Merge remote-tracking branch 'origin-orion/rename_paths'

Author: paren8esis

README.md

@@ -104,7 +104,7 @@ Every script inherits settings from the aforementioned files.
 **For PAD:**
 1. Run `pad_experiments.py` with the appropriate arguments. Example:
    ```
-   python pad_experiments.py --train --model convlstm --parcel_loss --weighted_loss --root_path_coco <coco_folder_path> --prefix_coco <coco_file_prefix> --prefix <run_prefix> --num_epochs 10 --batch_size 32 --bands B02 B03 B04 B08 --saved_medians --img_size 61 61 --requires_norm --num_workers 16 --num_gpus 1 --fixed_window
+   python pad_experiments.py --train --model convlstm --parcel_loss --weighted_loss --root_path_coco <coco_folder_path> --prefix_coco <coco_file_prefix> --netcdf_path <netcdf_folder_path> --prefix <run_prefix> --num_epochs 10 --batch_size 32 --bands B02 B03 B04 B08 --saved_medians --img_size 61 61 --requires_norm --num_workers 16 --num_gpus 1 --fixed_window
    ```
    The above command is for training the **ConvLSTM** model using the **weighted parcel loss** described in the associated publication. Training will continue for **10 epochs** with **batch size 32**, using the Sentinel-2 **bands Blue (B02), Green (B03), Red (B04) and NIR (B08)**. The **input image size is 61x61**, the **precomputed medians are used** to speed up training and all input data are **normalized**. Finally, a **fixed window** is used containing months 4 (April) through 9 (September). Please use the `--help` argument to find information on all available parameters.
 2. Optionally, after training run `visualize_predictions.py` to visualize the image, ground truth and prediction for a specific model and image.

compute_class_weights.py

@@ -18,6 +18,8 @@
                         help='Prefix of the COCO file. Default "exp1_patches2000_strat".')
     parser.add_argument('--medians_prefix', type=str, default='exp1_patches2000_strat_61x61', required=False,
                         help='Prefix of the medians directory. Default "exp1_patches2000_strat_61x61".')
+    parser.add_argument('--netcdf_path', type=str, default='dataset/netcdf',
+                        help='The path containing the netcdf files. Default "dataset/netcdf".')
     parser.add_argument('--out_prefix', type=str, required=False,
                         help='The prefix to use for the class weights file. Default none.')
     parser.add_argument('--ignore_zero', default=False, action='store_true', required=False,
@@ -30,6 +32,7 @@
     root_path_coco = Path(args.coco_path)
     coco_train = root_path_coco / f'{args.coco_prefix}_coco_train.json'
     coco_val = root_path_coco / f'{args.coco_prefix}_coco_val.json'
+    netcdf_path = Path(args.netcdf_path)
 
     if args.out_prefix is not None:
         out_name = f'{args.out_prefix}_class_weights.pkl'
@@ -46,7 +49,7 @@
     else:
         # Create Data Module
         dm = PADDataModule(
-            root_path_coco=root_path_coco,
+            netcdf_path=netcdf_path,
             path_train=coco_train,
             path_val=coco_val,
             group_freq='1MS',

pad_experiments.py

@@ -131,6 +131,9 @@ def main():
     parser.add_argument('--prefix_coco', type=str, default=None, required=False,
                              help='The prefix to use for the COCO file. Default none.')
 
+    parser.add_argument('--netcdf_path', type=str, default='dataset/netcdf',
+                        help='The path containing the netcdf files. Default "dataset/netcdf".')
+
     parser.add_argument('--prefix', type=str, default=None, required=False,
                              help='The prefix to use for dumping data files. If none, the current timestamp is used')
 
@@ -196,6 +199,8 @@ def main():
     # Normalize paths for different OSes
     root_path_coco = Path(args.root_path_coco)
 
+    netcdf_path = Path(args.netcdf_path)
+
     # Check existence of data folder
     if not root_path_coco.is_dir():
         print(f'{font_colors.RED}Coco path doesn\'t exist!{font_colors.ENDC}')
@@ -387,7 +392,7 @@ def main():
     if args.train:
         # Create Data Modules
         dm = PADDataModule(
-            root_path_coco=root_path_coco,
+            netcdf_path=netcdf_path,
             path_train=path_train,
             path_val=path_val,
             group_freq=args.group_freq,
@@ -453,7 +458,7 @@ def main():
     else:
         # Create Data Module
         dm = PADDataModule(
-            root_path_coco=root_path_coco,
+            netcdf_path=netcdf_path,
             path_test=path_test,
             group_freq=args.group_freq,
             prefix=prefix,

utils/PAD_datamodule.py

@@ -50,14 +50,14 @@ def __init__(
         '''
         Parameters
         ----------
-        root_path_coco: Path or str
-            The path containing the COCO files.
         netcdf_path: Path or str
             The path containing the training data (netCDF files).
+        path_train: Path or str
+            The COCO file path containing the training data.
         path_val: Path or str
-            The file path containing the validation data.
+            The COCO file path containing the validation data.
         path_test: Path or str
-            The file path containing the testing data.
+            The COCO file path containing the testing data.
         bands: list of str, default None
             A list of the bands to use. If None, then all available bands are
             taken into consideration. Note that the bands are given in a two-digit

visualize_predictions.py

@@ -60,6 +60,9 @@ def get_window(idx, window_len, image_size, coco_file):
     parser.add_argument('--prefix_coco', type=str, default=None, required=False,
                              help='The prefix to use for the COCO file. Default none.')
 
+    parser.add_argument('--netcdf_path', type=str, default='dataset/netcdf',
+                        help='The path containing the netcdf files. Default "dataset/netcdf".')
+
     parser.add_argument('--prefix', type=str, default=None, required=False,
                              help='The prefix to use for dumping data files. If none, the current timestamp is used')
 
@@ -117,6 +120,7 @@ def get_window(idx, window_len, image_size, coco_file):
 
     # Normalize paths for different OSes
     root_path_coco = Path(args.root_path_coco)
+    netcdf_path = Path(netcdf_path)
 
     # Check existence of data folder
     if not root_path_coco.is_dir():
@@ -175,7 +179,7 @@ def get_window(idx, window_len, image_size, coco_file):
 
     # Create Data Module for testing images
     dm = PADDataModule(
-        root_path_coco=root_path_coco,
+        netcdf_path=netcdf_path,
         path_test=path_test,
         group_freq=args.group_freq,
         prefix=args.prefix,