Jungfraujoch/docs/PIXEL_MASK.md

# Pixel mask

## Mask format

Jungfraujoch generally follows the [NXmx format](https://manual.nexusformat.org/classes/applications/NXmx.html) 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](RUGNUX.md)).
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](CPU_DATA_ANALYSIS_IMAGE.md)): 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](CPU_DATA_ANALYSIS_IMAGE.md)).

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:

```python
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:
```shell
curl -v http://<jfjoch_broker http address>/config/user_mask.tiff -XPUT --data-binary @mask.tiff
```