-clut option 16-bit tiff to PNG

[mattaguirre]

Hello,
I am looking for a solution to convert a 16-bit grayscale TIFF image to a color PNG using a specific look-up table that I provide. The table varies per set of images and would need to be created automatically.

TIFF Image - 16-bit grayscale
- only bits 1-10 are used (0-1023 intensity range)

Table - generated automatically from database
TIFF Intensity RGB values (0-255 for R,G,B)
0 0,128,128
...
1023 255,0,0

Output Image - color PNG

I have looked into using the -clut option and a gradient images created using PBM format, but this is still not working for me (see link for where I discovered this idea). Some info on the PBM part:

redlist="0 ...1024 pixel values each ranging 0-255... 0"

echo "P2 1024 1 255 $redlist" | convert - redlut.gif

greenlist="0 ...1024 pixel values each ranging 0-255... 0"

echo "P2 1024 1 255 $greenlist" | convert - greenlut.gif

bluelist="0 ...1024 pixel values each ranging 0-255... 0"

echo "P2 1024 1 255 $bluelist" | convert - bluelut.gif

convert redlut.gif greenlut.gif bluelut.gif -combine clut.png
convert image.tif image.png
convert image.png clut.png -clut resultimage.png

Reference I used for attempting this solution:
viewtopic.php?f=1&t=18530

Let me know if it is helpful to provide more information.

[fmw42]

it would help to know why it is not working or an example of your input, lutimage and output. In principle, your use of clut should work. You might try adding -colorspace rgb before -combine.

Also what version of IM and what platform you are using?

I have not given this much thought, but at first glance the problem I see is that you have a 10-bit tiff image that does not span full 16-bit dynamic range. You may need to add -auto-level to your command to stretch the resulting png image to full dynamic range.

Again it would help to know more about what is wrong with your result or show us an example.

[mattaguirre]

Sure. When I open the clut image I see color exactly as I would expect, but in the resulting image I only see red to various degrees. The comment about the 10-bit range makes sense and in fact with my example it may not even use that range. Some background - this source image is created by instrument acquisition software to outline certain components analyzed from another image. Bits 1-10 are switched on and off to indicate a segmented portion of a separate image with the same dimensions (if all 10 switched on it is 1023).

I can provide examples, let me see the best way to post the tif (zipped it is <30kb), the actual script is below.

#!/bin/bash

redlist="0 255 255 255 64 64 64 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"

echo "P2 1024 1 255 $redlist" | convert - redlut.gif

greenlist="0 0 128 128 255 255 255 255 0 0 0 0 0 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 64 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"

echo "P2 1024 1 255 $greenlist" | convert - greenlut.gif

bluelist="0 0 255 255 0 0 0 0 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 255 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 128 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"

echo "P2 1024 1 255 $bluelist" | convert - bluelut.gif

convert redlut.gif greenlut.gif bluelut.gif -combine clut.png
convert image.tif image.png
convert image.png clut.png -clut resultimage.png

[mattaguirre]

Hopefully this DB link works for you. It has just the image.tif file example.

<link removed>

[fmw42]

Your tif image (and thus the png image) only has a few values all of which are in range 0-33 out 65535. So you are only seeing very low values to colorize.

identify -verbose image.tif

image.tif
Image: image.tif
Format: TIFF (Tagged Image File Format)
Class: DirectClass
Geometry: 512x512+0+0
Resolution: 72x72
Print size: 7.11111x7.11111
Units: PixelsPerInch
Type: Grayscale
Base type: Grayscale
Endianess: MSB
Colorspace: RGB
Depth: 16-bit
Channel depth:
gray: 16-bit
Channel statistics:
Gray:
min: 0 (0)
max: 33 (0.000503548)
mean: 3.69467 (5.63771e-05)
standard deviation: 10.1525 (0.000154917)
kurtosis: 3.89441
skewness: 2.42594
Colors: 7
Histogram:
222322: ( 0, 0, 0) #000000000000 black
8707: ( 1, 1, 1) #000100010001 rgb(0.0015259%,0.0015259%,0.0015259%)
932: ( 2, 2, 2) #000200020002 rgb(0.0030518%,0.0030518%,0.0030518%)
30: ( 8, 8, 8 ) #000800080008 rgb(0.0122072%,0.0122072%,0.0122072%)
314: ( 9, 9, 9) #000900090009 rgb(0.0137331%,0.0137331%,0.0137331%)
29788: ( 32, 32, 32) #002000200020 rgb(0.0488289%,0.0488289%,0.0488289%)
51: ( 33, 33, 33) #002100210021 rgb(0.0503548%,0.0503548%,0.0503548%)


Your colormap does have colors beyond that range and should show different colors. But I am concerned that your colormap has only 1000 values and not 65535. I think this fixes it. try the following


convert clut.png -background black -extent 65535x1 clut2.png
convert image.png clut2.png -clut resultimage2.png

[mattaguirre]

That's it! Wow, incredibly powerful. (I thought I would have to handle this pixel by pixel somehow).

Thank you so much for your help.