From f21346e9c320767ce5780248b4524786904f212d Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 19 Feb 2024 13:27:35 +0100
Subject: [PATCH] Roughed in test coverage of ilastik classification by patch
stack
---
.../extensions/ilastik/tests/test_ilastik.py | 29 +++++++++++++++++--
1 file changed, 26 insertions(+), 3 deletions(-)
diff --git a/model_server/extensions/ilastik/tests/test_ilastik.py b/model_server/extensions/ilastik/tests/test_ilastik.py
index 2c972e9d..c21e338d 100644
--- a/model_server/extensions/ilastik/tests/test_ilastik.py
+++ b/model_server/extensions/ilastik/tests/test_ilastik.py
@@ -4,9 +4,10 @@ import unittest
import numpy as np
-from model_server.conf.testing import czifile, ilastik_classifiers, output_path
-from model_server.base.accessors import CziImageFileAccessor, InMemoryDataAccessor, write_accessor_data_to_file
+from model_server.conf.testing import czifile, ilastik_classifiers, output_path, roiset_test_data
+from model_server.base.accessors import CziImageFileAccessor, generate_file_accessor, InMemoryDataAccessor, write_accessor_data_to_file
from model_server.extensions.ilastik import models as ilm
+from model_server.base.roiset import _get_label_ids, RoiSet, RoiSetMetaParams
from model_server.base.workflows import classify_pixels
from tests.test_api import TestServerBaseClass
@@ -270,4 +271,26 @@ class TestIlastikOverApi(TestServerBaseClass):
class TestIlastikObjectClassification(unittest.TestCase):
def setUp(self):
- pass
+ stack = generate_file_accessor(roiset_test_data['multichannel_zstack']['path'])
+ stack_ch_pa = stack.get_one_channel_data(roiset_test_data['pipeline_params']['patches_channel'])
+ seg_mask = generate_file_accessor(roiset_test_data['multichannel_zstack']['mask_path'])
+
+ self.roiset = RoiSet(
+ stack_ch_pa,
+ _get_label_ids(seg_mask),
+ params=RoiSetMetaParams(
+ mask_type='boxes',
+ filters={'area': {'min': 1e3, 'max': 1e4}},
+ expand_box_by=(64, 2)
+ )
+ )
+
+ self.object_classifier = ilm.PatchStackObjectClassifier(
+ params={'project_file': ilastik_classifiers['seg_to_obj']}
+ )
+
+ def test_classify_patches(self):
+ raw_patches = self.roiset.get_raw_patches()
+ patch_masks = self.roiset.get_patch_masks()
+ res = self.object_classifier.infer(raw_patches, patch_masks)
+ self.assertEqual(0, 1)
--
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