2012-03-21 09:31 aarpon * [r1161] /trunk/inc/Ldap.inc.php: Fixed a bug in how the search DN was assembled in inc/Ldap.inc.php. Added some error logging as well. 2012-03-22 08:57 aarpon * [r1162] /trunk/config/samples/ldap_config.inc.sample, /trunk/inc/Ldap.inc.php: Added possibility to define the base for the DN of the LDAP manager. 2012-03-23 08:57 aarpon * [r1163] /trunk/inc/Ldap.inc.php: One more bug fix in inc/Ldap.inc.php. 2012-04-02 12:34 aarpon * [r1164] /branches/HackathonQueueManager: Created branch HackathonQueueManager. 2012-04-03 09:45 aarpon * [r1165] /branches/HackathonQueueManager/run/QueueManagerUtils.tcl: QueueManagerUtils.tcl collects some networks/socket functionalities. It might be merged into QueueManager.tcl in a later stage. 2012-04-03 10:11 danielsevilla * [r1166] /branches/HackathonQueueManager/run/QueueManager.tcl: Added tcl prototype of a new Queue Manager. 2012-04-03 11:52 danielsevilla * [r1167] /branches/HackathonQueueManager/run/QueueManager.tcl: Read data input fed by the client. 2012-04-03 12:29 danielsevilla * [r1168] /branches/HackathonQueueManager/run/QueueManager.tcl: Read client data in one chunk, no while loop for the time being.. 2012-04-03 12:31 aarpon * [r1169] /branches/HackathonQueueManager/inc/SocketClient.inc.php, /branches/HackathonQueueManager/run/testSocketClient.php: Initial prototype of a PHP socket client. 2012-04-03 14:54 aarpon * [r1170] /branches/HackathonQueueManager/collect.php, /branches/HackathonQueueManager/inc/Collector.inc.php, /branches/HackathonQueueManager/inc/Dispatcher.inc.php, /branches/HackathonQueueManager/inc/SocketClient.inc.php, /branches/HackathonQueueManager/run/testSocketClient.php: (1) Renamed inc/SocketClient.inc.php to inc/Dispatecher.inc.php. (2) Added collect.php and inc/Collector.inc.php, that will take of parsing the reports sent by the queue manager on port 80. 2012-04-03 15:04 danielsevilla * [r1171] /branches/HackathonQueueManager/run/QueueManager.tcl: Send an Ok message to the client if the data transfer was successful. 2012-04-03 16:59 aarpon * [r1172] /branches/HackathonQueueManager/inc/Dispatcher.inc.php, /branches/HackathonQueueManager/run/testSocketClient.php: Modified Dispatcher to use stream_sockets instead of sockets. 2012-04-04 08:15 aarpon * [r1173] /branches/HackathonQueueManager/inc/Dispatcher.inc.php, /branches/HackathonQueueManager/run/testSocketClient.php: More tweaking of the Dispatcher class. 2012-04-04 08:26 danielsevilla * [r1174] /branches/HackathonQueueManager/run/QueueManager.tcl: Added exit signal to close the server if the client says so (testing). 2012-04-04 08:31 aarpon * [r1175] /branches/HackathonQueueManager/run/testSocketClient.php: Added test send() to shutdown the socket server. 2012-04-04 09:04 aarpon * [r1176] /branches/HackathonQueueManager/run/QueueManagerUtils.tcl: Small change to address the correct php file for parsing POSTs. 2012-04-04 11:09 danielsevilla * [r1177] /branches/HackathonQueueManager/run/QueueManager.tcl: Added ssh to the processing server (work in progress). 2012-04-04 13:37 danielsevilla * [r1178] /branches/HackathonQueueManager/run/QueueManager.tcl, /branches/HackathonQueueManager/run/QueueManagerUtils.tcl: First additions to enable the Queue Manager to report back to the PHP. 2012-04-04 15:50 aarpon * [r1179] /branches/HackathonQueueManager/capturing_parameter.php, /branches/HackathonQueueManager/css/cupertino_custom, /branches/HackathonQueueManager/css/cupertino_custom/images, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-bg_diagonals-thick_90_eeeeee_40x40.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-bg_flat_15_cd0a0a_40x100.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-bg_glass_100_e4f1fb_1x400.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-bg_glass_50_3baae3_1x400.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-bg_glass_80_d7ebf9_1x400.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-bg_highlight-hard_100_f2f5f7_1x100.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-bg_highlight-hard_70_000000_1x100.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-bg_highlight-soft_25_ffef8f_1x100.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-bg_highlight-soft_55_5c9ccc_1x100.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-icons_2694e8_256x240.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-icons_2e83ff_256x240.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-icons_3d80b3_256x240.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-icons_72a7cf_256x240.png, /branches/HackathonQueueManager/css/cupertino_custom/images/ui-icons_ffffff_256x240.png, /branches/HackathonQueueManager/css/cupertino_custom/jquery-ui-1.8.18.custom.css, /branches/HackathonQueueManager/header.inc.php, /branches/HackathonQueueManager/scripts/common.js, /branches/HackathonQueueManager/scripts/jquery-1.7.2.min.js, /branches/HackathonQueueManager/scripts/jquery-ui-1.8.18.min.js, /branches/HackathonQueueManager/select_parameter_settings.php, /branches/HackathonQueueManager/select_task_settings.php, /branches/HackathonQueueManager/task_parameter.php, /branches/HackathonQueueManager/user_management.php: (1) Added jQuery UI. (2) Replaced standard Javascript dialog with modal jQuery UI dialogs. 2012-04-04 16:03 danielsevilla * [r1180] /branches/HackathonQueueManager/run/QueueManager.tcl: Better handling of sockets and pipes for ssh connections. 2012-04-05 09:11 aarpon * [r1181] /branches/HackathonQueueManager/scripts/jquery-1.7.1.min.js: Removed old jQuery library version. 