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Hi, I am very new to programing in general and ran into this issue with using eiger2cbf. I am trying to convert the master .h5 file from the FMX beamline at brookhaven which has an eiger 16M detector. Below is the meta data when I try running any of the commands:

(base) kimberlyvish@TB285-03 20-11-3 % eiger2cbf 20-11_15712_master.h5 out.cbf
Traceback (most recent call last): ] 25% 20-11_15712_master.h5
File "/Users/kimberlyvish/Desktop/ENTER/bin/eiger2cbf", line 8, in
sys.exit(main())
File "/Users/kimberlyvish/Desktop/ENTER/lib/python3.8/site-packages/fabio/app/eiger2cbf.py", line 524, in main
succeeded = convert_all(args)
File "/Users/kimberlyvish/Desktop/ENTER/lib/python3.8/site-packages/fabio/app/eiger2cbf.py", line 414, in convert_all
finish_at = convert_one(filename, options, start_at)
File "/Users/kimberlyvish/Desktop/ENTER/lib/python3.8/site-packages/fabio/app/eiger2cbf.py", line 306, in convert_one
raise NotImplementedError("Please implement Eiger detector data format parsing or at least open an issue")
NotImplementedError: Please implement Eiger detector data format parsing or at least open an issue
(base) kimberlyvish@TB285-03 20-11-3 %

Any help will be greatly appriciated!

When pixel_mask_applied is TRUE, invalid pixels (e.g. gaps) are represented by (2 ** image_depth) - 1 in /entry/data/data_NNNNNN. So eiger2cbf converts this value to -1. However, heavily saturated pixels, too, can have this value. They can be distinguished by looking at pixel_mask.

Should we also convert them to -1? Or keep them as they are? The converter from Dectris takes the latter strategy.

Hi, I am trying to convert some data using your program and following is the outcome. When i import the output to imosflm all the output are empty and I cannot process them. Can you please let me know what I am doing wrong? these are the data we collect from eiger , esrf. I installed all the dependencies. Ireally appreciate if you could help me .

Many thanks.

./eiger2cbf W_50_570_master.h5 1:112 W_50
EIGER HDF5 to CBF converter (version 160415)
written by Takanori Nakane
see https://github.com/biochem-fan/eiger2cbf for details.

Going to convert frame 1 to 112.
Metadata in HDF5:
/entry/instrument/detector/description = Dectris Eiger 4M
/entry/instrument/detector/detector_number = E-08-0106
/entry/instrument/detector/detectorSpecific/software_version = 1.6.1
/entry/instrument/detector/bit_depth_image = 16
/entry/instrument/detector/detectorSpecific/saturation_value not present. Trying another place.
/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff = 38086
/entry/instrument/detector/sensor_thickness = 449999.988079 (um)
/entry/instrument/detector/detectorSpecific/{x,y}pixels_in_detector = (2070, 2167) (px)
/entry/instrument/detector/beam_center{x,y} = (0, 0) (px)
/entry/instrument/detector/count_time = 0.015000 (sec)
/entry/instrument/detector/frame_time = 0.015010 (sec)
/entry/instrument/detector/x_pixel_size = 0.000075 (m)
/entry/instrument/detector/distance not present. Trying another place.
/entry/instrument/detector/detector_distance not present.
WARNING: detector distance was not defined! "Detector distance" field in the output is set to -1.
/entry/sample/beam/incident_wavelength not present. Trying another place.
/entry/instrument/beam/wavelength not present. Trying another place.
/entry/instrument/monochromator/wavelength not present. Trying another place.
/entry/instrument/beam/incident_wavelength = 0.953725 (A)
WARNING: oscillation width was not defined. "Start_angle" field in the output is set to 0!

This dataset starts from data_000001.
The number of images per data block is 200.

File analysis completed.

Converting frame 1 (1 / 112)
/entry/sample/goniometer/omega[1] = 0.000 (1-indexed)
Converting frame 2 (2 / 112)
/entry/sample/goniometer/omega[2] = 0.000 (1-indexed)
Converting frame 3 (3 / 112)
...
Converting frame 111 (111 / 112)
/entry/sample/goniometer/omega[111] = 0.000 (1-indexed)
Converting frame 112 (112 / 112)
/entry/sample/goniometer/omega[112] = 0.000 (1-indexed)

All done!

I am at the Australian Synchrotron MX beamlines, when unpacking some of our full h5 libraries from the Eiger 16M, a couple of frames end up with no data.

Writing the single frame works fine, but the empty frames while doing image analysis, would error checking slow the unpackaging?

