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
59 lines
2.4 KiB
Markdown
59 lines
2.4 KiB
Markdown
# Pixel mask
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## Mask format
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Jungfraujoch generally follows the [NXmx format](https://manual.nexusformat.org/classes/applications/NXmx.html) for the pixel mask.
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The pixel mask is a 32-bit unsigned integer array of the same size as the image.
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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.
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Bit values are set as follows:
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Bit 0 - gap (pixel with no sensor)
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Bit 1 - error pixel (for PSI JUNGFRAU: pixel doesn't set proper gain during pedestal, for DECTRIS: pixel is part of detector pixel mask)
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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)
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Bit 8 - user defined mask
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Bit 9 - beam stop shadow (found by `rugnux --detect-beam-stop`, on by default; see [Rugnux](RUGNUX.md)).
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Unlike the other bits this one belongs to the run that found it, not to the dataset: Rugnux clears it
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at the start of every run, so a mask read back from a file that carries one starts clear. The user
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mask (bit 8) is left alone.
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Bit 10 - defective pixel found on the run's own frames (rotation data from a counting sensor; see
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[CPU data analysis §1.6](CPU_DATA_ANALYSIS_IMAGE.md)): lit above its resolution ring on more frames
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than one reflection or chance explains, or holding the detector's error value on most frames.
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Bit 11 - outside a CCD's active area, measured on the run's own frames (see
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[CPU data analysis §1.6](CPU_DATA_ANALYSIS_IMAGE.md)).
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Bit 30 - module edge (only for PSI systems)
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Bit 31 - chip edge interpolated pixel (multipixel)
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## Custom user mask
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Jungfraujoch allows a custom user mask to be uploaded. This happens in two steps. First create the mask in TIFF format:
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```python
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import numpy as np
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import tifffile as tiff
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# Create an array matching a 2068 x 2164 (width x height) image: 2164 rows, 2068 columns
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array = np.zeros((2164, 2068), dtype=np.uint32)
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# Mark the pixel at column 400, row 300 with the value 1
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array[300, 400] = 1
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# Save the array as a TIFF file
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tiff.imwrite('mask.tiff', array)
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```
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Pixels with non-zero value in the TIFF file will be marked as belonging to the user mask (bit 8).
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Then upload the mask to Jungfraujoch server:
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```shell
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curl -v http://<jfjoch_broker http address>/config/user_mask.tiff -XPUT --data-binary @mask.tiff
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```
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