[Gate-users] Ascii

jehangir khan jehangir.kahn at gmail.com
Fri Dec 14 14:03:05 CET 2012


Hello !

in Ascii Coincidenc.dat file certain columns
like 4-6,9-11,27-29,32-34 represents XYZ position of the annihilation in
world referential ? what does it mean?
which are the columns one should consider to see the image of the
simulation,
thanks


On Thu, Dec 13, 2012 at 10:32 PM, <
gate-users-request at lists.opengatecollaboration.org> wrote:

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> Today's Topics:
>
>    1. Re: about "Forbid" command in GATE simulation (?? ?)
>    2. Re: Voxelized source orientation (J?r?me Suhard)
>    3. Gate command menu (dme627b)
>    4. Re: Gate command menu (Carlos Uribe)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 13 Dec 2012 23:30:34 +0900
> From: ?? ?      <takuyama at med.hokudai.ac.jp>
> To: Kaiyang Li <kl780 at uowmail.edu.au>,  gate-users
>         <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] about "Forbid" command in GATE simulation
> Message-ID:
>         <CADb2yx9Vjttz8=
> NhQSVh+EJABf_2UWL5wdCOncqi2z2BKxnNOQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-2022-jp"
>
> Hello Kaiyang Li,
>
> I'm still struggling with "forbid".
>
> I tried the simple geometry, too, but my simulation stops with "***Break***
> segmentation violation" and I cannot proceed to even see the reconstructed
> image... this didn't happen before...
>
> Anyway, it seems the command is working somehow.
> When I tried to forbid the whole source by surrounding with the
> "forbidding" volume and start simulation, GATE gave me the message of
> "primaries were always generated in forbidden volumes!" and the simulation
> was shut down.
>
> Also, you can visualize the source by
> /gate/source/FictiveSource/visualize "count" "color" "size"
> This command should reflect the "forbid" as well, so we are supposed to be
> able to see the "forbidden" source... but...
>
> You can check how the "forbid" command works in GATE in
> GateSPSPosDistribution.cc line:150
>
> After all, I cannot give you any solution to this problem.
> I'll still work on with this, so if you find anything new, please let me
> know.
>
> Taku
>
> 2012/12/10 Kaiyang Li <kl780 at uowmail.edu.au>
>
> >  Hi Taku,
> >
> > My name is Kaiyang Li, a GATE user.
> > I have the problem of using "forbid" in my simulation. It seems that the
> > forbid area is simply
> > not forbidden at all.
> >
> > I have read all other questions, including yours. Have you figure it out
> > yet?
> > I have used GATE for half a year and run some other complex simulations
> > successfully but for this forbid one, it seems something is wrong.
> >
> > Here is my simple code followed by the GATE instruction:
> >
> > /gate/world/daughters/name cold_area
> > /gate/world/daughters/insert cylinder
> > /gate/cold_area/vis/forceWireframe
> > /gate/cold_area/vis/setColor green
> > /gate/cold_area/geometry/setRmax 2.0 mm
> > /gate/cold_area/geometry/setHeight 0.3 mm
> > /gate/cold_area/setMaterial Water
> >
> > /gate/run/initialize
> >
> > /gate/source/addSource number1
> > /gate/source/number1/setActivity 37000000. becquerel
> > /gate/source/number1/gps/particle gamma
> > /gate/source/number1/setType backtoback
> > /gate/source/number1/gps/monoenergy 511. keV
> > /gate/source/number1/setForcedUnstableFlag                     true
> > /gate/source/number1/setForcedHalfLife                6586 s
> > /gate/source/number1/gps/type Volume
> > /gate/source/number1/gps/shape Cylinder
> > /gate/source/number1/gps/radius 4. mm
> > /gate/source/number1/gps/halfz 0.15 mm
> > /gate/source/number1/gps/centre 0. 0. 0. mm
> > /gate/source/number1/gps/angtype iso
> > /gate/source/number1/gps/Forbid cold_area
> > /gate/source/number1/dump 1
> > /gate/source/list
> >
> > The reconstructed image shows that there is no forbidden area.
> > Probably the forbidden command is not working, what do you think?
> >
> >
> > Kind Regards,
> > Kaiyang Li
> >
>
>
>
> --
> Hokkaido University,  Graduate school of medicine, medical physics and
> engineering D1
> ????? ??? ????? ???????? D1
> Taku Yamanaka
> ?? ?
>
> takuyama at med.hokudai.ac.jp
> --
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> ------------------------------
>
> Message: 2
> Date: Thu, 13 Dec 2012 17:19:25 +0100
> From: J?r?me Suhard <jerome at suhard.fr>
> To: Tom Buitenhuis <hjt.buitenhuis at gmail.com>
> Cc: gate-users at lists.opengatecollaboration.org
> Subject: Re: [Gate-users] Voxelized source orientation
> Message-ID:
>         <CANCPmRcWPWs2Fvj_GBXUp+4D_nNmg_Q15=
> Khj+FauYPqOPK3Cw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> 2012/12/13 Tom Buitenhuis <hjt.buitenhuis at gmail.com>
>
> > According to the documentation of these file formats, data is stored in
> > row-major order. For example, for the InterFile 3.3 format, the specs can
> > be found here:
> > http://www.nucmed.si.mahidol.ac.th/nucmed1/pip/interfil1.html
> >
> > Relevant section:
> > "I.5. IMAGE DATA
> >
> > A. Image arrays are to be arranged with the first value (in the binary
> > data) corresponding to the pixel in the top left corner and with the
> value
> > corresponding to the pixel in the bottom right corner occurring last.
> Image
