diff --git a/model_server/extensions/chaeo/products.py b/model_server/extensions/chaeo/products.py
index 3027f97cbfd1215ed222a4e8117b5af9f3a6cdd7..4b0d197f6a859c7cc88c03d3089799542e8fa2d9 100644
--- a/model_server/extensions/chaeo/products.py
+++ b/model_server/extensions/chaeo/products.py
@@ -118,7 +118,7 @@ def get_patches_from_zmask_meta(
assert white_channel < raw.chroma
stack = raw.data[:, :, [white_channel, white_channel, white_channel], :]
else:
- stack = np.zeros([*raw.shape[0:1], 3, raw.shape[3]], dtype=raw.dtype)
+ stack = np.zeros([*raw.shape[0:2], 3, raw.shape[3]], dtype=raw.dtype)
for ii, ci in enumerate(rgb_overlay_channels):
if ci is None:
@@ -128,12 +128,24 @@ def get_patches_from_zmask_meta(
stack[:, :, ii, :] = _safe_add(
stack[:, :, ii, :], # either black or grayscale channel
rgb_overlay_weights[ii],
- stack[:, :, ci, :]
+ raw.data[:, :, ci, :]
)
else:
- if white_channel:
+ if white_channel: # interpret as just a single channel
assert white_channel < raw.chroma
- stack = raw.data[:, :, [white_channel], :]
+ annotate_rgb = False
+ for k in ['contour_channel', 'bounding_box_channel', 'mask_channel']:
+ ca = kwargs.get(k)
+ if ca is None:
+ continue
+ assert(ca < raw.chroma)
+ if ca != white_channel:
+ annotate_rgb = True
+ break
+ if annotate_rgb: # make RGB patches anyway to include annotation color
+ stack = raw.data[:, :, [white_channel, white_channel, white_channel], :]
+ else: # make monochrome patches
+ stack = raw.data[:, :, [white_channel], :]
else:
stack = raw.data
diff --git a/model_server/extensions/chaeo/tests/test_zstack.py b/model_server/extensions/chaeo/tests/test_zstack.py
index 816c3f25eb5e56f019741097486cc8e512c5ccc5..6cf76c9c9e783f06948d2a8c6c655aec752cf7b0 100644
--- a/model_server/extensions/chaeo/tests/test_zstack.py
+++ b/model_server/extensions/chaeo/tests/test_zstack.py
@@ -39,6 +39,17 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
)
write_accessor_data_to_file(output_path / 'seg_mask.tif', self.seg_mask)
+ id_map = get_label_ids(self.seg_mask)
+ self.roiset = RoiSet(
+ id_map,
+ self.stack,
+ params=RoiSetMetaParams(
+ expand_box_by=(128, 2),
+ mask_type='boxes',
+ filters={'area': {'min': 1e3, 'max': 1e4}},
+ )
+ )
+
def test_zmask_makes_correct_boxes(self, mask_type='boxes', **kwargs):
id_map = get_label_ids(self.seg_mask)
roiset = RoiSet(
@@ -159,34 +170,20 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
InMemoryDataAccessor(img)
)
- def _setup_multichannel_tests(self, mask_type='boxes', **kwargs):
- id_map = get_label_ids(self.seg_mask)
- return RoiSet(
- id_map,
- self.stack,
- params=RoiSetMetaParams(
- expand_box_by=(128, 2),
- mask_type=mask_type,
- filters={'area': {'min': 1e3, 'max': 1e4}},
- )
- )
-
- def test_make_mono_2d_patches_from_multichannel_zmask(self):
- roiset = self._setup_multichannel_tests()
+ def test_multichannel_to_mono_2d_patches(self):
files = export_multichannel_patches_from_zstack(
- output_path / 'test_make_mono_2d_patches_from_multichannel_zmask',
- roiset,
+ output_path / 'test_multichannel_to_mono_2d_patches',
+ self.roiset,
white_channel=3,
draw_bounding_box=True,
)
result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
self.assertEqual(result.chroma, 1)
- def test_make_rgb_annotated_mono_2d_patches_from_multichannel_zmask(self):
- roiset = self._setup_multichannel_tests()
+ def test_multichannnel_to_mono_2d_patches_rgb_bbox(self):
files = export_multichannel_patches_from_zstack(
- output_path / 'test_make_rgb_annotated_mono_2d_patches_from_multichannel_zmask',
- roiset,
+ output_path / 'multichannnel_to_mono_2d_patches_rgb_bbox',
+ self.roiset,
white_channel=3,
draw_bounding_box=True,
bounding_box_channel=1,
@@ -194,11 +191,10 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
self.assertEqual(result.chroma, 3)
- def test_make_multichannel_2d_patches_with_mask_overlay(self):
- roiset = self._setup_multichannel_tests()
+ def test_multichannnel_to_rgb_2d_patches_bbox(self):
files = export_multichannel_patches_from_zstack(
- output_path / 'test_make_multichannel_2d_patches_with_mask_overlay',
- roiset,
+ output_path / 'multichannnel_to_rgb_2d_patches_bbox',
+ self.roiset,
white_channel=4,
rgb_overlay_channels=(3, None, None),
draw_mask=True,
@@ -208,26 +204,24 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
self.assertEqual(result.chroma, 3)
- def test_make_multichannel_2d_patches_with_contour_overlay(self):
- roiset = self._setup_multichannel_tests()
+ def test_multichannnel_to_rgb_2d_patches_contour(self):
files = export_multichannel_patches_from_zstack(
- output_path / '2d_patches_chlorophyl_contour_overlay',
- # InMemoryDataAccessor(self.stack.data),
- roiset,
- rgb_white_channel=4,
- ch_rgb_overlay=(3, None, None),
+ output_path / 'multichannnel_to_rgb_2d_patches_contour',
+ self.roiset,
+ rgb_overlay_channels=(3, None, None),
draw_contour=True,
contour_channel=1,
- overlay_gain=(0.1, 1.0, 1.0)
+ rgb_overlay_weights=(0.1, 1.0, 1.0)
)
result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
self.assertEqual(result.chroma, 3)
+ self.assertEqual(result.get_one_channel_data(2).data.max(), 0) # blue channel is black
- def test_make_2d_patches_as_multichannel_tif(self):
- roiset = self._setup_multichannel_tests()
+ def test_multichannel_to_multichannel_tif_patches(self):
+ # roiset = self._setup_multichannel_tests()
files = export_multichannel_patches_from_zstack(
- output_path / '2d_patches_multichannel_tif',
- roiset,
+ output_path / 'multichannel_to_multichannel_tif_patches',
+ self.roiset,
)
result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
self.assertEqual(result.chroma, 5)