img2dcm(1)                        OFFIS DCMTK                       img2dcm(1)

NAME
       img2dcm - Convert standard image formats into DICOM format


SYNOPSIS
       img2dcm [options] imgfile-in... dcmfile-out

DESCRIPTION
       The  img2dcm  tool  serves  as  a conversion tool from a standard image
       format like JPEG (including JPEG-LS) or BMP to DICOM. Different  output
       SOP  Classes  can  be  selected.  The additional information (regarding
       patients, series,  etc.)  stored  in  the  DICOM  output  file  can  be
       extracted  from  other  DICOM files which serve as a 'template' for the
       resulting DICOM object.  img2dcm  can  also  be  configured  to  invent
       missing  DICOM  type  1  and type 2 attributes to work even without any
       template dataset.

PARAMETERS
       imgfile-in   image input filename

       dcmfile-out  DICOM output filename ("-" for stdout)

OPTIONS
   general options
         -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

   input options
       general:

         -i    --input-format  [i]nput file format: string
                 supported formats: JPEG (default), BMP

         -df   --dataset-from  [f]ilename: string
                 use dataset from DICOM file f

         -dx   --dataset-from-xml  [f]ilename: string
                 use dataset from XML file f

         -stf  --study-from  [f]ilename: string
                 read patient/study from DICOM file f

         -sef  --series-from  [f]ilename: string
                 read patient/study/series from DICOM file f

         -ii   --instance-inc
                 increase instance number read from DICOM file

       JPEG format:

         -dp   --disable-progr
                 disable support for progressive JPEG

         -de   --disable-ext
                 disable support for extended sequential JPEG

         -jf   --insist-on-jfif
                 insist on JFIF header existence

         -ka   --keep-appn
                 keep APPn sections (except JFIF)

         -rc   --remove-com
                 remove COM segment

       XML validation:

         +Vd   --validate-document
                 validate XML document against DTD

         +Vn   --check-namespace
                 check XML namespace in document root

   processing options
       attribute checking:

               --do-checks
                 enable attribute validity checking (default)

               --no-checks
                 disable attribute validity checking

         +i2   --insert-type2
                 insert missing type 2 attributes (default)
                 (only with --do-checks)

         -i2   --no-type2-insert
                 do not insert missing type 2 attributes
                 (only with --do-checks)

         +i1   --invent-type1
                 invent missing type 1 attributes (default)
                 (only with --do-checks)

         -i1   --no-type1-invent
                 do not invent missing type 1 attributes
                 (only with --do-checks)

       character set conversion of study/series file:

         -Ct   --transliterate
                 try to approximate characters that cannot be
                 represented through similar looking characters

         -Cd   --discard-illegal
                 discard characters that cannot be represented
                 in destination character set

       other processing options:

         -k    --key  [k]ey: gggg,eeee="str", path or dictionary name="str"
                 add further attribute

   output options
       target SOP class:

         -sc   --sec-capture
                 write Secondary Capture SOP class (default)

         -nsc  --new-sc
                 write new Secondary Capture SOP classes

         -vlp  --vl-photo
                 write Visible Light Photographic SOP class

         -oph  --oph-photo
                 write Ophthalmic Photography SOP classes

       output file format:

         +F    --write-file
                 write file format (default)

         -F    --write-dataset
                 write data set without file meta information

       group length encoding:

         +g=   --group-length-recalc
                 recalculate group lengths if present (default)

         +g    --group-length-create
                 always write with group length elements

         -g    --group-length-remove
                 always write without group length elements

       length encoding in sequences and items:

         +e    --length-explicit
                 write with explicit lengths (default)

         -e    --length-undefined
                 write with undefined lengths

       data set trailing padding (not with --write-dataset):

         -p    --padding-off
                 no padding (implicit if --write-dataset)

         +p    --padding-create  [f]ile-pad [i]tem-pad: integer
                 align file on multiple of f bytes
                 and items on multiple of i bytes

NOTES
   Attribute Sources
       For converting a general image format into DICOM  format,  the  img2dcm
       application may be fed with some additional input for filling mandatory
       (and optional) attributes in the new DICOM file like patient, study and
       series  information.  This information can be collected using different
       approaches, which can be combined and are applied to the result file in
       the following order:

