LUT Encoding

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LUT Encoding

• Dave Heaney
• A.L.I. Technologies, Inc.

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Image ModuleUS Image ModuleModality LUT
ModuleVOI LUTPresentation LUT
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Palette Color Table

• As used for 8 and 16 bit Color Images
• A highlight of significant points and commonly
  raised issues

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Requirements For Use

• Image Pixel Module
• Palette Color Lookup Table (For Ultrasound)

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Image Pixel Module
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Image Pixel Module (continued)
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Palette Color Data Encoding

• Depending on IOD, can be done using the Image
  Pixel Module or the Palette Color Lookup Table
  Module.
• This presentation will discuss the Palette Color
  Lookup Table Module as it contains all the same
  Elements and thus both Modules are covered.

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Each Table (Red, Green, Blue) has a Lookup Table
Descriptor with 3 Values
1. Number of Entries in Lookup Table (Note that
if the number of table entries is equal to 216
then this shall be 0. A common error is to not
handle this case). 2. First Stored Pixel Value
Mapped (Specifies which pixel value is mapped to
the first entry in the Lookup Table. Do not
assume for example that value 100 maps to the
100th or 101 entry, you must offset from this
second entry) This value can be signed as it has
the same VR as the Pixel Representation. 3.
Specifies the number of bits for each entry in
the Lookup Table Data (if the Palette Color
Lookup Module is used, as for Ultrasound, then
this must be 16). Note that the Lookup Table
values must map across the full intensity range.
There is no padding of the values so zero
intensity must map to 0 and maximum intensity
must map to 2max bits - 1. A common error is to
try and put 8 bit values into 16 bit table
entries, padding the extra bits with 0. This is
invalid and means that the decoder will not map
across the full pixel intensity range.
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Two Types of Tables

• Contiguous Data Tables (only type in Image Pixel
  Module)
• Segmented Data Tables as in the Palette Color
  Lookup Table Module

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Contiguous Data Tables

• Each Image pixel value (7FE0,0010) maps to a
  value in each of the Red, Green, and Blue Palette
  Tables using the second descriptor entry value
  for the offset.
• The Palette Color Table Entries are intensity
  values as explained earlier. There is no padding
  so, to use the full possible range of
  intensities, values must be scaled across the
  full range of possible values. Must values use
  the data representation indicated by the Pixel
  Representation? Supplement 33 proposes that all
  LUT output must be unsigned. This requires a
  formal change to Part 3 for clarification. (i.e.
  for 2s complement Pixel Representation and an 8
  bit LUT is the minimum output value -128 or 0?).

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Contiguous Palette Table Example 1
(0028,0002) Samples per Pixel 1 (0028,0004)
Photometric Interpretation PALETTE
COLOR (0028,0100) Bits Allocated 16 (0028,0101)
Bits Stored 16 (0028,0103) Pixel
Representation 0000H unsigned (0028,1101) Red
Palette Color Descriptor 256 entries 0
first value mapped 16 bits per
entry (0028,1102) Green Palette Color
Descriptor same as red (0028,1103) Blue Palette
Color Descriptor same as red (7FE0,0010) Pixel
Data (0028,1201) Red Palette (0028,1202)
Green Palette (0028,1203) Blue Palette
0000H0000H0001H0000H0005H0002H
0000H0101H0202H0303H0404H0505H
0000H0101H0202H0303H0404H0505H
0000H0101H0202H0303H0404H0505H
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Contiguous Palette Table Example 2
Non-Ultrasound Palette Color Image Complex
Example (0028,0002) Samples per
Pixel 1 (0028,0004) Photometric
Interpretation PALETTE COLOR (0028,0100) Bits
Allocated 16 (0028,0101) Bits
Stored 16 (0028,0103) Pixel Representation 00
01H signed (0028,1101) Red Palette Color
Descriptor 256 entries -100 first value
mapped 8 bits per entry (0028,1102) Green
Palette Color Descriptor same as red (0028,1103)
Blue Palette Color Descriptor same as
red (7FE0,0010) Pixel Data (0028,1201) Red
Palette (0028,1202) Green Palette (0028,1203)
Blue Palette BUT ARE OUTPUT VALUES UNSIGNED OR
2S COMPLEMENT?
-103 -100 -100 -99 -98 -96 -97 -96
FFFFH FFFAH FFF5H FFF0H FFEBH
FFFFH FFFFH FFFFH FFFFH FFFFH
FFFFH FFFFH FFFFH FFFFH FFFFH
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Segmented Palette Color Tables

