Pull request #3: Refactoring

Merge in RR/image-prediction from refactoring to master

Squashed commit of the following:

commit fc4e2efac113f2e307fdbc091e0a4f4e3e5729d3
Author: Matthias Bisping <matthias.bisping@iqser.com>
Date:   Wed Mar 16 14:21:05 2022 +0100

    applied black

commit 3baabf5bc0b04347af85dafbb056f134258d9715
Author: Matthias Bisping <matthias.bisping@iqser.com>
Date:   Wed Mar 16 14:20:30 2022 +0100

    added banner

commit 30e871cfdc79d0ff2e0c26d1b858e55ab1b0453f
Author: Matthias Bisping <matthias.bisping@iqser.com>
Date:   Wed Mar 16 14:02:26 2022 +0100

    rename logger

commit d76fefd3ff0c4425defca4db218ce4a84c6053f3
Author: Matthias Bisping <matthias.bisping@iqser.com>
Date:   Wed Mar 16 14:00:39 2022 +0100

    logger refactoring

commit 0e004cbd21ab00b8804901952405fa870bf48e9c
Author: Matthias Bisping <matthias.bisping@iqser.com>
Date:   Wed Mar 16 14:00:08 2022 +0100

    logger refactoring

commit 49e113f8d85d7973b73f664779906a1347d1522d
Author: Matthias Bisping <matthias.bisping@iqser.com>
Date:   Wed Mar 16 13:25:08 2022 +0100

    refactoring

commit 7ec3d52e155cb83bed8804d2fee4f5bdf54fb59b
Author: Matthias Bisping <matthias.bisping@iqser.com>
Date:   Wed Mar 16 13:21:52 2022 +0100

    applied black

commit 06ea0be8aa9344e11b9d92fd526f2b73061bc736
Author: Matthias Bisping <matthias.bisping@iqser.com>
Date:   Wed Mar 16 13:21:20 2022 +0100

    refactoring

config.yaml

@@ -5,6 +5,7 @@ webserver:
 
 service:
   logging_level: $LOGGING_LEVEL_ROOT|DEBUG  # Logging level for service logger
+  progressbar: True  # Whether a progress bar over the pages of a document is displayed while processing
   batch_size: $BATCH_SIZE|32  # Number of images in memory simultaneously
   verbose: $VERBOSE|True  # Service prints document processing progress to stdout
   run_id: $RUN_ID|fabfb1f192c745369b88cab34471aba7  # The ID of the mlflow run to load the model from
@@ -25,4 +26,3 @@ filters:
     max: $MAX_IMAGE_FORMAT|10  # Maximum permissible
 
   min_confidence: $MIN_CONFIDENCE|0.5  # Minimum permissible prediction confidence
-

image_prediction/flask.py

@@ -0,0 +1,43 @@
+from typing import Callable
+
+from flask import Flask, request, jsonify
+
+from image_prediction.utils import get_logger
+
+logger = get_logger()
+
+
+def make_prediction_server(predict_fn: Callable):
+
+    app = Flask(__name__)
+
+    @app.route("/ready", methods=["GET"])
+    def ready():
+        resp = jsonify("OK")
+        resp.status_code = 200
+        return resp
+
+    @app.route("/health", methods=["GET"])
+    def healthy():
+        resp = jsonify("OK")
+        resp.status_code = 200
+        return resp
+
+    @app.route("/", methods=["POST"])
+    def predict():
+        pdf = request.data
+
+        logger.debug("Running predictor on document...")
+        try:
+            predictions = predict_fn(pdf)
+            response = jsonify(predictions)
+            logger.info("Analysis completed.")
+            return response
+        except Exception as err:
+            logger.error("Analysis failed.")
+            logger.exception(err)
+            response = jsonify("Analysis failed.")
+            response.status_code = 500
+            return response
+
+    return app

image_prediction/locations.py

@@ -2,12 +2,8 @@ from os import path
 
 MODULE_DIR = path.dirname(path.abspath(__file__))
 PACKAGE_ROOT_DIR = path.dirname(MODULE_DIR)
-REPO_ROOT_DIR = path.dirname(path.dirname(PACKAGE_ROOT_DIR))
-
-DOCKER_COMPOSE_FILE = path.join(REPO_ROOT_DIR, "docker-compose.yaml")
 
 CONFIG_FILE = path.join(PACKAGE_ROOT_DIR, "config.yaml")
-LOG_FILE = "/tmp/log.log"
 
 DATA_DIR = path.join(PACKAGE_ROOT_DIR, "data")
 MLRUNS_DIR = path.join(DATA_DIR, "mlruns")

image_prediction/predictor.py

@@ -1,4 +1,3 @@
-import logging
 from itertools import chain
 from operator import itemgetter
 from typing import List, Dict, Iterable
@@ -7,11 +6,14 @@ import numpy as np
 
 from image_prediction.config import CONFIG
 from image_prediction.locations import MLRUNS_DIR, BASE_WEIGHTS
+from image_prediction.utils import temporary_pdf_file, get_logger
 from incl.redai_image.redai.redai.backend.model.model_handle import ModelHandle
 from incl.redai_image.redai.redai.backend.pdf.image_extraction import extract_and_stitch
 from incl.redai_image.redai.redai.utils.mlflow_reader import MlflowModelReader
 from incl.redai_image.redai.redai.utils.shared import chunk_iterable
 