       • Using  the  --dataset-from  option  img2dcm  is  forced   to   import
         attributes from an existing DICOM file. The given DICOM file is fully
         imported  and  serves as the basis for all further export operations.
         As an exception, the SOP Instance UID is not copied by  this  option.
         Also  image  related data like Rows, Columns etc. is exchanged during
         conversion. Note that img2dcm does  not  check  any  other  attribute
         values  for  validity,  e.g. it does not look into sequences to adapt
         any attributes to the new object (referenced images etc.). Therefore,
         it is recommended to use the templates  in  the  data  directory  for
         (old)  SC  and VLP objects. See also section 'Input Templates'. As an
         alternative to option --dataset-from the  mutually  exclusive  option
         --dataset-from-xml  can be used. In this case, however, the file must
         contain XML data in the format as produced by dcm2xml.

       • The --study-from and --series-from options  can  be  used  to  import
         patient, study and series information from an existing DICOM file. If
         --series-from  is  specified,  then the given DICOM file is opened by
         img2dcm and all mandatory information down to  the  series  level  is
         imported.   Note   that  this  includes  patient,  study  and  series
         information. In case  of  --study-from,  the  series  information  is
         excluded.  Using --study-from and --series-from at the same time does
         make sense. If both options are provided on  the  command  line,  the
         rightmost option wins. The following attributes are taken over:

             Patient Level:
               Patient's Name
               Patient ID
               Patient's Sex
               Patient's Birth Date
               Specific Character Set

             Study Level:
               Study Instance UID
               Study Date
               Study Time
               Referring Physician's Name
               Study ID
               Accession Number

             Series Level (only in case of option --series-from):
               Series Instance UID
               Series Number
               Manufacturer

       • With  the --insert-type2 and --invent-type1 options (both enabled per
         default), missing  attributes  (type  2  attributes)  and/or  missing
         attribute  values (for type 1 attributes) are automatically added and
         invented  by  img2dcm.  Please  note  that  these  options  are  only
         evaluated  if  option  --do-checks is enabled (default). If the --no-
         checks options is enabled, no automatic attribute insertion will take
         place.

       • The --key option can be used to add further attributes to  the  DICOM
         output  file.  It  is  also  possible to specify sequences, items and
         nested attributes using the --key option. In these cases,  a  special
         'path'  notation has to be used. Details on this path notation can be
         found in the documentation of  dcmodify.  The  --key  option  can  be
         present  more than once. The value part (after the '=') may be absent
         causing the attribute to be set with zero length. Please  be  advised
         that  the --key option is applied at the very end, just before saving
         the DICOM file, so there is no value checking whatsoever.

   UIDs
       New Study and Series Instance UIDs are  generated  if  necessary  after
       applying  the --study-from and --series-from options. If Study Instance
       UID or Series Instance UID are not present after these steps, they  are
       newly generated, independently from each other.

       A  contrary  behavior is chosen for the SOP Instance UID that one could
       expect to be taken over when using  the  --dataset-from  or  --dataset-
       from-xml  option.  This  is  not  the case, the SOP Instance UID is not
       copied to the new object. This should be  the  desirable  behavior  for
       most  use  cases.  However,  if  a  certain  SOP Instance UID should be
       inserted into the new object, the --key option should be used.

   Input Templates
       For supporting the conversion into DICOM, img2dcm comes with some  pre-
       defined  templates which can be used for the --dataset-from option (see
       sample files SC.dump and VLP.dump). These templates  should  be  filled
       with  the desired values and then must be dumped (converted) to a DICOM
       file before actually being used with img2dcm. Use dump2dcm  to  convert
       the dump to DICOM. Example:

         dump2dcm SC.dump SC.dcm

       For  Ophthalmic  Photography  images,  XML  templates are provided (see
       sample file OP_template_utf_8.xml and OP_template_latin_1.xml).

       It is possible to use any DICOM file as a template.  Please  note  that
       the  complete  DICOM  dataset  is imported; hence, it should be assured
       that  only  attributes  are  present  which  should  be  part  of   the
       constructed  DICOM  object.  The  SOP  Class  UID  and  the  Pixel Data
       attributes (including attributes  like  Rows,  Columns  etc.)  are  not
       copied but replaced by img2dcm during conversion.

