Image calibration, processing and RAW conversion - Linux

General discussion about StarTools.

Image calibration, processing and RAW conversion - Linux

Postby Rowland » Wed May 13, 2015 11:18 pm

Here for a completely revamped interface with a selection of processing options.

If you are a Linux user and would like to try it out, I'd be interested in feedback.

The script performs several tasks on bias dark (optional) flat and light frames.

RAW converter - Fuji X-Trans support.
RAW - image calibration
RAW - preprocessing and stacking - two methods
non-RAW preprocessing and stacking - use jpeg png tiff bmp etc...

UPDATE: link to latest - no version number - easier to administrate - several other improvements

FAICS

Manual

Install Remove video (short)
UPDATE: changes to super pixel debayer.

Unconfigured.png
Unconfigured.png (64.05 KiB) Viewed 1009 times





Legacy content follows. Very much out of date and very much a learning experience.

RAWPREPRO is a Linux based DSLR RAW image conversion and data reduction/calibration script. It was originally intended a means of converting DSLR RAW images to 16bit integer tiff (CFA monochrome, no flip/rotation) files for use in programs such as DSS, to be imported into StarTools. It has grown into a GUI based conversion and image calibration utility. RAWPREPRO uses DCRAW for conversion and ImageMagick to perform the image calibration/reduction/preprocessing steps - DCRAW, ImageMagick and zenity must be installed to take advantage of all preprocessing options.

Unzip file and type go to the rawprepro folder open a terminal and type ./INSTALL.sh - Installs to /usr/local/bin. Or just run from the unzipped folder by typing ./rawprepro in the terminal. If it complains about permissions type chmod -x rawprepro or chmod u+x rawprepro for user only use.

What's going on under the hood/bonnet

Besides data conversion and calibration, RAWPREPRO orders the image preprocessing task through a folder structure, placing files in predictable places for easy access. It keeps things in one place under a project name, renaming files accordingly. All DSLR RAW data files are preserved. Files can be added or removed and the project run over and again, as required. Temporary files and the uncalibrated TIFF files can be deleted at the end of the script to save disk space.

Post #4 has an explanation of the basic maths applied to rawprepro - the bias-in-the-dark method, which is better suited to DSLR RAW data. Tested extensively, it is kind to data.

What follows may be useful - retained just in case - mostly development stuff - teething problems - demonstration - proof of concept!

If you use 0.82 onward, the read me will explain more. There are 4 files to be copied to the folder in which rawprepro will be run. The additional files do the file-by-file processing for image calibration. The parallel processing section is limited to 1 core for multi-core processors and doesn't hang waiting for processes to complete - a little slower but preferable for low resource systems.
Last edited by Rowland on Sat Dec 24, 2016 12:33 am, edited 102 times in total.
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Re: DSLR RAW 16bit CFA conversion script - master frame crea

Postby Rowland » Sun May 24, 2015 12:40 am

Calibration comparison - rawprepro , left, and Regim. The rawprepro result is better balanced and did not require noise reduction. Both files were processed using the same processes in ST. Image Magick has done an excellent job. This is a particularly bad image set.

I used a proprietary program to debayer, register and align the rawprepro calibrated files, with similar settings to Regim. I couldn't get Regim to process the rawprepro calibrated files. It didn't recognise that the frames were not debayered. Use the converted tiff files and/or the master frames with Regim.
M8-rawprepro - other programe calibration.jpg
M8-rawprepro - other programe calibration.jpg (193.13 KiB) Viewed 4520 times
Last edited by Rowland on Thu May 28, 2015 8:49 pm, edited 8 times in total.
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Re: DSLR RAW 16bit CFA conversion script - master frame crea

Postby Rowland » Mon May 25, 2015 11:27 pm

EDIT: I found in more recent tests that ImageMagick does a superb job of flat division on RGB images without normalisation. The reason being;

-auto-level is not necessarily required. From what I can see IM produces a set of normalised images anyway;

convert image.tiff -auto-level output.tiff

is what IM calls perfect normalisation. Not to be confused with;

convert image.tiff -normalize output.tiff

The two are close but not identical and grayscale normalistion seems to have a different effect on different sets of flats.


Posted a couple of flat frame crops, before and after IM flat division, and a crop of the flat as well. IM seems to have done an effective job of flat division.

