diff --git a/extensions/chaeo/tests/test_zstack.py b/extensions/chaeo/tests/test_zstack.py index c15fdfee209fce56d09d0b49a846de2c49b8acc9..357a0ca6feba201097a27782c4ca4d4717f3729f 100644 --- a/extensions/chaeo/tests/test_zstack.py +++ b/extensions/chaeo/tests/test_zstack.py @@ -5,6 +5,7 @@ import numpy as np from conf.testing import output_path from extensions.chaeo.conf.testing import multichannel_zstack, pixel_classifier, pipeline_params +from extensions.chaeo.params import RoiSetExportParams from extensions.chaeo.products import export_patches_from_zstack, export_multichannel_patches_from_zstack, export_patch_masks_from_zstack from extensions.chaeo.workflows import infer_object_map_from_zstack from extensions.chaeo.zmask import build_zmask_from_object_mask @@ -207,12 +208,21 @@ class TestZStackDerivedDataProducts(unittest.TestCase): self.pxmodel, DummyInstanceSegmentationModel(), ] + export_params = RoiSetExportParams(**{ + 'pixel_probabilities': True, + 'patches_3d': {}, + # 'patches_2d_for_annotation': { + # 'draw_bounding_box': True, + # 'rgb_overlay_channels': [4, 2, None] + # } + }) infer_object_map_from_zstack( multichannel_zstack['path'], - output_path, + output_path / 'workflow', models, pxmap_foreground_channel=pp['pxmap_channel'], pxmap_threshold=pp['pxmap_threshold'], segmentation_channel=pp['segmentation_channel'], patches_channel=pp['patches_channel'], + # exports=export_params, ) \ No newline at end of file diff --git a/extensions/chaeo/workflows.py b/extensions/chaeo/workflows.py index 284a773a34fdd5c986ad131358318896447e358e..46e693b159ea33d2b6b431ef66b3554a9d71ad77 100644 --- a/extensions/chaeo/workflows.py +++ b/extensions/chaeo/workflows.py @@ -283,7 +283,7 @@ def infer_object_map_from_zstack( # make zmask rois = RoiSet( obmask.get_one_channel_data(pxmap_foreground_channel), - stack.get_one_channel_data(segmentation_channel), + stack, mask_type=zmask_type, filters=zmask_filters, expand_box_by=kwargs.get('zmask_expand_box_by', (0, 0)), diff --git a/extensions/chaeo/zmask.py b/extensions/chaeo/zmask.py index 1f93151a437244f0c1f28700ddf56d82840681e4..886dcf1c7ab5a713d5064706441f5ac2707b0be8 100644 --- a/extensions/chaeo/zmask.py +++ b/extensions/chaeo/zmask.py @@ -152,7 +152,7 @@ class RoiSet(object): return projected def get_raw_patches(self, channel): - return get_patches_from_zmask_meta(self.acc_raw, self.zmask_meta) + return get_patches_from_zmask_meta(self.acc_raw, self.zmask_meta).get_one_channel_data(channel) def get_patch_masks(self): return get_patch_masks_from_zmask_meta(self.acc_raw, self.zmask_meta) @@ -224,7 +224,7 @@ def build_zmask_from_object_mask( """ # validate inputs - assert zstack.chroma == 1 + # assert zstack.chroma == 1 assert mask_type in ('contours', 'boxes'), mask_type assert obmask.is_mask() assert obmask.chroma == 1