docs(scripts): add logging and informative messages to the octseg app…

…lication

README.md

@@ -100,5 +100,5 @@ docker load -i image_name.tar.gz
 To use the image you need to start a container from the image, having the data mounted you want to process.
 
 ```shell
-docker run -u $(id -u):$(id -g) -v YOUR_DATA_PATH:/home/data -it medvisbonn/octseg:0.1-cpu
+docker run -u $(id -u):$(id -g) --gpus=all -v YOUR_DATA_PATH:/home/data -it medvisbonn/octseg:0.1-gpu
 ```

octseg/scripts/commands/check.py

@@ -0,0 +1,53 @@
+import click
+import logging
+from octseg.scripts.utils import find_volumes
+
+from tqdm import tqdm
+import numpy as np
+import eyepy as ep
+
+logger = logging.getLogger("octseg.check")
+logger.setLevel("INFO")
+
+
+@click.command()
+@click.pass_context
+def check(
+    ctx: click.Context,
+):
+    """Check XML exports for common problems"""
+
+    input_path = ctx.obj["input_path"]
+
+    volumes = find_volumes(input_path)["xml"]
+
+    error_count_multiple = check_multiple_exports(volumes)
+    error_count_white = check_white_background(volumes)
+
+    if error_count_white + error_count_multiple == 0:
+        msg = "All XML exports are checked and 0 problems were found."
+        logger.info(msg)
+    else:
+        msg = f"Please fix {error_count_white+error_count_multiple} errors before processing your data."
+        logger.info(msg)
+
+    click.echo(msg)
+
+
+def check_multiple_exports(v_paths):
+    errors = 0
+    for p in tqdm(v_paths, desc="Check for double exports: "):
+        if len(list(p.glob("*.xml"))) != 1:
+            logger.warning(f"{p.name}: Folder contains more than 1 XML export.")
+            errors += 1
+    return errors
+
+
+def check_white_background(v_paths):
+    errors = 0
+    for p in tqdm(v_paths, desc="Check for inverted contrast: "):
+        data = ep.Oct.from_heyex_xml(p)
+        if np.mean(data[0].scan) > 128:
+            logger.warning(f"{p.name}: B-scans have inverted contrast.")
+            errors += 1
+    return errors

octseg/scripts/drusen.py → octseg/scripts/commands/drusen.py

@@ -12,7 +12,7 @@
 from octseg.scripts.utils import find_volumes
 from octseg.grids import grid
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger("octseg.drusen")
 
 
 @click.command()
@@ -91,10 +91,18 @@ def drusen(ctx: click.Context, drusen_threshold, radii, sectors, offsets):
             results.append(quantify_drusen(data, radii, sectors, offsets))
 
     # Save quantification results as csv
-    csv = pd.DataFrame.from_records(results)
-    csv = csv.set_index(["Visit", "Laterality"])
-    csv = csv.sort_index()
-    csv.to_csv(output_path / f"drusen_results.csv")
+    if len(results) > 0:
+        csv = pd.DataFrame.from_records(results)
+        csv = csv.set_index(["Visit", "Laterality"])
+        csv = csv.sort_index()
+        csv.to_csv(output_path / f"drusen_results.csv")
+
+        click.echo(f"Drusen quantification saved for {len(csv)} volumes.")
+
+    if len(no_layers_volumes) > 0:
+        click.echo(
+            f"No retinal layers found for {len(no_layers_volumes)} volumes. To predict layers run the 'layers' command."
+        )
 
 
 def quantify_drusen(oct_obj, radii, n_sectors, offsets):

octseg/scripts/layers.py → octseg/scripts/commands/layers.py

@@ -1,5 +1,4 @@
 import click
-from pathlib import Path
 import logging
 
 from importlib import resources
@@ -13,7 +12,7 @@
 import eyepy as ep
 import pickle
 
-logger = logging.getLogger(__name__)
+logger = logging.getLogger("octseg.layers")
 
