From a1b48e945486da56a7c91a29c751dd43da4e1c1c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Sun, 23 Aug 2026 12:42:47 +0200
Subject: [PATCH] Mark unreadable frames in the reprocessing virtual dataset
 too

The master's own virtual dataset fills with the error marker, so a source file that cannot be
resolved reads as masked rather than as zero counts. The virtual dataset rugnux writes into
_process.h5 was left at HDF5's default fill of zero, which is a legitimate count - the same silent
failure, one file along.

The helper moves above its first user; it has to be set before SetVirtual.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01VfYvJT5Nb71suJCowRBn5z
---
 writer/HDF5NXmx.cpp | 53 +++++++++++++++++++++++++--------------------
 1 file changed, 29 insertions(+), 24 deletions(-)

diff --git a/writer/HDF5NXmx.cpp b/writer/HDF5NXmx.cpp
index e0f1f2ae..351c2edb 100644
--- a/writer/HDF5NXmx.cpp
+++ b/writer/HDF5NXmx.cpp
@@ -194,6 +194,30 @@ void NXmx::LinkToData_VDS(const StartMessage &start, const EndMessage &end) {
     }
 }
 
+namespace {
+    void SetFillValue(HDF5Dcpl &dcpl, const HDF5DataType &data_type,
+                      const std::optional<int64_t> &fill_value) {
+        if (!fill_value.has_value())
+            return;
+        const int64_t value = fill_value.value();
+        if (data_type.IsSigned()) {
+            switch (data_type.GetElemSize()) {
+                case 1: dcpl.SetFillValue8(static_cast<int8_t>(value)); break;
+                case 2: dcpl.SetFillValue16(static_cast<int16_t>(value)); break;
+                case 4: dcpl.SetFillValue32(static_cast<int32_t>(value)); break;
+                default: break;
+            }
+        } else {
+            switch (data_type.GetElemSize()) {
+                case 1: dcpl.SetFillValueU8(static_cast<uint8_t>(value)); break;
+                case 2: dcpl.SetFillValueU16(static_cast<uint16_t>(value)); break;
+                case 4: dcpl.SetFillValueU32(static_cast<uint32_t>(value)); break;
+                default: break;
+            }
+        }
+    }
+}
+
 void NXmx::LinkToData_ProcessingVDS(const StartMessage &start, const EndMessage &end) {
     if (start.hdf5_source_data.empty() || end.max_image_number == 0)
         return;
@@ -207,6 +231,11 @@ void NXmx::LinkToData_ProcessingVDS(const StartMessage &start, const EndMessage
     HDF5DataSpace full_data_space({total_images, height, width});
     HDF5Dcpl dcpl;
     dcpl.SetChunking({1, height, width});
+    // Same reason as the master's own virtual dataset: a source file that cannot be resolved reads
+    // as the fill value, and HDF5's default fill is zero - which is a legitimate count. Fill with the
+    // error marker instead, so an unreadable frame is masked rather than integrated as blank. Must be
+    // set before SetVirtual.
+    SetFillValue(dcpl, HDF5DataType(start.bit_depth_image / 8, start.pixel_signed), start.error_value);
 
     for (const auto &mapping: start.hdf5_source_data) {
         if (mapping.image_count == 0)
@@ -282,30 +311,6 @@ void NXmx::LinkToReflections_VDS(const StartMessage &start, const EndMessage &en
     }
 }
 
-namespace {
-    void SetFillValue(HDF5Dcpl &dcpl, const HDF5DataType &data_type,
-                      const std::optional<int64_t> &fill_value) {
-        if (!fill_value.has_value())
-            return;
-        const int64_t value = fill_value.value();
-        if (data_type.IsSigned()) {
-            switch (data_type.GetElemSize()) {
-                case 1: dcpl.SetFillValue8(static_cast<int8_t>(value)); break;
-                case 2: dcpl.SetFillValue16(static_cast<int16_t>(value)); break;
-                case 4: dcpl.SetFillValue32(static_cast<int32_t>(value)); break;
-                default: break;
-            }
-        } else {
-            switch (data_type.GetElemSize()) {
-                case 1: dcpl.SetFillValueU8(static_cast<uint8_t>(value)); break;
-                case 2: dcpl.SetFillValueU16(static_cast<uint16_t>(value)); break;
-                case 4: dcpl.SetFillValueU32(static_cast<uint32_t>(value)); break;
-                default: break;
-            }
-        }
-    }
-}
-
 std::unique_ptr<HDF5DataSet> NXmx::VDS(const StartMessage &start,
                                        const std::string &name,
                                        const std::vector<hsize_t> &dim,