Edit: I discovered later that the flats associated with this image set were not good quality and the results were obtained by not normalising the flats. This is the exception. However, with a good set of flats normalisation is a necessary step in producing a quality master flat. Link to no normalisation version down the thread.
Attachments
M8_divide_flat.jpeg
M8_divide_flat.jpeg (91.35 KiB) Viewed 4458 times
M8_no_flat.jpeg
M8_no_flat.jpeg (77.09 KiB) Viewed 4458 times
flat.jpeg
flat.jpeg (29.19 KiB) Viewed 4477 times
Last edited by Rowland on Mon Nov 14, 2016 4:30 am, edited 3 times in total.
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Re: DSLR RAW 16bit CFA conversion script - master frame crea

Postby Rowland » Sat May 30, 2015 12:31 am

8.206 median combines the flats, which reduces noise in the master flat. Light division with a good flat is perfect from what I can see.

I am using 3 image sets (3x bias, dark, flat and light frames) to test and compare rawprepro output.

A good set - Eta Carina
A poorly acquired set - M8
A set with mismatched darks - Rho Ophiuchus

rawprepro wont fix poor acquisition technique and each set displays expected outcomes. Dark frame mismatch being the predominant contributor, with gradient removal and color calibration (white point) being virtually impossible. Confirming a long held suspicion about the use of mismatched dark frames - not to mention the obvious noise issues.

The script handles the data this way - reference is Jim Solomon's Astrophotography Cookbook - great reading. And just to avoid any confusion, the term 'dark flat' is interchangeable with 'bias', where flats are taken at fast shutter speeds (say 0.25 - 0.5 seconds), and dark noise is not an issue. However, if as in the explanation below you have a slow system and take flats over several seconds, then 'dark flats' are applicable. In this case, just substitute dark flats for bias frames in rawprepro.
The formula that relates these physical phenomenon, and the actual frames we'll collect over a night of imaging, are as follows:

(1) Light = (Signal * Flat Signal) + Dark + Offset

where Signal is the image of the target object we wish we could collect under ideal circumstances, and Light is the image we actually captured. Rearranging the terms, we have:


(2) Signal = Light - (Dark + Offset)/Flat Signal

But realize that the Flats we capture with the camera will, in turn, be "polluted" by Darks and Offsets in their own right, and so we must subtract Flat Darks and Flat Offsets from the Flat Lights as follows:

(3) Flat Signal = Flat Light - (Flat Dark + Flat Offset)

So, plugging equation (3) into equation (2), yields this general formula:


(4) Signal = Light - (Dark + Offset)/Flat Light - (Flat Dark + Flat Offset)

Here, "Dark" refers to the thermal noise signal of the imaging camera; i.e., the noise signal that varies in proportion to temperature, ISO, and exposure length. Note, however, that any exposure we take with a digital camera contains the Offset, and "Darks" are no exception. So, if we define Dark' to be an exposure of some length with the body cap in place, then Dark' = Dark + Offset, and, similarly, Flat Dark' = Flat Dark + Offset. Plugging these values into Equation 4 yields the following simplified form:


(5) Signal = Light - Dark'/Flat Light - Flat Dark'

And just to make things even simpler, let's drop the prime indicators (the apostrophes) that we stuck on "Dark" and "Flat Dark", and just remember that by "Dark" and "Flat Dark" we mean frames captured with the body cap in place but with the same ISO and exposure length as the Lights and Flat Lights, respectively. That gives us our final form:


(6) Signal = Light - Dark/Flat Light - Flat Dark (bias) - editor's comment

Equation 6 gives us our marching orders for astrophotography, providing us with a set of Frames that must be captured for each imaging session. The actual order in which I choose to capture these frames is as follows, the reasons for which will be made clear in the acquisition section below:

Flat Darks (bias) editor's comment
Flat Lights
Lights
Darks
Last edited by Rowland on Thu Jun 11, 2015 10:51 pm, edited 5 times in total.
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Re: DSLR RAW 16bit CFA conversion script - master frame crea

Postby Rowland » Sun May 31, 2015 3:43 am

A bit more testing - warts and all - what's going on under the hood - normalization in image magick.

I have narrowed down what I think are the best imagemagick calibration options.