2012-04-05 13:11 danielsevilla * [r1182] /branches/HackathonQueueManager/run/QueueManager.tcl: Fixed a number of issues at the server side. It should be a bit more robust now. 2012-04-05 13:51 danielsevilla * [r1183] /branches/HackathonQueueManager/run/QueueManager.tcl: Few little on the Queue Manager. 2012-04-05 13:51 aarpon * [r1184] /branches/HackathonQueueManager/inc/ajax, /branches/HackathonQueueManager/inc/ajax/ajax.php, /branches/HackathonQueueManager/scripts/ajax_utils.js, /branches/HackathonQueueManager/scripts/common.js, /branches/HackathonQueueManager/select_parameter_settings.php: Added framework for ajax requests. Prototype action to get the parameter values implemented (to be extended). 2012-04-05 14:03 danielsevilla * [r1185] /branches/HackathonQueueManager/run/QueueManager.tcl, /branches/HackathonQueueManager/run/testSocketClient.php: Forgot to replace one variable declaration. Stop using the sendAndReceive function for the time being. 2012-04-06 08:56 danielsevilla * [r1186] /branches/HackathonQueueManager/run/QueueManager.tcl: Added controls to execute a job template. 2012-04-06 09:46 aarpon * [r1187] /branches/HackathonQueueManager/aberration_correction.php, /branches/HackathonQueueManager/capturing_parameter.php, /branches/HackathonQueueManager/css/default.css, /branches/HackathonQueueManager/css/default_ie.css, /branches/HackathonQueueManager/image_format.php, /branches/HackathonQueueManager/inc/ajax/ajax.php, /branches/HackathonQueueManager/microscope_parameter.php, /branches/HackathonQueueManager/select_psf.php, /branches/HackathonQueueManager/task_parameter.php: (1) Minor modification to the preview of the template parameters (still needs proper formatting). (2) The name of the parameter set is displayed at the top of the editing pages. 2012-04-06 12:36 danielsevilla * [r1188] /branches/HackathonQueueManager/run/QueueManager.tcl: Work on the tasks handled by the Queue Manager/Job Dispatcher. 2012-04-06 12:36 aarpon * [r1189] /branches/HackathonQueueManager/inc/Setting.inc.php, /branches/HackathonQueueManager/inc/ajax/ajax.php, /branches/HackathonQueueManager/scripts/ajax_utils.js, /branches/HackathonQueueManager/select_parameter_settings.php, /branches/HackathonQueueManager/select_task_settings.php: Added support for getting a preview of the parameters also to the task settings. 2012-04-06 13:42 aarpon * [r1190] /branches/HackathonQueueManager/create_job.php, /branches/HackathonQueueManager/inc/Setting.inc.php, /branches/HackathonQueueManager/inc/ajax/ajax.php: Added some simple formatting to the parameter preview. 2012-04-06 13:58 aarpon * [r1191] /branches/HackathonQueueManager/inc/ajax/ajax.php, /branches/HackathonQueueManager/scripts/ajax_utils.js: Made action and function names consistent in inc/ajax/ajax.php and scripts/ajax_utils.js. 2012-04-06 14:14 danielsevilla * [r1192] /branches/HackathonQueueManager/run/QueueManager.tcl: Initial work on the preview generation which will be handled as a first priority task in the future Queue Manager. 2012-04-06 14:36 danielsevilla * [r1193] /branches/HackathonQueueManager/run/QueueManager.tcl: Added basics of the SNR estimation task to the future Queue Manager. Added process id linked to all the server requests coming from clients. 2012-04-06 15:12 danielsevilla * [r1194] /branches/HackathonQueueManager/run/QueueManager.tcl: Register more information related to process id's, socket id's, client id's, etc. 2012-04-06 15:13 aarpon * [r1195] /branches/HackathonQueueManager/css/default.css, /branches/HackathonQueueManager/css/default_ie.css, /branches/HackathonQueueManager/inc/Util.inc.php: (1) Added function to check for IE version 8 and older. (2) Set monospace font for the textarea. 2012-04-09 14:18 aarpon * [r1196] /branches/HackathonQueueManager/scripts/ajax_utils.js, /branches/HackathonQueueManager/select_parameter_settings.php, /branches/HackathonQueueManager/select_task_settings.php: Fixed (yet) another IE8 inconsistency. 2012-04-09 14:20 danielsevilla * [r1197] /branches/HackathonQueueManager/run/QueueManager.tcl: Added a 'dispatchId' counter which will keep track of the number of processes dealt with by the server. 2012-04-09 14:38 danielsevilla * [r1198] /branches/HackathonQueueManager/run/QueueManager.tcl: Added a 'stop' procedure for when users want to delete existing tasks. 2012-04-09 14:57 danielsevilla * [r1199] /branches/HackathonQueueManager/run/QueueManager.tcl: Make use of the 'flushDispatchId' procedure to remove id's that no longer should exist. 2012-05-30 12:38 danielsevilla * [r1200] /branches/hrmColoc: HRM+Coloc 2012-05-30 13:52 danielsevilla * [r1201] /branches/hrmColoc/home.php, /branches/hrmColoc/select_images.php: First changes for a different order of the HRM steps to launch a deconvolution job. 2012-05-30 15:48 danielsevilla * [r1202] /branches/hrmColoc/select_images.php: The image selection page is now the first step of the deconvolution job workflow. 2012-05-30 16:17 danielsevilla * [r1203] /branches/hrmColoc/select_images.php, /branches/hrmColoc/select_parameter_settings.php: More work done to rearrange the stages necessary to launch a job. 2012-05-30 16:28 danielsevilla * [r1204] /branches/hrmColoc/create_job.php, /branches/hrmColoc/image_format.php, /branches/hrmColoc/select_parameter_settings.php, /branches/hrmColoc/select_task_settings.php: The basis of the new stage order is now finished. More work coming to improve these changes. 