Develop bugfixes

ledsa/core/image_reading.py

@@ -26,6 +26,25 @@ def read_channel_data_from_img(filename: str, channel: int) -> np.ndarray:
         channel_array = _read_channel_data_from_raw_file(filename, channel)
     return channel_array
 
+def read_img_array_from_img(filename: str, channel: int) -> np.ndarray:
+    """
+    Returns a 2D array of the image for all color channels.
+
+
+    :param filename: The path of the image file to read.
+    :type filename: str
+    :param channel: The color channel used for calculating black level values.
+    :type channel: int
+    :return: A 2D array containing the processed image data for all color channels.
+    :rtype: np.ndarray
+    """
+    extension = os.path.splitext(filename)[-1]
+    if extension in ['.JPG', '.JPEG', '.jpg', '.jpeg', '.PNG', '.png']:
+        img_array = _read_grayscale_img_array_from_img_file(filename)
+    elif extension in ['.CR2', '.CR3']:
+        img_array, _ = _read_img_array_from_raw_file(filename, channel)
+    return img_array
+
 
 def _read_channel_data_from_img_file(filename: str, channel: int) -> np.ndarray:
     """
@@ -38,7 +57,7 @@ def _read_channel_data_from_img_file(filename: str, channel: int) -> np.ndarray:
     :return: A 2D numpy array containing the data of the specified color channel from the image.
     :rtype: np.ndarray
     """
-    img_array = read_img_array_from_img_file(filename)
+    img_array = _read_img_array_from_img_file(filename)
     return img_array[:, :, channel]
 
 
@@ -54,15 +73,15 @@ def _read_channel_data_from_raw_file(filename: str, channel: int) -> np.ndarray:
     :return: A 2D numpy array representing the extracted channel, with all other channel values masked or set to zero.
     :rtype: np.ndarray
     """
-    img_array, filter_array = read_img_array_from_raw_file(filename, channel)
+    img_array, filter_array = _read_img_array_from_raw_file(filename, channel)
     if channel == 0 or channel == 2:
         channel_array = np.where(filter_array == channel, img_array, 0)
     elif channel == 1:
         channel_array = np.where((filter_array == 1) | (filter_array == 3), img_array, 0)
     return channel_array
 
 
-def read_img_array_from_raw_file(filename: str, channel: int) -> np.ndarray:
+def _read_img_array_from_raw_file(filename: str, channel: int) -> np.ndarray:
     # TODO: channel is only relevant for black level, consider individually!
     with rawpy.imread(filename) as raw:
         data = raw.raw_image_visible.copy()
@@ -74,10 +93,16 @@ def read_img_array_from_raw_file(filename: str, channel: int) -> np.ndarray:
     img_array = np.clip(img_array, 0, white_level)
     return img_array, filter_array
 
-def read_img_array_from_img_file(filename: str) -> np.ndarray:
+def _read_img_array_from_img_file(filename: str) -> np.ndarray:
     img_array = plt.imread(filename)
     return img_array
 
+def _read_grayscale_img_array_from_img_file(filename: str) -> np.ndarray:
+    img_array = plt.imread(filename)
+    weights = np.array([0.2989, 0.5870, 0.1140])
+    gray = np.dot(img_array[..., :3], weights).astype(np.uint8)
+    return gray
+
 
 def get_exif_entry(filename: str, tag: str) -> str:
     """

ledsa/data_extraction/DataExtractor.py

@@ -3,6 +3,7 @@
 import os
 
 import matplotlib.pyplot as plt
+from matplotlib.colors import LogNorm
 import numpy as np
 from tqdm import tqdm
 
@@ -26,7 +27,9 @@ class DataExtractor:
     :vartype channels: Tuple
     :ivar fit_leds: Whether to fit LEDs or not.
     :vartype fit_leds: bool
-    :ivar search_areas: 2D numpy array with dimension (# of LEDs) x (LED_id, x, y).
+     :ivar fit_leds: Whether to fit LEDs or not.
+    :vartype threshold: float, optional   
+    :ivar threshold: The threshold value used for LED detection.
     :vartype search_areas: numpy.ndarray, optional
     :ivar line_indices: 2D list with dimension (# of LED arrays) x (# of LEDs per array) or None.
     :vartype line_indices: list[list[int]], optional
@@ -46,6 +49,7 @@ def __init__(self, channels=(0), load_config_file=True, build_experiment_infos=T
         self.config = ConfigData(load_config_file=load_config_file)
         self.channels = list(channels)
         self.fit_leds = fit_leds
+        self.threshold = None
 
