Merge pull request #54 from IBM/improve/bands_definition

Improve/bands definition

Author: Joao-L-S-Almeida

terratorch/datamodules/generic_pixel_wise_data_module.py

@@ -91,9 +91,9 @@ def __init__(
         test_split: Path | None = None,
         ignore_split_file_extensions: bool = True,
         allow_substring_split_file: bool = True,
-        dataset_bands: list[HLSBands | int] | None = None,
-        predict_dataset_bands: list[HLSBands | int] | None = None,
-        output_bands: list[HLSBands | int] | None = None,
+        dataset_bands: list[HLSBands | int | tuple[int, int] | str] | None = None,
+        predict_dataset_bands: list[HLSBands | int | tuple[int, int] | str ] | None = None,
+        output_bands: list[HLSBands | int | tuple[int, int] | str] | None = None,
         constant_scale: float = 1,
         rgb_indices: list[int] | None = None,
         train_transform: A.Compose | None | list[A.BasicTransform] = None,
@@ -330,9 +330,9 @@ def __init__(
         test_split: Path | None = None,
         ignore_split_file_extensions: bool = True,
         allow_substring_split_file: bool = True,
-        dataset_bands: list[HLSBands | int] | None = None,
-        predict_dataset_bands: list[HLSBands | int] | None = None,
-        output_bands: list[HLSBands | int] | None = None,
+        dataset_bands: list[HLSBands | int | tuple[int, int] | str ] | None = None,
+        predict_dataset_bands: list[HLSBands | int | tuple[int, int] | str ] | None = None,
+        output_bands: list[HLSBands | int | tuple[int, int] | str ] | None = None,
         constant_scale: float = 1,
         rgb_indices: list[int] | None = None,
         train_transform: A.Compose | None | list[A.BasicTransform] = None,

terratorch/datasets/generic_pixel_wise_dataset.py

@@ -1,23 +1,19 @@
 # Copyright contributors to the Terratorch project
 
-"""Module containing generic dataset classes
-"""
+"""Module containing generic dataset classes"""
+
 import glob
 import os
 from abc import ABC
-from functools import partial
 from pathlib import Path
 from typing import Any
 
 import albumentations as A
 import matplotlib as mpl
 import numpy as np
 import rioxarray
-import torch
 import xarray as xr
-from albumentations.pytorch import ToTensorV2
 from einops import rearrange
-from matplotlib import cm
 from matplotlib import pyplot as plt
 from matplotlib.figure import Figure
 from matplotlib.patches import Rectangle
@@ -43,8 +39,8 @@ def __init__(
         ignore_split_file_extensions: bool = True,
         allow_substring_split_file: bool = True,
         rgb_indices: list[int] | None = None,
-        dataset_bands: list[HLSBands | int] | None = None,
-        output_bands: list[HLSBands | int] | None = None,
+        dataset_bands: list[HLSBands | int | tuple[int, int] | str] | None = None,
+        output_bands: list[HLSBands | int | tuple[int, int] | str] | None = None,
         constant_scale: float = 1,
         transform: A.Compose | None = None,
         no_data_replace: float | None = None,
@@ -73,8 +69,8 @@ def __init__(
                 that must be present in file names to be included (as in mmsegmentation), or exact
                 matches (e.g. eurosat). Defaults to True.
             rgb_indices (list[str], optional): Indices of RGB channels. Defaults to [0, 1, 2].
-            dataset_bands (list[HLSBands | int] | None): Bands present in the dataset.
-            output_bands (list[HLSBands | int] | None): Bands that should be output by the dataset.
+            dataset_bands (list[HLSBands | int | tuple[int, int] | str] | None): Bands present in the dataset. This parameter names input channels (bands) using HLSBands, ints, int ranges, or strings, so that they can then be refered to by output_bands. Defaults to None.
+            output_bands (list[HLSBands | int | tuple[int, int] | str] | None): Bands that should be output by the dataset as named by dataset_bands.
             constant_scale (float): Factor to multiply image values by. Defaults to 1.
             transform (Albumentations.Compose | None): Albumentations transform to be applied.
                 Should end with ToTensorV2(). If used through the generic_data_module,
@@ -88,6 +84,7 @@ def __init__(
                 expected 0. Defaults to False.
         """
         super().__init__()
+
         self.split_file = split
 
         label_data_root = label_data_root if label_data_root is not None else data_root
@@ -120,19 +117,24 @@ def __init__(
             )
         self.rgb_indices = [0, 1, 2] if rgb_indices is None else rgb_indices
 