The top image compares the use of -auto-level for normalization of the lights after calibration with a median combined flat, and no -auto-level of the lights.

A comparison of the calibrated light subs shows values 0 - 65535 (0 - 1) whether -auto-level is used or not.

Following calibration in rawprepro the light frames were debayered (VNG), aligned (bicubic bspline), and stacked (additive, average and percentile pixel rejection - due to only 3 frames).

In ST - the -auto-level stack; Devel 80%, Dark Anomaly 15; Wipe - Vignetting 85%, Dark Anomoly 2; Devel 83%; Color - scientific (1st option) Cap Green to Yellow; Save

The NO -auto-level stack required a dark anomaly in Devel of 17 to obtain the same luminance (visually) as the -auto-level stack.

The frames were not cropped and I did not pursue complete gradient removal, with a small residue in the corners.

The results are identical (I didn't mix up the frames - I was very careful about that) - pixel peeping comparison shows pixel values for the most neutral pixel (I could find) zoomed in. Concluding that normalization is probably not required when imagemagick is used in this way.

Average combination of lights and flats as in 8.204 with a 3 frame stack did not respond to color saturation in the color module - and if it did - the difference was negligible. Strangely, the only stack that color calibrated properly in the proprietary program was the average stack. ST handled all three stacks without missing a beat. Perhaps the difference between linear color calibration and the ST model.

I will let you good folk be the judge, but I am more confident that the calibrated light frames produced by 8.206 onwards - if that ever happens - are very useable.
Attachments
autolevelNOautolevel.jpg
autolevelNOautolevel.jpg (59.99 KiB) Viewed 4396 times
medianflatAUTOLEVELandNoautolevel.jpg
medianflatAUTOLEVELandNoautolevel.jpg (238.53 KiB) Viewed 4396 times
Last edited by Rowland on Sat Jul 04, 2015 1:27 am, edited 1 time in total.
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Re: DSLR RAW 16bit CFA conversion script - master frame crea

Postby Rowland » Sun May 31, 2015 9:56 am

And here is the first big image set with version 8.206 of the rawprepro script. Very basic minimalist approach so as not to mask flaws - as raw as possible to test the quality of preprocessing. It shaped up very well, from what I can see.

I chose this image for a number of reasons, mainly because it displays a variety of features, from dark areas of dust to bright areas around the keyhole. The vast star field demonstrates a variety of star colour, with attractive areas of blue reflection nebula. I didn't go to a lot of trouble dealing with the bright areas.

Very basic - calibration in rawprepro - debayer, align and stack in a proprietary preprocessing program - basic settings - nothing special.

StarTools processing - Develop, Wipe, Develop, HDR Reveal, Color, Sharp - as below - no noise reduction

