Bug 1059 - Analyze Particles and Bug Report not working
Analyze Particles and Bug Report not working
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: ImageJ1
unspecified
Macintosh Mac OS
: P5 enhancement
Assigned To: Wayne Rasband
Depends on:
Blocks:
 
Reported: 2015-04-23 16:23 CDT by Liz
Modified: 2015-04-25 14:38 CDT
3 users (show)

See Also:
Description Liz 2015-04-23 16:23:32 CDT 
Hi, 

I recently updated FIJI, and now analyze particles isn't working on single images. It works on stacks. I've tried with a macro and manually, and neither way is working. Here's what I'm doing:

Macro:

run("Set Measurements...", "area mean standard median limit redirect=None decimal=3");
setAutoThreshold("Default dark");
//run("Threshold...");
setThreshold(0.0100, 10);
run("Analyze Particles...", "size=10-infinity pixel display summarize");
run("Distribution...", "parameter=Median or=20 and=0-3");

Exception:

(Fiji Is Just) ImageJ 2.0.0-rc-29/1.49r; Java 1.6.0_65 [64-bit]; Mac OS X 10.10.2; 27MB of 2279MB (1%)
 
java.lang.ArrayIndexOutOfBoundsException: -1
	at ij.process.FloatStatistics.getMedian(FloatStatistics.java:240)
	at ij.process.FloatStatistics.<init>(FloatStatistics.java:38)
	at ij.plugin.filter.ParticleAnalyzer.getStatistics(ParticleAnalyzer.java:888)
	at ij.plugin.filter.ParticleAnalyzer.analyzeParticle(ParticleAnalyzer.java:838)
	at ij.plugin.filter.ParticleAnalyzer.analyze(ParticleAnalyzer.java:572)
	at ij.plugin.filter.ParticleAnalyzer.run(ParticleAnalyzer.java:254)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:263)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:112)
	at ij.IJ.runPlugIn(IJ.java:171)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)\



ALSO, when I tried to submit the bug report through FIJI, I got the following error messages: 


--------------------------

Submission Reply Page:

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
                      "http://www.w3.org/TR/html4/loose.dtd">
<html lang="en">
  <head>
    <title>Suspicious Action</title>

      <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">


<link rel="Top" href="http://fiji.sc/bugzilla/">

  


  


  
    <link rel="Saved&nbsp;Searches" title="My Bugs"
          href="buglist.cgi?resolution=---&amp;emailassigned_to1=1&amp;emailreporter1=1&amp;emailtype1=exact&amp;email1=esf%40stanford.edu">



    
    <link href="../css/global.cssquot;
          rel="alternate stylesheet" 
          title="Classic"><link href="../css/global.cssquot; rel="stylesheet"
        type="text/css" ><link href="../css/global.cssquot; rel="stylesheet"
        type="text/css" ><!--[if lte IE 7]>
      


  <link href="skins/standard/IE-fixes.css" rel="stylesheet"
        type="text/css" >
<![endif]-->

    <link href="../css/dusk.cssquot; rel="stylesheet"
        type="text/css" title="Dusk"><link href="../css/dusk.cssquot; rel="stylesheet"
        type="text/css" title="Dusk">

    

    

    
<script type="text/javascript" src="js/yui/yahoo-dom-event/yahoo-dom-event.js"></script><script type="text/javascript" src="js/yui/cookie/cookie-min.js"></script><script type="text/javascript" src="js/global.js"></script>

    <script type="text/javascript">
    <!--
        YAHOO.namespace('bugzilla');
        YAHOO.util.Event.addListener = function (el, sType, fn, obj, overrideContext) {
               if ( ("onpagehide" in window || YAHOO.env.ua.gecko) && sType === "unload") { sType = "pagehide"; };
               var capture = ((sType == "focusin" || sType == "focusout") && !YAHOO.env.ua.ie) ? true : false;
               return this._addListener(el, this._getType(sType), fn, obj, overrideContext, capture);
         };
        if ( "onpagehide" in window || YAHOO.env.ua.gecko) {
            YAHOO.util.Event._simpleRemove(window, "unload", 
                                           YAHOO.util.Event._unload);
        }
        
        function unhide_language_selector() { 
            YAHOO.util.Dom.removeClass(
                'lang_links_container', 'bz_default_hidden'
            ); 
        } 
        YAHOO.util.Event.onDOMReady(unhide_language_selector);

        
        var BUGZILLA = {
            param: {
                cookiepath: '\/bugzilla\/',
                maxusermatches: 1000
            },
            constant: {
                COMMENT_COLS: 80
            },
            string: {
                

                attach_desc_required:
                    'You must enter a Description for this attachment.',
                component_required:
                    'You must select a Component for this bug.',
                description_required:
                    'You must enter a Description for this bug.',
                short_desc_required:
                    'You must enter a Summary for this bug.',
                version_required:
                    'You must select a Version for this bug.'
            }
        };

