RE: AreaDetector Defective Pixel Correction Plugin

[Mark Rivers via Tech-talk <tech-talk at aps.anl.gov>]

Hi David,

 

I have created a new issue for this in ADCore.

 

https://github.com/areaDetector/ADCore/issues/471 

 

Mark

 

 

From: Mark Rivers
Sent: Wednesday, April 21, 2021 7:34 AM
To: David Vine <dvine at sigray.com>
Cc: tech-talk at aps.anl.gov
Subject: Re: AreaDetector Defective Pixel Correction Plugin

 

Hi David,

 

A bad pixel correction plugin would be very useful and is something I have been thinking about for a while. It seems like using a median filter around each bad pixel would be a good approach.

 

Here are some cases that should be handled:

1. - The neighboring pixels in the median filter happen to include other bad pixels.  They need to be excluded.
2. - Only a portion of the detector is being read out.  
3. - The detector is binned when being read out.
4. - The detector readout is reversed in X or Y

The NDArray NDDimension structures contain all of the information required to handle cases 2-4:

 

/** Structure defining a dimension of an NDArray */

typedef struct NDDimension {

    size_t size;    /**< The number of elements in this dimension of the array */

    size_t offset;  /**< The offset relative to the origin of the original data source (detector, for example).

                      * If a selected region of the detector is being read, then this value may be > 0.

                      * The offset value is cumulative, so if a plugin such as NDPluginROI further selects

                      * a subregion, the offset is relative to the first element in the detector, and not

                      * to the first element of the region passed to NDPluginROI. */

    int binning;    /**< The binning (pixel summation, 1=no binning) relative to original data source (detector, for example)

                      * The offset value is cumulative, so if a plugin such as NDPluginROI performs binning,

                      * the binning is expressed relative to the pixels in the detector and not to the possibly

                      * binned pixels passed to NDPluginROI.*/

    int reverse;    /**< The orientation (0=normal, 1=reversed) relative to the original data source (detector, for example)

                      * This value is cumulative, so if a plugin such as NDPluginROI reverses the data, the value must

                      * reflect the orientation relative to the original detector, and not to the possibly

                      * reversed data passed to NDPluginROI. */

} NDDimension_t;

 

Some drivers probably don’t set those NDDimension fields as they should, so they will need to be fixed to handle those cases.

 

I think the plugin should handle:

-          All NDArray data types

-          2-D NDArrays and 3-D NDArrays with ColorMode=RGB1

 

Mark

 

 

---

From: Tech-talk <tech-talk-bounces at aps.anl.gov> on behalf of David Vine via Tech-talk <tech-talk at aps.anl.gov>
Sent: Tuesday, April 20, 2021 6:58 PM
To: tech-talk at aps.anl.gov
Subject: AreaDetector Defective Pixel Correction Plugin

 

Hi all,

 

Both the Andor Ikon and Teledyne Shadobox detectors I use have defective pixel maps that need to be corrected. Currently these maps are specified in a text file listing bad pixels, rows or columns. They would typically be corrected with an appropriate median filter.

 

I was thinking about implementing the correction as a plugin. Has anyone done that already? 

 

Thanks,

David

 

 

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