   Multiframe Images
       It  is  possible  to  convert  multiple  input  files  into  one  DICOM
       multiframe image if the selected DICOM SOP class  supports  multiframe.
       In  particular,  the  Multi-frame Secondary Capture SOP Classes support
       this feature. They are  selected  through  the  --new-sc  command  line
       option.

   Character Sets
       When  an  input  template  is loaded using --dataset-from or --dataset-
       from-xml, the specific character set of that template is used  for  the
       generated  DICOM file. If the --study-from or --series-from options are
       used additionally, img2dcm will try to convert  the  character  set  of
       these  attributes  to that of the template, and will report an error if
       that is not possible.

       If the  --study-from  or  --series-from  options  are  used  without  a
       template,  the  specific  character  set of this source is used for the
       generated DICOM file. Any keys specified on the command line  with  the
       --key  option are treated as raw bytes and override any attributes that
       may already  be  present  due  to  a  template  or  study/series  file.
       Therefore, care should be taken to not specify a specific character set
       on  the  command  line  if one might be loaded from another file. It is
       also  the  user's  responsibility  to  ensure  that  attribute   values
       specified  on  the  command  line  use  the  correct  encoding,  as  no
       conversion will take place before the values are stored  in  the  DICOM
       file.

   Input Plugins
       The  img2dcm  application  currently supports the JPEG, JPEG-LS and the
       BMP image format as input.

   JPEG Input Plugin
       For JPEG, the original JPEG from the source file  is  not  decoded  but
       extracted  and  slightly  transformed  (e.g. JFIF header is cut off) to
       allow fast conversion of even  big  JPEG  files  without  the  need  of
       decoding  and re-encoding. The JPEG plugin chooses the necessary output
       transfer syntax automatically depending on the actual encoding  of  the
       data  inside  the JPEG file. Therefore, the following Transfer Syntaxes
       (and their corresponding JPEG encodings) are used by the JPEG plugin:

       • JPEG Coding Process 1
          Baseline, Lossy, Non-Hierarchical, Sequential, DCT, Huffman, 8 Bit
          Transfer Syntax UID = 1.2.840.10008.1.2.4.50

       • JPEG Coding Process 2 (8-bit) and 4 (12-bit)
          Extended, Lossy, Non-Hierarchical, Sequential,  DCT,  Huffman,  8/12
         Bit
          Transfer Syntax UID = 1.2.840.10008.1.2.4.51

       • JPEG Coding Process 10 (8-bit) and 12 (12-bit)
          Full  Progression,  lossy, Non-Hierarch., Progressive, DCT, Huffman,
         8/12 Bit
          Transfer Syntax UID = 1.2.840.10008.1.2.4.55

       Color and grayscale images are supported.

       The support for the Extended  JPEG  Transfer  Syntax  can  be  disabled
       (--disable-ext  option)  as  well  as  the  support  for  the (retired)
       Progressive JPEG Transfer Syntax (--disable-progr option).

       JPEG lossless encoding as well as any arithmetic or  hierarchical  JPEG
       encoding modes are not supported by the plugin.

       JFIF  (JPEG  File  Interchange Format) information facilitates optional
       APPn markers in a JPEG file. Many digital cameras do not integrate such
       JFIF information into the JPEG output they create.  For  example,  JFIF
       contains  information  about  the  pixel aspect ratio of the compressed
       image. If you want the img2dcm application to insist on a  JFIF  header
       in  the JPEG stream, you can use the option --insist-on-jfif which will
       abort if no JFIF information can be found.  By  default,  missing  JFIF
       information is ignored.

       For  DICOM it is kind of a 'gray zone', whether the integration of JFIF
       (or any other APPn) data into the DICOM object's internal  JPEG  stream
       is  allowed or not. However, the most reliable approach is to cut those
       markers and their information off the JPEG  stream.  This  approach  is
       also taken by the img2dcm application. By default, all APPn markers are
       cut  off  from  the  original JPEG stream. However, if you want to keep
       other APPn markers than JFIF (e.g. EXIF information) inside  the  DICOM
       stream,  the  option  --keep-appn  does  the  trick.  It should also be
       slightly faster than cutting off APPn information, because  it  is  not
       necessary  to  scan  the  whole  JPEG  stream  for such data. As stated
       before, JFIF information is always removed by  img2dcm.  However,  when
       using  this  option,  the APP2 marker is retained, but img2dcm does not
       create an equivalent ICC Profile (0028,2000) attribute.

