From 91091b3da7705dfa4523c73937f6228a802321ee Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 6 Sep 2023 11:53:48 +0200
Subject: [PATCH] Pixel classification in 3D works, but pixel maps are not
aligned with original image, suspect X-Y flipped
---
examples/ilastik3d.py | 45 ++++++++++++++++---------------------------
1 file changed, 17 insertions(+), 28 deletions(-)
diff --git a/examples/ilastik3d.py b/examples/ilastik3d.py
index c377a507..8733d0e6 100644
--- a/examples/ilastik3d.py
+++ b/examples/ilastik3d.py
@@ -30,21 +30,22 @@ if __name__ == '__main__':
resp_paths = requests.get(uri + 'paths')
paths = resp_paths.json()
+ def request_put(endpoint, params):
+ resp = requests.put(uri + endpoint, params=params)
+ assert resp.status_code == 200, resp.content.decode()
+ return resp.json()
+
# load ilastik pixel model
- resp_load_px = requests.put(
- uri + 'models/ilastik/pixel_classification/load/',
- params={'project_file': px3d_ilp},
- )
- assert resp_load_px.status_code == 200, resp_load_px.content.decode()
- model_id_px = resp_load_px.json()['model_id']
+ model_id_px = request_put(
+ 'models/ilastik/pixel_classification/load/',
+ {'project_file': px3d_ilp}
+ )['model_id']
# load ilastik object model
- resp_load_ob = requests.put(
- uri + 'models/ilastik/object_classification/load/',
- params={'project_file': ob3d_ilp},
- )
- assert resp_load_ob.status_code == 200, resp_load_ob.content.decode()
- model_id_ob = resp_load_ob.json()['model_id']
+ model_id_ob = request_put(
+ 'models/ilastik/object_classification/load/',
+ {'project_file': ob3d_ilp}
+ )['model_id']
# copy files from network storage to processing directory
for ff in czis:
@@ -53,26 +54,14 @@ if __name__ == '__main__':
copyfile(infile, outfile)
# infer pixel maps
- resp_infer_px = requests.put(
- uri + f'infer/from_image_file',
- params={
+ request_put(
+ 'infer/from_image_file',
+ {
'model_id': model_id_px,
'input_filename': ff,
'channel': channel,
- },
- )
- assert resp_infer_px == 200, resp_load_px.content.decode()
-
- # infer object maps
- resp_infer_ob = requests.put(
- uri + f'infer/from_image_file',
- params={
- 'model_id': model_id_ob,
- 'input_filename': ff,
- 'channel': channel,
- },
+ }
)
- assert resp_infer_ob == 200, resp_infer_ob.content.decode()
resp_models = requests.get(uri + 'models')
--
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