Merge remote-tracking branch 'origin/fix/3.2.2'

aarpon · Jun 28, 2015 · e62336c · e62336c
2 parents 8690c31 + 346975b
commit e62336c
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Showing 16 changed files with 325 additions and 139 deletions.
diff --git a/config/samples/hrm.conf.sample b/config/samples/hrm.conf.sample
@@ -6,14 +6,14 @@
 # Copyright and license notice: see license.txt
 
 # HRM install directory
-HRM_HOME="/path/to/hrm/home"
+HRM_HOME="/var/www/html/hrm"
 
 # HRM image share
-HRM_DATA="/path/to/hrm/data"
+HRM_DATA="/scratch/hrm_data"
 
 # Source and destination folder names
-HRM_SOURCE="huygens_src"
-HRM_DEST="huygens_dst"
+HRM_SOURCE="src"
+HRM_DEST="dst"
 
 # file mode to use for user directories
 FILE_MODE=0775
@@ -28,7 +28,7 @@ HRM_LOG="/var/log/hrm"
 
 # Interaction with OMERO (if switched on in hrm/config).
 # OMERO_PKG specifies the path where the "OMERO.server" package is installed
-OMERO_PKG="/path/to/OMERO.server"
+OMERO_PKG="/opt/OMERO/OMERO.server-5.0.3-ice34-b41.linux"
 OMERO_HOSTNAME="localhost"
 OMERO_PORT="4064"
 

diff --git a/estimate_snr_from_image.php b/estimate_snr_from_image.php
@@ -48,11 +48,11 @@ function showFileBrowser() {
 
     $additionalHTMLElements = "
              <!-- SNR estimation algorithm -->
-             <fieldset class=\"setting\"
-               onmouseover=\"javascript:changeQuickHelp( 'method' );\" >
+             <fieldset class=\"setting\" >
 
                  <legend>
-                     <a href=\"javascript:openWindow('#')\">
+                     <a href=\"javascript:openWindow(
+                       'http://www.svi.nl/HuygensRemoteManagerHelpSNREstimationAlgorithm')\">
                        <img src=\"images/help.png\" alt=\"?\" /></a>
                        SNR estimation algorithm
                  </legend>
@@ -104,7 +104,10 @@ function showFileBrowser() {
             <p>Select a raw image to estimate the Signal-to-Noise Ratio (SNR).
                You can then use the estimated SNR values in the Restoration
                Settings to deconvolve similar images, acquired under similar
-               conditions.</p>';
+               conditions.</p>
+
+            <p>You have a choice of two SNR estimation algorithms. Please click
+               on the corresponding help button for additional information.</p>';
 
     if ($type != "") {
         $info .= "<p>Only images of type <b>$type</b>, as set in the image
@@ -138,10 +141,6 @@ function showFileBrowser() {
 // validity of the estimate.
 function estimateSnrFromFile($file) {
 
-    // If using IE make sure to enforce IE7 Document Mode
-    if ( using_IE( ) ) {
-        $meta = "<meta http-equiv=\"X-UA-Compatible\" content=\"IE=7.5\" >";
-    }
     include("header.inc.php");
 
     $top_nav_left = get_wiki_link('HuygensRemoteManagerHelpSnrEstimator');

diff --git a/header.inc.php b/header.inc.php
@@ -17,8 +17,8 @@
 <head>
 <?php
 
-if (isset($meta)) {
-  echo "    ".$meta;
+if (using_IE()) {
+    echo '<meta http-equiv="X-UA-Compatible" content="IE=Edge"/>';
 }
 
 ?>
@@ -85,17 +85,13 @@
 
 
 ?>
-    <style type="text/css">
-
-<?php
-    if (using_IE () ) {
-        echo '@import url("css/default_ie.css");';
-    } else {
-        echo '@import url("css/default.css");';
-    }
-?>
-
-    </style>
+    <link rel="stylesheet" href="css/default.css">
+    <!--[if lt IE 9]>
+    <h3>This browser is OBSOLETE and is known to have important issues with the HRM.
+        Please upgrade to a later version of Internet Explorer or to a new
+        broswer altogether.</h3>
+    <link rel="stylesheet" href="css/default_ie.css">
+    <![endif]-->
 
 </head>
 

diff --git a/image_format.php b/image_format.php
@@ -71,7 +71,7 @@
  **************************************************************************** */
 
