Detect mappings (#136)

* finished implemention, example mappings needed

* added another assert with comment

* finished tests

* formatted files

Author: MartinBuessemeyer

testdata/test_metadata/segmentation/mappings/test_mapping_1.json

@@ -0,0 +1,37 @@
+{
+   "name": "test",
+   "classes": [
+	[
+       461032,
+       461089,
+       1643267,
+       1643289
+     ],
+     [
+       15029780,
+       15029823,
+       15029824,
+       15029832,
+       15029833,
+       15029842,
+       15029849,
+       15029913
+     ],
+     [
+       15029853,
+       15029859,
+       15029897,
+       15029914
+     ],
+     [
+       15030077,
+       15030188,
+       15030198,
+       15030209,
+       15030210,
+       15030254,
+       15030273,
+       15030310
+     ]
+  ]
+}

testdata/test_metadata/segmentation/mappings/test_mapping_2.json

@@ -0,0 +1,37 @@
+{
+   "name": "test",
+   "classes": [
+	[
+       461032,
+       461089,
+       1643267,
+       1643289
+     ],
+     [
+       15029780,
+       15029823,
+       15029824,
+       15029832,
+       15029833,
+       15029842,
+       15029849,
+       15029913
+     ],
+     [
+       15029853,
+       15029859,
+       15029897,
+       15029914
+     ],
+     [
+       15030077,
+       15030188,
+       15030198,
+       15030209,
+       15030210,
+       15030254,
+       15030273,
+       15030310
+     ]
+  ]
+}

testdata/test_metadata/segmentation/mappings/test_mapping_3.json

@@ -0,0 +1,37 @@
+{
+   "name": "test",
+   "classes": [
+	[
+       461032,
+       461089,
+       1643267,
+       1643289
+     ],
+     [
+       15029780,
+       15029823,
+       15029824,
+       15029832,
+       15029833,
+       15029842,
+       15029849,
+       15029913
+     ],
+     [
+       15029853,
+       15029859,
+       15029897,
+       15029914
+     ],
+     [
+       15030077,
+       15030188,
+       15030198,
+       15030209,
+       15030210,
+       15030254,
+       15030273,
+       15030310
+     ]
+  ]
+}

testdata/test_metadata/segmentation/mappings/test_mapping_4.json

@@ -0,0 +1,37 @@
+{
+   "name": "test",
+   "classes": [
+	[
+       461032,
+       461089,
+       1643267,
+       1643289
+     ],
+     [
+       15029780,
+       15029823,
+       15029824,
+       15029832,
+       15029833,
+       15029842,
+       15029849,
+       15029913
+     ],
+     [
+       15029853,
+       15029859,
+       15029897,
+       15029914
+     ],
+     [
+       15030077,
+       15030188,
+       15030198,
+       15030209,
+       15030210,
+       15030254,
+       15030273,
+       15030310
+     ]
+  ]
+}

testdata/test_metadata/segmentation/mappings/test_mapping_5.json

@@ -0,0 +1,37 @@
+{
+   "name": "test",
+   "classes": [
+	[
+       461032,
+       461089,
+       1643267,
+       1643289
+     ],
+     [
+       15029780,
+       15029823,
+       15029824,
+       15029832,
+       15029833,
+       15029842,
+       15029849,
+       15029913
+     ],
+     [
+       15029853,
+       15029859,
+       15029897,
+       15029914
+     ],
+     [
+       15030077,
+       15030188,
+       15030198,
+       15030209,
+       15030210,
+       15030254,
+       15030273,
+       15030310
+     ]
+  ]
+}

tests/test_metadata.py

@@ -8,6 +8,7 @@
     refresh_metadata,
     read_datasource_properties,
     read_metadata_for_layer,
+    detect_mappings,
 )
 
 
@@ -66,5 +67,38 @@ def write_custom_layer(target_path, layer_name, dtype, num_channels):
         dataset.write(off=(0, 0, 0), data=data)
 
 
+def test_mapping_detection():
+    # NOTE: the mappings do not match do the actual wkw data. Therefore do not use them
+    expected_mappings = [
+        "test_mapping_1.json",
+        "test_mapping_2.json",
+        "test_mapping_3.json",
+        "test_mapping_4.json",
+        "test_mapping_5.json",
+    ]
+    datapath_with_mappings = "testdata/test_metadata"
+    layer_name_with_mapping = "segmentation"
+    detected_mappings = detect_mappings(datapath_with_mappings, layer_name_with_mapping)
+
+    # test if all detected mappings are int the expected_mappings
+    assert all(
+        detected_mapping in expected_mappings for detected_mapping in detected_mappings
+    ), "Found unexpected mapping(s)."
+    # test if all mappings were detected
+    assert len(expected_mappings) == len(
+        detected_mappings
+    ), "Did not find all mappings."
+
+    datapath_without_mappings = "testdata/WT1_wkw"
+    layer_name_without_mapping = "color"
+    detected_mappings = detect_mappings(
+        datapath_without_mappings, layer_name_without_mapping
+    )
+    assert (
+        len(detected_mappings) == 0
+    ), "Found mapping(s) even though there should not be any mapping."
+
+
 if __name__ == "__main__":
     test_element_class_convertion()
+    test_mapping_detection()

wkcuber/metadata.py

@@ -3,6 +3,7 @@
 import wkw
 import logging
 import numpy as np
+import glob
 
 from argparse import ArgumentParser
 from glob import iglob
@@ -268,13 +269,20 @@ def detect_standard_layer(
     }
 
 
+def detect_mappings(dataset_path, layer_name):
+    pattern = path.join(dataset_path, layer_name, "mappings", "*.json")
+    mapping_files = glob.glob(pattern)
+    mapping_file_names = [path.basename(mapping_file) for mapping_file in mapping_files]
+    return mapping_file_names
+
+
 def detect_segmentation_layer(
     dataset_path, layer_name, max_id, compute_max_id=False, exact_bounding_box=None
 ):
     layer_info = detect_standard_layer(
         dataset_path, layer_name, exact_bounding_box, category="segmentation"
     )
-    layer_info["mappings"] = []
+    layer_info["mappings"] = detect_mappings(dataset_path, layer_name)
     layer_info["largestSegmentId"] = max_id
 
     if compute_max_id: