<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>So if there is no intrinsic plotting utility, is there any way to access plots (or their data) from macros or plugins? That is perhaps my main complaint about using JFreeChart (that and no log axes for some reason). I currently use my own version of Wayne’s PlotWindow which I then access from other plugins via reflection (not the best way, I know). Wayne doesn’t want to support it because of lack of backward function compatibility, but perhaps IJ2 is an opportunity to implement this in a more robust manner. This approach has been very rewarding. For example, I can do some really cool things like create dynamic histograms where I can change the bin size on the fly, visualize thresholds via a 1D or 2D histogram, etc. It becomes easy to implement some of the gating that people use for cytometry analysis for example. Anyway, not sure if IJ2 is the place for this kind of development, but it is an intriguing possibility.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Jay<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> ctrueden.wisc@gmail.com [mailto:ctrueden.wisc@gmail.com] <b>On Behalf Of </b>Curtis Rueden<br><b>Sent:</b> Tuesday, April 10, 2012 1:52 PM<br><b>To:</b> Unruh, Jay<br><b>Cc:</b> imagej-devel@imagej.net; Grant Harris<br><b>Subject:</b> Re: [ImageJ-devel] plot window support<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Jay,<br><br>On Tue, Apr 10, 2012 at 10:28 AM, Unruh, Jay <<a href="mailto:jru@stowers.org">jru@stowers.org</a>> wrote:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Firstly, is there a good way to search this list (other than downloading all of the text)?<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><o:p> </o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Unfortunately, the only way to do this is using a search engine such as Google.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><o:p> </o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>That is, searching with the "site:" keyword; e.g.:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> site:<a href="http://imagej.net/pipermail/imagej-devel">http://imagej.net/pipermail/imagej-devel</a> legacy<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><o:p> </o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Unfortunately, the Google index is more than a month behind the latest messages.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><o:p> </o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>For more information, see:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <a href="http://wiki.list.org/pages/viewpage.action?pageId=4030520">http://wiki.list.org/pages/viewpage.action?pageId=4030520</a><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><o:p> </o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><o:p> </o:p></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Secondly, (and I would know this if I could search the list) has there been any discussion of plot window support in ImageJ2? The beta version I downloaded as is doesn’t support it—perhaps because it relies on an awt panel within the imagewindow frame, but perhaps there is awt support somewhere that I’m not seeing.<o:p></o:p></p></blockquote><p class=MsoNormal style='margin-bottom:12.0pt'><br>There are plans to create a UI-agnostic plotting system, which will be driven by JFreeChart for the Swing UI, but pluggable differently for other UIs.<br><br>However, you is correct that at the moment, there is essentially no facility for plotting, other than legacy support for IJ1 plugins, which is limited and sometimes non-functional for custom AWT-based windows.<br><br>-Curtis<br><br><o:p></o:p></p><div><p class=MsoNormal>On Tue, Apr 10, 2012 at 1:17 PM, Grant B. Harris <<a href="mailto:gharris@mbl.edu">gharris@mbl.edu</a>> wrote:<o:p></o:p></p><p class=MsoNormal>Jay --<br>The Analyse::Histogram plugin uses JFreeChart (I wrote an earlier version of it.) You might have a look at that to see how you might use it in a plugin. I believe it is our intention to use JFreeChart as the default plotting system for the Swing-based implementation (But I may be corrected on this by people still more involved in the design ;-) I'd be interested to follow how you might use it and to he of help, if I can.<br>-- Grant<o:p></o:p></p><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><p class=MsoNormal>On Tue, Apr 10, 2012 at 10:28 AM, Unruh, Jay <<a href="mailto:jru@stowers.org">jru@stowers.org</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Firstly, congrats on the beta release.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Several questions after my first download: Firstly, is there a good way to search this list (other than downloading all of the text)? Secondly, (and I would know this if I could search the list) has there been any discussion of plot window support in ImageJ2? The beta version I downloaded as is doesn’t support it—perhaps because it relies on an awt panel within the imagewindow frame, but perhaps there is awt support somewhere that I’m not seeing.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thanks,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Jay<o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p></div></div></div></div></body></html>