    // -->
    </script>


    

    
    <link rel="search" type="application/opensearchdescription+xml"
                       title="Bugzilla" href="./search_plugin.cgi">
    <link rel="shortcut icon" href="images/favicon.ico" >
  </head>



  <body onload=""
        class="fiji-sc-bugzilla yui-skin-sam">



<div id="header">
<div id="banner">
  </div>

<table border="0" cellspacing="0" cellpadding="0" id="titles">
<tr>
    <td id="title">
      <p>Bugzilla &ndash; Suspicious Action</p>
    </td>


</tr>
</table>

<table id="lang_links_container" cellpadding="0" cellspacing="0"
       class="bz_default_hidden"><tr><td>
</td></tr></table>
<ul class="links">
  <li><a href="./">Home</a></li>
  <li><span class="separator">| </span><a href="enter_bug.cgi">New</a></li>
  <li><span class="separator">| </span><a href="query.cgi">Search</a></li>

  <li class="form">
    <span class="separator">| </span>
    <form action="buglist.cgi" method="get"
        onsubmit="if (this.quicksearch.value == '')
                  { alert('Please enter one or more search terms first.');
                    return false; } return true;">
    <input type="hidden" id="no_redirect_top" name="no_redirect" value="0">
    <script type="text/javascript">
      if (history && history.replaceState) {
        var no_redirect = document.getElementById("no_redirect_top");
        no_redirect.value = 1;
      }
    </script>
    <input class="txt" type="text" id="quicksearch_top" name="quicksearch" 
           title="Quick Search" value="">
    <input class="btn" type="submit" value="Search" 
           id="find_top"></form>

  <li><span class="separator">| </span><a href="report.cgi">Reports</a></li>

  <li></li>

    <li><span class="separator">| </span><a href="userprefs.cgi">Preferences</a></li>


    <li>
      <span class="separator">| </span>
        <a href="index.cgi?logout=1">Log&nbsp;out</a>
        esf&#64;stanford.edu</li>
</ul>
</div> 



  

    

      ⚠
      
        

        NOTICE! This is a static HTML version of a legacy Fiji BugZilla bug.
        

        

        The Fiji project now
        uses GitHub Issues for issue tracking.
        

        

        Please
        file all new issues
        there.
        

      		
    

  




<div id="bugzilla-body">

  <div class="throw_error">
    It looks like you didn't come from the right page (you have no valid token for
    the <em>create_bug</em> action while processing the
    'post_bug.cgi' script). The reason could be one of:<br>
    <ul>
      <li>You clicked the "Back" button of your web browser after having successfully
      submitted changes, which is generally not a good idea (but harmless).</li>
      <li>You entered the URL in the address bar of your web browser directly,
      which should be safe.</li>
      <li>You clicked on a URL which redirected you here <b>without your consent</b>,
      in which case this action is much more critical.</li>
    </ul>
    Are you sure you want to commit these changes anyway? This may result in
    unexpected and undesired results.
  </div>

  <form name="check" id="check" method="post" action="post_bug.cgi"><input type="hidden" name="priority"
             value="P4">
  
      <input type="hidden" name="bug_file_loc"
             value="http://">
  
      <input type="hidden" name="cc"
             value="esf&#64;stanford.edu">
  
      <input type="hidden" name="rep_platform"
             value="Macintosh">
  
      <input type="hidden" name="blocked"
             value="">
  
      <input type="hidden" name="assigned_to"
             value="">
  
      <input type="hidden" name="short_desc"
             value="Analyze particles not working">
  
      <input type="hidden" name="token"
             value="KwbNebQZqN">
  
      <input type="hidden" name="bug_severity"
             value="normal">
  
      <input type="hidden" name="bug_status"
             value="NEW">
  
      <input type="hidden" name="version"
             value="unspecified">
  
      <input type="hidden" name="estimated_time"
             value="">
  
      <input type="hidden" name="deadline"
             value="">
  
      <input type="hidden" name="comment"
             value="Hi, &#013;&#013;I recently updated FIJI, and now analyze particles isn't working on single images. It works on stacks. I've tried with a macro and manually, and neither way is working. Here's what I'm doing:&#013;&#013;Macro:&#013;&#013;run(&quot;Set Measurements...&quot;, &quot;area mean standard median limit redirect=None decimal=3&quot;);&#013;setAutoThreshold(&quot;Default dark&quot;);&#013;//run(&quot;Threshold...&quot;);&#013;setThreshold(0.0100, 10);&#013;run(&quot;Analyze Particles...&quot;, &quot;size=10-infinity pixel display summarize&quot;);&#013;run(&quot;Distribution...&quot;, &quot;parameter=Median or=20 and=0-3&quot;);&#013;&#013;Exception:&#013;&#013;(Fiji Is Just) ImageJ 2.0.0-rc-29/1.49r; Java 1.6.0_65 [64-bit]; Mac OS X 10.10.2; 27MB of 2279MB (1%)&#013; &#013;java.lang.ArrayIndexOutOfBoundsException: -1&#013;	at ij.process.FloatStatistics.getMedian(FloatStatistics.java:240)&#013;	at ij.process.FloatStatistics.&lt;init&gt;(FloatStatistics.java:38)&#013;	at ij.plugin.filter.ParticleAnalyzer.getStatistics(ParticleAnalyzer.java:888)&#013;	at ij.plugin.filter.ParticleAnalyzer.analyzeParticle(ParticleAnalyzer.java:838)&#013;	at ij.plugin.filter.ParticleAnalyzer.analyze(ParticleAnalyzer.java:572)&#013;	at ij.plugin.filter.ParticleAnalyzer.run(ParticleAnalyzer.java:254)&#013;	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:263)&#013;	at ij.plugin.filter.PlugInFilterRunner.&lt;init&gt;(PlugInFilterRunner.java:112)&#013;	at ij.IJ.runPlugIn(IJ.java:171)&#013;	at ij.Executer.runCommand(Executer.java:131)&#013;	at ij.Executer.run(Executer.java:64)&#013;	at java.lang.Thread.run(Thread.java:695)&#013;&#013;Information about your version of Java:&#013;&#013;  os.arch =&gt; x86_64&#013;  os.name =&gt; Mac OS X&#013;  os.version =&gt; 10.10.2&#013;  java.version =&gt; 1.6.0_65&#013;  java.vendor =&gt; Apple Inc.&#013;  java.runtime.name =&gt; Java(TM) SE Runtime Environment&#013;  java.runtime.version =&gt; 1.6.0_65-b14-466.1-11M4716&#013;  java.vm.name =&gt; Java HotSpot(TM) 64-Bit Server VM&#013;  java.vm.version =&gt; 20.65-b04-466.1&#013;  java.vm.vendor =&gt; Apple Inc.&#013;  java.vm.info =&gt; mixed mode&#013;  java.awt.graphicsenv =&gt; apple.awt.CGraphicsEnvironment&#013;  java.specification.name =&gt; Java Platform API Specification&#013;  java.specification.version =&gt; 1.6&#013;  sun.cpu.endian =&gt; little&#013;  sun.desktop =&gt; null&#013;  file.separator =&gt; /&#013;&#013;The up-to-date check says: REMIND_LATER&#013;&#013;Information relevant to JAVA_HOME related problems:&#013;&#013;  JAVA_HOME is set to: null&#013;  imagej.dir =&gt; /Applications/Fiji.app&#013;&#013;Information about the version of each plugin:&#013;&#013;Activated update sites:&#013;ImageJ: http://update.imagej.net/ (last check:20150421185343)&#013;Fiji: http://fiji.sc/update/ (last check:20150422041240)&#013;&#013;Files not up-to-date:&#013;  1ad3be0d (LOCAL_ONLY) 20140902085109 jars/jpedalSTD.jar&#013;">
  
      <input type="hidden" name="component"
             value="Plugins">
  
      <input type="hidden" name="dependson"
             value="">
  
      <input type="hidden" name="hidden"
             value="enter_bug&#013;">
  
      <input type="hidden" name="target_milestone"
             value="---">
  
      <input type="hidden" name="product"
             value="Fiji">
  
      <input type="hidden" name="commentprivacy"
             value="0">
  
      <input type="hidden" name="op_sys"
             value="Mac OS">
    <input type="submit" id="confirm" value="Confirm Changes">
  </form>
  <p>Or throw away these changes and go back to <a href="index.cgi">index.cgi</a>.</p>
</div>