   JPEG-LS Input Plugin
       The JPEG-LS plugin has been integrated  directly  into  the  main  JPEG
       plugin. There is no need for the user to explicitly state in advance if
       input is JPEG or JPEG-LS.

       For  JPEGL-LS, the original JPEG-LS from the source file is not decoded
       but extracted and slightly transformed (e. g. APP8 marker is  cut  off)
       to  allow fast conversion of even big JPEG-LS files without the need of
       decoding and re-encoding.

       The  JPEG-LS  plugin  chooses  the  necessary  output  transfer  syntax
       automatically  depending  on the actual encoding of the data inside the
       JPEG-LS file. Therefore, the following  Transfer  Syntaxes  (and  there
       corresponding JPEG-LS encodings) are used by the JPEG-LS plugin:

       • JPEG-LS Lossless Image Compression
          Transfer Syntax UID = 1.2.840.10008.1.2.4.80

       • JPEG-LS Lossy (Near-Lossless) Image Compression
          Transfer Syntax UID = 1.2.840.10008.1.2.4.81

       Color  and  grayscale  images  are  supported. CP-1843 enforce that the
       value of Planar  Configuration  (0028,0006)  is  irrelevant  since  the
       manner of encoding components is specified in the JPEG-LS bit stream as
       component,  line  or  sample  interleaved,  hence it shall be set to 0.
       Since no color transformation specific for JPEG-LS is currently defined
       in DICOM, it is assumed that the JPEG-LS stream is encoded in RGB color
       space.

       For DICOM it is clear that SPIFF header should not be  present  in  the
       DICOM  object's internal JPEG-LS stream. The plugin will simply rejects
       any input JPEG-LS file containing a SPIFF header at marker APP8.

       By default, all APPn markers are cut  off  from  the  original  JPEG-LS
       stream.  However,  if you want to keep APPn markers (e.g. APP8/HP color
       transform information, aka 'mrfx') inside the DICOM stream, the  option
       --keep-appn  does  the  trick. Pay attention that the plugin will check
       the actual color transform specified in the APP8/HP marker. Since DICOM
       does not allow any color transform to be specified in the APP8  marker,
       only a value of 0 (no color transform) is accepted.

   BMP Input Plugin
       img2dcm  supports  BMP  as  input format. However, so far only the most
       common BMP images are supported. In particular, BMP  images  which  use
       bit  fields  or  run  length encoding will be rejected. Such images are
       uncommon. Input images will either be converted into a DICOM image with
       RGB color model  and  a  bit  depth  of  24,  or  into  an  image  with
       MONOCHROME2  color  model  an  8  bits per pixel. There are no specific
       options for fine-tuning BMP format conversion.

   Output Plugins
       The desired output SOP Class can  be  selected  on  the  command  line.
       Currently,  export  plugins  for  the Secondary Capture Image SOP Class
       (default, option -sc), the  Multi-frame  Secondary  Capture  Image  SOP
       Classes  (option  -nsc),  Visible  Light  Photographic  Image SOP Class
       (option -vl), and the Ophthalmic Photography Image SOP Classes  (option
       -oph)  are  available.  Please  note  that  the first one is deprecated
       according to the DICOM standard but is selected as a default because it
       is widely supported. Future versions of img2dcm might  provide  further
       output plugins for other SOP Classes.

       For  the  new  Secondary  Capture  SOP  Classes,  it is not possible to
       specify which specific SOP Class should be used  for  output.  That  is
       because  these  new  SOP  classes are differentiated from each other by
       color depth (1/8/16) and the fact whether the image is  black/white  or
       color.  That is why img2dcm decides during conversion, which output SOP
       Class is suitable for a given source image.

EXAMPLES
       Here are some examples that show how the  img2dcm  application  can  be
       used.