> > arrays in V3.3 remain 2-D. The order of the pixel data shall increment by
> > column from left to right, and then (for each such row) by row, from top
> to
> > bottom. This is also known as row major order."
> >
> > more info on row-major order:
> http://en.wikipedia.org/wiki/Row-major_order
> >
> > However, when I simulate a voxelized source, the activity seems to have
> > the y-axis inverted, i.e. it seems that GATE ignores this row-major part
> of
> > the InterFile specification. An example of this can be seen in the
> attached
> > image. On the left, there is a window where I display the InterFile
> source
> > in AMIDE, which correctly interprets the specs. The top, white, part of
> the
> > source has an activity of 10 Bq, where the bottom, green, part has an
> > activity of 500 Bq. On the right of the image, I display the root output
> of
> > the source-position of simulated coincidences, where we can see that the
> > top-part now has the higher activity, instead of the bottom part.
> >
> > The same seems to hold for the Analyze 7.5 voxelized phantom. When we
> > center both the source and the phantom, this shouldn't be a problem in a
> > cylindrical symmetric PET-scanner, but when we translate one with respect
> > to the other, this could be problematic. The fix is ofcourse easy, i.e.
> > translate in the -y instead of the +y direction, but when this is
> > undocumented, incorrect simulations will be performed.
> >
> > Does anyone else have any experience with this? Am I making a mistake, or
> > is this a bug in the implementation of the file specs in GATE?
> >
>
> GATE doesn't conform to InterFile specs. It just parses some keys according
> to the function GateSourceVoxelInterfileReader::ReadKey(FILE* fp) in
> source/physics/src/GateSourceVoxelInterfileReader.cc .
>
> Here are the relevant portions:
>
> if ( key ==  "matrix size [1]" ) {
>     sscanf(value,"%d",m_dim);
>   } else if ( key ==  "matrix size [2]" ) {
>     sscanf(value,"%d",m_dim+1);
>   } else if ( ( key ==  "number of slices" ) || (key ==  "number of
> images") ) {
>     sscanf(value,"%d",&m_numPlanes);
>   } else if ( key ==  "scaling factor (mm/pixel) [1]" ) {
>     sscanf(value,"%f",m_pixelSize);
>   } else if ( key ==  "scaling factor (mm/pixel) [2]" ) {
>     sscanf(value,"%f",m_pixelSize+1);
>   } else if ( key ==  "slice thickness (pixels)" ) {
>     sscanf(value,"%f",&m_planeThickness);
>   } else if ( key ==  "name of data file" ) {
>     m_dataFileName = std::string(value);
>   } else if ( key ==  "number format" ) {
>     if ( (strcmp(value,"float")==0) || (strcmp(value,"FLOAT")==0) )
>       m_dataTypeName = "FLOAT";
>     else if ( (strcmp(value,"unsigned integer")==0) ||
> (strcmp(value,"UNSIGNED INTEGER")==0) )
>       m_dataTypeName = "UNSIGNED INTEGER";
>     else
>       G4cout << "Unrecognised type name '" << value << "'" << G4endl;
>   } else if (key == "imagedata byte order") {
>         if ( strcmp(value,"BIGENDIAN") == 0 )
>                 m_dataByteOrder = "BIGENDIAN";
>         else if ( strcmp(value,"LITTLEENDIAN") == 0)
>                 m_dataByteOrder = "LITTLEENDIAN";
>         else
>                 G4cerr << "Unrecognized data byte order '" +
> G4String(value) + "', assuming default BIGENDIAN\n" << G4endl;
>   } else {
>     // G4cout << "Key not processed: '" << key << "'" << G4endl;
>   }
>
>
> Best regards,
> --
> J?r?me Suhard
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> ------------------------------
>
> Message: 3
> Date: Thu, 13 Dec 2012 13:32:54 -0800
> From: dme627b <dme627b at gmail.com>
> To: "gate-users at lists.opengatecollaboration.org"
>         <gate-users at lists.opengatecollaboration.org>
> Subject: [Gate-users] Gate command menu
> Message-ID: <201212131332533900771 at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi everyone,
>
> I am a new gate user. I do not know if there is a Gate command menu which
> includes all the gate command, because I think it will be very helpful. Any
> other document of Gate command is also appreciate.
>
> Can anyone help me? Thank you in advance.
>
> Best Regards,
>
> Jeremy
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> ------------------------------
>
> Message: 4
> Date: Thu, 13 Dec 2012 13:37:44 -0800
> From: Carlos Uribe <carluri at phas.ubc.ca>
> To: dme627b <dme627b at gmail.com>
> Cc: "gate-users at lists.opengatecollaboration.org"
>         <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] Gate command menu
> Message-ID:
>         <
> CAPJy_1TQZ-9D1kVAretM++14bnKnY+4AiYvbKrQHYPaNYXT03g at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Jeremy,
>
> you can try typing  "Gate" in your terminal   then   "help".
>
> does that work?
>
>
>
>
> On Thu, Dec 13, 2012 at 1:32 PM, dme627b <dme627b at gmail.com> wrote:
>
> > **
> > Hi everyone,
> >
> > I am a new gate user. I do not know if there is a Gate command menu which
> > includes all the gate command, because I think it will be very helpful.
> Any
> > other document of Gate command is also appreciate.
> >
> > Can anyone help me? Thank you in advance.
> >
> > Best Regards,
> >
> > Jeremy
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >
> > --
> > Carlos F Uribe
> >
> >
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