print to logger

mapreader/annotate/annotator.py

@@ -3,6 +3,7 @@
 import functools
 import hashlib
 import json
+import logging
 import os
 import random
 import string
@@ -20,12 +21,15 @@
 
 from ..load.loader import load_patches
 
+# Ignore warnings
 warnings.filterwarnings("ignore", category=UserWarning)
 
 _CENTER_LAYOUT = widgets.Layout(
     display="flex", flex_flow="column", align_items="center"
 )
 
+# Set up logging
+logger = logging.getLogger(__name__)
 
 class Annotator:
     """
@@ -218,7 +222,7 @@
 
         # Test for existing patch annotation file
         if os.path.exists(annotations_file):
-            print("[INFO] Loading existing patch annotations.")
+            logger.info("Loading existing patch annotations.")
             patch_df = self._load_annotations(
                 patch_df=patch_df,
                 annotations_file=annotations_file,

mapreader/annotate/utils.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 from __future__ import annotations
 
+import logging
 import os
 import random
 import sys
@@ -25,10 +26,14 @@
 
 from mapreader import load_patches, loader
 
+# Ignore warnings
 warnings.filterwarnings("ignore")
-# warnings.filterwarnings(
+#   (
 #     "ignore", message="Pandas doesn't allow columns to be created via a new attribute name")
 
+# Set up logging
+logger = logging.getLogger(__name__)
+
 
 def prepare_data(
     df: pd.DataFrame,
@@ -708,4 +713,4 @@
         print(f"[INFO] {new_labels} labels were not already stored")
         print(f"[INFO] Total number of saved annotations: {len(image_df)}")
     else:
-        print("[INFO] No annotations to save!")
+        logger.info("No annotations to save!")

mapreader/classify/classifier.py

@@ -2,6 +2,7 @@
 from __future__ import annotations
 
 import copy
+import logging
 import os
 import random
 import socket
@@ -29,6 +30,9 @@
 # from tqdm.autonotebook import tqdm
 # from torch.nn.modules.module import _addindent
 
+# Set up logging
+logger = logging.getLogger(__name__)
+
 
 class ClassifierContainer:
     def __init__(
@@ -147,7 +151,7 @@
             self.labels_map = labels_map
 
             # set up model and move to device
-            print("[INFO] Initializing model.")
+            logger.info("Initializing model.")
             if isinstance(model, nn.Module):
                 self.model = model.to(self.device)
                 self.input_size = input_size
@@ -733,12 +737,12 @@
                 print_info_batch_freq=print_info_batch_freq,
             )
         except KeyboardInterrupt:
-            print("[INFO] Exiting...")
+            logger.info("Exiting...")
             if os.path.isfile(self.tmp_save_filename):
                 print(f'[INFO] Loading "{self.tmp_save_filename}" as model.')
                 self.load(self.tmp_save_filename, remove_after_load=remove_after_load)
             else:
-                print("[INFO] No checkpoint file found - model has not been updated.")
+                logger.info("No checkpoint file found - model has not been updated.")
 
     def train_core(
         self,
@@ -834,7 +838,7 @@
                 print(
                     "[WARNING] Could not import ``SummaryWriter`` from torch.utils.tensorboard"  # noqa
                 )
-                print("[WARNING] Continuing without tensorboard.")
+                logger.warning("Continuing without tensorboard.")
                 tensorboard_path = None
 
         start_epoch = self.last_epoch + 1
@@ -1812,7 +1816,7 @@
             The number of worker threads to use for loading data, by default 0.
         """
         if sampler and shuffle:
-            print("[INFO] ``sampler`` is defined so train dataset will be unshuffled.")
+            logger.info("``sampler`` is defined so train dataset will be unshuffled.")
 
         dataloader = DataLoader(
             dataset,

mapreader/classify/load_annotations.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 from __future__ import annotations
 
+import logging
 import os
 from decimal import Decimal
 from typing import Callable
@@ -16,6 +17,9 @@
 
 from .datasets import PatchContextDataset, PatchDataset
 
+# Set up logging
+logger = logging.getLogger(__name__)
+
 
 class AnnotationsLoader:
     def __init__(self):
@@ -452,7 +456,7 @@
             if user_input_ids.lower() in ["exit", "end", "stop"]:
                 break
 
-        print("[INFO] Exited.")
+        logger.info("Exited.")
 
     def show_sample(self, label_to_show: str, num_samples: int | None = 9) -> None:
         """Show a random sample of images with the specified label (tar_label).
@@ -629,7 +633,7 @@
         self.datasets = datasets
         self.dataset_sizes = dataset_sizes
 
-        print("[INFO] Number of annotations in each set:")
+        logger.info("Number of annotations in each set:")
         for set_name in datasets.keys():
             print(f"    - {set_name}:   {dataset_sizes[set_name]}")
 
@@ -761,15 +765,15 @@
 
         if isinstance(sampler, str):
             if sampler == "default":
-                print("[INFO] Using default sampler.")
+                logger.info("Using default sampler.")
                 sampler = self._define_sampler()
             else:
                 raise ValueError(
                     '[ERROR] ``sampler`` can only be a PyTorch sampler, ``"default"`` or ``None``.'
                 )
 
         if sampler and shuffle:
-            print("[INFO] ``sampler`` is defined so train dataset will be un-shuffled.")
+            logger.info("``sampler`` is defined so train dataset will be un-shuffled.")
 
         dataloaders = {
             set_name: DataLoader(

mapreader/download/sheet_downloader.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import json
+import logging
 import os
 import re
 import shutil
@@ -21,6 +22,9 @@
 from .tile_loading import DEFAULT_TEMP_FOLDER, TileDownloader
 from .tile_merging import TileMerger
 
