[Gate-users] Gate-users Digest, Vol 61, Issue 16
Kevin
hust.est at gmail.com
Thu Jun 23 06:59:23 CEST 2011
Does anyone know how to specify the yttrium-*90 point source*
for simulation?
thanks
2011/6/22 <gate-users-request at lists.opengatecollaboration.org>
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> Today's Topics:
>
> 1. Forbid problem (Pablo Aguiar)
> 2. Hello! (yangmeng412721)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 21 Jun 2011 11:33:53 +0200
> From: Pablo Aguiar <pablo.aguiar.fernandez at sergas.es>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Forbid problem
> Message-ID: <BANLkTi=jHcs9+fFJoEXAchJwTYi-=JtNzA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear colleagues,
> There are several messages in GATE_v6 gate-users mailing list about
> problems
> with the "Forbid" command but so far we could not found a solution to this
> problem. We are simulating the image quality phantom from NEMA NU standards
> but "Forbid" command causes a segmentation fault when is included into our
> simulations to simulate two cold regions within the phantom. However, all
> works fine if it is removed.
>
> Other colleagues have found the same problem from the last year (messages
> posted dated 2010-04-14, 2010-10-01, 2010-12-16 and 2011-01-05). Is this
> really a bug in the code? or are we doing something wrong?
>
> Thank you in advance,
>
> Regards,
> --
> Pablo Aguiar, PhD
>
> Fundaci?n IDICHUS, Complexo Hospitalario Universitario de Santiago
> Phone: 0034 981951427 email: pablo.aguiar.fernandez at sergas.es
>
> Facultade de F?sica, Universidade de Santiago de Compostela.
> Phone: 0034 981563100 (ext 13543) email: pablo.aguiar at usc.es
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 22 Jun 2011 11:24:51 +0800 (CST)
> From: yangmeng412721 <yangmeng412721 at 126.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Hello!
> Message-ID:
> <65e25a06.122d8.130b56101dd.Coremail.yangmeng412721 at 126.com>
> Content-Type: text/plain; charset=UTF-8
>
>
>
>
> -------- Forwarding messages --------
> From: yangmeng412721 <yangmeng412721 at 126.com>
> Date: 2011-06-22 09:24:10
> To: wugc <wuguocheng at neusoft.com>
> Subject: Hello!
> I have solved the problem which has stuck for several days. But there are
> any question. when I execute "make" successfully, there is a "Gate" in
> /home/administrator/Gate5/gate_v5.0.0.p01/bin/Linux-g++. go into this
> directory, I perform "./Gate" in the terminal. the following is the result:
> root at ubuntu:/home/administrator/Gate5/gate_v5.0.0_p01/bin/Linux-g++#
> ./Gate
>
> *************************************************************
> Geant4 version Name: geant4-09-02-patch-04 (16-September-2010)
> Copyright : Geant4 Collaboration
> Reference : NIM A 506 (2003), 250-303
> WWW : http://cern.ch/geant4
> *************************************************************
>
> /home/administrator/Gate5/gate_v5.0.0_p01/Materials.xml:1: parser error :
> Document is empty
>
> ^
> /home/administrator/Gate5/gate_v5.0.0_p01/Materials.xml:1: parser error :
> Start tag expected, '<' not found
>
> ^
> GateMaterialDatabase: did not find the Materials.xml file: no properties
> read for material 'Air'
> This is only a problem when OPTICAL PHOTONS are transported in this
> material.'
> Visualization Manager instantiating...
> Visualization Manager initialising...
> Registering graphics systems...
>
> You have successfully registered the following graphics systems.
> Current available graphics systems are:
> ASCIITree (ATree)
> DAWNFILE (DAWNFILE)
> G4HepRep (HepRepXML)
> G4HepRepFile (HepRepFile)
> RayTracer (RayTracer)
> VRML1FILE (VRML1FILE)
> VRML2FILE (VRML2FILE)
> OpenGLImmediateX (OGLIX)
> OpenGLStoredX (OGLSX)
>
> Registering model factories...
>
> You have successfully registered the following model factories.