• Data is stored in each Table as a series of
  segments
• When the segments are expanded into the actual
  lookup table data, it shall have the number of
  table entries specified by the first value of the
  respective Descriptor, Number of Table Entries
• Shall be used only when segmented lookup table
  data use is desirable and there is a single
  sample per pixel in the image

When To Use? Segmented Palette Color Tables are
useful if the Palette Color Data includes
repeated blocks of values and/or blocks of values
which are related linearly. By repeatedly
referencing a single block of values rather than
repeating the entire block and/or representing
linearly related values by their mathematical
relationship significant resource savings can be
made. Segmented Palette Color Tables are a means
of implementing non-lossy compression for Palette
Color Data but is only possible with very
specific data sets. Note that they may not be
widely supported by viewing systems.
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Segmented Palette Color Tables
Compresses Palette Color Lookup Table
Data Currently there are 3 types of segments
discrete, linear, and indirect. The segments type
is identified by opcodes. Segment
Types Opcode Segment Type 0
Discrete 1
Linear 2 Indirect 3 Above
Reserved
Segment 0 Segment 1 Segment 2 Segment 3
Segment N
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Discrete Segment Type
Used to represent a series of palette components
which are not monotonic with respect to their
predecessors or successors. i.e. Use this type
of segment for data which is non-linear with
respect to preceding or following values. These
values cannot be compressed but can be repeated
so if there are repeating non-linear blocks then
make them into separate Discrete
Segments. Discrete Segment Type Data Format
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Linear Segment Type
The linear segment represents a series of palette
components whose values may be represented by a
straight line. X palette address, Y Value
contained in the palette. (X0, Y0) end of the
previous segment (X0 SegmentLength, Y1) end
of this linear segment Where Y1 is contained in
the data portion of this segment. During
expansion the application should connect the
previous segments endpoint (X0, Y0) with this
segments endpoint, (X0 SegmentLength, Y1)
using a straight line, by computing the values
for each point between the endpoints. Note Becau
se the linear segment uses the end point from the
previous segment, a linear segment can not
be the first segment. Linear Segment Type Data
Format
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Indirect Segment Type
The indirect segment allows the re-use of
repetitive regions within the lookup table
without respecifying the segment. The opcode is
followed by the number of segments to copy and
one offset pointer to the first segment to copy.
The byte offset is relative to the beginning of
the lookup table. For example, if an indirect
segment wants to point to the first segment, then
the offset will be zero. The offset is a 32 bit
value but is stored in the segment as a least
significant 16 bit value followed by a most
significant 16 bit value. An indirect segment
shall not point to or copy another indirect
segment, to avoid recursion and infinite
loops. Indirect Segment Type Data Format
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Modality LUT

• The Modality LUT allows the manipulation of the
  image data in two different manners. In both
  cases it is implied that the manipulation can
  only occur for grayscale data.
• 1. The data can be manipulated by the application
  of a single LUT. The LUT is similar to one used
  for Palette Color Data. The LUT has a descriptor
  (0028,3002) with the same elements as for a color
  LUT
• Number of Entries in Lookup Table.
• First Stored Pixel Value Mapped (Note Has same
  VR as Pixel Representation).
• Specifies the number of bits for each entry in
  the Lookup Table Data (8 or 16).
• The LUT data itself (0028,3006) has output
  values defined by the Modality LUT Type
  (0028,3004). Currently the only defined type is
  OD, the number in the LUT represents thousands of
  optical density.

