ImageMagick "invalid colormap index" on greyscale image - c++

Question

I'm attempting to use ImageMagick 6.9.3-1 to convert a medical X-ray format into a more common one, be it a png, bmp or whatever. I have zero documentation on this file format. I have zero access to the software that loads the image. I'm hoping this wonderful community can help me out here.
So far I have determined it is a grey scale jfif with 12 bits per pixel.
I have compiled ImageMagick to enable decompression of 12 bit jfifs, which is where the problem may lie, but more on that later.
ImageMagick identify outputs no errors
C:\libjpeg\ImageMagick-6.9.3-1\VisualMagick\bin>identify.exe C:\Users\alexander\
Desktop\708_885_5856.xdr
C:\Users\alexander\Desktop\708_885_5856.xdr JPEG 1896x1368 1896x1368+0+0 12-bit
Gray 4096c 659KB 0.000u 0:00.000
However, ImageMagick identify -verbose reports the error "invalid colormap index"
C:\libjpeg\ImageMagick-6.9.3-1\VisualMagick\bin>identify.exe -verbose C:\Users\a
lexander\Desktop\708_885_5856.xdr
Image: C:\Users\alexander\Desktop\708_885_5856.xdr
Format: JPEG (Joint Photographic Experts Group JFIF format)
Mime type: image/jpeg
Class: PseudoClass
Geometry: 1896x1368+0+0
Units: Undefined
Type: Grayscale
Endianess: Undefined
Colorspace: Gray
Depth: 12/16-bit
Channel depth:
gray: 16-bit
Channel statistics:
Pixels: 2593728
Gray:
min: 0 (0)
max: 319.989 (0.0781415)
mean: 0.0593298 (1.44883e-05)
standard deviation: 2.68324 (0.000655247)
kurtosis: 3867.56
skewness: 57.5931
entropy: 0.00257194
Colormap entries: 4096
Colormap:
Rendering intent: Undefined
Gamma: 0.454545
Background color: gray(255)
Border color: gray(223)
Matte color: gray(189)
Transparent color: gray(0)
Interlace: None
Intensity: Undefined
Compose: Over
Page geometry: 1896x1368+0+0
Dispose: Undefined
Iterations: 0
Compression: JPEG
Quality: 84
Orientation: Undefined
Properties:
comment: ♦
date:create: 2016-01-12T12:53:56-05:00
date:modify: 2016-01-19T16:41:03-05:00
jpeg:colorspace: 1
jpeg:sampling-factor: 1x1
signature: f913f28ee8f54a718a3224d8b097f5cf3086509c6e4229974f4ce8570fd97f6e
Artifacts:
filename: C:\Users\alexander\Desktop\708_885_5856.xdr
verbose: true
Tainted: False
Filesize: 659KB
Number pixels: 2.594M
Pixels per second: 41.2KB
User time: 62.672u
Elapsed time: 1:04.010
Version: ImageMagick 6.9.3-1 Q16 x64 2016-01-19 http://www.imagemagick.org
identify.exe: Invalid colormap index `C:\Users\alexander\Desktop\708_885_5856.xd
r' # error/colormap-private.h/ConstrainColormapIndex/34.
This seems strange to me because identify was able to calculate the statistics for the gray channel, and "Colormap entries" registers as 4096.
When I attempt to use ImageMagick to convert one of these images, I end up with a appropriately sized grey scale image that is 100% black pixels, and I get the "invalid colormap index" message.
C:\libjpeg\ImageMagick-6.9.3-1\VisualMagick\bin>convert.exe -verbose C:\Users\al
exander\Desktop\708_885_5856.xdr C:\Users\alexander\Desktop\output.png
C:\Users\alexander\Desktop\708_885_5856.xdr JPEG 1896x1368 1896x1368+0+0 12-bit
Gray 4096c 659KB 61.844u 1:02.400
C:\Users\alexander\Desktop\708_885_5856.xdr=>C:\Users\alexander\Desktop\output.p
ng JPEG 1896x1368 1896x1368+0+0 16-bit Gray 22c 9.73KB 0.391u 0:00.187
convert.exe: Invalid colormap index `C:\Users\alexander\Desktop\708_885_5856.xdr
' # error/colormap-private.h/ConstrainColormapIndex/34.
The block of code referenced in the "invalid colormap index" error is
static inline IndexPacket ConstrainColormapIndex(Image *image,
const size_t index)
{
if ((index < image->colors) && ((ssize_t) index >= 0))
return((IndexPacket) index);
(void) ThrowMagickException(&image->exception,GetMagickModule(),
CorruptImageError,"InvalidColormapIndex","`%s'",image->filename);
return((IndexPacket) 0);
}
Which seems to make sense, index is coming in > 4095 or < 0.
I'm not very familiar with Visual Studio or c++, so please bear with me.
When I was setting libjpeg to read 12 bit images, I came across a line of code in jdct.h that caught my attention. The middle word "UINT32" on the middle line was underlined in red.
typedef INT32 DCTELEM; /* must have 32 bits */
typedef UINT32 UDCTELEM;
typedef unsigned long long UDCTELEM2;
Visual Studio does not recognize UINT32 as a valid data type.
In the process of getting the project loaded into Visual Studio, I had to "convert" the project from Visual Studio 2010 to Visual Studio 2015. I fear that something got messed up when I "Converted" the project from Visual Studio 2010 to Visual Studio 2015. Or it may be a red herring.
In conclusion, I guess my questions really are:
How can I print the value of index? (like java "System.println.out(index);")
Isn't there something I can include in C & C++ for standard data types like cstd.h or something?
Why do I even need a color map index? If identify can calculate an average for the pixel values, it can obviously read each one, and if it can read each one, why does it fail?
Would obtaining Visual Studio 2010 most likely solve my problem?

Answer 1

The maximum value in your image is only 319 on a 12-bit range, i.e. 319 out of a possible 4095, or just 7% brightness, so your image is dark and will look black.
Try setting the contrast higher like this:
convert "C:\Users\alexander\Desktop\708_885_5856.xdr" -auto-level result.png