2012-05-31 08:56 danielsevilla * [r1205] /branches/hrmColoc/select_images.php: Hacked the "select_images" script to get a working version of the job launching workflow. The file selection does not work yet. 2012-06-01 13:53 danielsevilla * [r1206] /branches/hrmColoc/select_images.php: Javascript additions to filter the list of available images by their extensions. This occurs now at the client side. Several aspects of this functionality don't work properly yet, so improvements are still necessary. 2012-06-05 14:08 danielsevilla * [r1207] /branches/hrmColoc/inc/Database.inc.php, /branches/hrmColoc/inc/Setting.inc.php: Removed file format constraints. These must be set somewhere else, but not in the parameter settings, as the file format will not be a microscopic parameter setting any longer. With this change it is already possible to launch deconvolution jobs successfully. The link between confidence levels and file format does not work yet though. 2012-06-05 14:51 danielsevilla * [r1208] /branches/hrmColoc/select_images.php: Remove any selected files when choosing an image file format different from the currently selected format. 2012-06-07 07:53 danielsevilla * [r1209] /branches/hrmColoc/inc/Setting.inc.php, /branches/hrmColoc/select_images.php, /branches/hrmColoc/select_parameter_settings.php: More work to rearrange the stage order necessary to launch a deconvolution job. The confidence levels do work now and are linked to the file format chosen in the first state. Saving the image parameters does not work yet. 2012-06-07 08:51 danielsevilla * [r1210] /branches/hrmColoc/select_parameter_settings.php: Saving new image parameter settings works now properly. The new workflow is now functional and can be tested. 2012-06-07 09:19 danielsevilla * [r1211] /branches/hrmColoc/create_job.php, /branches/hrmColoc/select_images.php, /branches/hrmColoc/select_parameter_settings.php, /branches/hrmColoc/select_task_settings.php: The postprocessing steps will be inserted in the "restoration" stage which will also be renamed as "processing" stage. Go back to 4 stages instead of 5. 2012-06-07 09:43 danielsevilla * [r1212] /branches/hrmColoc/select_parameter_settings.php, /branches/hrmColoc/select_task_settings.php, /branches/hrmColoc/task_parameter.php: Renamed step '3/4 - Restoration parameters' as '3/4 - Processing parameters'. 2012-06-08 09:27 danielsevilla * [r1213] /branches/hrmColoc/inc/Setting.inc.php, /branches/hrmColoc/post_processing.php, /branches/hrmColoc/task_parameter.php: Added post-processing page to the tasks template. Starting to implement the Colocalization subsection. 2012-06-08 10:54 danielsevilla * [r1214] /branches/hrmColoc/inc/System.inc.php, /branches/hrmColoc/post_processing.php, /branches/hrmColoc/setup/dbupdate.php: First dbupdate changes to include the new Colocalization parameters. 2012-06-08 13:35 danielsevilla * [r1215] /branches/hrmColoc/inc/Parameter.inc.php, /branches/hrmColoc/inc/Setting.inc.php, /branches/hrmColoc/post_processing.php, /branches/hrmColoc/scripts/settings.js, /branches/hrmColoc/setup/dbupdate.php: Created a new parameter class 'ColocAnalysis'. 2012-06-08 14:49 danielsevilla * [r1216] /branches/hrmColoc/inc/Setting.inc.php, /branches/hrmColoc/post_processing.php: Saving the colocalization parameters works now. The post processing step is now fully functional. More parameters to be added soon. 2012-06-11 14:02 danielsevilla * [r1217] /branches/hrmColoc/inc/HuygensTemplate.inc.php: Added "colocalization" to the HuygensTemplate class. This is the first working version of this feature. It still contains hardcoded values of several parameters, which needs to be corrected. The Hucore version necessary to run the colocalization analysis is a special build of release 4.2.1p3. 2012-06-11 14:20 danielsevilla * [r1218] /branches/hrmColoc/inc/HuygensTemplate.inc.php: Minor change on the colocalization subtask function: check whether colocalization is needed before proceeding to put the subtask together. 2012-06-12 15:49 danielsevilla * [r1219] /trunk/inc/Job.inc.php: Corrected a few faulty breakline tags. These tags were not properly interpreted by Firefox, showing a far too long sentence in the Parameters tab (image preview). 2012-06-19 13:10 danielsevilla * [r1220] /branches/hrmColoc/css/default.css, /branches/hrmColoc/css/default_ie.css, /branches/hrmColoc/home.php, /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/HuygensTemplate.inc.php, /branches/hrmColoc/inc/Job.inc.php: Second part of Terry Langeveld's internship work on colocalization analysis which adds a colocalization tab to the image preview in HRM. Subsequent corrections by Daniel Sevilla are also committed here. 2012-06-19 14:02 danielsevilla * [r1221] /branches/hrmColoc/css/default.css, /branches/hrmColoc/css/default_ie.css, /branches/hrmColoc/inc/Fileserver.inc.php: Minor changes on the appearance of the colocalization tab. 2012-06-20 09:44 danielsevilla * [r1222] /branches/hrmColoc/footer.inc.php, /branches/hrmColoc/inc/Fileserver.inc.php: (1) Somewhat better code for the coloc tabs. (2) Replaced 2011 with 2012 in the footer. 2012-06-22 16:51 danielsevilla * [r1223] /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/HuygensTemplate.inc.php: Added colocalization maps and 2D histograms to the HuygensTemplate class. This class still contains hardcoded values for several parameters, which has to be corrected the moment that UI asks for those parameters. 2012-07-04 13:29 aarpon * [r1224] /trunk/resources/hrmd.plist.sample: Restored original defaults in resources/hrmd.plist.sample. 