         # 2D numpy array with dimension (# of LEDs) x (LED_id, x, y)
         self.search_areas = None
@@ -95,12 +99,13 @@ def find_search_areas(self) -> None:
         max_num_leds = int(config['max_num_leds'])
         pixel_value_percentile = float(config['pixel_value_percentile'])
         if channel == 'all':
-            data, _ = ledsa.core.image_reading.read_img_array_from_raw_file(in_file_path, channel=0) # TODO: Channel to be removed here!
+            # TODO this currently only works for RAW files but should work for JPG files as well
+            data = ledsa.core.image_reading.read_img_array_from_img(in_file_path, channel=0) # TODO: Channel to be removed here!
         else:
             channel = int(channel)
             data = ledsa.core.image_reading.read_channel_data_from_img(in_file_path, channel=channel)
 
-        self.search_areas = ledsa.data_extraction.step_1_functions.find_search_areas(data, search_area_radius=search_area_radius, max_n_leds=max_num_leds, pixel_value_percentile=pixel_value_percentile)
+        self.search_areas, self.threshold = ledsa.data_extraction.step_1_functions.find_search_areas(data, search_area_radius=search_area_radius, max_n_leds=max_num_leds, pixel_value_percentile=pixel_value_percentile)
         self.write_search_areas()
         self.plot_search_areas()
         ledsa.core.file_handling.remove_flag('reorder_leds')
@@ -122,12 +127,14 @@ def plot_search_areas(self, reorder_leds=False) -> None:
             self.load_search_areas()
 
         in_file_path = os.path.join(config['img_directory'], config['img_name_string'].format(int(config['ref_img_id'])))
-        data = ledsa.core.image_reading.read_channel_data_from_img(in_file_path, channel=0)
+        # TODO this currently only works for RAW files but should work for JPG files as well
+        data = ledsa.core.image_reading.read_img_array_from_img(in_file_path, channel=0)
         search_area_radius = int(config['search_area_radius'])
         plt.figure(dpi=1200)
         ax = plt.gca()
         ledsa.data_extraction.step_1_functions.add_search_areas_to_plot(self.search_areas, search_area_radius, ax)
-        plt.imshow(data, cmap='Greys')
+        plt.imshow(data, norm=LogNorm(vmin=self.threshold, vmax=data.max()), cmap='Grays')
+
         plt.xlim(self.search_areas[:, 2].min() - 5 * search_area_radius, self.search_areas[:, 2].max() + 5 * search_area_radius)
         plt.ylim(self.search_areas[:, 1].max() + 5 * search_area_radius, self.search_areas[:, 1].min() - 5 * search_area_radius)
         plt.colorbar()

ledsa/data_extraction/step_1_functions.py

@@ -1,9 +1,13 @@
+from typing import Any
+
 import numpy as np
 from matplotlib import pyplot as plt
 import cv2
+from numpy import ndarray, dtype, floating
 
 
-def find_search_areas(image: np.ndarray, search_area_radius, pixel_value_percentile=99.875, max_n_leds=1300) -> np.ndarray:
+def find_search_areas(image: np.ndarray, search_area_radius, pixel_value_percentile=99.875, max_n_leds=1300) -> tuple[
+    ndarray[Any, dtype[Any]], floating[Any]]:
     """
     Identifies and extracts locations of LEDs in an image.
 
@@ -15,8 +19,10 @@ def find_search_areas(image: np.ndarray, search_area_radius, pixel_value_percent
     :type pixel_value_percentile: float
     :param max_n_leds: The maximum number of LED locations to identify in the image.
     :type max_n_leds: int
-    :return: A numpy array of identified LED locations, each represented as (LED ID, y-coordinate, x-coordinate).
-    :rtype: np.ndarray
+    :return: A tuple containing:
+             - A numpy array of identified LED locations, each represented as (LED ID, y-coordinate, x-coordinate).
+             - The threshold value used for LED detection.
+    :rtype: tuple[np.ndarray, float]
     """
     (_, max_pixel_value, _, max_pixel_loc) = cv2.minMaxLoc(image)
     threshold = np.percentile(image, pixel_value_percentile)
@@ -34,7 +40,7 @@ def find_search_areas(image: np.ndarray, search_area_radius, pixel_value_percent
             led_id += 1
     print('\n')
     print(f"Found {led_id} LEDS")
-    return np.array(search_areas_list)
+    return np.array(search_areas_list), threshold
 
 
 def add_search_areas_to_plot(search_areas: np.ndarray, search_area_radius: int, ax: plt.axes) -> None: