support NEF/ARW/DNG raw formats and zero-padded image IDs

ledsa/core/ConfigData.py

@@ -415,7 +415,7 @@ def get_start_time(self) -> None:
         Updates the 'DEFAULT' key with the 'start_time' computed.
 
         """
-        exif_entry = get_exif_entry(os.path.join(self['DEFAULT']['img_directory'] + self['DEFAULT']['img_name_string'].format(
+        exif_entry = get_exif_entry(os.path.join(self['DEFAULT']['img_directory'], self['DEFAULT']['img_name_string'].format(
             self['DEFAULT']['first_img_experiment_id'])), 'DateTimeOriginal')
         date, time_meta = exif_entry.split(' ')
         time_img = _get_datetime_from_str(date, time_meta)

ledsa/core/image_handling.py

@@ -3,6 +3,26 @@
 from ledsa.core.file_handling import read_table
 
 
+def format_img_name(img_name_string: str, img_id) -> str:
+    """
+    Build an image file name from the config template and an image ID.
+
+    Plain ``{}`` placeholders keep the ID as given, so zero-padded IDs such as
+    '0001' (e.g. DSC_0001.NEF) are preserved. Numeric format specifications
+    such as ``{:04d}`` require an integer, for which the ID is cast.
+
+    :param img_name_string: Name template from the config, e.g. 'DSC_{}.CR3'.
+    :type img_name_string: str
+    :param img_id: The image ID, as string or integer.
+    :return: The formatted image file name.
+    :rtype: str
+    """
+    try:
+        return img_name_string.format(img_id)
+    except ValueError:
+        return img_name_string.format(int(img_id))
+
+
 def get_img_name(img_id: str) -> str:
     """
     Retrieves the image path corresponding to a given image ID.

ledsa/core/image_reading.py

@@ -22,8 +22,10 @@ def read_channel_data_from_img(filename: str, channel: int) -> np.ndarray:
     extension = os.path.splitext(filename)[-1]
     if extension in ['.JPG', '.JPEG', '.jpg', '.jpeg', '.PNG', '.png']:
         channel_array = _read_channel_data_from_img_file(filename, channel)
-    elif extension in ['.CR2', '.CR3']:
+    elif extension in ['.CR2', '.CR3', '.NEF', '.ARW', '.DNG']:
         channel_array = _read_channel_data_from_raw_file(filename, channel)
+    else:
+        raise ValueError(f"Unsupported image format '{extension}' of file {filename}.")
     return channel_array
 
 def read_img_array_from_img(filename: str, channel: int) -> np.ndarray:
@@ -41,8 +43,10 @@ def read_img_array_from_img(filename: str, channel: int) -> 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']:
+    elif extension in ['.CR2', '.CR3', '.NEF', '.ARW', '.DNG']:
         img_array, _ = _read_img_array_from_raw_file(filename, channel)
+    else:
+        raise ValueError(f"Unsupported image format '{extension}' of file {filename}.")
     return img_array
 
 

ledsa/data_extraction/DataExtractor.py

@@ -93,7 +93,7 @@ def find_search_areas(self) -> None:
         Identify all LEDs in the reference image and define the areas where LEDs will be searched in the experiment images.
         """
         config = self.config['find_search_areas']
-        in_file_path = os.path.join(config['img_directory'], config['img_name_string'].format(int(config['ref_img_id'])))
+        in_file_path = os.path.join(config['img_directory'], ledsa.core.image_handling.format_img_name(config['img_name_string'], config['ref_img_id']))
         channel = config['channel']
         search_area_radius = int(config['search_area_radius'])
         max_num_leds = int(config['max_num_leds'])
@@ -126,7 +126,7 @@ def plot_search_areas(self, reorder_leds=False) -> None:
         if self.search_areas is None:
             self.load_search_areas()
 
-        in_file_path = os.path.join(config['img_directory'], config['img_name_string'].format(int(config['ref_img_id'])))
+        in_file_path = os.path.join(config['img_directory'], ledsa.core.image_handling.format_img_name(config['img_name_string'], config['ref_img_id']))
         # 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'])

ledsa/data_extraction/init_functions.py

@@ -3,6 +3,7 @@
 from typing import List
 
 from ledsa.core.ConfigData import ConfigData
+from ledsa.core.image_handling import format_img_name
 from ledsa.core.image_reading import get_exif_entry
 
 
@@ -114,7 +115,7 @@ def _calc_experiment_and_real_time(build_type: str, config: ConfigData, tag: str
     :rtype: tuple
     """
     exif_entry = get_exif_entry(os.path.join(config['DEFAULT']['img_directory'],
-                                config['DEFAULT']['img_name_string'].format(int(img_number))), tag)
+                                format_img_name(config['DEFAULT']['img_name_string'], img_number)), tag)
     date, time_meta = exif_entry.split(' ')
     date_time_img = _get_datetime_from_str(date, time_meta)
 
@@ -201,7 +202,7 @@ def _build_img_data_string(build_type: str, config: ConfigData) -> str:
     for img_id in img_id_list:
         tag = 'DateTimeOriginal'
         experiment_time, time = _calc_experiment_and_real_time(build_type, config, tag, img_id)
-        img_data += (str(img_idx) + ',' + config[build_type]['img_name_string'].format(int(img_id)) +
+        img_data += (str(img_idx) + ',' + format_img_name(config[build_type]['img_name_string'], img_id) +
                      ',' + time.strftime('%H:%M:%S') + ',' + str(experiment_time) + '\n')
         img_idx += 1
     return img_data

ledsa/tests/UnitTests/test_raw_format_compat.py

@@ -0,0 +1,41 @@
+import numpy as np
+import pytest
+
+import ledsa.core.image_reading as image_reading
+from ledsa.core.image_handling import format_img_name
+
+
+class TestRawExtensionRouting:
+    @pytest.fixture
+    def raw_reader_stub(self, monkeypatch):
+        calls = []
+
+        def stub(filename, channel):
+            calls.append(filename)
+            return np.zeros((4, 4))
+
+        monkeypatch.setattr(image_reading, '_read_channel_data_from_raw_file', stub)
+        return calls
+
+    @pytest.mark.parametrize('extension', ['.CR2', '.CR3', '.NEF', '.ARW', '.DNG'])
+    def test_raw_formats_are_routed_to_raw_reader(self, raw_reader_stub, extension):
+        image_reading.read_channel_data_from_img(f'img_0001{extension}', channel=0)
+        assert raw_reader_stub == [f'img_0001{extension}']
+
+    def test_unsupported_format_raises(self):
+        with pytest.raises(ValueError, match='Unsupported image format'):
+            image_reading.read_channel_data_from_img('img_0001.xyz', channel=0)
+
+
+class TestFormatImgName:
+    def test_plain_placeholder_preserves_leading_zeros(self):
+        assert format_img_name('DSC_{}.NEF', '0001') == 'DSC_0001.NEF'
+
+    def test_plain_placeholder_with_int_id(self):
+        assert format_img_name('test_img_{}.jpg', 7) == 'test_img_7.jpg'
+
+    def test_numeric_format_spec_with_string_id(self):
+        assert format_img_name('IMG_{:04d}.CR2', '7') == 'IMG_0007.CR2'
+
+    def test_numeric_format_spec_with_int_id(self):
+        assert format_img_name('IMG_{:04d}.CR2', 7) == 'IMG_0007.CR2'