Code: Select all
StarTools 1.4.302
Sun May 31 17:25:07 2015
-----------------------------------------------------------
File loaded [/home/geoland/Pictures/Eta_Carina/EtaCarina.tiff].
---
--- Bin
Parameter [Scale] set to [(scale/noise reduction 50.00%)/(400.00%)/(+2.00 bits)]
--- Crop
Parameter [X1] set to [61 pixels]
Parameter [Y1] set to [42 pixels]
Parameter [X2] set to [2761 pixels (-56)]
Parameter [Y2] set to [1842 pixels (-34)]
--- Develop
Parameter [White Calibration] set to [Use Stars]
Parameter [Gamma] set to [1.00]
Parameter [Skyglow] set to [0 %]
Parameter [Digital Development] set to [83.00 %]
Parameter [Blue Luminance Contrib.] set to [100 %]
Parameter [Green Luminance Contrib.] set to [100 %]
Parameter [Red Luminance Contrib.] set to [100 %]
Parameter [Dark Anomaly Headroom] set to [5 %]
Parameter [Dark Anomaly Filter] set to [5.0 pixels]
--- Wipe
Parameter [Mode] set to [Correct Color & Brightness]
Parameter [UNKNOWN] set to [Yes]
Parameter [Precision] set to [256 x 256 pixels]
Parameter [Dark Anomaly Filter] set to [2 pixels]
Parameter [Drop Off Point] set to [0 %]
Parameter [Corner Aggressiveness] set to [100 %]
Parameter [Aggressiveness] set to [75 %]
--- Develop
Parameter [White Calibration] set to [Use Stars]
Parameter [Gamma] set to [1.00]
Parameter [Skyglow] set to [0 %]
Parameter [Digital Development] set to [90.00 %]
Parameter [Blue Luminance Contrib.] set to [100 %]
Parameter [Green Luminance Contrib.] set to [100 %]
Parameter [Red Luminance Contrib.] set to [100 %]
Parameter [Dark Anomaly Headroom] set to [5 %]
Parameter [Dark Anomaly Filter] set to [Off]
--- HDRStarTools 1.4.302
Sun May 31 17:25:07 2015
-----------------------------------------------------------
File loaded [/home/geoland/Pictures/Eta_Carina/EtaCarina.tiff].
---
--- Bin
Parameter [Scale] set to [(scale/noise reduction 50.00%)/(400.00%)/(+2.00 bits)]
--- Crop
Parameter [X1] set to [61 pixels]
Parameter [Y1] set to [42 pixels]
Parameter [X2] set to [2761 pixels (-56)]
Parameter [Y2] set to [1842 pixels (-34)]
--- Develop
Parameter [White Calibration] set to [Use Stars]
Parameter [Gamma] set to [1.00]
Parameter [Skyglow] set to [0 %]
Parameter [Digital Development] set to [83.00 %]
Parameter [Blue Luminance Contrib.] set to [100 %]
Parameter [Green Luminance Contrib.] set to [100 %]
Parameter [Red Luminance Contrib.] set to [100 %]
Parameter [Dark Anomaly Headroom] set to [5 %]
Parameter [Dark Anomaly Filter] set to [5.0 pixels]
--- Wipe
Parameter [Mode] set to [Correct Color & Brightness]
Parameter [UNKNOWN] set to [Yes]
Parameter [Precision] set to [256 x 256 pixels]
Parameter [Dark Anomaly Filter] set to [2 pixels]
Parameter [Drop Off Point] set to [0 %]
Parameter [Corner Aggressiveness] set to [100 %]
Parameter [Aggressiveness] set to [75 %]
--- Develop
Parameter [White Calibration] set to [Use Stars]
Parameter [Gamma] set to [1.00]
Parameter [Skyglow] set to [0 %]
Parameter [Digital Development] set to [90.00 %]
Parameter [Blue Luminance Contrib.] set to [100 %]
Parameter [Green Luminance Contrib.] set to [100 %]
Parameter [Red Luminance Contrib.] set to [100 %]
Parameter [Dark Anomaly Headroom] set to [5 %]
Parameter [Dark Anomaly Filter] set to [Off]
--- HDR
Parameter [Small Detail Precision] set to [Max]
Parameter [Channels] set to [Brightness Only]
Parameter [Algorithm] set to [Reveal DSO Core]
Parameter [Dark/Bright Response] set to [Full]
Parameter [Detail Size Range] set to [64 pixels]
Parameter [Strength] set to [1.0]
Undo.
Redo.
Undo.
Redo.
--- Color
Parameter [Cap Green] set to [To Yellow]
Parameter [Bias Slider Mode] set to [Sliders Reduce Color Bias]
Parameter [Style] set to [Scientific (Color Constancy)]
Parameter [LRGB Method Emulation] set to [RGB Ratio, CIELab Luminance Retention]
Parameter [Dark Saturation] set to [3.00]
Parameter [Bright Saturation] set to [Full]
Parameter [Saturation Amount] set to [200 %]
Parameter [Blue Bias Reduce] set to [1.33]
Parameter [Green Bias Reduce] set to [1.00]
Parameter [Red Bias Reduce] set to [1.21]StarTools 1.4.302
Sun May 31 17:25:07 2015
-----------------------------------------------------------
File loaded [/home/geoland/Pictures/Eta_Carina/EtaCarina.tiff].
---
--- Bin
Parameter [Scale] set to [(scale/noise reduction 50.00%)/(400.00%)/(+2.00 bits)]
--- Crop
Parameter [X1] set to [61 pixels]
Parameter [Y1] set to [42 pixels]
Parameter [X2] set to [2761 pixels (-56)]
Parameter [Y2] set to [1842 pixels (-34)]