2012-07-04 14:13 aarpon * [r1225] /branches/hrmColoc/resources/hrmd.plist.sample: Restored original defaults in resources/hrmd.plist.sample. 2012-07-04 14:16 aarpon * [r1226] /branches/HackathonQueueManager/resources/hrmd.plist.sample: Restored original defaults in resources/hrmd.plist.sample. 2012-07-04 14:18 aarpon * [r1227] /branches/hrmOmero/resources/hrmd.plist.sample: Restored original defaults in resources/hrmd.plist.sample. 2012-07-10 10:30 aarpon * [r1228] /trunk/inc/User.inc.php, /trunk/resources: (1) Bug fixes in User.inc.php. (2) Ignored *.plist in resources. 2012-07-12 14:01 aarpon * [r1229] /branches/hrmColoc/resources: Ignored *.plist files. 2012-07-13 14:07 danielsevilla * [r1230] /trunk/inc/HuygensTemplate.inc.php: Lif subimages other than the first of the series were not deconvolved. This was due to the use of the wrong Huygens template keyword 'subImage' where it should read 'subImg'. 2012-07-13 14:26 danielsevilla * [r1231] /trunk/inc/Job.inc.php: Minor: blank missing between words in warning message. 2012-07-16 11:29 danielsevilla * [r1232] /branches/hrmColoc/inc/Job.inc.php: Slightly better code for the html coloc table. 2012-07-17 08:18 danielsevilla * [r1233] /branches/hrmColoc/css/default.css, /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/Job.inc.php: The 2D histograms should now be properly shown next to the coefficients table in the colocalization tab. 2012-07-19 11:38 danielsevilla * [r1234] /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/HuygensTemplate.inc.php: First version showing colocalization maps. The code will be further improved. 2012-07-19 13:06 danielsevilla * [r1235] /branches/hrmColoc/css/default.css, /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/Job.inc.php: The parameter and colocalization coefficient tables are now shown without borders. 2012-07-19 15:41 danielsevilla * [r1236] /branches/hrmColoc/setup/dbupdate.php: Added more colocalization paramaters to the dbsetup script. The database will be set to revision 10 after this update. 2012-07-20 12:32 danielsevilla * [r1237] /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/Parameter.inc.php, /branches/hrmColoc/inc/Setting.inc.php, /branches/hrmColoc/post_processing.php, /branches/hrmColoc/scripts/settings.js: Added colocalization parameters to the colocalization GUI. Added corresponding classes as well. The chosen parameter values are not yet properly saved to the database along with the other task settings. 2012-07-20 14:14 danielsevilla * [r1238] /branches/hrmColoc/post_processing.php: The colocalization coefficients can now be stored and displayed again when loading a previously saved parameter setting. There are limitations though that have to be corrected: the number of reloaded coefficients is limitied by the number of channels selected in the microscopic template. This is due to internal checks on the parameter classes, which should not apply to this case. 2012-07-20 14:34 danielsevilla * [r1239] /branches/hrmColoc/setup/dbupdate.php: Added more coloc maps options to the dbupdate script. 2012-07-20 14:57 danielsevilla * [r1240] /branches/hrmColoc/inc/Parameter.inc.php, /branches/hrmColoc/post_processing.php: More coloc maps available in the GUI. The choice of coloc maps is now exclusive: only one map can be chosen from the group. 2012-07-23 13:43 danielsevilla * [r1241] /branches/hrmColoc/inc/Parameter.inc.php, /branches/hrmColoc/inc/Setting.inc.php, /branches/hrmColoc/inc/Util.inc.php, /branches/hrmColoc/post_processing.php: Added channel selection to the colocalization post-processing page. 2012-07-24 10:33 danielsevilla * [r1242] /branches/hrmColoc/create_job.php, /branches/hrmColoc/inc/HuygensTemplate.inc.php, /branches/hrmColoc/setup/dbupdate.php: Corrected several colocalization parameter names in the database. Extended the HuygensTemplate class to handle the 'coloc' task appropriately, without hardcoded stuff. 2012-07-24 12:48 danielsevilla * [r1243] /branches/hrmColoc/inc/HuygensTemplate.inc.php: More corrections: the 2D histograms are now generated following the parameters passed in the Huygens template. No hardcoded values any more. 2012-07-24 13:38 danielsevilla * [r1244] /branches/hrmColoc/inc/HuygensTemplate.inc.php: Fixed bug in the 'HuygensTemplate' class. The channels count for colocalization and histogram tasks would be faulty if channel 0 was not included in the user selection. 2012-07-24 16:27 danielsevilla * [r1245] /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/Job.inc.php: Fixed coloc output layout. It was rather messed up when showing several coloc runs on the same image, i.e., several channel combinations. 2012-07-25 10:07 danielsevilla * [r1246] /branches/hrmColoc/css/default.css, /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/Job.inc.php: Fixed remaining issues on the colocalization output layout. These issues were mainly visible when several coloc runs (mixing different channels) where executed in a job. 2012-07-25 12:29 danielsevilla * [r1247] /branches/hrmColoc/inc/Fileserver.inc.php: Improvements in the colocalization maps page. The multiple runs case (more than 2 channels) had several layout problems. 2012-07-26 10:36 danielsevilla * [r1248] /branches/hrmColoc/css/default.css, /branches/hrmColoc/inc/Fileserver.inc.php: Work in progress: CSS additions for the colocalization maps page. 2012-07-26 10:55 danielsevilla * [r1249] /branches/hrmColoc/css/default.css, /branches/hrmColoc/css/default_ie.css, /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/Job.inc.php: Better css naming. Exported several new css entries to the IE CSS version. 