mx/Jungfraujoch
2
1
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 67 Wiki Activity

reader: take the stored image bit depth from the file, not the DECTRIS default

Browse Source 
DetectorSetup hardcodes bit_depth_image = 16 for every DECTRIS detector
(DetectorSetup.cpp:78), and GetByteDepthImage() consults that BEFORE the depth
the reader takes from the file - so a file storing 32-bit images had its
overflow computed as a 16-bit one. With the reader also declaring the images
signed, GetOverflow() returned INT16_MAX and GetSaturationLimit() became
min(file value, 32767).

Every count above 32767 was therefore marked saturated, and because the
integration accept gate requires ALL inner pixels valid, the whole reflection
was discarded. That silently removes the strongest reflections of a strong
crystal - the low-resolution ones that anchor scaling - while the file itself
declares saturation at 105000-133000.

Measured on a lysozyme rotation set (200 frames), before -> after:

  saturated pixels per frame   0.815 -> 0.000
  brightest accepted pixel     32738 -> 87633
  mean per-frame maximum       26218 -> 37390

i.e. the ceiling was exactly INT16_MAX and nothing genuine reached it.

Which datasets this touches depends on how bright they are: measured pixels
above the old ceiling range from 0.0 per frame on some rotation sets to 6.1 on
others, so the fix is a no-op on weak data and only ever adds reflections.

Rotation battery, 33 crystals: no point group changed (30/33 before and after)
and no run failed. Four crystals move on quality, in both directions - ISa
1.90 -> 2.40 and 3.29 -> 4.80 on two, 2.97 -> 1.85 and 20.83 -> 18.47 on two
others; three of the four are the battery's known weak or run-to-run-unstable
crystals. The one strong crystal that moves gains 136 observations out of
1.9 million and loses 2.4 ISa: the reflections restored are by construction the
brightest ones, and they carry the systematic error that the strongest
reflections always carry. That is a real cost, but it is the cost of MEASURING
them rather than discarding them unseen, and a lower asymptotic I/sigma on data
that are now complete is preferable to a flattering one on data that quietly
are not.

Only the offline file reader is affected; the online path builds its detector
setup from configuration.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-07-28 17:49:14 +02:00
co-authored by Claude Opus 5
parent 6f4917dcee
commit b81c6f00b7
1 changed files with 9 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files
reader/HDF5MetadataSource.cpp
+9
View File
@@ -661,6 +661,15 @@ HDF5MetadataSource::OpenResult HDF5MetadataSource::Open(const std::string &filen
if (master_file->Exists("/entry/instrument/detector/sensor_material"))
detector.SensorMaterial(master_file->GetString("/entry/instrument/detector/sensor_material"));
detector.SaturationLimit(master_file->GetInt("/entry/instrument/detector/saturation_value"));
// The container depth of the stored images, NOT the detector's counter depth. DetectorSetup
// defaults DECTRIS to 16 bits, and GetByteDepthImage() prefers that over the value the image
// format carries - so without this an EIGER2 file that stores 32-bit images has its overflow
// computed as a 16-bit one and every count above 32767 is called saturated. The integration
// accept gate then drops the WHOLE reflection, which silently removes the strongest
// reflections of a strong crystal (measured on a lysozyme set: max accepted pixel 32738
// against a declared saturation of 108833).
if (master_file->Exists("/entry/instrument/detector/bit_depth_image"))
detector.BitDepthImage(master_file->GetInt("/entry/instrument/detector/bit_depth_image"));
detector.MinFrameTime(std::chrono::microseconds(0));
detector.MinCountTime(std::chrono::microseconds(0));
detector.ReadOutTime(std::chrono::nanoseconds(0));