Now just running into broadcast errors, presumably on patch mask boundaries

model_server/base/roiset.py

@@ -223,13 +223,19 @@ class RoiSet(object):
             acc_raw: GenericImageDataAccessor,
             df: pd.DataFrame,
             patch_masks: dict, # dict of ndarray, where key is integer label
+            params: RoiSetMetaParams = RoiSetMetaParams(),
     ):
         assert len(df) == len(patch_masks)
-        se_patch_masks = pd.Series(patch_masks)
-        # df_merged = pd.merge(df, se_patch_masks)
-        assert all(patch_masks.keys())
-        assert df.apply(lambda x: x, axis=1)
-        assert False
+        zmask = np.zeros((*acc_raw.hw, 1, acc_raw.nz), dtype=bool)
+
+        def _label_obj(r):
+            sl = np.s_[r.ebb_y0:r.ebb_y1, r.ebb_x0:r.ebb_x1, :, r.zi:r.zi + 1]
+            zmask[sl] = patch_masks[r.label]
+
+        df.apply(lambda x: _label_obj(x), axis=1)
+        obj_ids = _get_label_ids(zmask, allow_3d=True, connect_3d=False)
+        return RoiSet(acc_raw, obj_ids, params)
+
 
     @staticmethod
     def filter_df(df: pd.DataFrame, filters: RoiFilter = None) -> pd.DataFrame:

tests/test_roiset.py

@@ -3,6 +3,8 @@ import unittest
 import numpy as np
 from pathlib import Path
 
+import pandas as pd
+
 from model_server.conf.testing import output_path, roiset_test_data
 
 from model_server.base.roiset import RoiSetExportParams, RoiSetMetaParams
@@ -303,3 +305,36 @@ class TestRoiSetFromZmask(unittest.TestCase):
         )
         self.assertEqual(roiset.count, id_map.data.max())
         self.assertGreater(len(roiset.get_df()['zi'].unique()), 1)
+        return roiset
+
+    def test_create_roiset_from_df_and_patch_masks(self):
+        ref_roiset = self.test_create_roiset_from_2d_obj_ids()
+        res = ref_roiset.run_exports(
+            output_path / 'roiset_from_3d',
+            roiset_test_data['pipeline_params']['segmentation_channel'],
+            'ref',
+            params=RoiSetExportParams(patch_masks={'pad_to': 256}, dataframe=True)
+        )
+        where_df = output_path / 'roiset_from_3d' / 'dataframe' / 'ref.csv'
+        self.assertTrue(where_df.exists())
+
+        df_test = pd.read_csv(where_df)
+
+        # zmask = np.zeros((*self.stack.hw, 1, self.stack.nz), dtype=bool)
+        print('hi')
+
+        fn = output_path / 'roiset_from_3d' / 'patch_masks' / 'ref-la{:04d}-zi{:04d}.png'
+        patch_masks = {}
+
+        def _label_obj(r):
+            sl = np.s_[r.ebb_y0:r.ebb_y1, r.ebb_x0:r.ebb_x1, :, r.zi:r.zi + 1]
+            self.assertEqual(str(sl), r.slice)
+            patch_masks[r.label] = generate_file_accessor(str(fn).format(r.label, r.zi)).data
+            # zmask[sl] = True
+
+        df_test.apply(lambda x: _label_obj(x), axis=1)
+
+        roiset_test = RoiSet.from_df_and_patch_masks(self.stack, df_test, patch_masks)
+        print('')
+
+