<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=windows-1252">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<p>Hello Kajal,</p>
<p>The <i>-opti-stat</i> option will output several image-based
information for each image update (iterations or subsets). Namely,
the mean voxel value and standard deviation over all voxels in the
new image estimation (<i>New image estimate</i> line), and the
same figures of merit for the difference image between the new
image estimation and the previous one (<i>Image update step</i>
line). Just to let you know, you can also configure the output
number format (scientific/fixed format, and precision ) with the
option <i>-onbp.</i><br>
</p>
<p>The first lines display the initial parameters of the <i>optimizer</i>
you use (MLEM by default). The data space denominator threshold if
the threshold under which estimated forward values are discarded
(it is used to avoid division by 0, and could be modified if you
have low-stat data, leading to very low forward-projeted values).
It is used during the data updates ( <i>iOptimizerMLEM::DataSpaceSpecificOperations()</i>
). Minimum (and Maximum) update factors are some thresholds used
for the same purposes during the image data step (<i>
iOptimizerMLEM::ImageSpaceSpecificOperations() </i>). All these
parameters can be modified in the command-line options (using
-opti MLEM,a,b,c,d where a,b,c,d are the initial image value,
denominator threshold, minimum image update and maximum image
update values respectively), or directly in the MLEM configuration
file in config/optimizer/.<br>
<br>
The <i>-opti-fom</i> option computes some data-space based
figures of merit, such as log-likelihood and RMSE. As these are
computed from the data and forward model estimation for each bin,
this option is restricted to histogram data. There is currently no
implementation of image-based figures of merit besides global mean
and standard deviation computations, however it should be quite
straightforward to implement some in the vOptimizer class (by
creating and initializing a variable following the example of <i>mp_imageStatMean</i>
in vOptimizer.hh and vOptimizer.cc files, then implementing its
behavior in the <i>vOptimizer::ImageUpdateStep()</i> function and
outputing the result). <br>
</p>
<p>Hope this helps !</p>
<p>Best regards,</p>
<p>Thibaut<br>
</p>
<div class="moz-forward-container"><br>
<br>
<br>
-------- Forwarded Message --------
<table class="moz-email-headers-table" border="0" cellpadding="0"
cellspacing="0">
<tbody>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject:
</th>
<td>Re: [Castor-users] Problem in crystal index</td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Date: </th>
<td>Fri, 25 May 2018 10:00:22 +0200</td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">From: </th>
<td>Kajal Aggarwal <a class="moz-txt-link-rfc2396E" href="mailto:kajal792@gmail.com"><kajal792@gmail.com></a></td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">To: </th>
<td>tmerlin <a class="moz-txt-link-rfc2396E" href="mailto:Thibaut.Merlin@univ-brest.fr"><Thibaut.Merlin@univ-brest.fr></a></td>
</tr>
</tbody>
</table>
<br>
<br>
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>Hello,<br>
</div>
<br>
</div>
I am trying to verify the convergence of
reconstructed image for each iteration, and to do
the same while reconstructing the image I wrote an
option of "-opti-stat" . (not really clear what this
option is doing)<br>
<br>
</div>
In the log file, because of this option, I got the
following lines:<br>
<br>
<b>--> Initial image value: 1<br>
--> Data space denominator threshold: 1e-10<br>
--> Minimum image update factor: 0.01<br>
.<br>
.<br>
.<br>
.<br>
<br>
vOptimizer::ImageUpdateStep() -> Start image
update<br>
--> Image update step | mean: -0.99 | stdv: 0<br>
--> New image estimate | mean: 0.01 | stdv: 0 |
min/max: 0.01/1<br>
.<br>
.<br>
.<br>
.<br>
<br>
vOptimizer::ImageUpdateStep() -> Start image
update<br>
--> Image update step | mean: -0.0099 | stdv:
0<br>
--> New image estimate | mean: 0.0001 | stdv: 0
| min/max: 0.0001/0.01<br>
</b><br>
</div>
I tried to look into the vOptimizer.cc file for these
parameters, but I did not really understand to what
factors the 'mean' and 'standard deviation' corresponds
to. Could you tell me?<br>
<br>
</div>
I am looking to get the value of likelihood of each
iteration, is it possible to get the value of likelihood
in list-mode?<br>
<br>
</div>
Thank you.<br>
<br>
</div>
Regards,<br>
</div>
Kajal <br>
<div>
<div>
<div>
<div>
<div>
<div>
<div><br clear="all">
<div class="gmail_extra"><br>
-- <br>
<div class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>Thanking you.</div>
<div> </div>
<div>Yours sincerely,</div>
<div>Kajal Aggarwal</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>