New script for converting WALN to JSON format

Script for converting Waln files from Webalign and Webwarp to VisuAlign compatible JSON files. The intention is to use the script for testing purposes (make sure the online tools produce the same results as the offline tools).

scripts/waln_to_json.py

@@ -0,0 +1,61 @@
+import json
+import re
+import os
+
+'''
+Sharon Yates, 04.04.24.
+This is a script for converting WALN and WWRP files from WebAlign and WebWarp to VisuAlign compatible JSON files.
+To be used for testing purposes. 
+'''
+
+def waln_to_json(filename):
+    with open(filename) as f:
+        vafile = json.load(f)
+    if filename.endswith(".waln") or filename.endswith("wwrp"):
+        slices = vafile["sections"] # define slices as "section" in waln
+        vafile["slices"] = slices 
+
+        for slice in slices:
+            print(slice) # this prints info from waln to screen.
+            if "filename" in slice:
+                base_name = os.path.basename(slice["filename"]).split('.')[0]
+                new_filename = base_name + '.png'
+                slice["filename"] = new_filename
+            slice["nr"] = int(re.search(r"_s(\d+)", slice["filename"]).group(1))
+            if "ouv" in slice:
+                slice["anchoring"] = slice["ouv"]        
+
+        '''
+        for slice in slices:
+            print(slice) # this prints info from waln to screen.
+            if "filename" in slice:
+                name, old_extension = slice["filename"].rsplit('.',1)
+                new_filename = name + '.png'
+                slice["filename"] = new_filename
+            slice["nr"] = int(re.search(r"_s(\d+)", slice["filename"]).group(1))
+            if "ouv" in slice:
+                slice["anchoring"] = slice["ouv"]
+        '''
+
+        name = os.path.basename(filename)
+        va_compat_file = {
+            "name": name.replace(".waln",".json"),
+            "target": vafile["atlas"] + '.cutlas',
+            "target-resolution": [456, 528, 320],
+            "slices": slices
+        }
+        # save with .json extension need to see if i can remove this
+        with open(
+            filename.replace(".waln", ".json").replace(".wwrp", ".json"), "w"
+        ) as f:
+            #json.dump(va_compat_file, f, indent=4) 
+            json.dump(va_compat_file, f, indent=4)
+
+        print("Waln or Wwrp converted successfully to JSON")
+
+    else:
+        pass
+
+waln_to_json("PyNutil_test_2.waln")    
+
+

testOOP.py

@@ -6,9 +6,9 @@
 
 pnt = PyNutil(settings_file=r"PyNutil/test/test10_PyNutil_web.json")
 
-##Use flat can be set to True if you want to use the flat file
-# instead of the visualign json (this is only useful for testing and will be removed)
-pnt.get_coordinates(object_cutoff=0, method="per_pixel")
+##use_flat can be set to True if you want to use the flat file
+## for method select between "all", "per_pixel" and "per_object"
+pnt.get_coordinates(object_cutoff=0, method="per_pixel", use_flat=False)
 
 pnt.quantify_coordinates()
 

test_data/PyNutil_test_2.waln

@@ -0,0 +1 @@
+{"atlas":"ABA_Mouse_CCFv3_2017_25um","sections":[{"filename":"PyNutil_test/test_s001.dzip","width":1500,"height":1000,"snr":1,"format":"png","current":0,"tilesize":254,"overlap":1,"mode":0,"ouv":[-5.145275115966797,361.8014440433213,331.1490739071843,456,0,0,0,0,-320],"markers":[[440.0000000000001,289,450,323]]},{"filename":"PyNutil_test/test_s002.dzip","width":1500,"height":1000,"snr":2,"format":"png","current":0,"tilesize":254,"overlap":1,"mode":0,"ouv":[-3.8589563369750977,318.7157039711191,340.24552914037605,456,0,0,0,0,-320],"markers":[[636.8098159509204,603.4958601655935,672.6993865030674,593.3762649494021],[902.9868982011025,615.5567336628567,843.8650306748466,610.8555657773691],[561.2609204260139,750.3661510917975,558.5889570552147,775.5289788408462]]},{"filename":"PyNutil_test/test_s003.dzip","width":1500,"height":1000,"snr":3,"format":"png","current":0,"tilesize":254,"overlap":1,"mode":0,"ouv":[-2.8942172527313232,275.6299638989171,350.0189942541106,456,0,0,0,0,-320],"markers":[[761.0429447852762,629.2548298068077,741,500],[204.29447852760745,613.6154553817848,365.3374233128834,612.695492180313],[482.6376861494953,714.9876920193675,623.0061349693251,747.0101195952162],[434.00208292806684,606.7676930120547,578.8343558282207,601.6559337626494],[959.8159509202455,636.6145354185834,980.0613496932516,628.3348666053357],[957.8161415293836,523.3987679117937,953.3742331288344,547.3781048758049]]},{"filename":"PyNutil_test/test_s004.dzip","width":1500,"height":1000,"snr":4,"format":"png","current":0,"tilesize":254,"overlap":1,"mode":0,"ouv":[-3.0282087922096252,232.54422382671487,364.1366059225139,456,0,0,0,0,-320],"markers":[[522.6993865030674,712.9714811407543,530.6338374725239,715.7313707451705],[630.6438500513034,523.1833943062713,550.3067484662577,519.7792088316469],[916.4047791164191,534.1886045162021,962.5766871165645,523.4590616375344],[950.8076359295408,705.46368100121,925,668],[1096.1208774051677,649.3153717520049,1115,675],[1030.2378410339393,594.2011916220456,1065.644171779141,604.4158233670653]]},{"filename":"PyNutil_test/test_s005.dzip","width":1500,"height":1000,"snr":5,"format":"png","current":0,"tilesize":254,"overlap":1,"mode":0,"ouv":[-0.6163610816001892,189.45848375451277,374.2485759765199,456,0,0,0,0,-320]}],"bucket":"ewb-3d1dc41f-4256-4db5-bc75-0642369e1354"}