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Modality LUT (Cont.)

• Optical density is always positive so a question
  arises as to whether this defined type indicates
  that the LUT values are unsigned regardless of
  the Pixel Representation?
• The issue of output type is an important one
  when one or more LUTs are applied to the original
  image data. It would be optimal if each LUT
  descriptor indicated the representation of the
  expected output values. Currently the Standard is
  ambiguous in regards to this issue. A proposal is
  to treat all output values as unsigned. Another
  possibility is to always conform to the Pixel
  Representation unless the conversion is clear
  based on the output Type (i.e. Hounsfeld Units
  are signed, Optical Density is unsigned).
• For now, I suggest to those encoding the data
  that they choose options to encode data
  unambiguously if possible. For example, 16 bit
  values may have to be used instead of just 8 bits
  because of this interpretation issue (the encoder
  wants output values which use the full 8 bit
  unsigned output range, 0 to 255, but Pixel
  Representation is 2s complement. Thus 16 bits
  are allocated to unambiguously define the
  unsigned values 0 to 255.).

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Modality LUT (Cont.)
A second type of data manipulation can be
specified in the Modality LUT Module 2. The data
can be manipulated by applying a linear LUT
represented by two values, Slope and Intercept.
Output Units Slope Image Value
Intercept These values can be signed or unsigned
regardless of the specified Pixel Representation.
Because the Rescale Types are not defined or
enumerated care must be taken to ensure proper
interpretation of the modified values and one
must ensure that underflow or overflow does not
occur due to a change in data representation. For
CT image data Slope and Intercept are used to
convert to Hounsfeld Units which are signed
values.
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VOI LUT
Another LUT module is the VOI LUT Module. This
Module also allows the specification of how the
data should be manipulated in 2 different
manners. This manipulation must always occur
after the application of the Modality LUT if one
exists. 1. The data can be manipulated using a
single LUT similar to the Modality LUT. This type
of LUT contains a description element as
specified for the other types of LUT. In
addition, there is a LUT explanation but there
are no defined or enumerated values. Again, the
issue of output value type is raised. As the
purpose of this LUT is to usually map a certain
range of data to the viewable intensities I
currently treat all output values as unsigned.
This may cause compatibility issues however.
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VOI LUT
2. The data can be manipulated by applying a
linear LUT represented by two values, Window
Center and Window Width. Window Center
(0028,1050) and Window Width (0028,1051) specify
a linear conversion of data values by specifying
a visible Window of values which are to be
mapped to the range of intensities. All those
values less than the minimum value in the Window
are to be mapped to minimum intensity while all
those greater than the maximum value in the
Window are to be mapped to maximum intensity. The
values in between are mapped linearly to the full
available range of intensities. Window Center
contains the pixel value that is the center of
the Window and Window Width contains the width of
the window. If multiple pairs are specified then
they should be applied independently.
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Presentation LUT

• The objective of the Presentation LUT is to
  realize tailored image display. It is used to
  prepare image pixel data for devices that conform
  to the Grayscale Standard Display Function
  defined in PS 3.14. The output of the
  Presentation LUT is Presentation Values
  (P-Values) which are approximately related to
  human perceptual responses. They are intended to
  facilitate common input for hardcopy and softcopy
  devices. This is the final LUT to be applied to
  the pixel data. The modality LUT being applied
  first if present, followed by the VOI LUT and
  finally the Presentation LUT.
• The data can be manipulated using a single LUT
  similar to the Modality LUT or a single Palette
  Color LUT. This type of LUT contains a
  description element containing the 3 values as
  specified for the other types of LUT. The values
  encoded in the LUT are always P-Values and thus
  the output data representation is always
  unsigned, regardless of Pixel Representation.
• A further element of this Module is the
  Presentation LUT Shape which indicates the type
  of input to the Presentation LUT
• IDENTITY input is in P-Values, no further
  translation is required.
• LIN OD input is in linear optical density over
  the range of Min Density (2010, 0120) and Max
  Density (2010,1030) - as from Modality LUT.