<div id="footer">
  <div class="intro"></div>




<ul id="useful-links">
  <li id="links-actions"><ul class="links">
  <li><a href="./">Home</a></li>
  <li><span class="separator">| </span><a href="enter_bug.cgi">New</a></li>
  <li><span class="separator">| </span><a href="query.cgi">Search</a></li>

  <li class="form">
    <span class="separator">| </span>
    <form action="buglist.cgi" method="get"
        onsubmit="if (this.quicksearch.value == '')
                  { alert('Please enter one or more search terms first.');
                    return false; } return true;">
    <input type="hidden" id="no_redirect_bottom" name="no_redirect" value="0">
    <script type="text/javascript">
      if (history && history.replaceState) {
        var no_redirect = document.getElementById("no_redirect_bottom");
        no_redirect.value = 1;
      }
    </script>
    <input class="txt" type="text" id="quicksearch_bottom" name="quicksearch" 
           title="Quick Search" value="">
    <input class="btn" type="submit" value="Search" 
           id="find_bottom"></form>

  <li><span class="separator">| </span><a href="report.cgi">Reports</a></li>

  <li></li>

    <li><span class="separator">| </span><a href="userprefs.cgi">Preferences</a></li>


    <li>
      <span class="separator">| </span>
        <a href="index.cgi?logout=1">Log&nbsp;out</a>
        esf&#64;stanford.edu</li>
</ul>
  </li>

  
    
    <li id="links-saved">
      <ul class="links">
          <li><a href="buglist.cgi?resolution=---&amp;emailassigned_to1=1&amp;emailreporter1=1&amp;emailtype1=exact&amp;email1=esf%40stanford.edu">My Bugs</a></li>

      </ul>
    </li>


  
</ul>

  <div class="outro"></div>
</div>


</body>
</html>

--------------------------

--------------------------

Login Reply Page:

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
                      "http://www.w3.org/TR/html4/loose.dtd">
<html lang="en">
  <head>
    <title>Enter Bug</title>

      <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">


<link rel="Top" href="http://fiji.sc/bugzilla/">

  


  


  
    <link rel="Saved&nbsp;Searches" title="My Bugs"
          href="buglist.cgi?resolution=---&amp;emailassigned_to1=1&amp;emailreporter1=1&amp;emailtype1=exact&amp;email1=esf%40stanford.edu">



    
    <link href="../css/global.cssquot;
          rel="alternate stylesheet" 
          title="Classic"><link href="../css/global.cssquot; rel="stylesheet"
        type="text/css" ><!--[if lte IE 7]>
      


  <link href="skins/standard/IE-fixes.css" rel="stylesheet"
        type="text/css" >
<![endif]-->

    <link href="../css/dusk.cssquot; rel="stylesheet"
        type="text/css" title="Dusk">

    

    

    
<script type="text/javascript" src="js/yui/yahoo-dom-event/yahoo-dom-event.js"></script><script type="text/javascript" src="js/yui/cookie/cookie-min.js"></script><script type="text/javascript" src="js/global.js"></script>

    <script type="text/javascript">
    <!--
        YAHOO.namespace('bugzilla');
        YAHOO.util.Event.addListener = function (el, sType, fn, obj, overrideContext) {
               if ( ("onpagehide" in window || YAHOO.env.ua.gecko) && sType === "unload") { sType = "pagehide"; };
               var capture = ((sType == "focusin" || sType == "focusout") && !YAHOO.env.ua.ie) ? true : false;
               return this._addListener(el, this._getType(sType), fn, obj, overrideContext, capture);
         };
        if ( "onpagehide" in window || YAHOO.env.ua.gecko) {
            YAHOO.util.Event._simpleRemove(window, "unload", 
                                           YAHOO.util.Event._unload);
        }
        
        function unhide_language_selector() { 
            YAHOO.util.Dom.removeClass(
                'lang_links_container', 'bz_default_hidden'
            ); 
        } 
        YAHOO.util.Event.onDOMReady(unhide_language_selector);

        
        var BUGZILLA = {
            param: {
                cookiepath: '\/bugzilla\/',
                maxusermatches: 1000
            },
            constant: {
                COMMENT_COLS: 80
            },
            string: {
                

                attach_desc_required:
                    'You must enter a Description for this attachment.',
                component_required:
                    'You must select a Component for this bug.',
                description_required:
                    'You must enter a Description for this bug.',
                short_desc_required:
                    'You must enter a Summary for this bug.',
                version_required:
                    'You must select a Version for this bug.'
            }
        };