-        self.dataset_bands = dataset_bands
-        self.output_bands = output_bands
+        self.dataset_bands = self._generate_bands_intervals(dataset_bands)
+        self.output_bands = self._generate_bands_intervals(output_bands)
+
         if self.output_bands and not self.dataset_bands:
             msg = "If output bands provided, dataset_bands must also be provided"
             return Exception(msg)  # noqa: PLE0101
 
+        # There is a special condition if the bands are defined as simple strings.
         if self.output_bands:
             if len(set(self.output_bands) & set(self.dataset_bands)) != len(self.output_bands):
                 msg = "Output bands must be a subset of dataset bands"
                 raise Exception(msg)
+
             self.filter_indices = [self.dataset_bands.index(band) for band in self.output_bands]
+
         else:
             self.filter_indices = None
+
         # If no transform is given, apply only to transform to torch tensor
         self.transform = transform if transform else lambda **batch: to_tensor(batch)
         # self.transform = transform if transform else ToTensorV2()
@@ -141,7 +143,7 @@ def __len__(self) -> int:
         return len(self.image_files)
 
     def __getitem__(self, index: int) -> dict[str, Any]:
-        image = self._load_file(self.image_files[index], nan_replace = self.no_data_replace).to_numpy()
+        image = self._load_file(self.image_files[index], nan_replace=self.no_data_replace).to_numpy()
         # to channels last
         if self.expand_temporal_dimension:
             image = rearrange(image, "(channels time) h w -> channels time h w", channels=len(self.output_bands))
@@ -151,9 +153,12 @@ def __getitem__(self, index: int) -> dict[str, Any]:
             image = image[..., self.filter_indices]
         output = {
             "image": image.astype(np.float32) * self.constant_scale,
-            "mask": self._load_file(self.segmentation_mask_files[index], nan_replace = self.no_label_replace).to_numpy()[0],
+            "mask": self._load_file(self.segmentation_mask_files[index], nan_replace=self.no_label_replace).to_numpy()[
+                0
+            ],
             "filename": self.image_files[index],
         }
+
         if self.reduce_zero_label:
             output["mask"] -= 1
         if self.transform:
@@ -166,6 +171,26 @@ def _load_file(self, path, nan_replace: int | float | None = None) -> xr.DataArr
             data = data.fillna(nan_replace)
         return data
 
+    def _generate_bands_intervals(self, bands_intervals: list[int | str | HLSBands | tuple[int]] | None = None):
+        if bands_intervals is None:
+            return None
+        bands = []
+        for element in bands_intervals:
+            # if its an interval
+            if isinstance(element, tuple):
+                if len(element) != 2:  # noqa: PLR2004
+                    msg = "When defining an interval, a tuple of two integers should be passed, defining start and end indices inclusive"
+                    raise Exception(msg)
+                expanded_element = list(range(element[0], element[1] + 1))
+                bands.extend(expanded_element)
+            else:
+                bands.append(element)
+        # check the expansion didnt result in duplicate elements
+        if len(set(bands)) != len(bands):
+            msg = "Duplicate indices detected. Indices must be unique."
+            raise Exception(msg)
+        return bands
+
 