--- Develop
Parameter [White Calibration] set to [Use Stars]
Parameter [Gamma] set to [1.00]
Parameter [Skyglow] set to [0 %]
Parameter [Digital Development] set to [83.00 %]
Parameter [Blue Luminance Contrib.] set to [100 %]
Parameter [Green Luminance Contrib.] set to [100 %]
Parameter [Red Luminance Contrib.] set to [100 %]
Parameter [Dark Anomaly Headroom] set to [5 %]
Parameter [Dark Anomaly Filter] set to [5.0 pixels]
--- Wipe
Parameter [Mode] set to [Correct Color & Brightness]
Parameter [UNKNOWN] set to [Yes]
Parameter [Precision] set to [256 x 256 pixels]
Parameter [Dark Anomaly Filter] set to [2 pixels]
Parameter [Drop Off Point] set to [0 %]
Parameter [Corner Aggressiveness] set to [100 %]
Parameter [Aggressiveness] set to [75 %]
--- Develop
Parameter [White Calibration] set to [Use Stars]
Parameter [Gamma] set to [1.00]
Parameter [Skyglow] set to [0 %]
Parameter [Digital Development] set to [90.00 %]
Parameter [Blue Luminance Contrib.] set to [100 %]
Parameter [Green Luminance Contrib.] set to [100 %]
Parameter [Red Luminance Contrib.] set to [100 %]
Parameter [Dark Anomaly Headroom] set to [5 %]
Parameter [Dark Anomaly Filter] set to [Off]
--- HDR
Parameter [Small Detail Precision] set to [Max]
Parameter [Channels] set to [Brightness Only]
Parameter [Algorithm] set to [Reveal DSO Core]
Parameter [Dark/Bright Response] set to [Full]
Parameter [Detail Size Range] set to [64 pixels]
Parameter [Strength] set to [1.0]
Undo.
Redo.
Undo.
Redo.
--- Color
Parameter [Cap Green] set to [To Yellow]
Parameter [Bias Slider Mode] set to [Sliders Reduce Color Bias]
Parameter [Style] set to [Scientific (Color Constancy)]
Parameter [LRGB Method Emulation] set to [RGB Ratio, CIELab Luminance Retention]
Parameter [Dark Saturation] set to [3.00]
Parameter [Bright Saturation] set to [Full]
Parameter [Saturation Amount] set to [200 %]
Parameter [Blue Bias Reduce] set to [1.33]
Parameter [Green Bias Reduce] set to [1.00]
Parameter [Red Bias Reduce] set to [1.21]
Parameter [Mask Fuzz] set to [1.0 pixels]
--- Wavelet Sharpen
Parameter [Intelligent Enhance] set to [Yes]
Parameter [Scale 1] set to [100 %]
Parameter [Scale 2] set to [100 %]
Parameter [Scale 3] set to [100 %]
Parameter [Scale 4] set to [100 %]
Parameter [Scale 5] set to [100 %]
Parameter [Mask Fuzz] set to [8.0 pixels]
Parameter [Amount] set to [100 %]
Parameter [Small Detail Bias] set to [75 %]
Undo.
Redo.
File saved [/home/geoland/Pictures/Eta_Carina/EtaCarinaST.tiff].
Parameter [Mask Fuzz] set to [1.0 pixels]
--- Wavelet Sharpen
Parameter [Intelligent Enhance] set to [Yes]
Parameter [Scale 1] set to [100 %]
Parameter [Scale 2] set to [100 %]
Parameter [Scale 3] set to [100 %]
Parameter [Scale 4] set to [100 %]
Parameter [Scale 5] set to [100 %]
Parameter [Mask Fuzz] set to [8.0 pixels]
Parameter [Amount] set to [100 %]
Parameter [Small Detail Bias] set to [75 %]
Undo.
Redo.
File saved [/home/geoland/Pictures/Eta_Carina/EtaCarinaST.tiff].
Parameter [Small Detail Precision] set to [Max]
Parameter [Channels] set to [Brightness Only]
Parameter [Algorithm] set to [Reveal DSO Core]
Parameter [Dark/Bright Response] set to [Full]
Parameter [Detail Size Range] set to [64 pixels]
Parameter [Strength] set to [1.0]
Undo.
Redo.
Undo.
Redo.
--- Color
Parameter [Cap Green] set to [To Yellow]
Parameter [Bias Slider Mode] set to [Sliders Reduce Color Bias]
Parameter [Style] set to [Scientific (Color Constancy)]
Parameter [LRGB Method Emulation] set to [RGB Ratio, CIELab Luminance Retention]
Parameter [Dark Saturation] set to [3.00]
Parameter [Bright Saturation] set to [Full]
Parameter [Saturation Amount] set to [200 %]
Parameter [Blue Bias Reduce] set to [1.33]
Parameter [Green Bias Reduce] set to [1.00]
Parameter [Red Bias Reduce] set to [1.21]
Parameter [Mask Fuzz] set to [1.0 pixels]
--- Wavelet Sharpen
Parameter [Intelligent Enhance] set to [Yes]
Parameter [Scale 1] set to [100 %]
Parameter [Scale 2] set to [100 %]
Parameter [Scale 3] set to [100 %]
Parameter [Scale 4] set to [100 %]
Parameter [Scale 5] set to [100 %]
Parameter [Mask Fuzz] set to [8.0 pixels]
Parameter [Amount] set to [100 %]
Parameter [Small Detail Bias] set to [75 %]
Undo.
Redo.
File saved [/home/geoland/Pictures/Eta_Carina/EtaCarinaST.tiff].
Attachments
EtaCarinaSTIM.jpeg
EtaCarinaSTIM.jpeg (432.11 KiB) Viewed 4386 times
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Re: DSLR RAW 16bit CFA conversion script - master frame crea

