Merge branch '49-document-algorithm-functions-and-classes' into 'master'

Resolve "Document algorithm functions and classes"

Closes #49

See merge request !52

algorithm/SalamanderImage.py

-class SalamanderImage():
-	descriptors = []
-	filename = ''
+from cv2 import cv2
+import numpy as np
+import algorithm.dsift as dsift
 
-	def __init__(self, filename):
-		self.filename
+
+class SalamanderImage:
+    descriptors = []
+    filename = ''
+
+    def __init__(self, filename):
+        self.filename = filename
+        self.descriptors = self.calculate_descriptors()
+
+    def calculate_descriptors(self):
+        """
+        Calculates the descriptors of the member image
+
+        Returns: The calculated descriptors
+
+        """
+
+        image = cv2.imdecode(np.fromfile(self.filename, dtype=np.uint8), cv2.IMREAD_GRAYSCALE)
+
+        if image is None:
+            raise FileNotFoundError("Cannot find image file " + self.filename)
+        return dsift.compute_descriptors(image)

algorithm/brute_force_matching.py

 import os
 from cv2 import cv2
-from algorithm.imageprocessing import create_salamander_image
 import glob
-
-min_good_match = 15
-match_dist = 0.75
+from algorithm.SalamanderImage import SalamanderImage
 
 
 def match_single_image(input_salamander, match_salamander):
+    """
+    Compares two SalamanderImages and determines if they are similar enough to be a match
+
+    Args:
+        input_salamander: SalamanderImage of input salamander
+        match_salamander: SalamanderImage of salamander from the database
+
+    Returns:
+        Boolean value indicating if the comparison was a match and the number of hits gotten in the comparison
+    """
+
+    min_good_match = 15
+    match_dist = 0.75
+
     match = cv2.BFMatcher().knnMatch(input_salamander.descriptors, match_salamander.descriptors, k=2)
 
     goodmatch = []
@@ -20,16 +31,28 @@ def match_single_image(input_salamander, match_salamander):
 
 
 def match_file_structure(input_image: str, match_directory: str):
+    """
+    Loops through a given directory of salamanders represented by folders containing their images, and finds the best
+    match (if any) based on an input image
+
+    Args:
+        input_image: SalamanderImage of input salamander
+        match_directory: Path of directory to looped through
+
+    Returns:
+        The ID of the best matched salamander or None if no match is found
+    """
+
     best_match = -1
     match_count = 0
 
     # check if input path is valid:
     if os.path.isfile(input_image):
-        input_salamander = create_salamander_image(input_image)
+        input_salamander = SalamanderImage(input_image)
         for folder in os.listdir(match_directory):
             name_list = glob.glob(os.path.join(match_directory, folder, "*_str.*"))
             for filename in name_list:
-                res, num_matches = match_single_image(input_salamander, create_salamander_image(filename))
+                res, num_matches = match_single_image(input_salamander, SalamanderImage(filename))
                 if res and num_matches > match_count:
                     match_count = num_matches
                     best_match = int(folder)

algorithm/dsift.py

@@ -7,6 +7,15 @@ sift = cv2.SIFT_create()
 
 
 def compute_descriptors(image):
-	dense = sift.compute(image,kp)
+	"""
+	Computes the descriptors of an incoming image
+	Args:
+		image: Image from openCV
+
+	Returns:
+		Descriptors of image
+	"""
+
+	dense = sift.compute(image, kp)
 	des = dense[1]
 	return des

algorithm/imageprocessing.py

-from cv2 import cv2
-import numpy as np
-
-from algorithm.SalamanderImage import SalamanderImage
-
-import algorithm.dsift as dsift
-import algorithm.segmentation as segmentation
-
-
-def create_salamander_image(filename: str):
-    salamander_image = SalamanderImage(filename)
-
-    salamander_image.filename = filename
-    salamander_image.descriptors = get_descriptors(filename)
-
-    return salamander_image
-
-
-def get_descriptors(filename: str):
-    image = get_straightened_image(filename)
-    return calculate_descriptors(image)
-
-
-# Reads, straightens, resizes the image and returns it
-def get_straightened_image(filename: str):
-    straightened_filename = filename  # [0:-4] + '_str.jpg'
-    image = get_image(straightened_filename)
-
-    return image
-
-
-# Should return a binary image (numpy ndarray) with 1 for "Part of salamander"
-# and 0 for "Not part of the salamander".
-def get_segmented_image(filename: str):
-    image = get_image(filename)
-    return segmentation.get_salamander_mask(image)
-
-
-def get_image(filename):
-    img = cv2.imdecode(np.fromfile(filename, dtype=np.uint8), cv2.IMREAD_GRAYSCALE)
-
-    if img is None:
-        raise FileNotFoundError("Cannot find image file " + filename)
-
-    return img
-
-
-# Calculates descriptors from preprocessed image
-def calculate_descriptors(image):
-    return dsift.compute_descriptors(image)

