Error processing new Eiger Data with XDS

[jkclegg]

I'm trying to run xds on some new data and I'm getting the following error:

***** XDS ***** (VERSION Jan 19, 2025 BUILT=20251103) 23-Mar-2026
Author: Wolfgang Kabsch
Copy licensed until 1-Aug-2026 to
academic users for non-commercial applications
No redistribution.

master_file=/Users/jack/Frames/synchrotron/AS/MX3/bendy_flexible/4f4m-s1/crystal_0/4f4m-s1_0_master.h5
[generic_data_plugin] - INFO - generic_open
+ library = </usr/local/bin/dectris-neggia.so>
+ template_name = </Users/jack/Frames/synchrotron/AS/MX3/bendy_flexible/4f4m-s1/crystal_0/4f4m-s1_0_master.h5>
+ dll_filename = </usr/local/bin/dectris-neggia.so>
+ image_data_filename = </Users/jack/Frames/synchrotron/AS/MX3/bendy_flexible/4f4m-s1/crystal_0/4f4m-s1_0_master.h5>
This is neggia 1.2.0 (Copyright Dectris 2020)
[generic_data_plugin] - INFO - generic_get_header
Assertion failed: (chunkShape() == std::vector<size_t>({1, _dim[1], _dim[2]})), function chunkDataSize, file Dataset.cpp, line 103.

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:

Could not print backtrace: executable file is not an executable
#0 0x105065347
#1 0x105064703
#2 0x19e90d6a3
#3 0x19e8d3847
#4 0x19e7dc9e3
#5 0x19e7dbc17
#6 0x10526d3bb
#7 0x10526d5df
#8 0x105268ab7
#9 0x105265e0f
#10 0x105265487
#11 0x104f9b297
#12 0x105063ecb
#13 0x104fcd767
#14 0x10504e007
#15 0x104fa2fa7
#16 0x1050645d7
#17 0x105099f7f
Abort trap: 6

I compile the neggia library freshly using cmake .. -DCMAKE_OSX_ARCHITECTURES="arm64" as I am on a new M3 mac. Any ideas?

[diego-gaemperle]

@jkclegg From the error message it sounds like the HDF5 wasn't written in a way that is supported by neggia. Could you please check the output of following command on your data file?

h5dump -p -H dataFile.h5

The DATASET CHUNKED has to (1, x, y) otherwise neggia cannot work with it as is.

         DATASET "data" {
            DATATYPE  H5T_STD_U32LE
            DATASPACE  SIMPLE { ( 900, 3269, 3110 ) / ( H5S_UNLIMITED, 3269, 3110 ) }
            STORAGE_LAYOUT {
               CHUNKED ( 1, 3269, 3110 )
               SIZE 20930799279 (1.749:1 COMPRESSION)
            }

[jkclegg]

Thanks @diego-gaemperle it seems like it might be a compilation issue. I swapped to a pre-compiled dectris-neggia-Apple-arm64.so and it now seems to be working.