> Registered model factories:
> generic
> drawByCharge
> drawByParticleID
> drawByOriginVolume
> drawByAttribute
>
> Registered filter factories:
> chargeFilter
> particleFilter
> originVolumeFilter
> attributeFilter
>
> Time set to (s) 0
>
>
> **********************************************************************
> GATE version name: gate_v5.0.0 (1-May-2009)
> Copyright : OpenGATE Collaboration
> Reference : Phys. Med. Biol. 49 (2004) 4543-4561
> WWW : http://opengatecollaboration.healthgrid.org/
> **********************************************************************
>
> /control/saveHistory
> /run/verbose 2
> /event/verbose 1
> /tracking/verbose 1
> /gate/timing/setTime 0. s
> Time set to (s) 0
> /gate/application/setTimeSlice 1. s
> PreInit>
>
>
> I don't know whether gate is installed successfully, because there still
> some errors which I write in red. Will these errors affect my future work?
> How I solve this problem?
>
>
>
> At 2011-06-21 16:47:58?wugc <wuguocheng at neusoft.com> wrote:
> ?
> Hi,yangmeng412721
>
>
> I can try to control, but I?m not sure to login in your computer.
>
>
>
> 2011-06-21
>
> ???? yangmeng412721
> ????? 2011-06-21 16:37:48
> ???? wugc
> ???
> ??? Hello!
> can you use remote control my computer to help me correct the error?
>
>
> At 2011-06-21 16:15:57?wugc <wuguocheng at neusoft.com> wrote:
> ?
> Hi,yangmeng412721
>
>
> Your right, there need export before PATH.
>
>
>
> 2011-06-21
>
> ???? yangmeng412721
> ????? 2011-06-21 16:09:20
> ???? wugc
> ???
> ??? Re:Re: Re:Fw: Re: Re:Re: Hello! (yangmeng412721)
> this is the photo of my folder. Can you give me the exact LD_LIBRARY_PATH
> and PATH variable . In additon, is there no need to add "export" before
> PATH?
>
>
> At 2011-06-21 16:01:28?wugc <wuguocheng at neusoft.com> wrote:
> ?
> Hi,yangmeng412721
>
> Just like follows,but not limit to.
>
> PATH=$PATH:$HOME/bin:/home/admin/gate_instal/gate_v5.0.0
> export LD_LIBRARY_PATH=/home/admin/gate_instal/Root/lib:$LD_LIBRARY_PATH
>
>
> 2011-06-21
>
> ???? yangmeng412721
> ????? 2011-06-21 15:54:16
> ???? wugc
> ???
> ??? Re:Fw: Re: Re:Re: Hello! (yangmeng412721)
> The following is my .bashrc.sh. How I add LD_LIBRARY_PATH and PATH into it
> ?
>
> # ~/.bashrc: executed by bash(1) for non-login shells.
> # see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
> # for examples
>
> # If not running interactively, don't do anything
> [ -z "$PS1" ] && return
>
> # don't put duplicate lines in the history. See bash(1) for more options
> # ... or force ignoredups and ignorespace
> HISTCONTROL=ignoredups:ignorespace
>
> # append to the history file, don't overwrite it
> shopt -s histappend
>
> # for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
> HISTSIZE=1000
> HISTFILESIZE=2000
>
> # check the window size after each command and, if necessary,
> # update the values of LINES and COLUMNS.
> shopt -s checkwinsize
>
> # make less more friendly for non-text input files, see lesspipe(1)
> [ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"
>
> # set variable identifying the chroot you work in (used in the prompt
> below)
> if [ -z "$debian_chroot" ] && [ -r /etc/debian_chroot ]; then
> debian_chroot=$(cat /etc/debian_chroot)
> fi
>
> # set a fancy prompt (non-color, unless we know we "want" color)
> case "$TERM" in
> xterm-color) color_prompt=yes;;
> esac
>
> # uncomment for a colored prompt, if the terminal has the capability;
> turned
> # off by default to not distract the user: the focus in a terminal window
> # should be on the output of commands, not on the prompt
> #force_color_prompt=yes
>
> if [ -n "$force_color_prompt" ]; then
> if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
> # We have color support; assume it's compliant with Ecma-48
> # (ISO/IEC-6429). (Lack of such support is extremely rare, and such
> # a case would tend to support setf rather than setaf.)
