From 5a770788202aa7fe296a83452b97464a6f115ca6 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 28 Sep 2023 15:06:54 +0200
Subject: [PATCH] Completed testing zmask module, including contour and filter
optional args
---
extensions/chaeo/test_zstack.py | 14 +++++++++-----
extensions/chaeo/zstack.py | 9 +++++++--
2 files changed, 16 insertions(+), 7 deletions(-)
diff --git a/extensions/chaeo/test_zstack.py b/extensions/chaeo/test_zstack.py
index ae13cb0f..4dfe7ec6 100644
--- a/extensions/chaeo/test_zstack.py
+++ b/extensions/chaeo/test_zstack.py
@@ -21,16 +21,17 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
mip = InMemoryDataAccessor(self.stack.get_one_channel_data(channel=0).data.max(axis=-1, keepdims=True))
self.pxmap, result = pxmodel.infer(mip)
- write_accessor_data_to_file(output_path / 'pxmap.tif', self.pxmap)
+ # write_accessor_data_to_file(output_path / 'pxmap.tif', self.pxmap)
self.obmap = InMemoryDataAccessor(self.pxmap.data > pipeline_params['threshold'])
- write_accessor_data_to_file(output_path / 'obmap.tif', self.obmap)
+ # write_accessor_data_to_file(output_path / 'obmap.tif', self.obmap)
- def test_zmask_makes_correct_boxes(self):
+ def test_zmask_makes_correct_boxes(self, mask_type='boxes', filters=None):
zmask, meta = build_stack_mask(
'test_zmask_with boxes',
self.obmap.get_one_channel_data(0),
self.stack.get_one_channel_data(0),
- mask_type='boxes',
+ mask_type=mask_type,
+ filters=filters,
)
zmask_acc = InMemoryDataAccessor(zmask)
self.assertTrue(zmask_acc.is_mask())
@@ -51,4 +52,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
self.assertGreaterEqual(sh[0] * sh[1], ar)
def test_zmask_makes_correct_contours(self):
- pass
\ No newline at end of file
+ return self.test_zmask_makes_correct_boxes(mask_type='contours')
+
+ def test_zmask_makes_correct_boxes_with_filters(self):
+ return self.test_zmask_makes_correct_boxes(filters={'area': (1e3, 1e4)})
\ No newline at end of file
diff --git a/extensions/chaeo/zstack.py b/extensions/chaeo/zstack.py
index 71bcd214..63152287 100644
--- a/extensions/chaeo/zstack.py
+++ b/extensions/chaeo/zstack.py
@@ -98,8 +98,13 @@ def build_stack_mask(desc, obmap: GenericImageDataAccessor, stack: GenericImageD
zi_st = np.zeros(stack.shape, dtype='bool')
if mask_type == 'contours':
zi_map = (lut[lamap] + 1.0).astype('int')
- idxs = np.array([zi_map]) - 1
- np.put_along_axis(zi_st, idxs, 1, axis=3)
+ idxs = np.array(zi_map) - 1
+ np.put_along_axis(
+ zi_st,
+ np.expand_dims(idxs, (2, 3)),
+ 1,
+ axis=3
+ )
# change background level from to 0 in final frame
zi_st[:, :, :, -1][lamap == 0] = 0
--
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