.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
.TH DGATE-DBASE "1" "April 2014" "Netherlands Cancer Institute" "ConQuest DICOM server"
.SH NAME
dgate-dbase \- UCDMC/NKI DICOM server thread and PACS utility application
.SH SYNOPSIS
.br
.B dgate
\-wDIR \-^LOGFILE
.br
Starts dgate with dicom.ini located at DIR and logging to LOGFILE
.PP

.B dgate
\-pPORT \-qIP \-\-COMMAND:ARGS
.br
Sends COMMAND with ARGS directly to dgate instance at IP:PORT
.SH DESCRIPTION
.PP
ConQuest is a full featured and Lua-scriptable DICOM server.
.PP
To check DICOM conformance, please check
.B /usr/share/doc/conquest-dicom-server/DicomConformance_FilesLST_Changes.pdf.gz
.PP
DGATE: UCDMC/NKI DICOM server thread and PACS utility application 1.4.17d
.SH OPTIONS
There are three common patterns to use
.B dgate.
And those patterns have different ways to interpret options, as follows.
Other options are described below.
.PP
Usage:
(1) DGATE <\-!#|\-v|\-u#|\-^#>    Report as in dicom.ini|stdout|UDP|File(#=port)
.TP
[\-p#|\-qIP|\-b]
Set port|Set target IP|run debug 1\-thread mode
.TP
[\-wDIR]
Set the working directory for dgate(ini,dic,...)
.TP
[\-i|\-r|\-arDEVICE]
Init|Init/regenerate DB|Regen single device
.TP
[\-d|\-m|\-k]
List (\fB\-d\fR) devices (\fB\-m\fR) AE map (\fB\-k\fR) DICOM.SQL
.TP
[\-t|\-o]
Test console|Test database
.TP
[\-sOpt|\-esap d u p]
Create ODBC source (WIN32), database with SApw
.TP
[\-nd|\-nc#|\-jd|\-jc#]
NKI de\-/compress#|JPEG de\-/compress# FILE
.TP
[\-j*##|\-j\-##FILE]
Recompress FILE to ##
.TP
[\-as#,N|\-amFROM,TO]
Select#KB to archive of MAGN|move device data
.TP
[\-au|\-aeFROM,TO]
Undo select for archiving|rename device
.TP
[\-av|\-atDEVICE]
Verify mirror disk|Test read files for DEVICE
.TP
[\-abJUKEBOX1.2,N]
Make cacheset to burn JUKEBOX1,CD2 from MAGN
.TP
[\-acJUKEBOX1.2]
Verify JUKEBOX1,CD2 against cacheset
.TP
[\-adJUKEBOX1.2]
Verify and delete cacheset for JUKEBOX1, CD2
.TP
[\-f<p|t|s|i>ID]
Delete DB for Patient, sTudy, Series, Image
.TP
[\-f<e|d|z>file]
Enter/Delete DB of file, Zap server file
.TP
[\-faFILE<,ID>]
Add file to server<optionally change PATID>
.TP
[\-zID]
Delete (zap) patient
.TP
[\-frDEVICE,DIR]
Regen single directory DIR on DEVICE
.TP
[\-f<c|k>PATID,file]
Change/Kopy PATID of file (irreversible/once)
.TP
[\-f?file|\-fu|\-c#]
get UID of file|Make new UID|UID helper(0..99)
.TP
[\-ff#]
Delete old patients until #MB free
.TP
[\-gSERVER,DATE]
grab images from SERVER of date not on here
Otherwise: run as threaded server, port=1111
.PP
(2) DGATE FileMapping         Run server child; shared memory has socket#
.PP
(3) DGATE <\-pPORT> <\-qIP> \fB\-\-command\fR:arguments
.TP
Send command to (this or other) running server
(works directly \- use with care)
.SH OTHER OPTIONS
.SS "Delete options:"
.TP
\fB\-\-deleteimagefile\fR:file
Delete given image file from server
.TP
\fB\-\-deletepatient\fR:patid
Delete given patient from server
.TP
\fB\-\-deletestudy\fR:patid:studyuid
Delete given study from server
.TP
\fB\-\-deletestudies\fR:date(range)
Delete studies from server on date
.TP
\fB\-\-deleteseries\fR:patid:seriesuid
Delete given series from server
.TP
\fB\-\-deleteimagefromdb\fR:file
Delete given file from db only
.TP
\fB\-\-deletesopfromdb\fR:pat,study,series,sop
Delete specified image from db only
.SS "DICOM move options:"
.TP
\fB\-\-movepatient\fR:source,dest,patid
Move patient, source e.g. (local)
.TP
\fB\-\-movestudy\fR:source,dest,patid:studyuid
Move study, patid: optional
.TP
\fB\-\-moveaccession\fR:source,dest,patid:acc
Move by Accession#, patid: optional
.TP
\fB\-\-movestudies\fR:source,dest,date(range)
Move studies on date
.TP
\fB\-\-moveseries\fR:src,dst,patid:seruid,stuid
Move series patid: optional
.SS "Modification of dicom objects:"
.TP
\fB\-\-modifypatid\fR:patid,file
Change patid of given file
.TP
\fB\-\-anonymize\fR:patid,file
Anonymize given file
.TP
\fB\-\-modifystudy\fR:p,s,script
Change items in patient or study
.TP
\fB\-\-modifyseries\fR:p,s,script
Change items in series
.TP
\fB\-\-modifyimage\fR:file,script
Change items in file
.TP
\fB\-\-mergestudy\fR:uid,uid,..
