[ImageJ-bugs] [Bug 1056] New: Problem opening TIFF files
bugzilla at fiji.sc
bugzilla at fiji.sc
Thu Apr 16 10:06:03 CDT 2015
http://fiji.sc/bugzilla/show_bug.cgi?id=1056
Bug ID: 1056
Summary: Problem opening TIFF files
Product: Fiji
Version: unspecified
Hardware: PC
OS: Windows
Status: NEW
Severity: enhancement
Priority: P5
Component: Bio-Formats
Assignee: imagej-bugs at imagej.net
Reporter: jmjxn at email.unc.edu
I have several 5D tiff stacks. Some open without an issue, but some open the
bioformats dialog (and will not open using the dialog). I have no clue why. I
uploaded a sample image that is giving me the error.
Also, I got the following errors when trying to submit this bug via Fiji:
<!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 Searches" title="My Bugs"
href="buglist.cgi?resolution=---&emailassigned_to1=1&emailreporter1=1&emailtype1=exact&email1=jmjxn%40email.unc.edu">
<link href="skins/standard/global.css"
rel="alternate stylesheet"
title="Classic"><link href="skins/standard/global.css"
rel="stylesheet"
type="text/css" ><link href="skins/standard/global.css"
rel="stylesheet"
type="text/css" ><!--[if lte IE 7]>
<link href="skins/standard/IE-fixes.css" rel="stylesheet"
type="text/css" >
<![endif]-->
<link href="skins/contrib/Dusk/global.css" rel="stylesheet"
type="text/css" title="Dusk"><link href="skins/contrib/Dusk/global.css"
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 – 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="describecomponents.cgi">Browse</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>
<a href="page.cgi?id=quicksearch.html" title="Quicksearch Help">[?]</a></li>
<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 out</a>
jmjxn@email.unc.edu</li>
</ul>
</div>
<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="jmjxn@email.unc.edu">
<input type="hidden" name="rep_platform"
value="PC">
<input type="hidden" name="blocked"
value="">
<input type="hidden" name="assigned_to"
value="">
<input type="hidden" name="short_desc"
value="Problem opening TIFF files">
<input type="hidden" name="token"
value="Yy9VYaC152">
<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="I have several 5D tiff stacks. Some open without an issue,
but some open the bioformats dialog (and will not open using the dialog). I
have no clue why. I uploaded two sample images, one which gives the error and
one which doesn't.
Information about your version of
Java:
os.arch => amd64
os.name => Windows 7
os.version => 6.1
java.version => 1.6.0_24
java.vendor
=> Sun Microsystems Inc.
java.runtime.name => Java(TM) SE Runtime
Environment
java.runtime.version => 1.6.0_24-b07
java.vm.name
=> Java HotSpot(TM) 64-Bit Server VM
java.vm.version =>
19.1-b02
java.vm.vendor => Sun Microsystems Inc.
java.vm.info
=> mixed mode
java.awt.graphicsenv =>
sun.awt.Win32GraphicsEnvironment
java.specification.name => Java
Platform API Specification
java.specification.version => 1.6
sun.cpu.endian => little
sun.desktop => windows
file.separator => \
The up-to-date check says:
CHECK_TURNED_OFF
Information relevant to JAVA_HOME related
problems:
JAVA_HOME is set to:
C:\Users\Matt\Desktop\Fiji.app/java/win64/jdk1.6.0_24//jre
imagej.dir
=> C:\Users\Matt\Desktop\Fiji.app
Information about the version
of each plugin:
Activated update sites:
ImageJ:
http://update.imagej.net/ (last check:20150203171720)
Fiji:
http://fiji.sc/update/ (last check:20150203171758)
Files not
up-to-date:
eb1fd0b1 (MODIFIED) 20150416105739 jars/ij-1.49m.jar
1ad3be0d (LOCAL_ONLY) 20141217044922 jars/jpedalSTD.jar
d3f6a936
(LOCAL_ONLY) 20150102161842 macros/AutoContrast.ijm
a587f1b3
(LOCAL_ONLY) 20141219111731 macros/BatchMacro.ijm
205b2a59 (LOCAL_ONLY)
20141219111154 macros/BatchRotat.txt
9a04d266 (LOCAL_ONLY)
20141219105247 macros/RotateLeft90.ijm
12e6f5b3 (LOCAL_ONLY)
20141219104949 macros/RotateLeft90.txt
2cd8b322 (LOCAL_ONLY)
20141219110909 macros/RotateLeft_batch.ijm
163c68ed (LOCAL_ONLY)
20150102175000 macros/Stitching+Analysis.ijm
d4d09e8f (LOCAL_ONLY)
20150108132410 macros/Stitching+Analysis_time.ijm
89f41efe (LOCAL_ONLY)
20150223145032
plugins/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3.class
b378efaf (LOCAL_ONLY) 20150223145032
plugins/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3/Matrice.class
