cleanup

model_server/extensions/chaeo/tests/test_zstack.py

@@ -75,7 +75,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
         ar = roiset.get_df().iloc[1]['area']
         self.assertGreaterEqual(sh[0] * sh[1], ar)
 
-    def test_zmask_works_on_non_zstacks(self, **kwargs):
+    def test_roiset_from_non_zstacks(self, **kwargs):
         acc_zstack_slice = InMemoryDataAccessor(self.stack_ch_pa.data[:, :, :, 0])
         self.assertEqual(acc_zstack_slice.nz, 1)
         id_map = get_label_ids(self.seg_mask)
@@ -86,23 +86,14 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
         zmask_acc = InMemoryDataAccessor(zmask)
         self.assertTrue(zmask_acc.is_mask())
 
-    def test_zmask_makes_correct_contours(self):
-        return self._make_roi_set(mask_type='contours')
-
-    def test_zmask_makes_correct_boxes_with_filters(self):
-        return self._make_roi_set()
-
-    def test_zmask_makes_correct_expanded_boxes(self):
-        return self._make_roi_set()
-
-    def test_zmask_slices_are_valid(self):
+    def test_slices_are_valid(self):
         roiset = self._make_roi_set()
         for s in roiset.get_slices():
             ebb = roiset.acc_raw.data[s]
             self.assertEqual(len(ebb.shape), 4)
             self.assertTrue(np.all([si >= 1 for si in ebb.shape]))
 
-    def test_zmask_rel_slices_are_valid(self):
+    def test_rel_slices_are_valid(self):
         roiset = self._make_roi_set()
         for roi in roiset:
             ebb = roiset.acc_raw.data[roi.slice]
@@ -112,7 +103,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
             self.assertEqual(len(rbb.shape), 4)
             self.assertTrue(np.all([si >= 1 for si in rbb.shape]))
 
-    def test_make_2d_patches_from_zmask(self):
+    def test_make_2d_patches(self):
         roiset = self._make_roi_set()
         files = export_patches_from_zstack(
             output_path / '2d_patches',
@@ -121,7 +112,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
         )
         self.assertGreaterEqual(len(files), 1)
 
-    def test_make_3d_patches_from_zmask(self):
+    def test_make_3d_patches(self):
         roiset = self._make_roi_set()
         files = export_patches_from_zstack(
             output_path / '3d_patches',
@@ -160,7 +151,7 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
             InMemoryDataAccessor(img)
         )
 
-    def test_make_binary_masks_from_zmask(self):
+    def test_make_binary_masks(self):
         roiset = self._make_roi_set()
         files = roiset.export_patch_masks(output_path / '2d_mask_patches', )
         self.assertGreaterEqual(len(files), 1)
@@ -303,9 +294,11 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
         self.assertEqual(result.chroma, 5)
 
     def test_multichannel_annotated_zstack(self):
-        self.roiset.export_annotated_zstack(
+        file = self.roiset.export_annotated_zstack(
             output_path / 'multichannel' / 'annotated_zstack',
             'test_multichannel_annotated_zstack',
-
         )
+        result = generate_file_accessor(Path(file['location']) / file['filename'])
+        self.assertEqual(result.chroma, self.stack.chroma)
+        self.assertEqual(result.nz, self.stack.nz)
 

model_server/extensions/chaeo/zmask.py

 from uuid import uuid4
 
-from math import floor
 import numpy as np
 import pandas as pd
-from pathlib import Path
 
-from skimage.measure import find_contours, label, regionprops_table
+from skimage.measure import label, regionprops_table
 from sklearn.preprocessing import PolynomialFeatures
 from sklearn.linear_model import LinearRegression
 
 from model_server.base.accessors import GenericImageDataAccessor, InMemoryDataAccessor, write_accessor_data_to_file
 from model_server.base.models import InstanceSegmentationModel
-from model_server.base.process import pad, rescale, resample_to_8bit
 
 from model_server.extensions.chaeo.annotators import draw_boxes_on_3d_image
 from model_server.extensions.chaeo.products import export_patches_from_zstack