Start merging studies with given studyuids
.TP
\fB\-\-mergestudyfile\fR:file
Use to process all files to merge
.TP
\fB\-\-mergeseries\fR:uid,uid,..
Start merging series with given seriesuids
.TP
\fB\-\-mergeseriesfile\fR:file
Use to process all files to merge
.TP
\fB\-\-attachanytopatient\fR:any,sample
Modify uids to attach any object to
.TP
\fB\-\-attachanytostudy\fR:any,sample
patient|study|series in sample file
.TP
\fB\-\-attachanytoseries\fR:any,sample
Do not attach same at different levels
.TP
\fB\-\-attachrtplantortstruct\fR:plan,struc
Attach rtplan to rtstruct
.SS "Maintenance options:"
.TP
\fB\-\-initializetables\fR:
Clear and create database
.TP
\fB\-\-initializetables\fR:1
Clear and create database without indices
.TP
\fB\-\-initializetables\fR:2
Clear and create worklist database
.TP
\fB\-\-regen\fR:
Re\-generate entire database
.TP
\fB\-\-regendevice\fR:device
Re\-generate database for single device
.TP
\fB\-\-regendir\fR:device,dir
Re\-generate database for single directory
.TP
\fB\-\-regenfile\fR:file
Re\-enter given file in database
.TP
\fB\-\-makespace\fR:#
Delete old patients to make #MB space
.TP
\fB\-\-quit\fR:
Stop the server
.TP
\fB\-\-safequit\fR:
Stop the server when not active
.SS "Logging options:"
.TP
\fB\-\-debuglog_on\fR:file/port
Start debug logging
.TP
\fB\-\-log_on\fR:file/port/pipe
Start normal logging
.TP
\fB\-\-debuglevel\fR:#
Set debug logging level
.TP
\fB\-\-display_status\fR:file
Display server status
.TP
\fB\-\-status_string\fR:file
Display status string of submit operation
.TP
\fB\-\-checklargestmalloc\fR:
Estimates DICOM object size limit
.TP
\fB\-\-get_freestore\fR:dev,fmt
Report free #Mb on device
.TP
\fB\-\-testmode\fR:#
Append # to dicom filenames
.TP
\fB\-\-echo\fR:AE,file
Echo server; show response
.SS "Configuration options:"
.TP
\fB\-\-get_param\fR:name,fmt
Read any parameter from DICOM.INI
.TP
\fB\-\-get_ini_param\fR:name,fmt
Read any parameter from DICOM.INI
.TP
\fB\-\-get_ini_num\fR:index,fmt
List any entry from DICOM.INI
.TP
\fB\-\-get_ini\fR:fmt
List all entries from DICOM.INI
.TP
\fB\-\-put_param\fR:name,value
Write any parameter to DICOM.INI
.TP
\fB\-\-delete_param\fR:name
Delete any parameter from DICOM.INI
.TP
\fB\-\-read_ini\fR:
Re\-read all parameters from DICOM.INI
.TP
\fB\-\-get_amap\fR:index,fmt
List any entry from ACRNEMA.MAP
.TP
\fB\-\-get_amaps\fR:fmt
List all entries from ACRNEMA.MAP
.TP
\fB\-\-put_amap\fR:i,AE,ip,p#,cmp
Write entry in memory for ACRNEMA.MAP
.TP
\fB\-\-delete_amap\fR:index
Delete entry in memory for ACRNEMA.MAP
.TP
\fB\-\-write_amap\fR:
Write ACRNEMA.MAP from memory to disk
.TP
\fB\-\-read_amap\fR:
Re\-read ACRNEMA.MAP from disk to memory
.TP
\fB\-\-get_sop\fR:index,fmt
List any accepted service class UID
.TP
\fB\-\-put_sop\fR:index,UID,name
Write/add accepted service class UID
.TP
\fB\-\-delete_sop\fR:index
Delete accepted service class UID
.TP
\fB\-\-get_transfer\fR:index,fmt
List any accepted transfer syntax