algorithm/predict_salamander_abdomen.py

@@ -21,7 +21,6 @@ def run_prediction_dlc(config: str, image: np.ndarray, shuffle: int = 1,
     if gputouse is not None:  # gpu selection
         os.environ['CUDA_VISIBLE_DEVICES'] = str(gputouse)
 
-    # tf.compat.v1.reset_default_graph()
     reset_default_graph()
     # record cwd to return to this directory in the end:
 
@@ -30,7 +29,6 @@ def run_prediction_dlc(config: str, image: np.ndarray, shuffle: int = 1,
     model_folder = os.path.join(cfg["project_path"],
                                 str(auxiliaryfunctions.GetModelFolder(train_fraction, shuffle, cfg)))
     path_test_config = Path(model_folder) / 'test' / 'pose_cfg.yaml'
-    # print(path_test_config)
     try:
         dlc_cfg = load_config(str(path_test_config))
     except FileNotFoundError:
@@ -58,24 +56,17 @@ def run_prediction_dlc(config: str, image: np.ndarray, shuffle: int = 1,
     increasing_indices = np.argsort([int(m.split('-')[1]) for m in snapshots])
     snapshots = snapshots[increasing_indices]
 
-    # print("Using %s" % snapshots[snapshot_index], "for model", model_folder)
-
     ##################################################
     # Load and setup CNN part detector
     ##################################################
 
     # Check if data already was generated:
     dlc_cfg['init_weights'] = os.path.join(model_folder, 'train', snapshots[snapshot_index])
-    trainingsiterations = (dlc_cfg['init_weights'].split(os.sep)[-1]).split('-')[-1]
 
     # Update batchsize (based on parameters in config.yaml)
     dlc_cfg['batch_size'] = 1
 
-    # Name for scorer:
-    # DLCscorer, DLCscorerlegacy = auxiliaryfunctions.GetScorerName(cfg,shuffle,trainFraction,trainingsiterations=trainingsiterations)
-    # return tensorflow session, input and outbut (whatever those are):
     sess, inputs, outputs = predict.setup_pose_prediction(dlc_cfg)
-    # sess, inputs, outputs = predict.setup_pose_prediction(dlc_cfg)
 
     # update number of outputs and adjust pandas indices
     dlc_cfg['num_outputs'] = cfg.get('num_outputs', 1)
@@ -86,26 +77,12 @@ def run_prediction_dlc(config: str, image: np.ndarray, shuffle: int = 1,
     ##################################################
     # Loading the images
     ##################################################
-    # Predicting data:
-    # print("session: ", sess)
-    # PredictedData,nframes,nx,ny=get_poses_deeplabcut_model(dlc_cfg, sess, inputs, outputs,image)
 
     ny, nx, nc = np.shape(image)
     nframes = 1
-    # print("Frame dimensions: ", nx,ny)
     PredictedData = np.zeros((nframes, dlc_cfg['num_outputs'] * 3 * len(dlc_cfg['all_joints_names'])))
 
-    # change from int:
     frame = img_as_ubyte(image)
     pose = predict.getpose(frame, dlc_cfg, sess, inputs, outputs)
     PredictedData[0, :] = pose.flatten()
-
-    stop = time.time()
-    # print("PredictedData done:\n")
-
-    # closing the session:
-    # device = cuda.get_current_device()
-    # device.reset()
-
-    # tf.Graph.reset_default_graph()
     return PredictedData[0], nframes, nx, ny

algorithm/segmentation.py

-from cv2 import cv2
-import numpy as np
-
-
-def get_salamander_mask(image):
-    ret, threshold = cv2.threshold(image, np.mean(image) - 40, 255, 0)
-
-    i, contours, hierarchy = cv2.findContours(threshold, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
-
-    largest_area, largest_contour_index = find_biggest_contour(contours, image.size)
-
-    cv2.drawContours(image, contours[largest_contour_index], -1, (0, 0, 255), 3)
-
-    mask = np.zeros(image.shape)
-
-    cv2.fillPoly(mask, pts=[contours[largest_contour_index]], color=(255, 255, 255))
-
-    return mask
-
-
-def find_biggest_contour(contours, imsize):
-    largest_area = 0
-    largest_contour_index = -1
-
-    i = 0
-    total_contours = len(contours)
-    while i < total_contours:
-        area = cv2.contourArea(contours[i])
-        if largest_area < area < imsize * 0.9:
-            largest_area = area
-            largest_contour_index = i
-
-        i += 1
-
-    return largest_area, largest_contour_index

algorithm/straighten_with_dlc.py

@@ -169,11 +169,14 @@ def straighten(image):
 def generate_map_from_bellycurve(curve, width=STRAIGTHENED_IMAGE_WIDTH):
     """
     Generates a map that can be passed to cv2.remap to extract the belly pattern
-    """
 