 // Javascript includes
-$script = array( "settings.js", "quickhelp/help.js" );
+$script = array( "settings.js", "quickhelp/help.js",  "quickhelp/imageFormat.js");
 
 include("header.inc.php");
 
@@ -323,9 +323,9 @@ function check($parameter, $value) {
             <h3>Quick help</h3>
 
             <div id="contextHelp">
-              <p>Here you are asked to define whether you want to use a theoretical
-              PSF, or if you instead want to use a measured PSF you distilled
-              with the Huygens software.</p>
+              <p>Here you are asked to define the number of channels in your
+                  data and whether you want to use a theoretical PSF or a
+                  measured PSF you distilled with the Huygens Software.</p>
             </div>
 
 

diff --git a/inc/FileBrowser.inc.php b/inc/FileBrowser.inc.php
@@ -71,7 +71,7 @@ function fileButton($type) {
       $class = "icon update";
       $tip = "Refresh image list";
       break;
-      
+
     case "omeroImport":
         $name    = "getOmeroData";
         $value   = "OMERO Data";
@@ -156,7 +156,7 @@ function fileButton($type) {
 }
 
 if (isset($_POST['getOmeroData']) || isset($_POST['exportToOmero'])) {
-    
+
     if (isset($omeroConnection)) {
         if ($omeroConnection->loggedIn) {
             $omeroTree = $omeroConnection->getLastOmeroTree();
@@ -165,7 +165,7 @@ function fileButton($type) {
 }
 
 if (isset($_POST['importFromOmero'])) {
-    
+
     if (isset($omeroConnection)) {
         if ($omeroConnection->loggedIn) {
             $omeroTree = $omeroConnection->getLastOmeroTree();
@@ -174,7 +174,7 @@ function fileButton($type) {
 }
 
 if (isset($_POST['refreshOmero'])) {
-    
+
     if (isset($omeroConnection)) {
         if ($omeroConnection->loggedIn) {
             $omeroTree = $omeroConnection->getUpdatedOmeroTree();
@@ -183,7 +183,7 @@ function fileButton($type) {
 }
 
     /************ End of code for the interaction with OMERO. **********/
-    
+
 
 
 // JavaScript
@@ -391,11 +391,6 @@ function imageAction (list) {
   $flag = " disabled=\"disabled\"";
 }
 
-// If using IE make sure to enforce IE7 Document Mode
-if ( using_IE( ) ) {
-    $meta = "<meta http-equiv=\"X-UA-Compatible\" content=\"IE=7.5\" >";
-}
-
 include("header.inc.php");
 
 
@@ -407,7 +402,11 @@ function imageAction (list) {
         <div id="navleft">
             <ul>
             <?php
-                wiki_link('HuygensRemoteManagerHelpFileManagement');
+                if (isset($top_nav_left)) {
+                    echo $top_nav_left;
+                } else {
+                    wiki_link('HuygensRemoteManagerHelpFileManagement');
+                }
             ?>
             </ul>
         </div>
@@ -438,20 +437,20 @@ function imageAction (list) {
 
 
     <div id="content" >
-    
+
     <?php if ($page_title == "Raw images") {
     $icon = "./images/rawdata_title.png";
 } else {
     $icon = "./images/results_title.png";
 } ?>
-        
+
 <h3><img alt=<?php echo $page_title;?> src=<?php echo $icon;?> width="40"/>
     &nbsp;&nbsp;<?php echo $page_title; ?></h3>
 
     <form method="post" action="?folder=<?php echo $browse_folder;?>"
         id="file_browser" onsubmit="return confirmSubmit()" >
 
-        <?php 
+        <?php
             // Add additional input elements if defined
             if (isset($additionalHTMLElements)) {
                 echo $additionalHTMLElements;
@@ -467,7 +466,7 @@ function imageAction (list) {
         <div id="userfiles" onmouseover="showPreview()">
           <select name="userfiles[]" id="fileSelection"
                   onchange="javascript:imageAction(this)"
-                  onkeyup="this.blur();this.focus();" 
+                  onkeyup="this.blur();this.focus();"
                   size="<?php echo $size;?>" <?php echo $multiple.$flag ?>>
           <?php
           // Populate the select field with the list of available images:
@@ -499,12 +498,12 @@ function imageAction (list) {
       </div>
       </form>
 
-      
+
       <?php
       include("./omero_UI.php");
-      ?>  
+      ?>
+
 
-
   <div id="upMsg"><!-- do not remove !--></div>