More test coverage of number of channels in multichannel export

model_server/extensions/chaeo/products.py

@@ -235,6 +235,7 @@ def export_patches_from_zstack(
         exported.append({
             'df_index': roi.Index,
             'patch_filename': fname,
+            'location': where.__str__(),
         })
 
     exported = []

model_server/extensions/chaeo/tests/test_zstack.py

 import unittest
 
 import numpy as np
+from pathlib import Path
 
 from model_server.conf.testing import output_path
 
@@ -131,9 +132,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
         )
         files = export_patches_from_zstack(
             output_path / '3d_patches',
-            # self.stack_ch_pa,
             roiset,
-            # roiset.zmask_meta,
             make_3d=True)
         self.assertGreaterEqual(len(files), 1)
 
@@ -145,8 +144,6 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
 
         from model_server.extensions.chaeo.zmask import project_stack_from_focal_points
 
-        # dff = df[df['keeper']]
-
         img = project_stack_from_focal_points(
             df['centroid-0'].to_numpy(),
             df['centroid-1'].to_numpy(),
@@ -168,49 +165,42 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
             id_map,
             self.stack,
             params=RoiSetMetaParams(
-                mask_type=mask_type, filters=kwargs.get('filters')
+                expand_box_by=(128, 2),
+                mask_type=mask_type,
+                filters={'area': {'min': 1e3, 'max': 1e4}},
             )
         )
 
     def test_make_multichannel_2d_patches_from_zmask(self):
-        roiset = self._setup_multichannel_tests(
-            filters={'area': {'min': 1e3, 'max': 1e4}},
-            expand_box_by=(128, 2)
-        )
+        roiset = self._setup_multichannel_tests()
         files = export_multichannel_patches_from_zstack(
             output_path / '2d_patches_chlorophyl_bbox_overlay',
-            # InMemoryDataAccessor(self.stack.data),
-            # roiset.zmask_meta,
             roiset,
-            rgb_white_channel=4,
+            white_channel=4,
             draw_bounding_box=True,
             bounding_box_channel=1,
         )
         self.assertGreaterEqual(len(files), 1)
+        result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
+        self.assertEqual(result.chroma, 1)
 
     def test_make_multichannel_2d_patches_with_mask_overlay(self):
-        roiset = self.test_zmask_makes_correct_boxes(
-            filters={'area': {'min': 1e3, 'max': 1e4}},
-            expand_box_by=(128, 2)
-        )
+        roiset = self._setup_multichannel_tests()
         files = export_multichannel_patches_from_zstack(
             output_path / '2d_patches_chlorophyl_mask_overlay',
-            # InMemoryDataAccessor(self.stack.data),
-            # roiset.zmask_meta,
             roiset,
-            rgb_white_channel=4,
-            ch_rgb_overlay=(3, None, None),
+            white_channel=4,
+            # rgb_overlay_channels=(3, None, None),
             draw_mask=True,
             mask_channel=0,
-            overlay_gain=(0.1, 1.0, 1.0)
+            # rgb_overlay_weights=(0.1, 1.0, 1.0)
         )
         self.assertGreaterEqual(len(files), 1)
+        result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
+        self.assertEqual(result.chroma, 1)
 
     def test_make_multichannel_2d_patches_with_contour_overlay(self):
-        roiset = self.test_zmask_makes_correct_boxes(
-            filters={'area': {'min': 1e3, 'max': 1e4}},
-            expand_box_by=(128, 2)
-        )
+        roiset = self._setup_multichannel_tests()
         files = export_multichannel_patches_from_zstack(
             output_path / '2d_patches_chlorophyl_contour_overlay',
             # InMemoryDataAccessor(self.stack.data),
@@ -222,6 +212,18 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
             overlay_gain=(0.1, 1.0, 1.0)
         )
         self.assertGreaterEqual(len(files), 1)
+        result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
+        self.assertEqual(result.chroma, 3)
+
+    def test_make_2d_patches_as_multichannel_tif(self):
+        roiset = self._setup_multichannel_tests()
+        files = export_multichannel_patches_from_zstack(
+            output_path / '2d_patches_chlorophyl_contour_overlay',
+            roiset,
+        )
+        self.assertGreaterEqual(len(files), 1)
+        result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
+        self.assertEqual(result.chroma, 5)
 
     # TODO: rewrite with direct call to RoiSet methods
     def test_make_binary_masks_from_zmask(self):