       1.  img2dcm image.jpg out.dcm
            Read  JPEG  file 'image.jpg', convert to the old Secondary Capture
           SOP Class and save the result to DICOM file 'out.dcm'. This is  the
           easiest  way  of  using  img2dcm.  Any type 1 and type 2 attributes
           required for writing valid objects of this SOP Class  are  inserted
           automatically.

       2.  img2dcm -i BMP image.bmp out.dcm
            Same  as  above  but  tells  img2dcm to read a BMP file instead of
           JPEG.

       3.  img2dcm image.jpg out.dcm -vlp -k 'PatientName=BondˆJames'
            Same as first example, but writes Visible Light Photographic Image
           object to 'out.dcm' and  sets  PatientName  to  'BondˆJames'  which
           otherwise would be left empty.

       4.  img2dcm    image.jpg    out.dcm   --series-from   template.dcm   -k
           'PatientName=BondˆJames'
            Same as 1),  but  imports  patient/study/series  information  from
           DICOM  file  'template.dcm'. Please note that attribute PatientName
           will contain 'BondˆJames' at the end, any value from 'template.dcm'
           will be overwritten. That is, because the -k option is  applied  at
           the very end of the conversion pipeline (see above).

       5.  img2dcm image.jpg out.dcm --no-checks
            Same  as  1),  but  does not perform any attribute checking and no
           type 1 and type 2 attribute insertion! So in this case, an  invalid
           DICOM  object  would  be  generated. This can be interesting if the
           output file is not meant to be completed but will  undergo  further
           transformations,  e.g.  adding  attributes using dcmodify. Only use
           option --no-checks if you know what you are doing!

       6.  img2dcm image.jpg out.dcm --no-type1-invent
            Same as 1), but does not insert missing type 1  attributes  and/or
           their values. Type 2 attributes will be inserted. Note that in this
           case  it must be assured that all type 1 attributes are provided by
           other means, i.e. by adding them with the --key option.  Otherwise,
           img2dcm will report an error and will stop converting.

       7.  img2dcm image.jpg out.dcm --keep-appn --insist-on-jfif
            Same  as  1),  but  takes over APPn information like EXIF into the
           DICOM object's resulting  JPEG  stream.  Further,  --insist-on-jfif
           will  force  img2dcm to abort if no JFIF information is existent in
           the source file.

       8.  img2dcm image1.jpg image2.jpg out.dcm --new-sc
            Read the JPEG files 'image1.jpg' and 'image2.jpg',  convert  to  a
           multiframe  image  of the appropriate Multi-frame Secondary Capture
           SOP Class, and save the result to DICOM file 'out.dcm'.

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  --verbose  also  informational messages like processing details
       are reported. Option --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 --log-level. In --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
       --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
       <etcdir>/logger.cfg.

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. @command.txt). 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.
       This simple but effective  approach  allows  one  to  summarize  common
       combinations  of  options/parameters  and  avoids longish and confusing
       command lines (an example is provided in file <datadir>/dumppat.txt).

ENVIRONMENT
       The img2dcm utility  will  attempt  to  load  DICOM  data  dictionaries
       specified  in the DCMDICTPATH environment variable. By default, i.e. if
       the  DCMDICTPATH  environment   variable   is   not   set,   the   file
       <datadir>/dicom.dic  will be loaded unless the dictionary is built into
       the application (default for Windows).

       The  default  behavior  should  be  preferred   and   the   DCMDICTPATH
       environment  variable  only used when alternative data dictionaries are
       required. The DCMDICTPATH environment variable has the same  format  as
       the  Unix  shell 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
       DCMDICTPATH environment variable. It is an error if no data  dictionary
       can be loaded.

FILES
       <datadir>/SC.dump - Sample dump file for Secondary Capture images
       <datadir>/VLP.dump  -  Sample  dump file for Visible Light Photographic
       images
       <datadir>/OP_template.xml  -  Sample  XML   template   for   Ophthalmic
       Photography images

SEE ALSO
       dcm2pnm(1),    dcmj2pnm(1),   dump2dcm(1),   dcmconv(1),   dcmodify(1),
       dcm2xml(1)

COPYRIGHT
       Copyright (C) 2007-2024 by OFFIS e.V., Escherweg  2,  26121  Oldenburg,
       Germany.

Version 3.6.9                   Wed Dec 11 2024                     img2dcm(1)