.TP
\fB\-\-put_transfer\fR:in,UID,nam
Write/add accepted transfer syntax
.TP
\fB\-\-delete_transfer\fR:index
Delete accepted transfer syntax
.TP
\fB\-\-get_application\fR:idx,fmt
List any accepted application UID
.TP
\fB\-\-put_application\fR:i,U,n
Write/add accepted application UID
.TP
\fB\-\-delete_application\fR:inde
Delete accepted application UID
.TP
\fB\-\-get_localae\fR:index,fmt
List any accepted local AE title
.TP
\fB\-\-put_localae\fR:in,AE,name
Write/add accepted local AE title
.TP
\fB\-\-delete_localae\fR:index
Delete accepted local AE title
.TP
\fB\-\-get_remoteae\fR:index,fmt
List any accepted remote AE title
.TP
\fB\-\-put_remoteae\fR:in,AE,name
Write/add accepted remote AE title
.TP
\fB\-\-delete_remoteae\fR:index
Delete accepted remote AE title
.TP
\fB\-\-get_dic\fR:index,fmt
List any dicom dictionary item
.TP
\fB\-\-get_sqldef\fR:level,in,fmt
List any database field definition
.SS "Communication options:"
.TP
\fB\-\-addimagefile\fR:file,patid
Copy file into server, optionally new patid
.TP
\fB\-\-addlocalfile\fR:file,patid
Copy local file into server, opt. new patid
.TP
\fB\-\-loadanddeletedir\fR:dir,patid
Load folder and delete its contents
.TP
\fB\-\-loadhl7\fR:file
Load HL7 data into worklist
.TP
\fB\-\-dump_header\fR:filein,fileout
Create header dump of file
.TP
\fB\-\-forward\fR:file,mode,server
Send file with compr. mode to server
.TP
\fB\-\-grabimagesfromserver\fR:AE,date
Update this server from other
.TP
\fB\-\-prefetch\fR:patientid
Prefetch all images for improved speed
.TP
\fB\-\-browsepatient\fR:searchstring
Select patient in windows GUI
.TP
\fB\-\-submit\fR:p,s,s,s,target,pw,scr
Immediate sftp submit of data
.TP
\fB\-\-submit2\fR:p,s,s,s,target,c,scr
Immediate submit with command line c
.TP
\fB\-\-export\fR:p,st,ser,sop,file,scr
Immediate process and zip/7z data
.TP
\fB\-\-scheduletransfer\fR:options
Background sftp transfer as above
.SS "Test options:"
.TP
\fB\-\-genuid\fR:
Generate an UID
.TP
\fB\-\-changeuid\fR:UID
Give new UID as generated now or before
.TP
\fB\-\-changeuidback\fR:UID
Give old UID from one generated above
.TP
\fB\-\-checksum\fR:string
Give checksum of string
.TP
\fB\-\-testcompress\fR:file
Enter file in server with many compressions
.TP
\fB\-\-clonedb\fR:AE
Clone db from server for testing
.SS "Conversion options:"
.TP
\fB\-\-convert_to_gif\fR:file,size,out,l/w/f
Downsize and convert to mono GIF
.TP
\fB\-\-convert_to_bmp\fR:file,size,out,l/w/f
Downsize and convert to color BMP
.TP
\fB\-\-convert_to_jpg\fR:file,size,out,l/w/f
Downsize and convert to color JPG
.TP
\fB\-\-convert_to_dicom\fR:file,size,comp,f
Downsize/compress/frame DICOM
.TP
\fB\-\-extract_frames\fR:file,out,first,last
Select frames of DICOM file
.TP
\fB\-\-count_frames\fR:file
report # frames in DICOM file
.TP
\fB\-\-uncompress\fR:file,out
Uncompress DICOM
.TP
\fB\-\-compress\fR:file,mode,out
Compress DICOM to mode e.g. J2
.TP
\fB\-\-wadorequest\fR:parameters
Internal WADO server