+# Set up logging
+logger = logging.getLogger(__name__)
+
 
 class SheetDownloader:
     """
@@ -504,7 +508,7 @@
             self.get_polygons()
 
         if len(self.found_queries) == 0:
-            print("[INFO] No query results found/saved.")
+            logger.info("No query results found/saved.")
         else:
             divider = 14 * "="
             print(f"{divider}\nQuery results:\n{divider}")

mapreader/download/tile_loading.py

@@ -10,8 +10,10 @@
 
 from .data_structures import GridBoundingBox, GridIndex
 
+# Set up logging
 logger = logging.getLogger(__name__)
 
+# Default values (constants)
 DEFAULT_TEMP_FOLDER = "_tile_cache/"  # must end with a "/"
 DEFAULT_IMG_DOWNLOAD_FORMAT = "png"
 

mapreader/download/tile_merging.py

@@ -10,8 +10,10 @@
 from .data_structures import GridBoundingBox, GridIndex
 from .tile_loading import DEFAULT_IMG_DOWNLOAD_FORMAT, DEFAULT_TEMP_FOLDER
 
+# Set up logging
 logger = logging.getLogger(__name__)
 
+# Default values (constants)
 DEFAULT_OUT_FOLDER = "./"
 DEFAULT_IMG_STORE_FORMAT = ("png", "PNG")
 

mapreader/load/geo_utils.py

@@ -1,11 +1,16 @@
 #!/usr/bin/env python
 from __future__ import annotations
 
+import logging
+
 import numpy as np
 import rasterio
 from geopy.distance import geodesic, great_circle
 from pyproj import Transformer
 
+# Set up logging
+logger = logging.getLogger(__name__)
+
 
 def extractGeoInfo(image_path):
     """Extract geographic information (shape, CRS and coordinates) from GeoTiff files
@@ -34,7 +39,7 @@ def extractGeoInfo(image_path):
         tiff_coord = tuple(tiff_src.bounds)
 
     print(f"[INFO] Shape: {tiff_shape}. \n[INFO] CRS: {tiff_proj}.")
-    print("[INFO] Coordinates: {:.4f} {:.4f} {:.4f} {:.4f}".format(*tiff_coord))
+    logger.info("Coordinates: {:.4f} {:.4f} {:.4f} {:.4f}".format(*tiff_coord))
 
     return tiff_shape, tiff_proj, tiff_coord
 
@@ -62,7 +67,7 @@ def reproject_geo_info(image_path, target_crs="EPSG:4326", calc_size_in_m=False)
     transformer = Transformer.from_crs(tiff_proj, target_crs, always_xy=True)
     coord = transformer.transform_bounds(*tiff_coord)
     print(f"[INFO] New CRS: {target_crs}")
-    print("[INFO] Reprojected coordinates: {:.4f} {:.4f} {:.4f} {:.4f}".format(*coord))
+    logger.info("Reprojected coordinates: {:.4f} {:.4f} {:.4f} {:.4f}".format(*coord))
 
     height, width, _ = tiff_shape
 

mapreader/load/images.py

@@ -5,6 +5,7 @@
 except ImportError:
     pass
 
+import logging
 import os
 import random
 import re
@@ -37,6 +38,9 @@
 # Ignore warnings
 warnings.filterwarnings("ignore")
 
+# Set up logging
+logger = logging.getLogger(__name__)
+
 
 class MapImages:
     """
@@ -518,7 +522,7 @@ def add_shape(self, tree_level: str | None = "parent") -> None:
             self._add_shape_id(image_id=image_id)
 
     def add_coords_from_grid_bb(self, verbose: bool = False) -> None:
-        print("[INFO] Adding coordinates, tree level: parent")
+        logger.info("Adding coordinates, tree level: parent")
 
         parent_list = self.list_parents()
 
@@ -552,7 +556,7 @@ def add_coord_increments(self, verbose: bool | None = False) -> None:
         pixel-wise delta longitude (``dlon``) and delta latitude (``dlat``)
         for the image and adds the data to it.
         """
-        print("[INFO] Add coord-increments, tree level: parent")
+        logger.info("Add coord-increments, tree level: parent")
 
         parent_list = self.list_parents()
 

mapreader/spot_text/deepsolo_runner.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import logging
 import os
 import pathlib
 import pickle
@@ -32,6 +33,9 @@
         "Please install DeepSolo from the following link: https://github.com/rwood-97/DeepSolo"
     )
 
+# Set up logging
+logger = logging.getLogger(__name__)
+
 
 class DeepSoloRunner:
     def __init__(
@@ -471,7 +475,7 @@
                 raise ValueError("[ERROR] Please provide a `parent_df`")
 
         if self.parent_predictions == {}:
-            print("[INFO] Converting patch pixel bounds to parent pixel bounds.")
+            logger.info("Converting patch pixel bounds to parent pixel bounds.")
             _ = self.convert_to_parent_pixel_bounds()
 
         for parent_id, prediction in self.parent_predictions.items():

mapreader/spot_text/dptext_detr_runner.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import logging
 import os
 import pathlib
 
@@ -31,6 +32,9 @@
         "Please install DPText-DETR from the following link: https://github.com/rwood-97/DPText-DETR"
     )
 
+# Set up logging
+logger = logging.getLogger(__name__)
+
 
 class DPTextDETRRunner:
     def __init__(
@@ -290,7 +294,7 @@
                 raise ValueError("[ERROR] Please provide a `parent_df`")
 
         if self.parent_predictions == {}:
-            print("[INFO] Converting patch pixel bounds to parent pixel bounds.")
+            logger.info("Converting patch pixel bounds to parent pixel bounds.")
             _ = self.convert_to_parent_pixel_bounds()
 
         for parent_id, prediction in self.parent_predictions.items():