leonarski_fandClaude Opus 5.5
12d6208126
The pixels rugnux measures as outside a CCD's active area shared bit 1 with the detector's own bad
pixels, so they could not be told from the device mask and pixel_sum left them out. They now have bit 11,
a run-determined bit like the shadow and the hot pixels: they stay masked in the image and the other
statistics, and pixel_sum counts them. The beam-stop finder still reads them as data.
A file written with this mask no longer shows them as bit 1. The jfjoch XDS plugin and DIALS mask any
bit, so they still mask them; Durin and Neggia, which ignore the bits from 8 up, no longer do.
(ported from rc184-2 e6baecda5)
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HVeDQsU5a8AJUdJPgWevAK
2.4 KiB
Pixel mask
Mask format
Jungfraujoch generally follows the NXmx format for the pixel mask. The pixel mask is a 32-bit unsigned integer array of the same size as the image. The conditions for masking a pixel are encoded by setting a particular bit to one. This makes it possible to record the reason why a pixel is included in the mask, and several reasons can be recorded for one pixel 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 10 - defective pixel found on the run's own frames (rotation data from a counting sensor; see CPU data analysis §1.6): lit above its resolution ring on more frames than one reflection or chance explains, or holding the detector's error value on most frames.
Bit 11 - outside a CCD's active area, measured on the run's own frames (see CPU data analysis §1.6).
Bit 30 - module edge (only for PSI systems)
Bit 31 - chip edge interpolated pixel (multipixel)
Custom user mask
Jungfraujoch allows a custom user mask to be uploaded. This happens in two steps. First create the mask in TIFF format:
import numpy as np
import tifffile as tiff
# Create an array matching a 2068 x 2164 (width x height) image: 2164 rows, 2068 columns
array = np.zeros((2164, 2068), dtype=np.uint32)
# Mark the pixel at column 400, row 300 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