2012-07-26 13:56 danielsevilla * [r1250] /branches/hrmColoc/css/default.css, /branches/hrmColoc/css/default_ie.css, /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/Job.inc.php: More layout work on the CSS files. 2012-07-26 15:40 danielsevilla * [r1251] /branches/hrmColoc/css/default.css, /branches/hrmColoc/css/default_ie.css, /branches/hrmColoc/inc/Fileserver.inc.php, /branches/hrmColoc/inc/Job.inc.php, /branches/hrmColoc/inc/Util.inc.php, /branches/hrmColoc/post_processing.php: If the user chose 'No Colocalization Analysis' the colocalization preview page should not be shown. This can be controlled when the Huygens output file is being parse to build the colocalization tables. If the parsing is not successful (because the coloc coefficients do not exist) we can skip saving the data to the coloc file. PS: Some parsing function have now grown out of proportion. The Job and Fileserver classes contain some ugly functions. It should be possible to improve this, though parsing code is often this ugly to look at. 2012-07-26 16:19 danielsevilla * [r1252] /branches/hrmColoc/inc/Parameter.inc.php, /branches/hrmColoc/inc/Setting.inc.php: Added constraints on the channel count selected for colocalization. At least two channels should be selected. 2012-07-27 09:45 danielsevilla * [r1253] /branches/hrmColoc/inc/Parameter.inc.php, /branches/hrmColoc/inc/Setting.inc.php: Adapted the 'ColocCoefficient' class so that it can hold more than 5 values (the parent can hold 5 values at most, since they are linked to the number of channels). Added constraints on the colocalization coefficient choice: at least one coefficient should be selected. 2012-07-27 10:44 danielsevilla * [r1254] /branches/hrmColoc/post_processing.php, /branches/hrmColoc/task_parameter.php: The post procesing page will be shown only if the user selected more than one channel for deconvolution. 2012-07-27 11:53 danielsevilla * [r1255] /branches/coloc: HRM+Coloc (v2.0) 2012-07-27 11:55 danielsevilla * [r1256] /branches/workflow: HRM (new workflow) 2012-07-27 12:02 danielsevilla * [r1257] /branches/newWorkflow, /branches/workflow: Rename branch. 2012-07-27 13:20 danielsevilla * [r1258] /branches/coloc/create_job.php, /branches/coloc/css/default.css, /branches/coloc/css/default_ie.css, /branches/coloc/footer.inc.php, /branches/coloc/home.php, /branches/coloc/inc/Fileserver.inc.php, /branches/coloc/inc/HuygensTemplate.inc.php, /branches/coloc/inc/Job.inc.php, /branches/coloc/inc/Parameter.inc.php, /branches/coloc/inc/Setting.inc.php, /branches/coloc/inc/System.inc.php, /branches/coloc/inc/Util.inc.php, /branches/coloc/post_processing.php, /branches/coloc/scripts/settings.js, /branches/coloc/select_task_settings.php, /branches/coloc/setup/dbupdate.php, /branches/coloc/task_parameter.php: The 'hrmColoc' branch ended up having partial results for other features as well, such as the new workflow design. This is of course not optimal, as we would rather like to keep different branches for different features. This commit includes the colocalization feature only. 2012-07-27 13:47 danielsevilla * [r1259] /branches/newWorkflow/create_job.php, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/footer.inc.php, /branches/newWorkflow/home.php, /branches/newWorkflow/image_format.php, /branches/newWorkflow/inc/Setting.inc.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php, /branches/newWorkflow/setup/dbupdate.php, /branches/newWorkflow/task_parameter.php: The 'hrmColoc' branch ended up having partial results for other features as well, such as the new workflow design. This is of course not optimal, as we would rather like to keep different branches for different features. This commit includes the 'new workflow' feature only. 2012-07-27 13:56 danielsevilla * [r1260] /branches/coloc+newWorkflow, /branches/hrmColoc: Renamed branch: more specific name. 2012-07-31 07:55 danielsevilla * [r1261] /branches/newWorkflow/scripts/common.js, /branches/newWorkflow/select_images.php: Better file matching. All file extensions are now properly recognized. Subimages still present a problem. 2012-07-31 09:02 danielsevilla * [r1262] /trunk/css/default.css, /trunk/css/default_ie.css, /trunk/inc/Parameter.inc.php, /trunk/inc/QueueManager.inc.php: Added confidence level 'asIs' which HuCore now reports for several microscopic parameters of HDF5 files. 2012-07-31 10:34 danielsevilla * [r1263] /branches/coloc/css/default.css, /branches/coloc/css/default_ie.css, /branches/coloc/inc/Parameter.inc.php, /branches/coloc/inc/QueueManager.inc.php: Also add the 'asIs' confidence level to this branch. This should include the same exact changes as the previous trunk commit. This should be handled via merge or when the two branches are finally merged, but is included into this branch now for simplicity and to be able to get the correct confidence levels of the HDF5 format. 2012-07-31 14:26 danielsevilla * [r1264] /branches/coloc/inc/Parameter.inc.php, /branches/coloc/inc/Setting.inc.php, /branches/coloc/post_processing.php, /branches/coloc/scripts/settings.js, /branches/coloc/setup/dbupdate.php: Starting to add a new (and hopefully last) colocalization parameter: colocalization threshold. This parameter will give the user the freedom to choose which percentage of the (background) signal to take into account in the colocalization analysis. 