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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">Dear Mas,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">You mention that you got a one-dimensional profile, and you show a screenshot of the root output. However, please note that
you select only the x-coordinates of the root output, that means, you select the x-coordinate of all particles intersecting your detector plane. Since you select only one variable, you will obtain a one-dimensional output.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">The phase space actor does not have a built-in function that separates scatter and primaries; you have to do this yourself.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">What you have to do is the following (and I hope that also answers your questions 2-3 as well): You have to extract the
(x,y) coordinates for all events, and then filter the events based on their distance to the centre of the detector. (I assume that the centre of the detector is the point at which the pencil beam is directed.) To be honest, I have never really used the root
object browser, so others might share more light on this. For my data analysis I use Python. There is a Python library called “<a href="https://uproot.readthedocs.io/en/latest/">uproot</a>”, which enables you to read the root files.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">Here's some example code to read the root file that is output by the phase space actor; in this example the file is called
“phaseSpace.root”.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas">import numpy as np<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas">import uproot<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas">import matplotlib.pyplot as plt<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"># Load the root file:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas">with uproot.open("phaseSpace.root") as rootfile:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> data = rootfile['PhaseSpace'].arrays(filter_name="*", library='np’)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # root files have a tree structure, like a trunk with many branches.<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # The “trunk” of a root file that is output by a phase space actor
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # is called ‘PhaseSpace’. With the function ‘arrays’ we can
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # access all the branches that we want. You can specify the
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # desired branches with the argument ‘filter_name’. If you use the
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # wildcard ‘*’, then all branches are loaded. If you just want the
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # x and y coordinate, you can do
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # filter_name = [‘X’, ‘Y’]<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # . The argument ‘library’ specifies whether you want to use numpy
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # or pandas. The former is better in terms of performance, the
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # latter is nicer for visualisation.
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"># Create a 2D histogram:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas">xbins = np.arange(-240, 241, 1)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas">ybins = np.arange(-240, 241, 1)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas">histData, histXbins, histYbins = np.histogram2d(data['X'], data['Y'], bins=[xbins, ybins])<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"># Plot the result:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas">fig, ax = plt.subplots()<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas">ax.imshow(histData, vmin=0, vmax=2)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # Please note that the origin of the plot does not coincide with the
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:10.0pt;font-family:Consolas"> # data origin, you would have to shift that manually<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><img border="0" width="675" height="473" style="width:7.0347in;height:4.9305in" id="_x0038_571008F-9A8A-4C3A-BC32-5D0EC3199CDA" src="cid:image001.png@01D8BEAB.5D291C50"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">(That little dot in the centre of the figure is not dust on your screen, it’s actually a very
faint signal…)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">Based the 2D histogram, you can now say that all events that are outside, for example, a 0.1 mm region around the origin,
are scatter.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">I hope that helps! If you need more help, let me know.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">David<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">PS: Sorry for writing your name incorrectly in my last mail!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> mas <fight1_fight2@yahoo.co.jp>
<br>
<b>Sent:</b> Friday, 2 September 2022 8:27 AM<br>
<b>To:</b> David Leibold <D.Leibold@tudelft.nl><br>
<b>Cc:</b> gate-users@lists.opengatecollaboration.org<br>
<b>Subject:</b> Re: Re: [Gate-users] How to measure the X-rays scattered by the phantom when they enter the detector?<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p>Dear David,<o:p></o:p></p>
<p><o:p> </o:p></p>
<p>Thanks to your reply, I understood that I should use the phase space actor.<o:p></o:p></p>
<p>After reading the documentation, I tried using phase space actor.<o:p></o:p></p>
<p><o:p> </o:p></p>
<p>I got a one-dimensional profile.<o:p></o:p></p>
<p>It was certainly like a point spread function.<o:p></o:p></p>
<p>However, some questions remained.<o:p></o:p></p>
<p><o:p> </o:p></p>
<p>1)The output is a one-dimensional profile, but how do I know which location on the detector is profiled?<o:p></o:p></p>
<p><o:p> </o:p></p>
