/*!

\if MANPAGES
\page dcmicmp Compare DICOM images and compute difference metrics
\else
\page dcmicmp dcmicmp: Compare DICOM images and compute difference metrics
\endif

\section dcmicmp_synopsis SYNOPSIS

\verbatim
dcmicmp [options] dcmfile-in-1 dcmfile-in-2
\endverbatim

\section dcmicmp_description DESCRIPTION

The \b dcmicmp utility reads two DICOM images, an original "reference
image" and a post-processed "test image", to which some kind of processing
such as a lossy image compression, followed by decompression, has been applied.
This tool requires that both images have the same resolution, the same number
of frames and are either both color or monochrome. Compressed images are
not supported.

The \b dcmicmp utility then compares both images and computes and prints
metrics that describe how similar or different both images are:

  - the maximum absolute error is the largest difference between an
    pixel value in the reference image and the corresponding pixel value in the
    test image.
  - the mean absolute error (MAE) is the average difference between original
    pixel value and test image pixel value
  - the root mean square error (RMSE) is computed by adding the squares of all
    difference values, then dividing by the number of values added, and
    then taking the square root.
  - The peak signal to noise ratio (PSNR) considers the reference image as
    a signal and the differences between reference and test image as noise.
    PSNR is the maximum signal strength (i.e. maximum pixel value in the
    reference image) divided by the RMSE, expressed on a logarithmic scale in
    dB.
  - The signal to noise ratio (PSNR) also considers the reference image as
    a signal and the differences between reference and test image as noise.
    SNR is the average signal strength divided by the RMSE, expressed on
    a logarithmic scale in dB.

All metrics are computed as defined in R.C. Gonzalez and R.E. Woods,
"Digital Image Processing," Prentice Hall 2008.

\section dcmicmp_parameters PARAMETERS

\verbatim
dcmfile-in-1  Reference DICOM image file for comparison

dcmfile-in-2  Test DICOM image file for comparison
\endverbatim

\section dcmicmp_options OPTIONS

\subsection dcmicmp_general_options general options
\verbatim
  -h    --help
          print this help text and exit

        --version
          print version information and exit

        --arguments
          print expanded command line arguments

  -q    --quiet
          quiet mode, print no warnings and errors

  -v    --verbose
          verbose mode, print processing details

  -d    --debug
          debug mode, print debug information

  -ll   --log-level  [l]evel: string constant
          (fatal, error, warn, info, debug, trace)
          use level l for the logger

  -lc   --log-config  [f]ilename: string
          use config file f for the logger
\endverbatim

\subsection dcmicmp_input_options input options
\verbatim
input file format:

  +f    --read-file
          read file format or data set (default)

  +fo   --read-file-only
          read file format only

  -f    --read-dataset
          read data set without file meta information

input transfer syntax:

  -t=   --read-xfer-auto
          use TS recognition (default)

  -td   --read-xfer-detect
          ignore TS specified in the file meta header

  -te   --read-xfer-little
          read with explicit VR little endian TS

  -tb   --read-xfer-big
          read with explicit VR big endian TS

  -ti   --read-xfer-implicit
          read with implicit VR little endian TS
\endverbatim

\subsection dcmicmp_image_processing_options image processing options
\verbatim
modality LUT transformation:

  +M    --use-modality
          use modality LUT transformation (default)

  -M    --no-modality
          ignore stored modality LUT transformation

VOI LUT transformation:

  -W    --no-windowing
          no VOI windowing (default)

  +Wi   --use-window  [n]umber: integer
          use the n-th VOI window from image file

  +Wl   --use-voi-lut  [n]umber: integer
          use the n-th VOI look up table from image file

  +Wm   --min-max-window
          compute VOI window using min-max algorithm
          on both images separately

  +Wn   --min-max-window-n
          compute VOI window using min-max algorithm
          on both images separately, ignoring extremes

  +Wr   --min-max-ref
          compute VOI window using min-max algorithm
          and use same window for the test image

  +Wq   --min-max-n-ref
          compute VOI window using min-max algorithm,
          ignoring extreme values
          and use same window for the test image

  +Ww   --set-window  [c]enter [w]idth: float
          compute VOI window using center c and width w

  +Wfl  --linear-function
          set VOI LUT function to LINEAR

  +Wfs  --sigmoid-function
          set VOI LUT function to SIGMOID

presentation LUT transformation:

  +Pid  --identity-shape
          set presentation LUT shape to IDENTITY

  +Piv  --inverse-shape
          set presentation LUT shape to INVERSE

  +Pod  --lin-od-shape
          set presentation LUT shape to LIN OD
\endverbatim

\subsection dcmicmp_image_comparison_metrics_options image comparison metrics options
\verbatim
  +ce   --check-error  [l]imit: integer
          check if max absolute error <= limit

  # Return exit code EXITCODE_LIMIT_EXCEEDED_MAX_ERROR if the computed
  # maximum absolute error is larger than the given limit.

