Basic unit tests, logging, exception refactoring

.gitignore

@@ -47,6 +47,7 @@ coverage.xml
 *.cover
 .hypothesis/
 .pytest_cache/
+/tests/reports/
 
 # Translations
 *.mo

.travis.yml

@@ -1,11 +1,15 @@
 language: python
+
 python:
   - "3.8"
 
+before_install:
+  - "pip install -U pip"
+  - "python setup.py install"
 install:
-  - pip install -e .
+  - pip install pytest pandas
 dist: xenial
 services:
   - xvfb
 
-script: eyeloop --video 'misc/travis-sample/Frmd7.m4v'
+script: pytest

MANIFEST.in

@@ -0,0 +1 @@
+include requirements.txt requirements_testing.txt tox.ini

README.md

@@ -187,6 +187,17 @@ The default graphical user interface in EyeLoop is [*minimum-gui*.](https://gith
 
 > EyeLoop is compatible with custom graphical user interfaces through its modular logic. [Click here](https://github.com/simonarvin/eyeloop/blob/master/eyeloop/guis/README.md) for instructions on how to build your own.
 
+## Running unit tests ##
+
+Install testing requirements by running in a terminal:
+
+`pip install -r requirements_testing.txt`
+
+Then run tox: `tox`
+
+Reports and results will be outputted to `/tests/reports`
+
+
 ## Known issues ##
 - [ ] Respawning/freezing windows when running *minimum-gui* in Ubuntu.
 

conftest.py

@@ -0,0 +1,2 @@
+# Extra configuration for pytest
+# The presence of this file in {project_dir} will force pytest to add the dir to PYTHONPATH

eyeloop/__init__.py

@@ -0,0 +1,7 @@
+__all__ = ["constants", "engine", "extractors", "guis", "importers", "utilities", "run_eyeloop", "config"]
+
+from eyeloop import utilities
+from eyeloop import constants
+from eyeloop import guis
+from eyeloop import importers
+from eyeloop import utilities

eyeloop/engine/engine.py

@@ -1,4 +1,6 @@
+import logging
 import time
+from typing import Optional
 
 import cv2
 
@@ -7,6 +9,8 @@
 from eyeloop.engine.processor import Shape
 from eyeloop.utilities.general_operations import to_int, tuple_int
 
+logger = logging.getLogger(__name__)
+
 
 class Engine:
     def __init__(self, eyeloop):
@@ -21,6 +25,7 @@ def __init__(self, eyeloop):
         else:  # Enables markers to remove artifacts. -m 1
             self.place_markers = self.real_place_markers
         self.marks = []
+        self.blink: Optional[int] = None
 
         if config.arguments.tracking == 0:  # Recording mode. --tracking 0
             self.iterate = self.record
@@ -103,7 +108,8 @@ def arm(self, width, height, image) -> None:
         self.norm_cr_artefact = int(6 * self.norm)
 
         self.mean = np.mean(image)
-        self.blink_threshold = 25.1*np.log(np.var(image)) - 182 #0.046 * np.var(image) - 68.11
+        # self.blink_threshold = 25.1 * np.log(np.var(image)) - 182  # 0.046 * np.var(image) - 68.11
+        self.blink_threshold = 0.046 * np.var(image) - 58
 
         self.base_mean = -1
         self.blink = 0
@@ -119,28 +125,35 @@ def arm(self, width, height, image) -> None:
         for cr_processor in self.cr_processors:
             cr_processor.binarythreshold = float(np.min(self.source)) * .7
 
-    def check_blink(self, threshold=5) -> bool:
+    def check_blink(self, threshold: Optional[float] = None) -> bool:
         """
         Analyzes the monochromatic distribution of the frame,
         to infer blinking. Change in mean during blinking is very distinct.
+        :returns: True if blink detected, False otherwise
         """
-
+        # TODO calculate threshold using another method?
+        if threshold is None:
+            threshold = self.blink_threshold
+            # print(f"threshold = {threshold}")
         mean = np.mean(self.source)
         delta = self.mean - mean
         self.mean = mean
 
-        #    print("delta", delta)
-        if abs(delta) > self.blink_threshold:
-            self.blink = 10
-            print("blink!")
-            return False
+        if threshold < 0:
+            raise ValueError(f"check_blink() threshold must be greater than 0! Threshold was {threshold}")
+
+        # print(f"blink delta = {abs(delta)}")
+        if abs(delta) > threshold:
+            self.blink = 10  # TODO does this parameter mean a blink lasts for 10 frames? Should this be here?
+            print("blink detected!")
+            return True
         elif self.blink != 0:
 
             self.blink -= 1
+            return True
+        else:
+            self.blink = 0
             return False
-        self.blink = 0
-
-        return True
 
     def track(self) -> None:
         """
@@ -154,10 +167,11 @@ def track(self) -> None:
 
         timestamp = time.time()
         cr_width = cr_height = cr_center = cr_angle = pupil_center = pupil_width = pupil_height = pupil_angle = -1
-        blink = 0
-        cr_log=self.cr_log_stock.copy()
 
-        if self.check_blink():
+        cr_log = self.cr_log_stock.copy()
+
+        if self.check_blink() is False:
+            blink = 0
             try:
                 pupil_area = self.pupil_processor.area
                 offsetx, offsety = -self.pupil_processor.corners[0]
@@ -176,7 +190,7 @@ def track(self) -> None:
                             cr_center, cr_width, cr_height, cr_angle, cr_dimensions_int = cr_processor.ellipse.parameters()
                             cr_log[i] = ((cr_width, cr_height), cr_center, cr_angle)
                     except:
-                        pass #for now, let's pass any errors arising from Shape().track() - this caused EyeLoop to crash when cr_processor.track() failed.
+                        pass  # for now, let's pass any errors arising from Shape().track() - this caused EyeLoop to crash when cr_processor.track() failed.
 