2012-08-01 08:18 danielsevilla * [r1265] /branches/coloc/inc/Parameter.inc.php, /branches/coloc/post_processing.php, /branches/coloc/setup/dbupdate.php: The colocalization threshold code resembles now that of the background offset, since both parameters follow the same choice structure. 2012-08-01 08:46 danielsevilla * [r1266] /branches/coloc/inc/Parameter.inc.php, /branches/coloc/inc/Setting.inc.php: Done with the new colocalization threshold parameter. The value/s of this parameters have now to be inserted into the HuygensTemplate class, so that HuCore can get the threshold information. 2012-08-01 09:12 danielsevilla * [r1267] /branches/coloc/css/default.css, /branches/coloc/css/default_ie.css, /branches/coloc/post_processing.php: Style changes to show the colocalization coefficient names aligned and next to the corresponding checkboxes. 2012-08-01 10:14 danielsevilla * [r1268] /branches/coloc/inc/HuygensTemplate.inc.php: Added the colocalization threshold options to the HuygensTemplate class. The Huygens templates created by HRM contain now all the necessary parameters for the proper colocalization processing. 2012-08-01 10:18 danielsevilla * [r1269] /branches/coloc/post_processing.php: Make sure the "manual" colocalization threshold radiobutton is automatically selected if the users clicks on one of the channel input boxes. 2012-08-01 13:52 danielsevilla * [r1270] /branches/coloc/inc/HuygensTemplate.inc.php: Replaced some 'bg' prefixes with 'thresh' prefixes. 2012-08-03 14:55 aarpon * [r1271] /branches/coloc/inc/System.inc.php, /branches/coloc/setup/dbupdate.php: Added support for Mac OS X Mountain Lion in the system view. 2012-08-03 15:14 danielsevilla * [r1272] /branches/coloc/inc/Job.inc.php: The coloc output by HuCore recently changed. Adapted the parsing functions of the Job class. Some code needs further writing. The coloc coefficients table has not two more columns, one per threshold parameter. Since these parameters are not colocalization coefficients as such they should be excluded from the highlight mechanism at the preview page -> colocalization results. To be continued. 2012-08-06 10:19 danielsevilla * [r1273] /branches/coloc/css/default.css, /branches/coloc/css/default_ie.css, /branches/coloc/inc/Fileserver.inc.php, /branches/coloc/inc/Job.inc.php: The highlight form in the colocalization preview page should only affect the colocalization coefficients, and not the threshold values. 2012-08-06 11:56 danielsevilla * [r1274] /branches/coloc/inc/Setting.inc.php: If the user chooses 'No colocalization analysis' the colocalization parameters should be checked upon posting the choice. 2012-08-06 12:03 danielsevilla * [r1275] /branches/coloc/inc/Setting.inc.php: Replaced capitals with lowercase in 'false' word. 2012-08-06 12:30 danielsevilla * [r1276] /branches/coloc/inc/HuygensTemplate.inc.php: Fixed wrongly named variable. 2012-08-09 13:07 aarpon * [r1277] /branches/2.0.3: Removed old branch 2.0.3. 2012-08-09 13:46 aarpon * [r1278] /trunk, /trunk/create_job.php, /trunk/css/default.css, /trunk/css/default_ie.css, /trunk/footer.inc.php, /trunk/home.php, /trunk/inc/Fileserver.inc.php, /trunk/inc/HuygensTemplate.inc.php, /trunk/inc/Job.inc.php, /trunk/inc/Parameter.inc.php, /trunk/inc/Setting.inc.php, /trunk/inc/System.inc.php, /trunk/inc/Util.inc.php, /trunk/post_processing.php, /trunk/scripts/settings.js, /trunk/select_task_settings.php, /trunk/setup/dbupdate.php, /trunk/task_parameter.php: (1) Merged back coloc branch. (2) Increased HRM version to 3.0. 2012-08-10 07:07 aarpon * [r1279] /trunk/ajax, /trunk/ajax/ajax.php, /trunk/capturing_parameter.php, /trunk/home.php, /trunk/images/logo_bsse.png, /trunk/inc/Shell.inc.php, /trunk/scripts/ajax_utils.js, /trunk/scripts/jquery-1.7.1.min.js, /trunk/scripts/jquery-1.7.2.min.js, /trunk/select_parameter_settings.php, /trunk/select_task_settings.php, /trunk/task_parameter.php: (1) Added AJAX- and timer-based update of the number of jobs in queue in the home page (to replace the original page refresh). (2) Added (AJAX-based) preview of parameters sets. (3) Updated jQuery library to version 1.7.2. 2012-08-10 08:29 danielsevilla * [r1280] /trunk/setup/dbupdate.php: Minor changes in the coloc part of the database setup script: coloc analysis is set to 'No' by default. Also, corrected typo. 2012-08-10 08:52 aarpon * [r1281] /branches/HackathonQueueManager/ajax, /branches/HackathonQueueManager/ajax/ajax.php, /branches/HackathonQueueManager/inc/ajax, /branches/HackathonQueueManager/scripts/ajax_utils.js: Changed the folder structure in the HackathonQueueManager branch to prevent problems when later merging back into trunk. 2012-08-10 10:28 aarpon * [r1282] /trunk/capturing_parameter.php, /trunk/header.inc.php, /trunk/home.php, /trunk/scripts/settings.js, /trunk/select_parameter_settings.php, /trunk/select_task_settings.php, /trunk/task_parameter.php: (1) jQuery is now added to all pages. (2) Fixed hiding/showing coloc parameter fields. 2012-08-10 11:36 aarpon * [r1283] /trunk/ajax/ajax.php, /trunk/home.php: Changed the text that is updated by the getNumberOfJobsInQueue() method in the home page. 2012-08-13 14:12 danielsevilla * [r1284] /trunk/inc/Fileserver.inc.php, /trunk/setup/dbupdate.php: (1) Added coloc run field to the statistics table. (2) Removed the beautiful "NEW" word next to 'colocalization'. 