-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
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).
- Loading branch information
Sharon Christine Yates
committed
Apr 4, 2024
1 parent
012c860
commit c1bd454
Showing
3 changed files
with
65 additions
and
3 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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") | ||
|
||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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"} |