> color_prompt=yes
> else
> color_prompt=
> fi
> fi
>
> if [ "$color_prompt" = yes ]; then
> PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$
> '
> else
> PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
> fi
> unset color_prompt force_color_prompt
>
> # If this is an xterm set the title to user at host:dir
> case "$TERM" in
> xterm*|rxvt*)
> PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
> ;;
> *)
> ;;
> esac
>
> # enable color support of ls and also add handy aliases
> if [ -x /usr/bin/dircolors ]; then
> test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval
> "$(dircolors -b)"
> alias ls='ls --color=auto'
> #alias dir='dir --color=auto'
> #alias vdir='vdir --color=auto'
>
> alias grep='grep --color=auto'
> alias fgrep='fgrep --color=auto'
> alias egrep='egrep --color=auto'
> fi
>
> # some more ls aliases
> alias ll='ls -alF'
> alias la='ls -A'
> alias l='ls -CF'
>
> # Add an "alert" alias for long running commands. Use like so:
> # sleep 10; alert
> alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal ||
> echo error)" "$(history|tail -n1|sed -e
> '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'
>
> # Alias definitions.
> # You may want to put all your additions into a separate file like
> # ~/.bash_aliases, instead of adding them here directly.
> # See /usr/share/doc/bash-doc/examples in the bash-doc package.
>
> if [ -f ~/.bash_aliases ]; then
> . ~/.bash_aliases
> fi
>
> # enable programmable completion features (you don't need to enable
> # this, if it's already enabled in /etc/bash.bashrc and /etc/profile
> # sources /etc/bash.bashrc).
> if [ -f /etc/bash_completion ] && ! shopt -oq posix; then
> . /etc/bash_completion
> fi
>
>
>
>
>
>
> At 2011-06-21 15:47:23?wugc <wuguocheng at neusoft.com> wrote:
> ?
> Hi,
>
>
> I encounter the problem, and I solved just as I told you last week, see
> below.
>
>
> 2011-06-21
>
> ???? wugc
> ????? 2011-06-17 15:45:46
> ???? yangmeng412721
> ???
> ??? Re: Re:Re: Hello! (yangmeng412721)
>
> Hi,yangmeng412721
>
>
> I think you need to add the environment variables ?$ LD_LIBRARY_PATH? in
> your build terminal or add the variables in your bashrc file.
>
> Hope this can helps.
>
>
> wugc
> 2011-06-17
>
> ???? yangmeng412721
> ????? 2011-06-17 15:12:29
> ???? wugc
> ???
> ??? Re:Re: Hello! (yangmeng412721)
> Hi, I have just tried it again as what you say,but it no use. And a new
> problem came out.the following is the error:
>
> /usr/bin/ld: cannot find -lGpad
> /usr/bin/ld: cannot find -lTree
> /usr/bin/ld: cannot find -lRint
> /usr/bin/ld: cannot find -lPostscript
> /usr/bin/ld: cannot find -lMatrix
> /usr/bin/ld: cannot find -lPhysics
> /usr/bin/ld: cannot find -lMathCore
> /usr/bin/ld: cannot find -lThread
> collect2: ld returned 1 exit status
> make: *** [bin/Linux-g++/Gate] ?? 1
>
> Have you any good advice about it? thank you advance!
>
>
>
> At 2011-06-16 17:23:21?wugc <wuguocheng at neusoft.com> wrote:
> ?
> Hi,
> maybe you can re-build the geant4, when you get the following information,
> you should select default.
>
>
>
> "Activates the configuration setup for allowing plugins to
>
> analysis tools based on AIDA (Astract Interfaces for Data
>
> Analysis). In order to use AIDA features and compliant analysis
>
> tools, the proper environment for these tools will have to be
>
> set (see documentation for the specific analysis tools).
>
> [n] n "
>
>
>
>
> Good Luck?
> Wugc
> 2011-06-16
>
> Email?wuguocheng at neusoft.com
> ???? gate-users-request
> ????? 2011-06-16 17:10:34
> ???? gate-users
> ???
> ??? Gate-users Digest, Vol 61, Issue 11
> Send Gate-users mailing list submissions to
> gate-users at lists.opengatecollaboration.org
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> or, via email, send a message with subject or body 'help' to
> gate-users-request at lists.opengatecollaboration.org
> You can reach the person managing the list at
> gate-users-owner at lists.opengatecollaboration.org
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Gate-users digest..."
> Today's Topics:
> 1. Hello! (yangmeng412721)
> 2. Re: Calculate Trues, Randoms and Scatter coincidences
> (giuseppe iaccarino)
> ----------------------------------------------------------------------
> Message: 1
> Date: Thu, 16 Jun 2011 15:19:54 +0800 (CST)
> From: yangmeng412721 <yangmeng412721 at 126.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Hello!
> Message-ID:
> <7367915a.164b6.13097520a76.Coremail.yangmeng412721 at 126.com>
> Content-Type: text/plain; charset=GBK
> Hello!