 class GenericNonGeoSegmentationDataset(GenericPixelWiseDataset):
     """GenericNonGeoSegmentationDataset"""
@@ -181,8 +206,8 @@ def __init__(
         ignore_split_file_extensions: bool = True,
         allow_substring_split_file: bool = True,
         rgb_indices: list[str] | None = None,
-        dataset_bands: list[HLSBands | int] | None = None,
-        output_bands: list[HLSBands | int] | None = None,
+        dataset_bands: list[HLSBands | int | tuple[int, int] | str] | None = None,
+        output_bands: list[HLSBands | int | tuple[int, int] | str] | None = None,
         class_names: list[str] | None = None,
         constant_scale: float = 1,
         transform: A.Compose | None = None,
@@ -348,8 +373,8 @@ def __init__(
         ignore_split_file_extensions: bool = True,
         allow_substring_split_file: bool = True,
         rgb_indices: list[int] | None = None,
-        dataset_bands: list[HLSBands | int] | None = None,
-        output_bands: list[HLSBands | int] | None = None,
+        dataset_bands: list[HLSBands | int | tuple[int, int] | str] | None = None,
+        output_bands: list[HLSBands | int | tuple[int, int] | str] | None = None,
         constant_scale: float = 1,
         transform: A.Compose | None = None,
         no_data_replace: float | None = None,

terratorch/datasets/generic_scalar_label_dataset.py

@@ -42,8 +42,8 @@ def __init__(
         ignore_split_file_extensions: bool = True,
         allow_substring_split_file: bool = True,
         rgb_indices: list[int] | None = None,
-        dataset_bands: list[HLSBands | int] | None = None,
-        output_bands: list[HLSBands | int] | None = None,
+        dataset_bands: list[HLSBands | int | tuple[int, int] | str] | None = None,
+        output_bands: list[HLSBands | int | tuple[int, int] | str] | None = None,
         constant_scale: float = 1,
         transform: A.Compose | None = None,
         no_data_replace: float = 0,
@@ -64,8 +64,8 @@ def __init__(
                 that must be present in file names to be included (as in mmsegmentation), or exact
                 matches (e.g. eurosat). Defaults to True.
             rgb_indices (list[str], optional): Indices of RGB channels. Defaults to [0, 1, 2].
-            dataset_bands (list[HLSBands | int] | None): Bands present in the dataset.
-            output_bands (list[HLSBands | int] | None): Bands that should be output by the dataset.
+            dataset_bands (list[HLSBands | int | tuple[int, int] | str] | None): Bands present in the dataset. This parameter names input channels (bands) using HLSBands, ints, int ranges, or strings, so that they can then be refered to by output_bands. Defaults to None.
+            output_bands (list[HLSBands | int | tuple[int, int] | str] | None): Bands that should be output by the dataset as named by dataset_bands.
             constant_scale (float): Factor to multiply image values by. Defaults to 1.
             transform (Albumentations.Compose | None): Albumentations transform to be applied.
                 Should end with ToTensorV2(). If used through the generic_data_module,
@@ -110,17 +110,21 @@ def is_valid_file(x):
 
         self.rgb_indices = [0, 1, 2] if rgb_indices is None else rgb_indices
 
-        self.dataset_bands = dataset_bands
-        self.output_bands = output_bands
+        self.dataset_bands = self._generate_bands_intervals(dataset_bands)
+        self.output_bands = self._generate_bands_intervals(output_bands)
+
         if self.output_bands and not self.dataset_bands:
             msg = "If output bands provided, dataset_bands must also be provided"
             return Exception(msg)  # noqa: PLE0101
 