 
 @click.command()
@@ -46,7 +45,7 @@ def layers(ctx: click.Context, model_id, overwrite, gpu):
     # Check if specified model is available
     if not model_id in list(resources.contents(weights_resources)):
         msg = f"A model with ID {model_id} is not available. Check 'octseg layers --help' for available models."
-        logging.error(msg)
+        logger.error(msg)
         raise ValueError(msg)
 
     # Find volumes
@@ -71,12 +70,15 @@ def layers(ctx: click.Context, model_id, overwrite, gpu):
         tf.config.experimental.set_visible_devices(gpus[gpu], "GPU")
     except IndexError:
         msg = "No GPU found, using the CPU instead."
-        logging.info(msg)
+        logger.warning(msg)
 
     data_readers = {"vol": ep.Oct.from_heyex_vol, "xml": ep.Oct.from_heyex_xml}
     # Predict layers and save
     for datatype, volumes in volumes.items():
-        for path in tqdm(volumes):
+        for path in tqdm(
+            volumes,
+            desc="Volumes: ",
+        ):
             # Load data
             data = data_readers[datatype](path)
 
@@ -88,6 +90,8 @@ def layers(ctx: click.Context, model_id, overwrite, gpu):
             with open(output_dir / ("layers.pkl"), "wb") as myfile:
                 pickle.dump(data.layers, myfile)
 
+    click.echo("\nPredicted OCT layers are saved. You can now use the 'drusen' command")
+
 
 def get_layers(data, model_id):
     layer_model, model_config = load_model(model_id, (512, data[0].shape[1], 1))

octseg/scripts/main.py

@@ -1,9 +1,19 @@
 import click
 from pathlib import Path
-from octseg.scripts.layers import layers
-from octseg.scripts.drusen import drusen
+from octseg.scripts.commands.layers import layers
+from octseg.scripts.commands.drusen import drusen
+from octseg.scripts.commands.check import check
 
 import logging
+import warnings
+
+logger = logging.getLogger("octseg")
+
+formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
+ch = logging.StreamHandler()
+ch.setLevel("WARNING")
+ch.setFormatter(formatter)
+logger.addHandler(ch)
 
 
 @click.group()
@@ -23,7 +33,7 @@
 @click.option(
     "--log-level",
     type=click.Choice(["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]),
-    default="INFO",
+    default="WARNING",
     help="Set the logging level for the script",
 )
 @click.pass_context
@@ -38,17 +48,28 @@ def main(ctx, input_path, output_path, log_level):
     """
     ctx.ensure_object(dict)
 
-    logger = logging.getLogger(__name__)
-    logger.setLevel(getattr(logging, log_level))
-
     if output_path is None:
         output_path = Path(input_path) / "processed"
     else:
         output_path = Path(output_path)
+    output_path.mkdir(parents=True, exist_ok=True)
+
+    fh = logging.FileHandler(output_path / "octseg.log")
+    fh.setLevel("DEBUG")
+    formatter = logging.Formatter(
+        "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+    )
+    fh.setFormatter(formatter)
+    logger.addHandler(fh)
+    logger.setLevel(log_level)
+
+    if log_level != logging.DEBUG:
+        warnings.filterwarnings("ignore")
 
     ctx.obj["input_path"] = Path(input_path)
     ctx.obj["output_path"] = Path(output_path)
 
 
 main.add_command(drusen)
 main.add_command(layers)
+main.add_command(check)

scripts/make_docker_image.sh

@@ -1,4 +1,4 @@
 poetry build
 DOCKER_BUILDKIT=1 docker build -t medvisbonn/octseg:0.1-gpu -f ./docker/Dockerfile --target gpu .
-docker save -o ./dist/octseg_gpu_docker.tar medvisbonn/octseg:0.1-cpu
-gzip ./dist/octseg_gpu_docker.tar
+docker save -o ./dist/docker_octseg-0.1-gpu.tar medvisbonn/octseg:0.1-gpu
+gzip ./dist/docker_octseg-0.1-gpu.tar