<p>2)Which function of the phase space actor is used to separate scattered and direct lines?<o:p></o:p></p>
<p>[/gate/actor/MyActor/storeOutgoingParticles true] is used?<o:p></o:p></p>
<p><o:p> </o:p></p>
<p>3)How do I output the actual values from the root file, e.g. a txt file? I am sorry that this is not the original question.<o:p></o:p></p>
<p><o:p> </o:p></p>
<p>Thank you.<o:p></o:p></p>
<p>mas<o:p></o:p></p>
<pre><o:p> </o:p></pre>
<p><o:p> </o:p></p>
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<p class="MsoNormal">----- Original Message -----<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><strong>From: </strong>"David Leibold" <<a href="mailto:D.Leibold@tudelft.nl">D.Leibold@tudelft.nl</a>><o:p></o:p></p>
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<p class="MsoNormal"><strong>To: </strong>"mas" <<a href="mailto:fight1_fight2@yahoo.co.jp">fight1_fight2@yahoo.co.jp</a>><o:p></o:p></p>
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<p class="MsoNormal"><strong>Cc: </strong>"<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>" <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>><o:p></o:p></p>
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<p class="MsoNormal"><strong>Date: </strong>2022/09/02 <span style="font-family:"MS Gothic"">
金</span> 00:35<o:p></o:p></p>
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<p class="MsoNormal"><strong>Subject: </strong>Re: [Gate-users] How to measure the X-rays scattered by the phantom when they enter the detector?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Dear Masa,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">May I summarise your requirements:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">1) You mention that you want to simulate a CsI detector, but with 100 % detection efficiency and no interaction within the detector. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">2) You would like to distinguish between scattered and primary rays.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">3) A monochromatic pencil beam enters a phantom.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">My suggestion:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I would suggest using a phase space actor (see the <a href="https://urldefense.com/v3/__https:/opengate.readthedocs.io/en/latest/tools_to_interact_with_the_simulation_actors.html*phase-space-actor__;Iw!!PAKc-5URQlI!_P9nlwtwj9dIeV2hHQtSbBZiOOlf2u0klOOSbhmmNrMhNxMxAJN4SgVVz_zaiEj0SQYvfHgXq2pNEPKPSyXWmZGQZIKttg$" target="_blank">documentation
here</a>), which registers each particle's energy, position, velocity etc. crossing its surface. Since you do not want to simulate interaction in your CsI detector material, there is no need to use it in the first place.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Since you are using a pencil beam, all primary photons will go straight through your phantom, intersecting your detector at, for example, point (0,0). All scattered radiation will intersect your detector away from point (0,0). Hence, you
can filter out the scatter and primary rays purely based on where they end up on your detector.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">To set up your detector, use e.g. a box volume with the desired size, fill it with vacuum, and attach a phase space actor to it. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If you need more help, please let us know.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best regards,<o:p></o:p></p>
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<p class="MsoNormal">David <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 30 Aug2022, at 00:46, mas <<a href="mailto:fight1_fight2@yahoo.co.jp" target="_blank">fight1_fight2@yahoo.co.jp</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<pre>Hi GATE users.<o:p></o:p></pre>
<pre>I am masa@japan and new to Gate.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I am currently working on a simple simulation.<o:p></o:p></pre>
<pre>I am trying to find the point spread function of the scattered rays detected by a CsI detector by injecting a pencil beam of monochromatic X-rays into an acrylic phantom.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Assuming a detector detection efficiency of 100%, I want to output the spread of scattered radiation when it enters the detector.<o:p></o:p></pre>
<pre>No interaction occurs with the detector.<span style="font-family:"MS Gothic""> </span>I also want to output scattered rays and primary rays separately.<o:p></o:p></pre>
<pre>How should I set up the detector in such a case?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Should I use Fluence Actor for detection?<o:p></o:p></pre>
<pre>Or should I use a sensitive detector?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I would appreciate it if you could help me.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Thank you.<o:p></o:p></pre>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt">_______________________________________________</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt">Gate-users mailing list</span><o:p></o:p></p>
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<p class="MsoNormal"><a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank"><span style="font-size:10.0pt">Gate-users@lists.opengatecollaboration.org</span></a><o:p></o:p></p>
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<p class="MsoNormal"><a href="https://urldefense.com/v3/__http:/lists.opengatecollaboration.org/mailman/listinfo/gate-users__;!!PAKc-5URQlI!5R6DdcwuD-nXX0bmvN3RckxZ2HEAgen9ExhbGuDcz_52hS9V1Rohx8vBP7HBR0msh9Bx0lNmj5dJ866ftlukHHjC8jk0_A$" target="_blank"><span style="font-size:10.0pt">https://urldefense.com/v3/__http://lists.opengatecollaboration.org/mailman/listinfo/gate-users__;!!PAKc-5URQlI!5R6DdcwuD-nXX0bmvN3RckxZ2HEAgen9ExhbGuDcz_52hS9V1Rohx8vBP7HBR0msh9Bx0lNmj5dJ866ftlukHHjC8jk0_A$</span></a><span style="font-size:10.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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