From 5dcc337fd92c6dc7928576ece2317e3884647133 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Paul=20M=C3=BCller?= <dev@craban.de>
Date: Wed, 10 Jan 2024 23:59:39 +0100
Subject: [PATCH] fix: RTDCWriter.rectify_metadata fails when image feature is
 empty

---
 CHANGELOG                    |  1 +
 dclab/rtdc_dataset/writer.py | 13 ++++++++-----
 tests/test_rtdc_writer.py    | 19 +++++++++++++++++++
 3 files changed, 28 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG b/CHANGELOG
index 9004c2b7..9ac9bc99 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,4 +1,5 @@
 0.57.1
+ - fix: RTDCWriter.rectify_metadata fails when image feature is empty
  - docs: improve documentation of hierarchy child mapper
 0.57.0
  - fix: integer overflow in downsample_grid
diff --git a/dclab/rtdc_dataset/writer.py b/dclab/rtdc_dataset/writer.py
index b81853f9..3c90e3c0 100644
--- a/dclab/rtdc_dataset/writer.py
+++ b/dclab/rtdc_dataset/writer.py
@@ -148,9 +148,12 @@ def rectify_metadata(self):
         else:
             raise ValueError(f"No features in '{self.path}'!")
 
-        # make sure that "trace" is not empty
-        if "trace" in feats and len(self.h5file["events"]["trace"]) == 0:
-            feats.remove("trace")
+        # ignore empty features in the checks further below
+        for feat in feats[:]:  # iterate over a copy of the list
+            obj = self.h5file["events"][feat]
+            if ((isinstance(feat, h5py.Group) and len(obj) == 0)  # groups
+                    or obj.shape[0] == 0):  # datasets
+                feats.remove(feat)
 
         # set samples per event
         if "trace" in feats:
@@ -166,9 +169,9 @@ def rectify_metadata(self):
                 self.h5file.attrs["fluorescence:channel count"] = chcount
 
         # set roi size x/y
-        if "image" in self.h5file["events"]:
+        if "image" in feats:
             shape = self.h5file["events"]["image"][0].shape
-        elif "mask" in self.h5file["events"]:
+        elif "mask" in feats:
             shape = self.h5file["events"]["mask"][0].shape
         else:
             shape = None
diff --git a/tests/test_rtdc_writer.py b/tests/test_rtdc_writer.py
index 0945ac0c..46116423 100644
--- a/tests/test_rtdc_writer.py
+++ b/tests/test_rtdc_writer.py
@@ -675,6 +675,25 @@ def test_real_time_single():
         assert len(logs["log1"]) == n
 
 
+def test_rectify_metadata_ignore_empty_image():
+    # test introduced in 0.39.7
+    rtdc_file = tempfile.mktemp(suffix=".rtdc",
+                                prefix="dclab_test_error_")
+    with h5py.File(rtdc_file, "a") as h5:
+        h5.require_group("events")
+        h5["events"].require_dataset(name="image",
+                                     shape=(0, 80, 100),
+                                     dtype=np.uint8)
+        h5["events/deform"] = np.linspace(.1, .12, 7)
+
+        # Initialize writer
+        hw = RTDCWriter(h5, mode="append")
+        # in previous versions, this did not work, because of the empty trace
+        hw.rectify_metadata()
+        # make sure that something happened
+        assert h5.attrs["experiment:event count"] == 7
+
+
 def test_rectify_metadata_ignore_empty_trace():
     # test introduced in 0.39.7
     rtdc_file = tempfile.mktemp(suffix=".rtdc",