From cdc3ea3596f53b13d7f6947d42a9b930ec650808 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 29 Sep 2023 13:27:57 +0200
Subject: [PATCH] Cleaned up patch export functino
---
extensions/chaeo/products.py | 5 -----
extensions/chaeo/tests/test_zstack.py | 5 ++---
2 files changed, 2 insertions(+), 8 deletions(-)
diff --git a/extensions/chaeo/products.py b/extensions/chaeo/products.py
index 1e10205c..88d8f3fa 100644
--- a/extensions/chaeo/products.py
+++ b/extensions/chaeo/products.py
@@ -56,7 +56,6 @@ def export_patches_from_zstack(
assert len(patch.shape) == 4
assert patch.shape[2] == stack.chroma
- # assert patch.shape[3] == 1 # should not get to zstacks by this point
if rescale_clip is not None:
patch = rescale(patch, rescale_clip)
@@ -68,10 +67,6 @@ def export_patches_from_zstack(
y1 = rbb['y1']
for zi in range(0, patch.shape[3]):
- # pilimg = Image.fromarray(patch[:, :, 0, zi]) # drawing modifies array in-place
- # draw = ImageDraw.Draw(pilimg)
- # draw.rectangle([(x0, y0), (x1, y1)], outline='white', width=kwargs.get('linewidth', 1))
- # patch[:, :, 0, zi] = np.array(pilimg)
patch[:, :, 0, zi] = draw_box_on_patch(
patch[:, :, 0, zi],
((x0, y0), (x1, y1)),
diff --git a/extensions/chaeo/tests/test_zstack.py b/extensions/chaeo/tests/test_zstack.py
index fcbbb3e1..8ea85d79 100644
--- a/extensions/chaeo/tests/test_zstack.py
+++ b/extensions/chaeo/tests/test_zstack.py
@@ -26,13 +26,12 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
self.obmap = InMemoryDataAccessor(self.pxmap.data > pipeline_params['threshold'])
# write_accessor_data_to_file(output_path / 'obmap.tif', self.obmap)
- def test_zmask_makes_correct_boxes(self, mask_type='boxes', filters=None, expand_box_by=None):
+ def test_zmask_makes_correct_boxes(self, mask_type='boxes', **kwargs):
zmask, meta = build_zmask_from_object_mask(
self.obmap.get_one_channel_data(0),
self.stack.get_one_channel_data(0),
mask_type=mask_type,
- filters=filters,
- expand_box_by=expand_box_by,
+ **kwargs,
)
zmask_acc = InMemoryDataAccessor(zmask)
self.assertTrue(zmask_acc.is_mask())
--
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