             self.refresh_pupil(self.pupil_source)  # lambda _: None when pupil not selected in gui.
             self.place_markers()  # lambda: None when markerless (-m 0).
@@ -188,13 +202,13 @@ def track(self) -> None:
 
         else:
             blink = 1
+
         self.blink_i = blink
 
         try:
             config.graphical_user_interface.update_track(blink)
         except Exception as e:
-            print("Error! Did you assign the graphical user interface (GUI) correctly?")
-            print("Error message: ", e)
+            logger.exception("Did you assign the graphical user interface (GUI) correctly? Attempting to release()")
             self.release()
             return
 
@@ -217,8 +231,8 @@ def activate(self) -> None:
         for extractor in self.extractors:
             try:
                 extractor.activate()
-            except:
-                pass
+            except AttributeError:
+                logger.warning(f"Extractor {extractor} has no activate() method")
 
     def release(self) -> None:
         """
@@ -231,14 +245,10 @@ def release(self) -> None:
         for extractor in self.extractors:
             try:
                 extractor.release()
-            except:
-                pass
-
-        try:
-            config.importer.release()
-        except:
-            pass
+            except AttributeError:
+                logger.warning(f"Extractor {extractor} has no release() method")
 
+        config.importer.release()
 
     def update_feed(self, img) -> None:
 

eyeloop/extractors/DAQ.py

@@ -1,22 +1,20 @@
 import json
-import time
+import logging
+from pathlib import Path
 
 
 class DAQ_extractor:
-    def __init__(self, dir):
-        self.dir = dir
-        timestamp = time.strftime("%Y%m%d-%H%M%S")
-        filename = "{}/log{}.json".format(dir, timestamp)
-        self.log = open(filename, 'w')
+    def __init__(self, output_dir):
+        self.output_dir = output_dir
+        self.datalog_path = Path(output_dir, f"datalog.json")
 
     def fetch(self, engine):
-        try:
-            self.log.write(json.dumps(engine.dataout) + "\n")
-        except:
-            pass
+        with open(self.datalog_path, "a") as datalog:
+            datalog.write(json.dumps(engine.dataout) + "\n")
 
     def release(self):
-        self.log.close()
+        logging.debug("DAQ_extractor.release() called")
+        pass
 
     # def set_digital_line(channel, value):
     # digital_output = PyDAQmx.Task()

eyeloop/guis/minimum/minimum_gui.py

@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 
 import numpy as np
 
@@ -224,7 +225,7 @@ def arm(self, width: int, height: int) -> None:
         self.binary_height = max(height, 200)
 
         fourcc = cv2.VideoWriter_fourcc(*'MPEG')
-        output_vid = config.arguments.output_dir / "output.avi"
+        output_vid = Path(config.file_manager.new_folderpath, "output.avi")
         self.out = cv2.VideoWriter(str(output_vid), fourcc, 50.0, (self.width, self.height))
 
         self.PStock = np.zeros((self.binary_height, self.binary_width))

eyeloop/importers/cv.py

@@ -1,15 +1,20 @@
+import logging
 from pathlib import Path
+from typing import Optional, Callable
 
 import cv2
 
 import eyeloop.config as config
 from eyeloop.importers.importer import IMPORTER
 
+logger = logging.getLogger(__name__)
+
 
 class Importer(IMPORTER):
 
     def __init__(self) -> None:
         super().__init__()
+        self.route_frame: Optional[Callable] = None  # Dynamically assigned at runtime depending on input type
 
     def first_frame(self) -> None:
         self.vid_path = Path(config.arguments.video)
@@ -31,7 +36,9 @@ def first_frame(self) -> None:
                 except:
                     image = image[..., 0]
             else:
-                raise ValueError("Failed to initialize video stream.\nMake sure that the video path is correct, or that your webcam is plugged in and compatible with opencv.")
+                raise ValueError(
+                    "Failed to initialize video stream.\n"
+                    "Make sure that the video path is correct, or that your webcam is plugged in and compatible with opencv.")
 
         elif self.vid_path.is_dir():
 
@@ -45,7 +52,8 @@ def first_frame(self) -> None:
                 height, width, _ = image.shape
                 image = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
                 self.route_frame = self.route_sequence_sing
-            except:  # TODO fix bare except
+            except Exception:  # TODO fix bare except
+                logger.exception("first_frame() error: ")
                 height, width = image.shape
                 self.route_frame = self.route_sequence_flat
 
@@ -57,14 +65,9 @@ def first_frame(self) -> None:
     def route(self) -> None:
         self.first_frame()
         while True:
-            try:
+            if self.route_frame is not None:
                 self.route_frame()
-            except ValueError:
-                config.engine.release()
-                print("Importer released (1).")
-                break
-            except TypeError:
-                print("Importer released (2).")
+            else:
                 break
 
     def proceed(self, image) -> None:
@@ -86,7 +89,6 @@ def route_sequence_flat(self) -> None:
 
         self.proceed(image)
 
-
     def route_cam(self) -> None:
         """
         Routes the capture frame to:
@@ -97,14 +99,15 @@ def route_cam(self) -> None:
         _, image = self.capture.read()
         if image is not None:
             image = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
+            self.proceed(image)
         else:
-            raise ValueError("No more frames.")
-            return
-
-        self.proceed(image)
+            logger.info("No more frames to process, exiting.")
+            self.release()
 
     def release(self) -> None:
+        logger.debug(f"cv.Importer.release() called")
         if self.capture is not None:
             self.capture.release()
 
-        self.route_frame = lambda _: None
+        self.route_frame = None
+        cv2.destroyAllWindows()