Stable tests

model_server/extensions/chaeo/products.py

@@ -55,7 +55,7 @@ def write_patch_to_file(where, fname, yxcz):
 
     else:
         raise Exception(f'Unsupported file extension: {ext}')
-    
+
 
 def get_patches_from_zmask_meta(
         stack: GenericImageDataAccessor,

model_server/extensions/chaeo/tests/test_zstack.py

@@ -72,7 +72,7 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
         self.assertEqual(interm['label_map'].shape, zmask.shape[0:2])
         self.assertEqual(interm['argmax'].shape, zmask.shape[0:2])
 
-        return zmask, meta
+        return roiset
 
     def test_zmask_works_on_non_zstacks(self, **kwargs):
         acc_zstack_slice = InMemoryDataAccessor(self.stack_ch_pa.data[:, :, :, 0])
@@ -95,27 +95,27 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
         return self.test_zmask_makes_correct_boxes(expand_box_by=(64, 2))
 
     def test_make_2d_patches_from_zmask(self):
-        zmask, meta = self.test_zmask_makes_correct_boxes(
+        roiset = self.test_zmask_makes_correct_boxes(
             filters={'area': {'min': 1e3, 'max': 1e4}},
             expand_box_by=(64, 2)
         )
         files = export_patches_from_zstack(
             output_path / '2d_patches',
             self.stack_ch_pa,
-            meta,
+            roiset.zmask_meta,
             draw_bounding_box=True,
         )
         self.assertGreaterEqual(len(files), 1)
 
     def test_make_3d_patches_from_zmask(self):
-        zmask, meta = self.test_zmask_makes_correct_boxes(
+        roiset = self.test_zmask_makes_correct_boxes(
             filters={'area': {'min': 1e3, 'max': 1e4}},
             expand_box_by=(64, 2),
         )
         files = export_patches_from_zstack(
             output_path / '3d_patches',
             self.stack_ch_pa,
-            meta,
+            roiset.zmask_meta,
             make_3d=True)
         self.assertGreaterEqual(len(files), 1)
 
@@ -145,14 +145,14 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
         )
 
     def test_make_multichannel_2d_patches_from_zmask(self):
-        zmask, meta = self.test_zmask_makes_correct_boxes(
+        roiset = self.test_zmask_makes_correct_boxes(
             filters={'area': {'min': 1e3, 'max': 1e4}},
             expand_box_by=(128, 2)
         )
         files = export_multichannel_patches_from_zstack(
             output_path / '2d_patches_chlorophyl_bbox_overlay',
             InMemoryDataAccessor(self.stack.data),
-            meta,
+            roiset.zmask_meta,
             ch_white=4,
             draw_bounding_box=True,
             bounding_box_channel=1,
@@ -160,14 +160,14 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
         self.assertGreaterEqual(len(files), 1)
 
     def test_make_multichannel_2d_patches_with_mask_overlay(self):
-        zmask, meta = self.test_zmask_makes_correct_boxes(
+        roiset = self.test_zmask_makes_correct_boxes(
             filters={'area': {'min': 1e3, 'max': 1e4}},
             expand_box_by=(128, 2)
         )
         files = export_multichannel_patches_from_zstack(
             output_path / '2d_patches_chlorophyl_mask_overlay',
             InMemoryDataAccessor(self.stack.data),
-            meta,
+            roiset.zmask_meta,
             ch_white=4,
             ch_rgb_overlay=(3, None, None),
             draw_mask=True,
@@ -177,14 +177,14 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
         self.assertGreaterEqual(len(files), 1)
 
     def test_make_multichannel_2d_patches_with_contour_overlay(self):
-        zmask, meta = self.test_zmask_makes_correct_boxes(
+        roiset = self.test_zmask_makes_correct_boxes(
             filters={'area': {'min': 1e3, 'max': 1e4}},
             expand_box_by=(128, 2)
         )
         files = export_multichannel_patches_from_zstack(
             output_path / '2d_patches_chlorophyl_contour_overlay',
             InMemoryDataAccessor(self.stack.data),
-            meta,
+            roiset.zmask_meta,
             ch_white=4,
             ch_rgb_overlay=(3, None, None),
             draw_contour=True,
@@ -194,17 +194,13 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
         self.assertGreaterEqual(len(files), 1)
 
     # TODO: rewrite with direct call to RoiSet methods
-    # def test_make_binary_masks_from_zmask(self):
-    #     zmask, meta = self.test_zmask_makes_correct_boxes(
-    #         filters={'area': {'min': 1e3, 'max': 1e4}},
-    #         expand_box_by=(128, 2)
-    #     )
-    #     files = export_patch_masks_from_zstack(
-    #         output_path / '2d_mask_patches',
-    #         InMemoryDataAccessor(self.stack.data),
-    #         meta,
-    #     )
-    #     self.assertGreaterEqual(len(files), 1)
+    def test_make_binary_masks_from_zmask(self):
+        roiset = self.test_zmask_makes_correct_boxes(
+            filters={'area': {'min': 1e3, 'max': 1e4}},
+            expand_box_by=(128, 2)
+        )
+        files = roiset.export_patch_masks_from_zstack(output_path / '2d_mask_patches', )
+        self.assertGreaterEqual(len(files), 1)
 
     def test_object_map_workflow(self):
         pp = pipeline_params

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
@@ -11,7 +12,7 @@ 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
+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, export_multichannel_patches_from_zstack
@@ -43,10 +44,8 @@ class RoiSet(object):
         self.object_id_labels = self.interm['label_map']
         self.object_class_map = None
 
-    def get_argmax(self):
-        return self.interm.argmax
 
-    def get_multichannel_projection(self):
+    def get_multichannel_projection(self):  # TODO: document and test
         dff = self.df[self.df['keeper']]
         if self.count:
             projected = project_stack_from_focal_points(
@@ -100,7 +99,7 @@ class RoiSet(object):
     def get_zmask(self): # TODO: on-the-fly generation of zmask array
         return self.zmask
 
-    def export_patch_masks_from_zstack(self, where: Path, pad_to: int = 256, prefix='mask'):
+    def export_patch_masks_from_zstack(self, where: Path, pad_to: int = 256, prefix='mask') -> List:
         patches_acc = self.get_patch_masks(pad_to=pad_to)
 
         exported = []