.SS "Database options:"
.TP
\fB\-\-query\fR:table|fields|where|fmt|file
Arbitrary query output to file
.TP
\fB\-\-query2\fR:tab|fld|whe|fmt|max|file
Same but limit output rows to max
.TP
\fB\-\-patientfinder\fR:srv|str|fmt|file
List patients on server
.TP
\fB\-\-studyfinder\fR:srv|str|fmt|file
List studies on server
.TP
\fB\-\-seriesfinder\fR:srv|str|fmt|file
List series on server
.TP
\fB\-\-imagefinder\fR:srv|str|fmt|file
List images on server
.TP
\fB\-\-serieslister\fR:srv|pat|stu|fmt|file
List series in a study
.TP
\fB\-\-imagelister\fR:srv|pat|ser|fmt|file
List (local) files in a series
.TP
\fB\-\-extract\fR:PatientID = 'id'
Extract all dbase tables to X..
.TP
\fB\-\-extract\fR:
Extract patient dbase table to XA..
.TP
\fB\-\-addrecord\fR:table|flds|values
Append record, values must be in ''
.TP
\fB\-\-deleterecord\fR:table,where
Delete record from table
.SS "For DbaseIII without ODBC:"
.TP
\fB\-\-packdbf\fR:
Pack database, recreate memory index
.TP
\fB\-\-indexdbf\fR:
Re\-create memory index
.SS "Archival options:"
.TP
\fB\-\-renamedevice\fR:from,to
Rename device in database
.TP
\fB\-\-verifymirrordisk\fR:device
Verify mirror disk for selected device
.TP
\fB\-\-testimages\fR:device
Test read all images on device
.TP
\fB\-\-movedatatodevice\fR:to,from
Move patients from one device to another
.TP
\fB\-\-moveseriestodevice\fR:to,from
Move series from one device to another
.TP
\fB\-\-selectlruforarchival\fR:kb,device
Step 1 for archival: to device.Archival
.TP
\fB\-\-selectseriestomove\fR:device,age,kb
Step 1 for archival: to device.Archival
.TP
\fB\-\-preparebunchforburning\fR:to,from
Step 2 for archival: moves to cache
.TP
\fB\-\-deletebunchafterburning\fR:deviceto
Step 3 for archival: deletes from cache
.HP
\fB\-\-comparebunchafterburning\fR:deviceto Part step 3 \- compare jukebox to cache
.TP
\fB\-\-restoremagflags\fR:
Undo archival sofar
.SS "Scripting options:"
.TP
\fB\-\-lua\fR:chunk
Run lua chunk in server, wait to finish
.TP
\fB\-\-luastart\fR:chunk
Run lua chunk in server, retn immediate
.TP
\fB\-\-dolua\fR:chunk
Run lua chunk in this dgate instance
.TP
\fB\-\-dolua\fR:filename
Run lua file in this dgate instance
.SH COMPRESSION
.B ConQuest
supports a lot of compression and downsizing methods. These can be declared
in the
.B acrnema.map
file, using directives 
.B DroppedFileCompression, IncomingCompression and ArchiveCompression
in
.B dicom.ini
file and/or by using modifiers to AE Title (check
.B AE TITLE
section below).
.PP
The following information was extracted from
.B section 7.7
of the manual (file
/user/share/doc/conquest-dicom-server/windowsmanual.pdf.gz in this package):
.PP
Files dropped into the server will optionally be compressed, decompressed
and/or recompressed. Supported values are (expected compression ratio stated
between brackets):
.TP
as
store images as is, e.g. without changing the compression.
.TP
is
store images as is, e.g. without changing the compression.