324f76ae (LOCAL_ONLY) 20150223145034
plugins/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3/poinToolbarBis.class
f73e543f (LOCAL_ONLY) 20150223145032
plugins/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3/pointActionBis.class
2937bc66 (LOCAL_ONLY) 20150223145032
plugins/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3/pointHandlerBis.class
1c0c7603 (LOCAL_ONLY) 20150223145034
plugins/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3/pointPickerClearAllBis.class
83dbc2b3 (LOCAL_ONLY) 20150223145034
plugins/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3/pointPickerColorSettingsBis.class
36975694 (LOCAL_ONLY) 20150223145034
plugins/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3/pointPickerFileBis.class
20c55e1c (LOCAL_ONLY) 20150223145034
plugins/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3/pointPickerTerminateBis.class
06ebfc11 (LOCAL_ONLY) 20150223145034
plugins/A_posteriori_shading_correction_514_v3/A_posteriori_shading_correction_514_v3/src/A_posteriori_shading_correction_514_v3.txt
54e92988 (LOCAL_ONLY) 20150103154517
plugins/ActionBar/ImageSelector_.txt
0786c282 (LOCAL_ONLY)
20150102182035 plugins/ActionBar/new_action_bar.txt
3ac631b6
(LOCAL_ONLY) 20150128094625 plugins/Calculator_Plus.class
203df37a
(LOCAL_ONLY) 20141230151731 plugins/Time_Series_Analyzer.jar
be06fe59
(LOCAL_ONLY) 20150102181404 plugins/action_bar202.jar
">
<input type="hidden" name="component"
value="Plugins">
<input type="hidden" name="dependson"
value="">
<input type="hidden" name="hidden"
value="enter_bug
">
<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="Windows">
<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="describecomponents.cgi">Browse</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>
<a href="page.cgi?id=quicksearch.html" title="Quicksearch Help">[?]</a></li>
<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 out</a>
jmjxn@email.unc.edu</li>
</ul>
</li>
<li id="links-saved">
<ul class="links">
<li><a
href="buglist.cgi?resolution=---&emailassigned_to1=1&emailreporter1=1&emailtype1=exact&email1=jmjxn%40email.unc.edu">My
Bugs</a></li>
</ul>
</li>
</ul>
<div class="outro"></div>
</div>
</body>
</html>
<!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 Searches" title="My Bugs"
href="buglist.cgi?resolution=---&emailassigned_to1=1&emailreporter1=1&emailtype1=exact&email1=jmjxn%40email.unc.edu">
<link href="skins/standard/global.css"
rel="alternate stylesheet"
title="Classic"><link href="skins/standard/global.css"
rel="stylesheet"
type="text/css" ><!--[if lte IE 7]>
<link href="skins/standard/IE-fixes.css" rel="stylesheet"
type="text/css" >
<![endif]-->
<link href="skins/contrib/Dusk/global.css" 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 – 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="describecomponents.cgi">Browse</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>
<a href="page.cgi?id=quicksearch.html" title="Quicksearch Help">[?]</a></li>
<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 out</a>
jmjxn@email.unc.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>:
</th>
<td valign="top">http://fiji.sc/</td>
</tr>
<tr>
<th align="right" valign="top">
<a href="enter_bug.cgi?product=ImageJ">ImageJ</a>:
</th>
<td valign="top">http://imagej.net/</td>
</tr>
<tr>
<th align="right" valign="top">
<a href="enter_bug.cgi?product=Website">Website</a>:
</th>
<td valign="top">http://imagej.net/</td>
</tr>
<tr>
<th colspan="2"> </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="describecomponents.cgi">Browse</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>
<a href="page.cgi?id=quicksearch.html" title="Quicksearch Help">[?]</a></li>
<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 out</a>
jmjxn@email.unc.edu</li>
</ul>
</li>
<li id="links-saved">
<ul class="links">
<li><a
href="buglist.cgi?resolution=---&emailassigned_to1=1&emailreporter1=1&emailtype1=exact&email1=jmjxn%40email.unc.edu">My
Bugs</a></li>
</ul>
</li>
</ul>
<div class="outro"></div>
</div>
</body>
</html>
--
You are receiving this mail because:
You are the assignee for the bug.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-bugs/attachments/20150416/76307d54/attachment-0001.html>
More information about the Imagej-bugs
mailing list