2012-08-13 14:40 danielsevilla * [r1285] /trunk/inc/Database.inc.php, /trunk/setup/dbupdate.php: The statistics table now keeps track of whether or not colocalization analysis was run on this job. 2012-08-13 15:42 danielsevilla * [r1286] /trunk/inc/Database.inc.php, /trunk/inc/Stats.inc.php: The administrator can now see pie charts with the number of colocalization runs per user and per group. To be fixed: coloc is counted even when it is not run. 2012-08-14 08:22 danielsevilla * [r1287] /trunk/inc/Stats.inc.php: (1) Added 'colocFilter' to the pie chart (statistics page). This is necessary to count the coloc runs only and to leave out the runs that didn't perform coloc analysis. (2) Reformatted some very long staments of the Stats class. 2012-08-14 09:21 aarpon * [r1288] /branches/newWorkflow, /branches/newWorkflow/ajax, /branches/newWorkflow/capturing_parameter.php, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/header.inc.php, /branches/newWorkflow/home.php, /branches/newWorkflow/images/logo_bsse.png, /branches/newWorkflow/inc/Database.inc.php, /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/inc/HuygensTemplate.inc.php, /branches/newWorkflow/inc/Job.inc.php, /branches/newWorkflow/inc/Parameter.inc.php, /branches/newWorkflow/inc/QueueManager.inc.php, /branches/newWorkflow/inc/Setting.inc.php, /branches/newWorkflow/inc/Shell.inc.php, /branches/newWorkflow/inc/Stats.inc.php, /branches/newWorkflow/inc/System.inc.php, /branches/newWorkflow/inc/Util.inc.php, /branches/newWorkflow/post_processing.php, /branches/newWorkflow/scripts/ajax_utils.js, /branches/newWorkflow/scripts/jquery-1.7.1.min.js, /branches/newWorkflow/scripts/jquery-1.7.2.min.js, /branches/newWorkflow/scripts/settings.js, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php, /branches/newWorkflow/setup/dbupdate.php, /branches/newWorkflow/task_parameter.php: Merged trunk (revision 1283) into the newWorkflow branch. 2012-08-14 09:55 aarpon * [r1289] /branches/newWorkflow/inc/System.inc.php: After internal discussion, set the HRM version to 2.2. 2012-08-14 09:57 aarpon * [r1290] /branches/coloc: Removed branches/coloc. 2012-08-14 09:57 aarpon * [r1291] /branches/coloc+newWorkflow: Removed branches/coloc+newWorkflow. 2012-08-14 11:36 aarpon * [r1292] /branches/newWorkflow/images/logo_bsse.png: Better bsse logo. 2012-08-14 13:53 danielsevilla * [r1293] /branches/newWorkflow/scripts/common.js: The image filter at the select images stage did not work properly for all lif images. This was due to a faulty pattern matching when the lif images contained subimages. Fixed. 2012-08-14 15:59 aarpon * [r1294] /branches/newWorkflow/aberration_correction.php, /branches/newWorkflow/account.php, /branches/newWorkflow/calculate_pixel_size.php, /branches/newWorkflow/capturing_parameter.php, /branches/newWorkflow/create_job.php, /branches/newWorkflow/footer.inc.php, /branches/newWorkflow/header.inc.php, /branches/newWorkflow/image_format.php, /branches/newWorkflow/job_queue.php, /branches/newWorkflow/microscope_parameter.php, /branches/newWorkflow/post_processing.php, /branches/newWorkflow/scripts/jquery.qtip-1.0.0-rc3.min.js, /branches/newWorkflow/scripts/wz_tooltip, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_psf.php, /branches/newWorkflow/select_task_settings.php, /branches/newWorkflow/task_parameter.php: Replaced Tooltip JavaScript Library by Walter Zorn with jQuery qTip. 2012-08-14 16:18 aarpon * [r1295] /branches/newWorkflow/footer.inc.php, /branches/newWorkflow/home.php: Fixed brace mismatch. 2012-08-15 06:35 aarpon * [r1296] /branches/newWorkflow/footer.inc.php: Added licensing information to the footer. 2012-08-15 06:47 aarpon * [r1297] /branches/newWorkflow/footer.inc.php: Minor cosmetic changes in the tooltip rendering. 2012-08-15 13:29 danielsevilla * [r1298] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/inc/Job.inc.php: Added text reporting scaling factors. This will be shown above the parameter tables, in the parameters tab. 2012-08-15 14:14 danielsevilla * [r1299] /branches/newWorkflow/create_job.php, /branches/newWorkflow/select_analysis_settings.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php: First step to add a new workflow stage 'Analysis'. The new file 'select_analysis_parameters' is at the moment very similar to 'select_task_parameters'. 2012-08-15 14:40 danielsevilla * [r1300] /branches/newWorkflow/coloc_analysis.php, /branches/newWorkflow/post_processing.php, /branches/newWorkflow/select_analysis_settings.php, /branches/newWorkflow/task_parameter.php: Moved the colocalization page from the restoration settings to the analysis settings. 2012-08-16 09:27 danielsevilla * [r1301] /branches/newWorkflow/coloc_analysis.php, /branches/newWorkflow/inc/Parameter.inc.php, /branches/newWorkflow/select_images.php: (1) Fixed bug where the chosen file format was reset upon posting data to the server. (2) The coloc analysis page shows the number of channels again, which first vanished after taking the coloc step out of the processing template. 2012-08-16 09:56 danielsevilla * [r1302] /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php: The confidence levels are now adapted to the file format chosen at stage 1. 2012-08-16 16:12 danielsevilla * [r1303] /branches/newWorkflow/select_images.php: Little improvement on the image selection page. The server contents are now shown more effectively. TODO: Improve the behaviour of the image transfers (up and down arrows, top and bottom selection boxes), better with Ajax? 2012-08-17 08:29 danielsevilla * [r1304] /branches/newWorkflow/setup/dbupdate.php: Extended the database script to add tables for the new 'analysis' templates. 2012-08-17 09:09 danielsevilla * [r1305] /branches/newWorkflow/setup/dbupdate.php: Minor: renamed analysis tables to better stick to the HRM 'standard'. 