diff --git a/config/samples/hrm.conf.sample b/config/samples/hrm.conf.sample index c09b64cc0..ea261d3a3 100644 --- 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 index d921aa6a0..9fdc7a0db 100644 --- a/estimate_snr_from_image.php +++ b/estimate_snr_from_image.php @@ -48,11 +48,11 @@ function showFileBrowser() { $additionalHTMLElements = " -
+
- + \"?\" SNR estimation algorithm @@ -104,7 +104,10 @@ function showFileBrowser() {

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.

'; + conditions.

+ +

You have a choice of two SNR estimation algorithms. Please click + on the corresponding help button for additional information.

'; if ($type != "") { $info .= "

Only images of type $type, as set in the image @@ -138,10 +141,6 @@ function showFileBrowser() { // validity of the estimate. function estimateSnrFromFile($file) { - // If using IE make sure to enforce IE7 Document Mode - if ( using_IE( ) ) { - $meta = ""; - } include("header.inc.php"); $top_nav_left = get_wiki_link('HuygensRemoteManagerHelpSnrEstimator'); diff --git a/header.inc.php b/header.inc.php index 2b13afef5..43d19985f 100644 --- a/header.inc.php +++ b/header.inc.php @@ -17,8 +17,8 @@ '; } ?> @@ -85,17 +85,13 @@ ?> - + + diff --git a/image_format.php b/image_format.php index bb52fd89a..b4ede3027 100644 --- a/image_format.php +++ b/image_format.php @@ -71,7 +71,7 @@ **************************************************************************** */ // Javascript includes -$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) {

Quick help

-

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.

+

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.

diff --git a/inc/FileBrowser.inc.php b/inc/FileBrowser.inc.php index aed773229..d51f48f4d 100644 --- 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 = ""; -} - include("header.inc.php"); @@ -407,7 +402,11 @@ function imageAction (list) { @@ -438,20 +437,20 @@ function imageAction (list) {
- + - +

<?php src= width="40"/>   

-