Legacy ImageMagick Discussions Archive

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

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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"

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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 99% black pixels, and I get the "invalid colormap index" message. I am aware that the maximum pixel value of 319 is ~7% of the range; I have run the command with -auto-levels and i'm still not seeing any satisfactory results.

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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

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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.

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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, so to compile, I tried defining UDCTELEM as an unsigned long, unsigned short, and an unsigned int, all with the same "invalid colormap index" result. I don't think UDCTELEM's datatype is the issue.

I found a program at http://www.imageconverterplus.com that can read and convert the image. This program confirms that it is indeed a 12bpp(12 bits per sample 1 sample per pixel) jpeg in "Extended sequential" mode, in the grayscale colorspace with DCT & Huffman compression.

Does anyone have any ideas? Please tell me I'm an idiot and all I have to do is add a flag or something!

I didn't know that IM could process 12-bit JPEGs. Perhaps it can't, and that's the fundamental problem

A developer would need to comment.

Well technically ImageMagick doesn't process the jpegs, a library that it uses does. I also compiled that library for 12 bpp jpegs. If you look in my first post, you'll see that it calculates an average pixel value, among other things.

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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

How can it come up with any of those values if ImageMagick can't read the data?

As you say, it clearly is reading the data. But is it reading the data correctly? I don't know. You say the output is 99% black, which is consistent with the low values reported by "identify". Is this the expected output?

A developer would need to comment.

Legacy ImageMagick Discussions Archive

6.9.3-0 hdri 12bpp jpeg "invalid colormap index"

6.9.3-0 hdri 12bpp jpeg "invalid colormap index"

Re: 6.9.3-0 hdri 12bpp jpeg "invalid colormap index"

Re: 6.9.3-0 hdri 12bpp jpeg "invalid colormap index"

Re: 6.9.3-0 hdri 12bpp jpeg "invalid colormap index"