> I am a new user of GATE. I have compiled the clhep_v2.0.4.2,
> geant4.9.2.p04 and root_5.24 successfully. However, when I type "make"in the
> terminal , I got the errors as follows. And I have tried some solutions
> proposed on the mailing list , but it's no use.
> /home/administrator/Gate5/geant4.9.2.p04/source/run/include/G4RunManager.hh:
> In member function ?void G4RunManager::SetRandomNumberStoreDir(G4String)?:
> /home/administrator/Gate5/geant4.9.2.p04/source/run/include/G4RunManager.hh:352:
> warning: ignoring return value of ?int system(const char*)?, declared with
> attribute warn_unused_result
> Compiling GateVGeometryVoxelReader.cc ...
> /bin/sh: aida-config: not found
> Compiling GateVGeometryVoxelReaderMessenger.cc ...
> /bin/sh: aida-config: not found
> Compiling GateVGeometryVoxelStore.cc ...
> /bin/sh: aida-config: not found
> Compiling GateVGeometryVoxelStoreMessenger.cc ...
> /bin/sh: aida-config: not found
> Compiling GateVGeometryVoxelTranslator.cc ...
> /bin/sh: aida-config: not found
> Compiling GateVoxelBoxParameterization.cc ...
> /bin/sh: aida-config: not found
> ......
> ......
> ompiling GateTranslationMove.cc ...
> /bin/sh: aida-config: not found
> Compiling GateTranslationMoveMessenger.cc ...
> /bin/sh: aida-config: not found
> Compiling GateUIcmdWithAnIntegerAndADouble.cc ...
> /bin/sh: aida-config: not found
> Compiling GateUIcmdWithTwoDouble.cc ...
> /bin/sh: aida-config: not found
> Compiling GateUIcontrolMessenger.cc ...
> /bin/sh: aida-config: not found
> Compiling GateUIterminal.cc ...
> /bin/sh: aida-config: not found
> Compiling GateVisAttributesMessenger.cc ...
> /bin/sh: aida-config: not found
> Compiling GateVisManager.cc ...
> /bin/sh: aida-config: not found
> Compiling GateXMLDocument.cc ...
> /bin/sh: aida-config: not found
> source/management finished
> Creating/replacing object files in ./tmp/Linux-g++/Gate/libGate.a ...
> ar: creating ./tmp/Linux-g++/Gate/libGate.a
> Compiling Gate.cc ...
> /bin/sh: aida-config: not found
> In file included from
> ./source/mandatory_G4_classes/include/GateRunManager.hh:46,
> from Gate.cc:18:
> /home/administrator/Gate5/geant4.9.2.p04/source/run/include/G4RunManager.hh:
> In member function ?void G4RunManager::SetRandomNumberStoreDir(G4String)?:
> /home/administrator/Gate5/geant4.9.2.p04/source/run/include/G4RunManager.hh:352:
> warning: ignoring return value of ?int system(const char*)?, declared with
> attribute warn_unused_result
> Using granular libraries ...
> Linking Gate
> /bin/sh: aida-config: not found
> /bin/sh: aida-config: not found
> /usr/bin/ld: cannot find -lLMF
> /usr/bin/ld: cannot find -lCore
> /usr/bin/ld: cannot find -lCint
> /usr/bin/ld: cannot find -lRIO
> /usr/bin/ld: cannot find -lNet
> /usr/bin/ld: cannot find -lHist
> /usr/bin/ld: cannot find -lGraf
> /usr/bin/ld: cannot find -lGraf3d
> /usr/bin/ld: cannot find -lGpad
> /usr/bin/ld: cannot find -lTree
> /usr/bin/ld: cannot find -lRint
> /usr/bin/ld: cannot find -lPostscript
> /usr/bin/ld: cannot find -lMatrix
> /usr/bin/ld: cannot find -lPhysics
> /usr/bin/ld: cannot find -lMathCore
> /usr/bin/ld: cannot find -lThread
> /usr/bin/ld: cannot find -lLMF
> /usr/bin/ld: cannot find -lecat
> collect2: ld returned 1 exit status
> make: *** [bin/Linux-g++/Gate] ?? 1
> root at ubuntu:/home/administrator/Gate5/gate_v5.0.0_p01#
> Any more help for the above issue will be appreciated!
> Thank you very much advance.
> ------------------------------
>
>
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> accompanying attachment(s)
> is intended only for the use of the intended recipient and may be
> confidential and/or privileged of
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> of this communication is
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