Merge branch 'staging' into 'master'

Changed formatting of object classification path results

See merge request !2

model_server/base/roiset.py

@@ -474,7 +474,15 @@ class RoiSet(object):
         dfe['patch'] = self._df.apply(lambda r: _make_patch(r), axis=1)
         return dfe
 
-    def run_exports(self, where, channel, prefix, params: RoiSetExportParams):
+    def run_exports(self, where: Path, channel, prefix, params: RoiSetExportParams) -> dict:
+        """
+        Export various representations of ROIs, e.g. patches, annotated stacks, and object maps.
+        :param where: path of directory in which to write all export products
+        :param channel: color channel of products to export
+        :param prefix: prefix of the name of each product's file or subfolder
+        :param params: RoiSetExportParams object describing which products to export and with which parameters
+        :return: dict of Path objects describing the location of single-file export products
+        """
         record = {}
         if not self.count:
             return
@@ -506,11 +514,10 @@ class RoiSet(object):
             if k == 'annotated_zstacks':
                 self.export_annotated_zstack(subdir, prefix=pr, **kp)
             if k == 'object_classes':
-                record[k] = {}
                 for kc, acc in self.object_class_maps.items():
                     fp = subdir / kc / (pr + '.tif')
                     write_accessor_data_to_file(fp, acc)
-                    record[k][kc] = fp.__str__()
+                    record[f'{k}_{kc}'] = fp
             if k == 'dataframe':
                 dfpa = subdir / (pr + '.csv')
                 dfpa.parent.mkdir(parents=True, exist_ok=True)

tests/test_roiset.py

@@ -148,9 +148,9 @@ class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):
             'obmap',
             RoiSetExportParams(object_classes=True)
         )
-        opa = record['object_classes']['dummy_class']
-        acc = generate_file_accessor(opa)
+        opa = record['object_classes_dummy_class']
         self.assertTrue(Path(opa).exists())
+        acc = generate_file_accessor(opa)
         self.assertTrue(all(np.unique(acc.data) == [0, 1]))