Jungfraujoch/docs/PIXEL_MASK.md

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