Postby Rowland » Sun Jun 07, 2015 6:45 am

Here is a crop from a set of 45 images taken with an unmodded, uncooled DSLR, some 4 years ago. Preprocessing/calibration in rawprepro followed by debayer, alignment and stacking in a proprietary program. Processing in ST using the same parameters as in the previous post.

This image set was the product of more than 12 months work getting unguided image acquisition in order and reliable.

All frames were dithered by > 15 pixels between shots.

ISO800, f5.6, 200mm prime lens, 45 x 210 seconds. Bias, dark and flat calibration frames.

Other than the variety of color in the star field, the luminosity around M8 and M20 is abundant. I know from previous attempts processing this set that the very subtle glow was not as obvious as it is in this screen shot.

I am quite satisfied with the process adopted for DSLR RAW calibration in rawprepro; that is, no pixel rejection during preprocessing of calibration files and light frames (as well as avoiding the data truncation flaw associated with 16bit processing techniques applied to DSLR data) is a very effective valid technique for DSLR RAW data, properly acquired.

Once again, I will let the reader be the judge of that. These frames were taken with a 5DMKII with no more than 10 seconds between frames to allow for the dithering process to complete. The dark frames were taken in the same way. The 5DMKII sensor gets very very hot during long exposures. The first 6 dark and light frames were discarded from the set because they were taken during sensor warm up and were not representative of the average image set.
Attachments
M8-M20nomodDSLR.jpeg
M8-M20nomodDSLR.jpeg (357.76 KiB) Viewed 4310 times
Last edited by Rowland on Sun Aug 09, 2015 12:18 am, edited 2 times in total.
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Re: Image calibration, processing and RAW conversion - Linux

Postby smokey688i » Tue Dec 13, 2016 4:41 pm

Rowland,

Old thread I know...I've just discovered how much better Regim is than DSS, but I came across your FAICS program and am working on setting a Linux virtual machine on my Win10 OS to give it a trial run. I notice you've recommended Regim fairly recently though - have you dropped this project, or do you still prefer the results out of FAICS over Regim?

-Chris
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Re: Image calibration, processing and RAW conversion - Linux

Postby Rowland » Fri Dec 16, 2016 11:35 pm

Hi Chris.

Regim is more mature than FAICS and I prefer Regim over DSS. Regim is an excellent, very flexible preprocessing utility. Regim can be set up for consumer digital camera RAW calibration and stacking, in the same way that FAICS processes RAW data, which is superior in my view to traditional 16bit linear processing, often applied to RAW data.

Signal = (light - dark inclusive of the bias)/(flat - bias) : better handles the non-linearity / firmware manipulation to which RAW data is subject before we get our hands on it.

FAICS is a little unconventional but does a very good job as a rule.

As you are using Windows stick with Regim.

Cheers

Rowland
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