Problem reading 16bit grayscale image

Hello

I have a strange problem when trying to read in a grayscale image of 16bit. So despite the fact that these images are well displayed in some other software I use, when I am trying to load them in Matlab as tiff files a very strange thing occurs.

So the images are read in as uint16 (which is correct). Some values such as the maximum are also detected correctly but the most of the rest values are imported as zeros, which is absolute wrong !

I trying to read them both with imread() and geotiffread() --- as these files are georeferenced images

Do you know what may be the reason for such a problem ?

Thanks in advance

[Dimitris M]

No one had similar problem before ?

Answer 1

[Sean de Wolski]

Perhaps they should be int16's and the values below zero are saturating to zero since they can't be represented as a uint16?

If you could attach an image, that would help.

More per size clarification

It sounds like the file might actually be a BigTIFF file. You could try using the MATLAB interface to LibTIFF to see if it can be read directly from there:

doc tiff

You can also read in just certain tiles at a time.

This blog may interest you as well:

http://blogs.mathworks.com/steve/2013/08/07/tiff-bigtiff-and-blockproc/

[Dimitris M]

Thank you for your answer but this is not the case ! The data are unsigned 16bit data and I can see this in the metadata file.

The image data are huge (more than 4giga per image) so I can not send them here. However I clipped a very small tile from the image to send it here and when I tried to read it I see that it works normally !!!

So I want to know if there is a limit on data size in the imread() function as this seems to be the problem ! If this is the case do you have any idea how I can overcome it ?

Thank you

[Sean de Wolski]

See More

[Dimitris M]

Thanks for the tip - I will look into it

Nevertheless this are the metadata I was able to retrieve with imfinfo()

If you see anyhing 'strange' with it let me know ( this is the small tile file)

                  FileSize: 9579

                         Format: 'tif'

                  FormatVersion: []

                          Width: 57

                         Height: 53

                       BitDepth: 16

                      ColorType: 'grayscale'

                FormatSignature: [73 73 42 0]

                      ByteOrder: 'little-endian'

                 NewSubFileType: 0

                  BitsPerSample: 16

                    Compression: 'Uncompressed'

      PhotometricInterpretation: 'BlackIsZero'

                   StripOffsets: []

                SamplesPerPixel: 1

                   RowsPerStrip: 4.2950e+09

                StripByteCounts: []

                    XResolution: 1

                    YResolution: 1

                 ResolutionUnit: 'None'

                       Colormap: []

            PlanarConfiguration: 'Chunky'

                      TileWidth: 64

                     TileLength: 64

                    TileOffsets: 8

                 TileByteCounts: 8192

                    Orientation: 1

                      FillOrder: 1

               GrayResponseUnit: 0.0100

                 MaxSampleValue: 65535

                 MinSampleValue: 0

                   Thresholding: 1

                         Offset: 8890

                       Software: [1x163 char]

                   SampleFormat: 'Unsigned integer'

             ModelPixelScaleTag: [1.2500 1.2500 0]

               ModelTiepointTag: [0 0 0 6.9696e+05 4.1508e+06 0]

             GeoKeyDirectoryTag: [1x24 double]

              GeoAsciiParamsTag: [1x130 char]

[Dimitris M]

This is my large file - with which I have a problem !

                FileSize: 3.9159e+09

                       Format: 'tif'

                FormatVersion: []

                        Width: 36800

                       Height: 53200

                     BitDepth: 16

                    ColorType: 'grayscale'

              FormatSignature: [77 77 0 42]

                    ByteOrder: 'big-endian'

               NewSubFileType: 0

                BitsPerSample: 16

                  Compression: 'Uncompressed'

    PhotometricInterpretation: 'BlackIsZero'

                 StripOffsets: [1x53200 double]

              SamplesPerPixel: 1

                 RowsPerStrip: 1

              StripByteCounts: [1x53200 double]

                  XResolution: []

                  YResolution: []

               ResolutionUnit: 'Inch'

                     Colormap: []

          PlanarConfiguration: 'Chunky'

                    TileWidth: []

                   TileLength: []

                  TileOffsets: []

               TileByteCounts: []

                  Orientation: 1

                    FillOrder: 1

             GrayResponseUnit: 0.0100

               MaxSampleValue: 65535

               MinSampleValue: 0

                 Thresholding: 1

                       Offset: 3.9155e+09

       ModelTransformationTag: [1.2500 0 0 662500 0 -1.2500 0 4214000 0 0 0 0 0 0 0 1]

           GeoKeyDirectoryTag: [1x52 double]

           GeoDoubleParamsTag: [0 500000 0.9996 117 0]

            GeoAsciiParamsTag: 'Zone utm50N|'

[Image Analyst]

Please attach the actual image file itself.