ae5808daab874740a37cf --- /dev/null +++ b/neo_reader/neo_reader.py @@ -0,0 +1,183 @@ +#!/usr/bin/env python3 +"""NEO Reader module""" +from __future__ import annotations +from pathlib import Path +from argparse import Namespace, ArgumentParser +from pprint import pprint +from natsort import natsorted +from loguru import logger +import numpy as np +from torch.utils.data import Dataset + +try: + from .neo_node import NEONode +except ImportError: + from neo_node import NEONode + +class NEOReader(Dataset): + """ + NEO Reader implementation. Reads data from npz files and returns them as a dict. + + Parameters: + - path: Path to the directory containing the npz files. + - nodes: List of nodes that are present in the dataset. + - handle_missing_data: Modes to handle missing data. Valid options are: + - drop: Drop the data point if any of the nodes is missing. + - fill_none: Fill the missing data with Nones. + + Expected directory structure: + path/ + - node_1/0.npz, ..., N.npz + - ... + - node_n/0.npz, ..., N.npz + + Names can be in a different format (i.e. 2022-01-01.npz), but must be consistent and equal across all nodes. + """ + # The default names and their corresponding types for NEO datasets (1week or 1month) + name_to_type = {"AOD": "AerosolOpticalDepth", "BS_ALBEDO": "Albedo", "CHLORA": "Chlorophyll", + "CLD_FR": "CloudFraction", "CLD_RD": "CloudParticleRadius", "CLD_WP": "CloudWaterContent", + "COT": "CloudOpticalThickness", "CO_M": "CarbonMonoxide", "FIRE": "Fire", + "INSOL": "SolarInsolation", "LAI": "LeafAreaIndex", "LSTD": "Temperature", + "LSTD_AN": "TemperatureAnomaly", "LSTN": "Temperature", "LSTN_AN": "TemperatureAnomaly", + "LWFLUX": "OutgoingLongwaveRadiation", "NDVI": "Vegetation", "NETFLUX": "NetRadiation", + "NO2": "NitrogenDioxide", "OZONE": "Ozone", "SNOWC": "SnowCover", "SST": "SeaSurfaceTemperature", + "SWFLUX": "ReflectedShortwaveRadiation", "WV": "WaterVapor"} + + def __init__(self, path: Path, nodes: list[str] | None = None, handle_missing_data: str = "fill_none"): + assert path.exists(), f"Provided path '{path}' doesn't exist!" + assert handle_missing_data in ("drop", "fill_none"), f"Invalid handle_missing_data mode: {handle_missing_data}" + self.path = Path(path).absolute() + self.files_per_node, self.file_names = self._build_dataset(handle_missing_data) + if nodes is None: + nodes = list(self.files_per_node.keys()) + logger.debug("No nodes provided. Using all of them as read from the paths.") + assert all(isinstance(x, str) for x in nodes), tuple(zip(nodes, (type(x) for x in nodes))) + + self.node_names = sorted(nodes) + logger.info(f"Nodes used in this reader: {self.node_names}") + self.nodes = [NEONode(NEOReader.name_to_type[x], x) for x in self.node_names] + self.handle_missing_data = handle_missing_data + + self._images_shape: tuple[int, int, int] | None = None + + # Public methods and properties + + @property + def images_shape(self) -> tuple[int, int, int]: + """Returns a triple of (H, W, C) for all images shape, which are assumed to be consistent for all data points""" + if self._images_shape is None: + i = 0 + while True: + for img in self[i][0].values(): + if img is not None: + self._images_shape = img.shape + assert len(self._images_shape) == 3 and self._images_shape[-1] == 1, self._images_shape + return self._images_shape + i += 1 + return self._images_shape + + # Private methods + + def _get_all_npz_files(self) -> dict[str, list[Path]]: + in_files = {} + nodes = [x for x in self.path.iterdir() if x.is_dir()] + for node in nodes: + dir_name = self.path / node.name + items = dir_name.glob("*.npz") + items = set(natsorted(items, key=lambda x: x.name)) + in_files[node.name] = items + assert not any(len(x) == 0 for x in in_files.values()), f"{ [k for k, v in in_files.items() if len(v) == 0] }" + return in_files + + def _build_dataset_drop(self) -> tuple[dict[str, list[Path]], list[str]]: + in_files = self._get_all_npz_files() + common = set(x.name for x in next(iter(in_files.values()))) + nodes = in_files.keys() + for node in nodes: + common = common.intersection([f.name for f in in_files[node]]) + assert len(common) > 0, f"Node '{node}' made the intersection null" + common = natsorted(list(common)) + logger.info(f"Found {len(common)} data points for each node ({len(nodes)} nodes).") + files_per_node = {node: [self.path / node / x for x in common] for node in nodes} + return files_per_node, common + + def _build_dataset_fill_none(self) -> tuple[dict[str, list[Path]], list[str]]: + in_files = self._get_all_npz_files() + all_files = set(x.name for x in next(iter(in_files.values()))) + nodes = in_files.keys() + for node in nodes: + all_files = all_files.union([f.name for f in in_files[node]]) + all_files = natsorted(list(all_files)) + logger.info(f"Found {len(all_files)} data points as union of all nodes' data ({len(nodes)} nodes).") + + files_per_node = {node: [] for node in nodes} + in_file_names = {node: [f.name for f in in_files[node]] for node in nodes} + for node in nodes: + for file_name in all_files: + file_path = self.path / node / file_name if file_name in in_file_names[node] else None + files_per_node[node].append(file_path) + return files_per_node, all_files + + def _build_dataset(self, handle_missing_data: str) -> tuple[dict[str, list[Path]], list[str]]: + logger.debug(f"Building dataset from: '{self.path}'") + if handle_missing_data == "drop": + return self._build_dataset_drop() + else: + return self._build_dataset_fill_none() + + def _read_node_data(self, node: NEONode, index: int) -> np.ndarray | None: + """Reads the npz data from the disk and transforms it properly""" + file_path = self.files_per_node[node.name][index] + if file_path is None: + return None + item = np.load(file_path, allow_pickle=True)["arr_0"] + transformed_item = node.load_from_disk(item) + return transformed_item + + # Python magic methods (pretty printing the reader object, reader[0], len(reader) etc.) + + def __getitem__(self, index: int) -> tuple[dict[str, np.ndarray], str, list[str]]: + """Read the data all the desired nodes""" + assert isinstance(index, int), type(index) + res = {} + item_name = self.file_names[index] + + for node in self.nodes: + item = self._read_node_data(node, index) + assert self.handle_missing_data == "fill_none" or item is not None, item_name + res[node.name] = item + return (res, item_name, self.node_names) + + def __len__(self) -> int: + return len(self.files_per_node[self.node_names[0]]) + + def __str__(self): + f_str = "[NGC Npz Reader]" + f_str += f"\n - Path: '{self.path}'" + f_str += f"\n - Only full data: {self.handle_missing_data == 'drop'}" + f_str += f"\n - Nodes ({len(self.nodes)}): {self.nodes}" + f_str += f"\n - Length: {len(self)}" + return f_str + + def __repr__(self): + return str(self) + +def get_args() -> Namespace: + """cli args""" + parser = ArgumentParser() + parser.add_argument("dataset_path", type=Path) + parser.add_argument("--handle_missing_data", choices=("drop", "fill_none"), default="fill_none") + args = parser.parse_args() + return args + +def main(args: Namespace): + """main fn""" + reader = NEOReader(args.dataset_path, nodes=None, handle_missing_data=args.handle_missing_data) + print(reader) + print(f"Shape: {reader.images_shape}") + data, name, node_names = reader[np.random.randint(len(reader))] + print(f"Name: {name}. Nodes: {node_names}") + pprint({k: (v.shape if v is not None else None) for k, v in data.items()}) + +if __name__ == "__main__": + main(get_args()) diff --git a/neo_viewer.ipynb b/neo_viewer.ipynb new file mode 100644 index 0000000000000000000000000000000000000000..451bdb22a301fd09849f4b12a821e9647f6de460 --- /dev/null +++ b/neo_viewer.ipynb @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:23c8ec700dc0df69d0ee88c6c0998e287fc76ef21b0ce2fc31d5697fb283e8b5 +size 11757180 diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..a8922e11e2b7d6b3aae2f5aef44072c2cf5e938a --- /dev/null +++ b/requirements.txt @@ -0,0 +1,10 @@ +numpy==1.23.5 +media-processing-lib==0.6.3 +loguru +lovely_numpy +natsort +torch>=2.0.0 +requests +bs4 +pandas +matplotlib