.TP
un
uncompress NKI and/or JPEG compressed images
.TP
n1
fast NKI private loss-less compression mode 1 (50%)
.TP
n2
as n1 but with CRC check for errors (50%)
.TP
n3
fast NKI private loss-less compression mode 3 (40%)
.TP
n4
as n3 but with CRC check for errors (40%)
.TP
j1
JPEGLossless (retired, use J2 instead) (33%)
.TP
j2
JPEGLosslessNH14 (33%)
.TP
j3
JPEG baseline 1 (8 bit) lossy (8%)
.TP
j4
JPEGExtended2and4 lossy (15%)
.TP
j5
JPEGSpectralNH6and8 lossy (15%)
.TP
j6
JPEGFulllNH10and12 lossy (14%)
.TP
j3NN
JPEG baseline 1 (8 bit) quality as defined (60..95 suggested)
.TP
j4NN
JPEGExtended2and4 quality as defined (60..95 suggested)
.TP
j5NN
JPEGSpectralNH6and8 quality as defined (60..95 suggested)
.TP
j6NN
JPEGFulllNH10and12 quality as defined (60..95 suggested)
.TP
jk
Lossless JPEG2000 (30%)
.TP
jl
Lossy JPEG2000 (20%)
.TP
jlNN
Lossy JPEG2000 bitrate as defined (1..20 suggested)
.TP
nj
Highest NKI mode; but leaves JPEG as is (variable)
.TP
uj
Uncompressed; but leaves JPEG as is (variable)
.TP
k1
Downsize image>1024 pixels wide/high to 1024 (variable)
.TP
k2
Downsize image>512 pixels wide/high to 512 (variable)
.TP
k4
Downsize image>256 pixels wide/high to 256 (variable)
.TP
k8
Downsize image>128 pixels wide/high to 128 (variable)
.TP
ka
Downsize image>64 pixels wide/high to 64 (variable)
.SH "AE TITLE"
The default AE Title for ConQuest DICOM server in this package is
.B CONQUESTSRV1
and this is the AE Title you should use in DICOM viewers pointing to it. As
a "bonus" feature, you can use AE Title to declare the type of compression
you'll be using between the viewer and the server. just add
.B ~XX
to ConQuest AE Title, where XX is the compression algo/level you wish to use.
For instance, to use
.B uncompressed
images, the AE Title
.B CONQUESTSRV1~un
can be declared in your DICOM node configuration in the viewer.
.SH FILES
All of the locations below can be configured in
.B dicom.ini
file. In this package
.B ConQuest
expects dicom.ini to be present in the
.B /etc/conquest-dicom-server
directory. This can be changed using
.B -w
option (see 
.B OPTIONS
above).
.TP 15
/etc/conquest-dicom-server/dicom.ini
Several self-explanatory configuration parameters for the server.
.TP
/etc/conquest-dicom-server/acrnema.map
Map of the DICOM nodes allowed to retrieve studies from ConQuest and their
compression methods
.TP
/etc/conquest-dicom-server/dicom.sql
Database schema for the server
.TP
/etc/conquest-dicom-server/dgate.dic
DICOM dictionary
.TP
/etc/conquest-dicom-server/dgatesop.lst
DICOM SOP Class List
.TP
/var/log/conquest-dicom-server/dgate.log
Log from the running server (equivalent to stderr)
.TP
/var/log/conquest-dicom-server/trouble.log
Errors from the running server
.TP
/var/log/conquest-dicom-server/user.log
Application user log
.TP
/var/lib/conquest-dicom-server/dbase/conquest.sqlite
Database of DICOM information on Patients, Studies, Series, etc
.TP
/var/lib/conquest-dicom-server/MAG0/*
Where images are placed
.SH AUTHOR
.B ConQuest DICOM Server
was written by Marcel van Herk and Lambert Zijp at Netherlands Cancer
Institute based on University of California at Davis Medical Center DICOM
code, originally developed by Mark Oskin.
.PP
This manpage was written by
.B help2man
with parts supplied by Pablo Lorenzzoni <spectra@debian.org> for the Debian
package.
.SH "REPORTING BUGS"
For ConQuest specific bugs, please first check their forum at
.B http://forum.image-systems.biz/viewforum.php?f=33
and, if needed, send email to
.B Lambert Zijp <zijp@nki.nl>.
.PP
For bugs in the Debian package, please use Debian's BTS at
.B http://bugs.debian.org
or the tool provided in
.B reportbug
package.