+        # There is a special condition if the bands are defined as simple strings.
         if self.output_bands:
             if len(set(self.output_bands) & set(self.dataset_bands)) != len(self.output_bands):
                 msg = "Output bands must be a subset of dataset bands"
                 raise Exception(msg)
+
             self.filter_indices = [self.dataset_bands.index(band) for band in self.output_bands]
+
         else:
             self.filter_indices = None
         # If no transform is given, apply only to transform to torch tensor

tests/manufactured-finetune_prithvi_swin_B_band_interval.yaml

@@ -0,0 +1,136 @@
+# lightning.pytorch==2.1.1
+seed_everything: 42
+trainer:
+  accelerator: auto
+  strategy: auto
+  devices: auto
+  num_nodes: 1
+  # precision: 16-mixed
+  logger:
+    class_path: TensorBoardLogger
+    init_args:
+      save_dir: tests/
+      name: all_ecos_random
+  callbacks:
+    - class_path: RichProgressBar
+    - class_path: LearningRateMonitor
+      init_args:
+        logging_interval: epoch
+    - class_path: EarlyStopping
+      init_args:
+        monitor: val/loss
+        patience: 100
+  max_epochs: 5
+  check_val_every_n_epoch: 1
+  log_every_n_steps: 20
+  enable_checkpointing: true
+  default_root_dir: tests/
+data:
+  class_path: GenericNonGeoPixelwiseRegressionDataModule
+  init_args:
+    batch_size: 2
+    num_workers: 4
+    train_transform:
+      - class_path: albumentations.HorizontalFlip
+        init_args:
+          p: 0.5      
+      - class_path: albumentations.Rotate
+        init_args:
+          limit: 30
+          border_mode: 0 # cv2.BORDER_CONSTANT
+          value: 0
+          # mask_value: 1
+          p: 0.5
+      - class_path: ToTensorV2
+    dataset_bands:
+      - [0, 11]
+    output_bands:
+      - [1, 3]
+      - [4, 6]
+    rgb_indices:
+      - 2
+      - 1
+      - 0
+    train_data_root: tests/
+    train_label_data_root: tests/
+    val_data_root: tests/
+    val_label_data_root: tests/
+    test_data_root: tests/
+    test_label_data_root: tests/ 
+    img_grep: "regression*input*.tif"
+    label_grep: "regression*label*.tif"
+    means:
+    - 547.36707
+    - 898.5121
+    - 1020.9082
+    - 2665.5352
+    - 2340.584
+    - 1610.1407
+    stds:
+    - 411.4701
+    - 558.54065
+    - 815.94025
+    - 812.4403
+    - 1113.7145
+    - 1067.641
+    no_label_replace: -1
+    no_data_replace: 0
+
+model:
+  class_path: terratorch.tasks.PixelwiseRegressionTask
+  init_args:
+    model_args:
+      decoder: UperNetDecoder
+      pretrained: true
+      backbone: prithvi_swin_B
+      backbone_pretrained_cfg_overlay:
+        file: tests/prithvi_swin_B.pt
+      backbone_drop_path_rate: 0.3
+      # backbone_window_size: 8
+      decoder_channels: 256
+      in_channels: 6
+      bands:
+        - BLUE
+        - GREEN
+        - RED
+        - NIR_NARROW
+        - SWIR_1
+        - SWIR_2
+      num_frames: 1
+      head_dropout: 0.5708022831486758
+      head_final_act: torch.nn.ReLU
+      head_learned_upscale_layers: 2
+    loss: rmse
+    #aux_heads:
+    #  - name: aux_head
+    #    decoder: IdentityDecoder
+    #    decoder_args:
+    #      decoder_out_index: 2
+    #      head_dropout: 0,5
+    #      head_channel_list:
+    #        - 64
+    #      head_final_act: torch.nn.ReLU
+    #aux_loss:
+    #  aux_head: 0.4
+    ignore_index: -1
+    freeze_backbone: true
+    freeze_decoder: false
+    model_factory: PrithviModelFactory
+
+    # uncomment this block for tiled inference
+    # tiled_inference_parameters:
+    #   h_crop: 224
+    #   h_stride: 192
+    #   w_crop: 224
+    #   w_stride: 192
+    #   average_patches: true
+optimizer:
+  class_path: torch.optim.AdamW
+  init_args:
+    lr: 0.00013524680528283027
+    weight_decay: 0.047782217873995426
+lr_scheduler:
+  class_path: ReduceLROnPlateau
+  init_args:
+    monitor: val/loss
+