From ff6547b22098cee4e5335ccb56db485fd2339f71 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 26 Apr 2024 15:49:00 +0200
Subject: [PATCH] ilastik workflow now interprets channel=None to use all input
channels
---
model_server/conf/testing.py | 5 +++--
.../extensions/ilastik/tests/test_ilastik.py | 20 +++++++++++++------
2 files changed, 17 insertions(+), 8 deletions(-)
diff --git a/model_server/conf/testing.py b/model_server/conf/testing.py
index 72b8816d..5fdea529 100644
--- a/model_server/conf/testing.py
+++ b/model_server/conf/testing.py
@@ -57,8 +57,9 @@ ilastik_classifiers = {
'px': root / 'ilastik' / 'demo_px.ilp',
'pxmap_to_obj': root / 'ilastik' / 'demo_obj.ilp',
'seg_to_obj': root / 'ilastik' / 'demo_obj_seg.ilp',
- 'px_color_zstack': root / 'ilastik' / 'px_color_zstack.ilp',
- 'ob_color_zstack': root / 'ilastik' / 'ob_color_zstack.ilp',
+ 'px_color_zstack': root / 'ilastik' / 'px-3d-color.ilp',
+ 'ob_pxmap_color_zstack': root / 'ilastik' / 'ob-pxmap-color-zstack.ilp',
+ 'ob_seg_color_zstack': root / 'ilastik' / 'ob-seg-color-zstack.ilp',
}
roiset_test_data = {
diff --git a/model_server/extensions/ilastik/tests/test_ilastik.py b/model_server/extensions/ilastik/tests/test_ilastik.py
index 2406cdbe..18e95a4d 100644
--- a/model_server/extensions/ilastik/tests/test_ilastik.py
+++ b/model_server/extensions/ilastik/tests/test_ilastik.py
@@ -325,8 +325,10 @@ class TestIlastikOnMultichannelInputs(TestServerBaseClass):
def setUp(self) -> None:
super(TestIlastikOnMultichannelInputs, self).setUp()
self.pa_px_classifier = ilastik_classifiers['px_color_zstack']
- self.pa_ob_classifier = ilastik_classifiers['ob_color_zstack']
+ self.pa_ob_pxmap_classifier = ilastik_classifiers['ob_pxmap_color_zstack']
+ self.pa_ob_seg_classifier = ilastik_classifiers['ob_seg_color_zstack']
self.pa_input_image = roiset_test_data['multichannel_zstack']['path']
+ self.pa_mask = roiset_test_data['multichannel_zstack']['mask_path_3d']
def _copy_input_file_to_server(self):
from shutil import copyfile
@@ -352,7 +354,7 @@ class TestIlastikOnMultichannelInputs(TestServerBaseClass):
def test_classify_objects(self):
pxmap = self.test_classify_pixels()
img = generate_file_accessor(self.pa_input_image)
- mod = ilm.IlastikObjectClassifierFromPixelPredictionsModel(params={'project_file': self.pa_ob_classifier})
+ mod = ilm.IlastikObjectClassifierFromPixelPredictionsModel(params={'project_file': self.pa_ob_pxmap_classifier})
obmap = mod.infer(img, pxmap)[0]
self.assertEqual(obmap.hw, img.hw)
self.assertEqual(obmap.nz, img.nz)
@@ -361,7 +363,7 @@ class TestIlastikOnMultichannelInputs(TestServerBaseClass):
return infer_px_then_ob_model(
self.pa_input_image,
ilm.IlastikPixelClassifierModel(params={'project_file': self.pa_px_classifier}),
- ilm.IlastikObjectClassifierFromPixelPredictionsModel(params={'project_file': self.pa_ob_classifier}),
+ ilm.IlastikObjectClassifierFromPixelPredictionsModel(params={'project_file': self.pa_ob_pxmap_classifier}),
output_path,
channel=channel,
)
@@ -369,8 +371,12 @@ class TestIlastikOnMultichannelInputs(TestServerBaseClass):
def test_workflow(self):
with self.assertRaises(ilm.IlastikInputShapeError):
self._call_workflow(channel=0)
-
res = self._call_workflow(channel=None)
+ acc_input = generate_file_accessor(self.pa_input_image)
+ acc_obmap = generate_file_accessor(res.object_map_filepath)
+ self.assertEqual(acc_obmap.hw, acc_input.hw)
+ self.assertEqual(len(acc_obmap._unique()[1]), 3)
+
def test_api(self):
resp_load = self._put(
@@ -382,7 +388,7 @@ class TestIlastikOnMultichannelInputs(TestServerBaseClass):
resp_load = self._put(
'ilastik/pxmap_to_obj/load/',
- query={'project_file': str(self.pa_ob_classifier)},
+ query={'project_file': str(self.pa_ob_pxmap_classifier)},
)
self.assertEqual(resp_load.status_code, 200, resp_load.json())
ob_model_id = resp_load.json()['model_id']
@@ -393,10 +399,12 @@ class TestIlastikOnMultichannelInputs(TestServerBaseClass):
'px_model_id': px_model_id,
'ob_model_id': ob_model_id,
'input_filename': self.pa_input_image,
- # 'channel': 0,
}
)
self.assertEqual(resp_infer.status_code, 200, resp_infer.content.decode())
+ acc_input = generate_file_accessor(self.pa_input_image)
+ acc_obmap = generate_file_accessor(resp_infer.json()['object_map_filepath'])
+ self.assertEqual(acc_obmap.hw, acc_input.hw)
class TestIlastikObjectClassification(unittest.TestCase):
--
GitLab