file: support loading a misclassified Kymo

changelog.md

@@ -7,6 +7,7 @@
 * Added more options for plotting color channels for images:
   * Shortcuts `"r"`, `"g"`, and `"b"` can now be used for plotting single color channels in addition to `"red"`, `"green"`, and `"blue"`.
   * Two-channel visualizations can be plotted using `"rg"`, `"gb"`, or `"rb"`.
+* Handle kymographs that were accidentally stored in the `Scan` field.
 
 #### Improvements
 

lumicks/pylake/file.py

@@ -275,7 +275,16 @@ def try_from_dataset(*args):
     @property
     def kymos(self) -> Dict[str, Kymo]:
         """Kymos stored in the file"""
-        return self._get_object_dictionary("Kymograph", Kymo)
+
+        # Due to an error in an earlier version of Bluelake, some Kymographs were stored in the
+        # `Scan` field. This reads those using a fallback mechanism.
+        scan_kymos = {
+            key: item
+            for key, item in self._get_object_dictionary("Scan", Kymo).items()
+            if item._metadata.num_axes == 1
+        }
+
+        return scan_kymos | self._get_object_dictionary("Kymograph", Kymo)
 
     @property
     def point_scans(self) -> Dict[str, Scan]:

lumicks/pylake/scan.py

@@ -30,6 +30,8 @@ class Scan(ConfocalImage, VideoExport, FrameIndex):
 
     def __init__(self, name, file, start, stop, metadata):
         super().__init__(name, file, start, stop, metadata)
+        if self._metadata.num_axes == 1:
+            raise RuntimeError("1D scans are not supported")
         if self._metadata.num_axes > 2:
             raise RuntimeError("3D scans are not supported")
 

lumicks/pylake/tests/test_file/conftest.py

@@ -191,3 +191,19 @@ def h5_file_invalid_version(tmpdir_factory):
     mock_file.attrs["File format version"] = 254
 
     return mock_file
+
+
+@pytest.fixture(scope="module", params=[MockDataFile_v2])
+def h5_kymo_as_scan(tmpdir_factory, request):
+    mock_class = request.param
+
+    tmpdir = tmpdir_factory.mktemp("pylake")
+    mock_file = mock_class(tmpdir.join("%s.h5" % mock_class.__class__.__name__))
+    mock_file.write_metadata()
+
+    json_kymo = generate_scan_json([{"axis": 1, "num of pixels": 4, "pixel size (nm)": 191.0}])
+    ds = mock_file.make_json_data("Scan", "Kymo1", json_kymo)
+    ds.attrs["Start time (ns)"] = np.int64(20e9)
+    ds.attrs["Stop time (ns)"] = np.int64(100e9)
+
+    return mock_file.file

lumicks/pylake/tests/test_file/test_file_items.py

@@ -117,3 +117,15 @@ def test_notes(h5_file):
         assert note.text == "Note content"
         assert note.start == 100
         assert note.stop == 100
+
+
+def test_kymos_in_scans(h5_kymo_as_scan):
+    """Tests whether Kymos accidentally put in Scan are loaded correctly"""
+    f = pylake.File.from_h5py(h5_kymo_as_scan)
+
+    assert len(f.kymos) == 1
+    assert f.kymos["Kymo1"].name == "Kymo1"
+
+    with pytest.warns():
+        scan_dict = f.scans
+        assert not scan_dict