+logger = get_logger()
+
 
 class Predictor:
     """`ModelHandle` wrapper. Forwards to wrapped model handle for prediction and produces structured output that is
@@ -36,7 +38,7 @@ class Predictor:
             self.classes_readable = np.array(self.model_handle.classes)
             self.classes_readable_aligned = self.classes_readable[self.classes[list(range(len(self.classes)))]]
         except Exception as e:
-            logging.info(f"Service estimator initialization failed: {e}")
+            logger.info(f"Service estimator initialization failed: {e}")
 
     def __make_predictions_human_readable(self, probs: np.ndarray) -> List[Dict[str, float]]:
         """Translates an n x m matrix of probabilities over classes into an n-element list of mappings from classes to
@@ -88,29 +90,33 @@ class Predictor:
 
         return predictions if probabilities else classes
 
+    def predict_pdf(self, pdf, verbose=False):
+        with temporary_pdf_file(pdf) as pdf_path:
+            image_metadata_pairs = self.__extract_image_metadata_pairs(pdf_path, verbose=verbose)
+            return self.__predict_images(image_metadata_pairs)
 
-def extract_image_metadata_pairs(pdf_path: str, **kwargs):
+    def __predict_images(self, image_metadata_pairs: Iterable, batch_size: int = CONFIG.service.batch_size):
-    def image_is_large_enough(metadata: dict):
+        def process_chunk(chunk):
-        x1, x2, y1, y2 = itemgetter("x1", "x2", "y1", "y2")(metadata)
+            images, metadata = zip(*chunk)
+            predictions = self.predict(images, probabilities=True)
+            return predictions, metadata
 
-        return abs(x1 - x2) > 2 and abs(y1 - y2) > 2
+        def predict(image_metadata_pair_generator):
+            chunks = chunk_iterable(image_metadata_pair_generator, n=batch_size)
+            return map(chain.from_iterable, zip(*map(process_chunk, chunks)))
 
-    yield from extract_and_stitch(pdf_path, convert_to_rgb=True, filter_fn=image_is_large_enough, **kwargs)
+        try:
+            predictions, metadata = predict(image_metadata_pairs)
+            return predictions, metadata
 
+        except ValueError:
+            return [], []
 
-def classify_images(predictor, image_metadata_pairs: Iterable, batch_size: int = CONFIG.service.batch_size):
+    @staticmethod
-    def process_chunk(chunk):
+    def __extract_image_metadata_pairs(pdf_path: str, **kwargs):
-        images, metadata = zip(*chunk)
+        def image_is_large_enough(metadata: dict):
-        predictions = predictor.predict(images, probabilities=True)
+            x1, x2, y1, y2 = itemgetter("x1", "x2", "y1", "y2")(metadata)
-        return predictions, metadata
 
-    def predict(image_metadata_pair_generator):
+            return abs(x1 - x2) > 2 and abs(y1 - y2) > 2
-        chunks = chunk_iterable(image_metadata_pair_generator, n=batch_size)
-        return map(chain.from_iterable, zip(*map(process_chunk, chunks)))
 
-    try:
+        yield from extract_and_stitch(pdf_path, convert_to_rgb=True, filter_fn=image_is_large_enough, **kwargs)
-        predictions, metadata = predict(image_metadata_pairs)
-        return predictions, metadata
-
-    except ValueError:
-        return [], []

image_prediction/response.py

@@ -1,11 +1,10 @@
 """Defines functions for constructing service responses."""
 
 
+import math
 from itertools import starmap
 from operator import itemgetter
 
-import numpy as np
-
 from image_prediction.config import CONFIG
 
 
@@ -15,8 +14,8 @@ def build_response(predictions: list, metadata: list) -> list:
 
 def build_image_info(prediction: dict, metadata: dict) -> dict:
     def compute_geometric_quotient():
-        page_area_sqrt = np.sqrt(abs(page_width * page_height))
+        page_area_sqrt = math.sqrt(abs(page_width * page_height))
-        image_area_sqrt = np.sqrt(abs(x2 - x1) * abs(y2 - y1))
+        image_area_sqrt = math.sqrt(abs(x2 - x1) * abs(y2 - y1))
         return image_area_sqrt / page_area_sqrt
 
     page_width, page_height, x1, x2, y1, y2, width, height = itemgetter(
@@ -36,7 +35,7 @@ def build_image_info(prediction: dict, metadata: dict) -> dict:
 
     min_confidence_breached = bool(max(prediction["probabilities"].values()) < CONFIG.filters.min_confidence)
     prediction["label"] = prediction.pop("class")  # "class" as field name causes problem for Java objectmapper
-    prediction["probabilities"] = {klass: np.round(prob, 6) for klass, prob in prediction["probabilities"].items()}
+    prediction["probabilities"] = {klass: round(prob, 6) for klass, prob in prediction["probabilities"].items()}
 