[email protected]

Hi
While installing eiger2cbf I get the following warning, but CBFLib 'make tests' gives no error. So I assumed that eiger2cbf would work. Could you please let me know if this warning matters or if the imported h5 files have problem? Thanks a lot for your time and help.

best regards

root@alipc:/home/ali/Downloads/eiger2cbf-master# make
/usr/bin/gcc -O3 -std=c99 -o eiger2cbf -g
-I/home/ali/Downloads/CBFlib-0.9.5.17/include
-L/home/ali/Downloads/CBFlib-0.9.5.17/lib -Ilz4
eiger2cbf.c
lz4/lz4.c lz4/h5zlz4.c
bitshuffle/bshuf_h5filter.c
bitshuffle/bshuf_h5plugin.c
bitshuffle/bitshuffle.c
/home/ali/Downloads/CBFlib-0.9.5.17/lib/libhdf5_hl.a
/home/ali/Downloads/CBFlib-0.9.5.17/lib/libhdf5.a
-lcbf -lm -lpthread -lz -ldl
bitshuffle/bitshuffle.c: In function ‘bshuf_decompress_lz4_block’:
bitshuffle/bitshuffle.c:1311:14: warning: implicit declaration of function ‘LZ4_decompress_fast’ [-Wimplicit-function-declaration]
nbytes = LZ4_decompress_fast((char*) in + 4, tmp_buf, size * elem_size);

To fill in missing metadata or overwrite wrong metadata.

I was trying to convert H5 file to cbf file using eiger2cbf.exe, but after few seconds of running the command the eiger2cbf stops working. Can anyone help me to solve the problem? I am attaching the metadata and the notification of stopping eiger2cbf.

Hello,
in a view of using eiger2cbf ta ID11 for the new Eiger2-4M, I am trying to learn eiger2cbf with a dataset form id30a (which perhaps should be working.)
When I run the command : eiger2cbf id30_eiger_0003.h5 1:1000 out i get the error at the end of this message.
My question is: is it because I need to modify the eiger2cbf.c in the section main with the right values?
Or can I add these info as arguments?
Is there a detailed manual?
Thanks a lot for your help!
Carlotta

EIGER HDF5 to CBF converter (version 160415)
written by Takanori Nakane
see https://github.com/biochem-fan/eiger2cbf for details.

HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 140442264835840:
#000: ../../../src/H5D.c line 358 in H5Dopen2(): not found
major: Dataset
minor: Object not found
#1: ../../../src/H5Gloc.c line 430 in H5G_loc_find(): can't find object
major: Symbol table
minor: Object not found
#2: ../../../src/H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#3: ../../../src/H5Gtraverse.c line 755 in H5G_traverse_real(): component not found
major: Symbol table
minor: Object not found
Going to convert frame 1 to 1000.
Metadata in HDF5:
/entry/instrument/detector/description =
/entry/instrument/detector/detector_number =
/entry/instrument/detector/detectorSpecific/software_version =
WARNING: /entry/instrument/detector/bit_depth_image is not avaialble. We assume 16 bit.
/entry/instrument/detector/detectorSpecific/saturation_value not present. Trying another place.
/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff not present. Trying another place.
/entry/instrument/detector/detectorSpecific/detectorModule_000/countrate_correction_count_cutoff not present.
As a last resort, we will put an arbitrary large number (65534) in the header.
You might want to change the OVERLOAD setting in your subsequent processing.
/entry/instrument/detector/sensor_thickness is not avaialble. We assume it is 450.000000 um
/entry/instrument/detector/detectorSpecific/{x,y}pixels_in_detector = (-1, -1) (px)
/entry/instrument/detector/beam_center{x,y} = (-1, -1) (px)
/entry/instrument/detector/count_time = -1.000000 (sec)
/entry/instrument/detector/frame_time = -1.000000 (sec)
/entry/instrument/detector/x_pixel_size = -1.000000 (m)
/entry/instrument/detector/distance not present. Trying another place.
/entry/instrument/detector/detector_distance not present.
WARNING: detector distance was not defined! "Detector distance" field in the output is set to -1.
/entry/sample/beam/incident_wavelength not present. Trying another place.
/entry/instrument/beam/wavelength not present. Trying another place.
/entry/instrument/monochromator/wavelength not present. Trying another place.
/entry/instrument/beam/incident_wavelength not present.
WARNING: wavelength was not defined! "Wavelength" field in the output is set to -1.
WARNING: oscillation width was not defined. "Start_angle" field in the output is set to 0!