Added and covered PatchStack dataframe with summary stats

model_server/base/accessors.py

@@ -3,6 +3,7 @@ import os
 from pathlib import Path
 
 import numpy as np
+import pandas as pd
 from skimage.io import imread, imsave
 
 import czifile
@@ -491,6 +492,18 @@ class PatchStack(InMemoryDataAccessor):
     def shape_dict(self):
         return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
 
+    @property
+    def df(self):
+        df = pd.DataFrame([
+            {
+                'label': i,
+                'area': (self.iat(i).data > 0).sum(),
+                'sum': self.iat(i).data.sum()
+            } for i in range(0, self.count)
+        ])
+        df['intensity_mean'] = df['sum'] / df['area']
+        return df
+
 
 def make_patch_stack_from_file(fpath):  # interpret t-dimension as patch position
     if not Path(fpath).exists():

tests/base/test_accessors.py

@@ -302,6 +302,9 @@ class TestPatchStackAccessor(unittest.TestCase):
         self.assertEqual(acc.hw, (h, w))
         self.assertEqual(acc.get_mono(channel=0).data_yxz.shape, (n, h, w, nz))
         self.assertEqual(acc.get_mono(channel=0, mip=True).data_yx.shape, (n, h, w))
+
+        # intensity means are centered around half of full range
+        self.assertTrue(np.all(((acc.df['intensity_mean'] / acc.dtype_max) - 0.5)**2 < 1e-3))
         return acc
 
     def test_get_one_channel(self):