     image_info = {
         "classification": prediction,

image_prediction/utils.py

@@ -0,0 +1,68 @@
+import logging
+import tempfile
+from contextlib import contextmanager
+
+from image_prediction.config import CONFIG
+
+
+@contextmanager
+def temporary_pdf_file(pdf: bytes):
+    with tempfile.NamedTemporaryFile() as f:
+        f.write(pdf)
+        yield f.name
+
+
+def make_logger_getter():
+
+    logger = logging.getLogger("imclf")
+    logger.propagate = False
+
+    handler = logging.StreamHandler()
+    handler.setLevel(CONFIG.service.logging_level)
+
+    log_format = "[%(levelname)s]: %(message)s"
+    formatter = logging.Formatter(log_format)
+
+    handler.setFormatter(formatter)
+    logger.addHandler(handler)
+
+    def get_logger():
+        return logger
+
+    return get_logger
+
+
+get_logger = make_logger_getter()
+
+
+def show_banner():
+    banner = '''
+    .....     .                            ...                ..          
+  .d88888Neu. 'L                        xH88"`~ .x8X    x .d88"    oec :  
+  F""""*8888888F    ..    .     :     :8888   .f"8888Hf  5888R    @88888  
+ *      `"*88*"   .888: x888  x888.  :8888>  X8L  ^""`   '888R    8"*88%  
+  -....    ue=:. ~`8888~'888X`?888f` X8888  X888h         888R    8b.     
+         :88N  `   X888  888X '888>  88888  !88888.       888R   u888888> 
+         9888L     X888  888X '888>  88888   %88888       888R    8888R   
+  uzu.   `8888L    X888  888X '888>  88888 '> `8888>      888R    8888P   
+,""888i   ?8888    X888  888X '888>  `8888L %  ?888   !   888R    *888>   
+4  9888L   %888>  "*88%""*88" '888!`  `8888  `-*""   /   .888B .  4888    
+'  '8888   '88%     `~    "    `"`      "888.      :"    ^*888%   '888    
+     "*8Nu.z*"                            `""***~"`        "%      88R    
+                                                                   88>    
+                                                                   48     
+                                                                   '8     
+    '''
+
+    logger = logging.getLogger(__name__)
+    logger.propagate = False
+
+    handler = logging.StreamHandler()
+    handler.setLevel(logging.INFO)
+
+    formatter = logging.Formatter("")
+
+    handler.setFormatter(formatter)
+    logger.addHandler(handler)
+
+    logger.info(banner)

src/serve.py

@@ -1,57 +1,29 @@
 import logging
-import tempfile
 
-from flask import Flask, request, jsonify
 from waitress import serve
 
 from image_prediction.config import CONFIG
-from image_prediction.predictor import Predictor, extract_image_metadata_pairs, classify_images
+from image_prediction.flask import make_prediction_server
+from image_prediction.predictor import Predictor
 from image_prediction.response import build_response
+from image_prediction.utils import get_logger, show_banner
+
+logger = get_logger()
 
 
 def main():
 
-    predictor = Predictor()
+    def predict(pdf):
-    logging.info("Predictor ready.")
+        predictions, metadata = predictor.predict_pdf(pdf, verbose=CONFIG.service.progressbar)
-
+        response = build_response(predictions, metadata)
-    app = Flask(__name__)
-
-    @app.route("/ready", methods=["GET"])
-    def ready():
-        resp = jsonify("OK")
-        resp.status_code = 200
-        return resp
-
-    @app.route("/health", methods=["GET"])
-    def healthy():
-        resp = jsonify("OK")
-        resp.status_code = 200
-        return resp
-
-    @app.route("/", methods=["POST"])
-    def predict():
-        pdf = request.data
-
-        logging.debug("Running predictor on document...")
-        with tempfile.NamedTemporaryFile() as tmp_file:
-            tmp_file.write(pdf)
-            image_metadata_pairs = extract_image_metadata_pairs(tmp_file.name)
-            try:
-                predictions, metadata = classify_images(predictor, image_metadata_pairs)
-            except Exception as err:
-                logging.warning("Analysis failed.")
-                logging.exception(err)
-                response = jsonify("Analysis failed.")
-                response.status_code = 500
-                return response
-            logging.debug(f"Found images in document.")
-
-        response = jsonify(build_response(list(predictions), list(metadata)))
-
-        logging.info("Analysis completed.")
         return response
 
-    run_prediction_server(app, mode=CONFIG.webserver.mode)
+    predictor = Predictor()
+    logger.info("Predictor ready.")
+
+    prediction_server = make_prediction_server(predict)
+
+    run_prediction_server(prediction_server, mode=CONFIG.webserver.mode)
 
 
 def run_prediction_server(app, mode="development"):
@@ -68,5 +40,9 @@ if __name__ == "__main__":
     logging.getLogger("urllib3").setLevel(logging.ERROR)
     logging.getLogger("werkzeug").setLevel(logging.ERROR)
     logging.getLogger("waitress").setLevel(logging.ERROR)
+    logging.getLogger("PIL").setLevel(logging.ERROR)
+    logging.getLogger("h5py").setLevel(logging.ERROR)
+
+    show_banner()
 
     main()