  +cm   --check-mae  [l]imit: float
          check if mean absolute error <= limit

  # Return exit code EXITCODE_LIMIT_EXCEEDED_MAE if the computed
  # mean absolute error is larger than the given limit.

  +cr   --check-rmse  [l]imit: float
          check if root mean square error <= limit

  # Return exit code EXITCODE_LIMIT_EXCEEDED_RMSE if the computed
  # root mean square error is larger than the given limit.

  +cp   --check-psnr  [l]imit: float
          check if PSNR >= limit

  # Return exit code EXITCODE_LIMIT_EXCEEDED_PSNR if the computed
  # peak signal to noise ratio is smaller than the given limit
  # (for PSNR, higher values mean better image quality)

  +cs   --check-snr  [l]imit: float
          check if SNR >= limit

  # Return exit code EXITCODE_LIMIT_EXCEEDED_PSNR if the computed
  # signal to noise ratio is smaller than the given limit
  # (for SNR, higher values mean better image quality)
\endverbatim

\subsection dcmicmp_output_options output options
\verbatim
  +sd   --save-diff  [f]ilename: string
          write secondary capture difference image

  # Create a Multiframe Secondary Capture image that contains a
  # difference image between reference and test image. For monochrome
  # images, one difference frame is created for each frame in the reference
  # image. For color images, three monochrome frames are created for each
  # frame in the reference image, corresponding to the differences in the
  # red, green and blue color plane. The difference image will have
  # BitsStored 8 or 16, depending on the properties of the reference image.

  +a    --amplify  [f]actor: float
          multiply diff image pixel values by f

  # This option can be used to amplify the grayscale values in the
  # difference image by multiplying each value with the given factor.
  # Alternatively, a DICOM VOI LUT window may be used when visualizing
  # the difference image.
\endverbatim

\section dcmicmp_notes NOTES

\subsection dcmicmp_notes_display_pipeline grayscale display pipeline

Monochrome DICOM images require that a multi-stage display pipeline is
executed in order to convert the raw pixel values to the so-called
presentation values (p-values) that are sent to the (possibly calibrated)
display. When comparing the similarity of images before and after
post-processing, it can be relevant to activate some stages of this
display pipeline before calculating the difference image and metrics.
The image processing options allow the caller to either activate or
deactivate the Modality LUT, VOI LUT and Presentation LUT transformations.
In any case, the same transformation is applied to both images, although
possibly with different parameters if for example the "first VOI LUT window"
stored in each image is applied. This assumes that the post-processing
algorithm (e.g. compression algorithm) has adapted the values of such windows
during compression such that the image display after applying the window
is as close as possible to the reference. For images with more than
8 bits/sample it may be important to known which VOI LUT transformation
will be applied by the user when viewing the image, because this may
affect the perceived image quality. Therefore, absolute Window parameters
can also be given with the --set-window option, which will then be
applied to both images.

\subsection dcmicmp_notes_diagnostics suitability of images for diagnostic purposes

The user should also note that the metrics computed by this tool
cannot predict or estimate the suitability of lossy compressed
image for diagnostic purposes. Much more complex image processing
and an understanding of the image content (e.g. body part) would be
needed for this purpose. The metrics computed provide an estimation
of the level of distortion caused by the post-processing - no more and
no less.

\section dcmicmp_transfer_syntaxes TRANSFER SYNTAXES

\b dcmicmp supports the following transfer syntaxes for input:

\verbatim
LittleEndianImplicitTransferSyntax             1.2.840.10008.1.2
LittleEndianExplicitTransferSyntax             1.2.840.10008.1.2.1
DeflatedExplicitVRLittleEndianTransferSyntax   1.2.840.10008.1.2.1.99 (*)
BigEndianExplicitTransferSyntax                1.2.840.10008.1.2.2
\endverbatim

The difference image file is always written in Little Endian Implicit Transfer Syntax.

