diff --git a/model_server/extensions/chaeo/conf/testing.py b/model_server/extensions/chaeo/conf/testing.py index c151234c73607bf5f8d5660b23d1187a80f72b84..cf1b4c642d4d9d24d676d9c4ccfc8c200ff4d4bd 100644 --- a/model_server/extensions/chaeo/conf/testing.py +++ b/model_server/extensions/chaeo/conf/testing.py @@ -8,6 +8,7 @@ multichannel_zstack = { 'h': 512, 'c': 5, 'z': 7, + 'mask_path': root / 'testing' / 'zmask-test-stack-mask.tif', } pixel_classifier = { diff --git a/tests/test_roiset.py b/tests/test_roiset.py index 5aa3c28ef61c81022630a8db096868be58a43a91..0a1490bd5227423b2108ced5f7fccbda706c7da5 100644 --- a/tests/test_roiset.py +++ b/tests/test_roiset.py @@ -15,27 +15,10 @@ from model_server.base.models import DummyInstanceSegmentationModel class BaseTestRoiSetMonoProducts(object): def setUp(self) -> None: - - # need test data incl obj map + # set up test raw data and segmentation from file self.stack = generate_file_accessor(multichannel_zstack['path']) - self.stack_ch_seg = self.stack.get_one_channel_data(pipeline_params['segmentation_channel']) self.stack_ch_pa = self.stack.get_one_channel_data(pipeline_params['patches_channel']) - - self.pxmodel = IlastikPixelClassifierModel( - {'project_file': pixel_classifier['path']}, - ) - mip = InMemoryDataAccessor( - self.stack_ch_seg.data.max(axis=-1, keepdims=True) - ) - pxmap, _ = self.pxmodel.infer(mip) - - write_accessor_data_to_file(output_path / 'pxmap.tif', pxmap) - self.seg_mask = InMemoryDataAccessor( - pxmap.get_one_channel_data( - pipeline_params['pxmap_channel'] - ).data > pipeline_params['pxmap_threshold'] - ) - write_accessor_data_to_file(output_path / 'seg_mask.tif', self.seg_mask) + self.seg_mask = generate_file_accessor(multichannel_zstack['mask_path']) class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):