leonarski_fandClaude Opus 5
a29c36600f
rugnux finds the beam stop and its holder in a projection of 60 images and marks them in the pixel mask as bit 9 (--detect-beam-stop[=N|off], on by default). Reflections behind the stop are attenuated but not flagged, so they integrate low with a plausible sigma and nothing downstream catches them: the signal-box gate requires 100% valid pixels and shadow pixels are valid, the background clip is high-side only, and the |zeta| cut applies only to the space-group search merge. The detection compares each pixel's background against the typical background at the same radius on two channels. An azimuthal one (the ring median) finds the holder arm, which is a minority of its ring; a radial one (the background just outside) finds the disk, which the ring median cannot see because inside a fully blocked ring the median is the shadow itself. Pixels are pooled over a 5x5 box and tested only where the background has actually been counted, so low-background data no longer masks the whole detector. Recorded reflections are carved back out - a beam stop cannot block a reflection that was measured. Bit 9 belongs to the run that found it, not to the dataset: it is cleared when a run starts, so a mask read back from a file that carries one starts clear. The user mask (bit 8) is left alone. Scaling and merging gain a low-resolution limit, default 50 A (--scaling-low-resolution <num>, 0 removes it), applied per observation before scaling so it also protects the per-frame scale fit and the space-group search. 50 A is the value XDS configurations use; rugnux_vs_xds.py now matches both of XDS's resolution limits instead of only the high one, so the lowest shell is the same shell in the two programs. The viewer draws the detected shadow in coral with a "Show beam stop" switch in the side panel, exposes the low-resolution limit in the settings dock, and offers detection in its processing jobs. Adding an image marker meant giving the reader a MIN_REAL_PXL_VALUE, because several places classify a pixel by range rather than by equality and would otherwise read the new marker as a very negative intensity. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2.0 KiB
Pixel mask
Mask format
Jungfraujoch follows generally NXmx format format for pixel mask. Pixel mask is described as 32-bit unsigned integer array of size the same as the image. Conditions to mask pixel are described by setting a particular bit to one. This way it is possible to encode reason why pixel is included in the pixel mask, also for one pixel there can be multiple reasons encoded at the same time.
Bit values are set as follows:
Bit 0 - gap (pixel with no sensor)
Bit 1 - error pixel (for PSI JUNGFRAU: pixel doesn't set proper gain during pedestal, for DECTRIS: pixel is part of detector pixel mask)
Bit 4 - noisy pixel (for PSI JUNGFRAU: pixel pedestal G0 RMS is over threshold, for DECTRIS: pixel was flagged with signal during dark data collection at initialization)
Bit 8 - user defined mask
Bit 9 - beam stop shadow (found by rugnux --detect-beam-stop, on by default; see rugnux).
Unlike the other bits this one belongs to the run that found it, not to the dataset: rugnux clears it
at the start of every run, so a mask read back from a file that carries one starts clear. The user
mask (bit 8) is left alone.
Bit 30 - module edge (only for PSI systems)
Bit 31 - chip edge interpolated pixel (multipixel)
Custom user mask
Jungfraujoch allows to upload custom user mask. This happens in two steps. First create mask in TIFF format:
import numpy as np
import tifffile as tiff
# Create a 2068x2164 numpy array filled with zeros, with 32-bit unsigned integers
array = np.zeros((2068, 2164), dtype=np.uint32)
# Mark the pixel (300, 400) with the value 1
array[300, 400] = 1
# Save the array as a TIFF file
tiff.imwrite('mask.tiff', array)
Pixels with non-zero value in the TIFF file will be marked as belonging to the user mask (bit 8).
Then upload the mask to Jungfraujoch server:
curl -v http://<jfjoch_broker http address>/config/user_mask.tiff -XPUT --data-binary @mask.tiff