(*) if compiled with zlib support enabled

\section dcmicmp_logging LOGGING

The level of logging output of the various command line tools and underlying
libraries can be specified by the user.  By default, only errors and warnings
are written to the standard error stream.  Using option \e --verbose also
informational messages like processing details are reported.  Option
\e --debug can be used to get more details on the internal activity, e.g. for
debugging purposes.  Other logging levels can be selected using option
\e --log-level.  In \e --quiet mode only fatal errors are reported.  In such
very severe error events, the application will usually terminate.  For more
details on the different logging levels, see documentation of module "oflog".

In case the logging output should be written to file (optionally with logfile
rotation), to syslog (Unix) or the event log (Windows) option \e --log-config
can be used.  This configuration file also allows for directing only certain
messages to a particular output stream and for filtering certain messages
based on the module or application where they are generated.  An example
configuration file is provided in <em>\<etcdir\>/logger.cfg</em>.

\section dcmicmp_command_line COMMAND LINE

All command line tools use the following notation for parameters: square
brackets enclose optional values (0-1), three trailing dots indicate that
multiple values are allowed (1-n), a combination of both means 0 to n values.

Command line options are distinguished from parameters by a leading '+' or '-'
sign, respectively.  Usually, order and position of command line options are
arbitrary (i.e. they can appear anywhere).  However, if options are mutually
exclusive the rightmost appearance is used.  This behavior conforms to the
standard evaluation rules of common Unix shells.

In addition, one or more command files can be specified using an '@' sign as a
prefix to the filename (e.g. <em>\@command.txt</em>).  Such a command argument
is replaced by the content of the corresponding text file (multiple
whitespaces are treated as a single separator unless they appear between two
quotation marks) prior to any further evaluation.  Please note that a command
file cannot contain another command file.

\section dcmicmp_exit_codes EXIT CODES

The \b dcmicmp utility uses the following exit codes when terminating.  This
enables the user to check for the reason why the application terminated.

\subsection dcmicmp_exit_codes_general general
\verbatim
EXITCODE_NO_ERROR                         0
EXITCODE_COMMANDLINE_SYNTAX_ERROR         1
\endverbatim

\subsection dcmicmp_exit_codes_input_file_errors input/output file errors
\verbatim
EXITCODE_INVALID_INPUT_FILE              22
EXITCODE_CANNOT_WRITE_OUTPUT_FILE        40
\endverbatim

\subsection dcmicmp_exit_codes_image_processing image processing errors
\verbatim
EXITCODE_INITIALIZE_DIFF_IMAGE           80
EXITCODE_DISPLAY_PIPELINE                81
EXITCODE_IMAGE_COMPARISON                82
\endverbatim

\subsection dcmicmp_exit_codes_limit_exceeded error codes for exceeded limits
\verbatim
EXITCODE_LIMIT_EXCEEDED_MAX_ERROR        90
EXITCODE_LIMIT_EXCEEDED_MAE              91
EXITCODE_LIMIT_EXCEEDED_RMSE             92
EXITCODE_LIMIT_EXCEEDED_PSNR             93
EXITCODE_LIMIT_EXCEEDED_SNR              94
\endverbatim

\section dcmicmp_environment ENVIRONMENT

The \b dcmicmp utility will attempt to load DICOM data dictionaries specified
in the \e DCMDICTPATH environment variable.  By default, i.e. if the
\e DCMDICTPATH environment variable is not set, the file
<em>\<datadir\>/dicom.dic</em> will be loaded unless the dictionary is built
into the application (default for Windows).

The default behavior should be preferred and the \e DCMDICTPATH environment
variable only used when alternative data dictionaries are required.  The
\e DCMDICTPATH environment variable has the same format as the Unix shell
\e PATH variable in that a colon (":") separates entries.  On Windows systems,
a semicolon (";") is used as a separator.  The data dictionary code will
attempt to load each file specified in the \e DCMDICTPATH environment variable.
It is an error if no data dictionary can be loaded.

\section dcmicmp_see_also SEE ALSO

<b>dcm2pnm</b>(1)

\section dcmicmp_copyright COPYRIGHT

Copyright (C) 2018 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.

*/