    // -->
    </script>


    

    
    <link rel="search" type="application/opensearchdescription+xml"
                       title="Bugzilla" href="./search_plugin.cgi">
    <link rel="shortcut icon" href="images/favicon.ico" >
  </head>



  <body onload=""
        class="fiji-sc-bugzilla yui-skin-sam">



<div id="header">
<div id="banner">
  </div>

<table border="0" cellspacing="0" cellpadding="0" id="titles">
<tr>
    <td id="title">
      <p>Bugzilla &ndash; Enter Bug</p>
    </td>


</tr>
</table>

<table id="lang_links_container" cellpadding="0" cellspacing="0"
       class="bz_default_hidden"><tr><td>
</td></tr></table>
<ul class="links">
  <li><a href="./">Home</a></li>
  <li><span class="separator">| </span><a href="enter_bug.cgi">New</a></li>
  <li><span class="separator">| </span><a href="query.cgi">Search</a></li>

  <li class="form">
    <span class="separator">| </span>
    <form action="buglist.cgi" method="get"
        onsubmit="if (this.quicksearch.value == '')
                  { alert('Please enter one or more search terms first.');
                    return false; } return true;">
    <input type="hidden" id="no_redirect_top" name="no_redirect" value="0">
    <script type="text/javascript">
      if (history && history.replaceState) {
        var no_redirect = document.getElementById("no_redirect_top");
        no_redirect.value = 1;
      }
    </script>
    <input class="txt" type="text" id="quicksearch_top" name="quicksearch" 
           title="Quick Search" value="">
    <input class="btn" type="submit" value="Search" 
           id="find_top"></form>

  <li><span class="separator">| </span><a href="report.cgi">Reports</a></li>

  <li></li>

    <li><span class="separator">| </span><a href="userprefs.cgi">Preferences</a></li>
<li>
        <span class="separator">| </span>
        <a href="docs/en/html/bugreports.html" target="_blank">Help</a>
      </li>

    <li>
      <span class="separator">| </span>
        <a href="index.cgi?logout=1">Log&nbsp;out</a>
        esf&#64;stanford.edu</li>
</ul>
</div> 

<div id="bugzilla-body">

<h2>First, you must pick a product on which to enter a bug: </h2>

<table>


    <tr>
      <th align="right" valign="top">
        <a href="enter_bug.cgi?product=Fiji">Fiji</a>:&nbsp;
      </th>

      <td valign="top">http://fiji.sc/</td>
    </tr>
    <tr>
      <th align="right" valign="top">
        <a href="enter_bug.cgi?product=ImageJ">ImageJ</a>:&nbsp;
      </th>

      <td valign="top">http://imagej.net/</td>
    </tr>
    <tr>
      <th align="right" valign="top">
        <a href="enter_bug.cgi?product=Website">Website</a>:&nbsp;
      </th>

      <td valign="top">http://imagej.net/</td>
    </tr>

  <tr>
    <th colspan="2">&nbsp;</th>
  </tr>

</table>
</div>



<div id="footer">
  <div class="intro"></div>




<ul id="useful-links">
  <li id="links-actions"><ul class="links">
  <li><a href="./">Home</a></li>
  <li><span class="separator">| </span><a href="enter_bug.cgi">New</a></li>
  <li><span class="separator">| </span><a href="query.cgi">Search</a></li>

  <li class="form">
    <span class="separator">| </span>
    <form action="buglist.cgi" method="get"
        onsubmit="if (this.quicksearch.value == '')
                  { alert('Please enter one or more search terms first.');
                    return false; } return true;">
    <input type="hidden" id="no_redirect_bottom" name="no_redirect" value="0">
    <script type="text/javascript">
      if (history && history.replaceState) {
        var no_redirect = document.getElementById("no_redirect_bottom");
        no_redirect.value = 1;
      }
    </script>
    <input class="txt" type="text" id="quicksearch_bottom" name="quicksearch" 
           title="Quick Search" value="">
    <input class="btn" type="submit" value="Search" 
           id="find_bottom"></form>

  <li><span class="separator">| </span><a href="report.cgi">Reports</a></li>

  <li></li>

    <li><span class="separator">| </span><a href="userprefs.cgi">Preferences</a></li>
<li>
        <span class="separator">| </span>
        <a href="docs/en/html/bugreports.html" target="_blank">Help</a>
      </li>

    <li>
      <span class="separator">| </span>
        <a href="index.cgi?logout=1">Log&nbsp;out</a>
        esf&#64;stanford.edu</li>
</ul>
  </li>

  
    
    <li id="links-saved">
      <ul class="links">
          <li><a href="buglist.cgi?resolution=---&amp;emailassigned_to1=1&amp;emailreporter1=1&amp;emailtype1=exact&amp;email1=esf%40stanford.edu">My Bugs</a></li>

      </ul>
    </li>


  
</ul>

  <div class="outro"></div>
</div>


</body>
</html>

--------------------------

Please help!

