Merge pull request #3 from DragaDoncila/sorting-timestamps

Sorting timestamps correctly

.gitignore

@@ -79,3 +79,6 @@ target/
 
 # written by setuptools_scm
 */_version.py
+
+# misc
+*/_tests/test_loading.py

napari_sentinel_zip/_tests/test_napari_sentinel_zip.py

@@ -15,6 +15,8 @@
 
 IM_SHAPES = [
     (1000, 1000, 3), #QKL
+    (10980, 10980), #Mask
+    (5490, 5490),   #Mask
     (5490, 5490),
     (5490, 5490),
     (10980, 10980),
@@ -50,7 +52,7 @@ def check_layer_list_structure(layer_list, num_ims, num_layers):
         # all elements in the layers must be tuples
         assert isinstance(layer, tuple), f"Layer list element {i} is not tuple"
 
-            # each data in tuples must have correct shape
+        # each data in tuples must have correct shape
         expected_shape = tuple([num_ims] + [im_axis_shape for im_axis_shape in IM_SHAPES[i]])
         assert layer[0].shape == expected_shape,\
         f"Layer {i} has shape {layer[0].shape}, expected {expected_shape}"
@@ -68,7 +70,7 @@ def check_viewer_open_structure(path, num_layers, num_dims):
 
 def test_reader_with_list():
     NUM_IMS = 10
-    NUM_LAYERS = 21
+    NUM_LAYERS = 23
     NUM_DIMS = 3
 
     reader = napari_get_reader(TEST_ZIP_PATH_LIST)
@@ -81,15 +83,15 @@ def test_reader_with_list():
     for layer in layer_list:
         v.add_image(layer[0], **layer[1])
 
-    # viewer must have 21 layers after opening
+    # viewer must have 23 layers after opening
     assert len(v.layers) == NUM_LAYERS, f"Expected {NUM_LAYERS} layers after opening in napari viewer, got {len(v.layers)}"
     # viewer should have 3 dimensions after opening
     assert v.dims.ndim == NUM_DIMS, f"Expected {NUM_DIMS} dimensions after opening in napari viewer, got {v.dims.ndim}"
 
 
 def test_reader_with_string_path():
     NUM_IMS = 1
-    NUM_LAYERS = 21
+    NUM_LAYERS = 23
     NUM_DIMS = 3
 
     reader = napari_get_reader(TEST_ONE_ZIP_PATH)
@@ -103,7 +105,7 @@ def test_reader_with_string_path():
 
 def test_reader_with_root_directory():
     NUM_IMS = 10
-    NUM_LAYERS = 21
+    NUM_LAYERS = 23
     NUM_DIMS = 3
 
     reader = napari_get_reader(TEST_TILE_PATH)

napari_sentinel_zip/napari_sentinel_zip.py

@@ -108,6 +108,18 @@ def ziptiff2array(zip_filename, path_to_tiff):
         image = tiff_f.pages[0].asarray()
     return image
 
+def sort_timestamps(path_list):
+    timestamp_regex = re.compile(".*([0-9]{8}-[0-9]{6}-[0-9]{3}).*.zip")
+    timestamp_dict = {}
+    for path in path_list:
+        match = timestamp_regex.match(path)
+        if match:
+            timestamp = match.groups()[0]
+            timestamp_dict[timestamp] = path
+    sorted_paths = []
+    for timestamp in sorted(timestamp_dict.keys()):
+        sorted_paths.append(timestamp_dict[timestamp])
+    return sorted_paths
 
 @napari_hook_implementation
 def napari_get_reader(path):
@@ -172,10 +184,12 @@ def reader_function(path):
         paths = [path]
     # list of sentinel zips
     elif isinstance(path, list):
-        paths = sorted(path)
+        paths = path
     # one root directory path with multiple sentinel zips inside
     else:
-        paths = sorted(filter(SENTINEL_PATH_REGEX.match, glob(path + "/*.zip")))
+        paths = list(filter(SENTINEL_PATH_REGEX.match, glob(path + "/*.zip")))
+
+    paths = sort_timestamps(paths)
 
     # stack all timepoints together for each band
     images = {}