-    # salamander_length = np.linalg.norm(curve[len(curve) - 1] - curve[0])
+    Args:
+        curve: Interpolated curve along the spine
+        width: Width of the abdominal pattern
+
+    Returns: Map generated from the curve
+    """
 
-    # salamander_width = salamander_length * STRAIGHTENED_IMAGE_ASPECT_RATIO
     salamander_width = width + SHOULDER_ESTIMATION_BUFFER
     gradient = np.gradient(curve, axis=0)
 
@@ -200,10 +203,16 @@ def get_smooth_curve(points, num_points):
     Takes in an array of 2-D points and returns a new set of points
     with numpoints elements where the missing points are interpolated
     using cubic interpolation
+
+    Args:
+        points:
+        num_points:
+
+    Returns: Interpolated points
+
     """
     # Calculate distance between all the points
     distance = np.sqrt(np.sum(np.diff(points, axis=0) ** 2, axis=1))
-    # print("distance, ", distance.shape)
     # Accumulate distance to use as parameter
     accumulated_distance = np.cumsum(distance)
 
@@ -223,7 +232,14 @@ def get_smooth_curve(points, num_points):
 
 def halfway_between(point1, point2):
     """
-    halfway_between() calculates a point between two points:
+    halfway_between() calculates a point between two points
+
+    Args:
+        point1:
+        point2:
+
+    Returns: A point between the two provided points
+
     """
     vec = [(point2[0] - point1[0]) / 2, (point2[1] - point1[1]) / 2]
     return [point1[0] + vec[0], point1[1] + vec[1]]

api/endpoints/editsalamander.py

@@ -10,7 +10,8 @@ import glob
 from shutil import move
 from path_constants import _ACCESS_DATABASE
 from image_encoder.image_encoder import *
-import cv2
+from cv2 import cv2
+import numpy as np
 
 """
 Endpoint for editing salamanders.
@@ -43,7 +44,10 @@ class EditSalamander(Resource):
                         basename = os.path.basename(path)
                         if basename.__contains__(str(image_id)):
 
-                            image = cv2.imread(path)
+                            image = cv2.imdecode(np.fromfile(path, dtype=np.uint8), cv2.IMREAD_UNCHANGED)
+                            if image is None:
+                                raise FileNotFoundError("Cannot find image file " + path)
+
                             if not basename.__contains__("str"):  # Scale only original to set size
 
                                 height, width, _ = image.shape

api/endpoints/findsalamanderinfo.py

@@ -2,7 +2,7 @@ from flask import request, jsonify
 from flask_restful import Resource
 from flask_jwt_extended import get_jwt_identity, jwt_required
 from algorithm.straighten_with_dlc import straighten
-import cv2
+from cv2 import cv2
 import os
 from api import limiter
 from image_encoder.image_encoder import *

api/endpoints/salamander.py

@@ -5,7 +5,8 @@ from api import db, limiter
 from api.models.dbmodels import Location, User, Salamander
 import os
 import glob
-import cv2
+import numpy as np
+from cv2 import cv2
 from image_encoder.image_encoder import *
 from path_constants import _ACCESS_DATABASE
 
@@ -33,8 +34,10 @@ class SalamanderEndpoint(Resource):
                     list_of_paths = glob.glob(os.path.join(path_to_salamander_images, '*.*'))
                     for path in list_of_paths:
                         if not path.__contains__("_str"):
+                            image = cv2.imdecode(np.fromfile(path, dtype=np.uint8), cv2.IMREAD_UNCHANGED)
 
-                            image = cv2.imread(path)
+                            if image is None:
+                                raise FileNotFoundError("Cannot find image file " + path)
 
                             # scaling to set size
                             height, width, _ = image.shape

run.py

 from api import app
 
 if __name__ == "__main__":
-    app.run(debug=True, host='0.0.0.0')
\ No newline at end of file
+    app.run(debug=True, host='0.0.0.0')