Thanks,
ESF
Comment 1 Mark Hiner 2015-04-24 07:52:39 CDT 
Hi Liz,

 Thanks for the report. We had seen the Bug Reporter issue before[1] but didn't realize it was a universal problem. I just confirmed I was unable to report a bug with the bug submitter as well, though.

 I am going to work on fixing the bug submitter immediately.

 In the mean time, I wasn't able to reproduce your analyze particles bug. Are you able to trigger that exception when running your macro on any of the sample images? ("File > Open Samples > ...")

Thanks again,
Mark

[1] https://github.com/fiji/Bug_Submitter/issues/4
Comment 2 Liz 2015-04-24 12:32:33 CDT 
(In reply to Mark Hiner from comment #1)
> Hi Liz,
> 
>  Thanks for the report. We had seen the Bug Reporter issue before[1] but
> didn't realize it was a universal problem. I just confirmed I was unable to
> report a bug with the bug submitter as well, though.
> 
>  I am going to work on fixing the bug submitter immediately.
> 
>  In the mean time, I wasn't able to reproduce your analyze particles bug.
> Are you able to trigger that exception when running your macro on any of the
> sample images? ("File > Open Samples > ...")
> 
> Thanks again,
> Mark
> 
> [1] https://github.com/fiji/Bug_Submitter/issues/4

Hi Mark, 

Thanks for looking into this! I ended up downloading a Life Line FIJI from Nov. 2014, and analyze particles worked on that for me, so (fortunately or unfortunately) I can no longer reproduce that issue. However, before I did that, I got the same errors for multiple different images multiple times in separate FIJI sessions. Does that help?

Thanks,
Liz
Comment 3 Curtis Rueden 2015-04-24 13:04:15 CDT 
I was also unable to reproduce using the given macro, with a fully updated Fiji from yesterday. I tested using the Blobs sample image.

I am closing as "works for me" -- but if you find a sample image which demonstrates the issue, feel free to reopen the bug with more details!
Comment 4 Mark Hiner 2015-04-24 13:08:38 CDT 
I was just able to reproduce with the given macro and the Shepp-Logan Phantom sample (with default params).

So, maybe it's a 32-bit float pixel type problem?
Comment 5 Liz 2015-04-24 13:12:32 CDT 
(In reply to Mark Hiner from comment #4)
> I was just able to reproduce with the given macro and the Shepp-Logan
> Phantom sample (with default params).
> 
> So, maybe it's a 32-bit float pixel type problem?

Could be - my images are also 32-bit float. I'm glad I'm not the only one seeing this error! Thankfully, earlier versions work, so I'll just use an older FIJI until it's fixed.
Comment 6 Mark Hiner 2015-04-24 13:25:42 CDT 
Oh, of course it requires float data. It's right there in the stack trace. Sorry I missed that.

Anyway, looks like this is a bug in ImageJ 1.x so I'm giving this to Wayne.

The problem is that the getMedian method in FloatStatistics checks for even or odd values: https://github.com/imagej/ImageJA/blob/v1.49r/src/main/java/ij/process/FloatStatistics.java#L239

When the pixel array is empty, size = 0 which tests as even.

This causes index "0 - 1" to be accessed of the pixel array here: https://github.com/imagej/ImageJA/blob/v1.49r/src/main/java/ij/process/FloatStatistics.java#L240

which causes the reported error.

Probably want to either return 0 or throw an exception if there are no pixels..?
Comment 7 Liz 2015-04-24 13:31:19 CDT 
Returning 0 (or NaN or something) if there are no pixels would be great. Thanks!
Comment 8 Wayne Rasband 2015-04-24 19:19:17 CDT 
This bug is fixed in the latest ImageJ daily build (1.49s5). A NaN value is now returned as the median when the pixel count is zero.
Comment 9 Liz 2015-04-25 14:38:35 CDT 
Wonderful, thanks!