2012-08-17 15:24 danielsevilla * [r1306] /branches/newWorkflow/coloc_analysis.php, /branches/newWorkflow/inc/Parameter.inc.php, /branches/newWorkflow/inc/Setting.inc.php, /branches/newWorkflow/inc/SettingEditor.inc.php, /branches/newWorkflow/select_analysis_settings.php: Done adding a new analysis settings editor, selector, etc. The new step is near functional. A few adaptations in the HuygensTemplate class are needed. 2012-08-20 09:25 danielsevilla * [r1307] /branches/newWorkflow/create_job.php, /branches/newWorkflow/select_analysis_settings.php: Added the analysis parameters summary to the 'Create a job' stage. 2012-08-20 09:26 danielsevilla * [r1308] /branches/newWorkflow/create_job.php: Forgot to add the analysis parameter set name to the summary. 2012-08-20 12:11 danielsevilla * [r1309] /branches/newWorkflow/create_job.php, /branches/newWorkflow/inc/Database.inc.php, /branches/newWorkflow/inc/HuygensTemplate.inc.php, /branches/newWorkflow/inc/JobDescription.inc.php, /branches/newWorkflow/inc/Setting.inc.php: Finished work on the new Analysis setting. 2012-08-20 13:46 danielsevilla * [r1310] /branches/newWorkflow/inc/JobDescription.inc.php, /branches/newWorkflow/inc/Setting.inc.php: The job analysis settings did not get copied into the database, which stopped the colocalization analysis from being executed. 2012-08-20 15:09 danielsevilla * [r1311] /branches/newWorkflow/create_job.php, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/images/Analysis.png, /branches/newWorkflow/images/Image_Parameters.png, /branches/newWorkflow/images/Launch.png, /branches/newWorkflow/images/Restoration.png, /branches/newWorkflow/images/Select_Images.png, /branches/newWorkflow/inc/FileBrowser.inc.php, /branches/newWorkflow/select_analysis_settings.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php: Trying a few more icons to throw clarity into the different workflow stages. This way the workflow stages are somewhat easier to distinguish at a first glance. Added the 'raw/deconvolved' icons to the corresponding file manager folders as well. 2012-08-20 16:14 danielsevilla * [r1312] /branches/newWorkflow/images/Analysis.png, /branches/newWorkflow/images/Image_Parameters.png, /branches/newWorkflow/images/Launch.png, /branches/newWorkflow/images/Restoration.png, /branches/newWorkflow/images/Select_Images.png, /branches/newWorkflow/images/analysis.png, /branches/newWorkflow/images/image_parameters.png, /branches/newWorkflow/images/launch.png, /branches/newWorkflow/images/restoration.png, /branches/newWorkflow/images/select_images.png: Corrected capital letters in image names. 2012-08-20 16:17 danielsevilla * [r1313] /branches/newWorkflow/create_job.php, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/select_analysis_settings.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php: Corrected capital letters in icon names. 2012-08-21 11:26 aarpon * [r1314] /branches/newWorkflow/ajax/ajax.php, /branches/newWorkflow/home.php, /branches/newWorkflow/job_queue.php, /branches/newWorkflow/scripts/ajax_utils.js: Added and fine-tuned Ajax functionalities to update total and user-owned number of jobs in the queue and to update the job queue table every 10 s. 2012-08-21 11:52 danielsevilla * [r1315] /branches/newWorkflow/create_job.php, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/images/deconvolved.png, /branches/newWorkflow/images/launch_start.png: Trying to polish yesterday's icon proposal. 2012-08-21 12:10 danielsevilla * [r1316] /branches/newWorkflow/inc/Setting.inc.php: Corrected wrong analysis table name. 2012-08-21 12:59 danielsevilla * [r1317] /branches/newWorkflow/create_job.php, /branches/newWorkflow/images/deconvolved.png, /branches/newWorkflow/images/select_images.png: More on the HRM icons. 2012-08-21 15:38 danielsevilla * [r1318] /branches/newWorkflow/aberration_correction.php, /branches/newWorkflow/capturing_parameter.php, /branches/newWorkflow/coloc_analysis.php, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/image_format.php, /branches/newWorkflow/microscope_parameter.php, /branches/newWorkflow/task_parameter.php: Formatting issues: there was too much space around the steps titles. 2012-08-21 15:51 danielsevilla * [r1319] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/image_format.php: Minor: set the 'Quick help' at the same height as the other titles. 2012-08-21 16:26 danielsevilla * [r1320] /branches/newWorkflow/coloc_analysis.php: Fixed a glitch in the coloc analysis page. The threshold percentage did not show the input fields. 2012-08-22 10:55 danielsevilla * [r1321] /branches/newWorkflow/home.php, /branches/newWorkflow/images/analysis.png: First steps to add the analysis template editor to the admin page. 2012-08-22 14:05 danielsevilla * [r1322] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/home.php: A few additions to the admin home panel. 2012-08-22 14:32 danielsevilla * [r1323] /branches/newWorkflow/coloc_analysis.php: The coloc analysis page now works with the number of channels precisely as the restoration parameters page. That is, the number of channels is set to 5 for the administrator and to the number of channels of the image setting for the regular users. This also fixed the Analysis template behaviour in the admin page. It should be optimal now. 2012-08-22 15:19 danielsevilla * [r1324] /branches/newWorkflow/select_parameter_settings.php: Because the image format is no longer chosen at the microscopic parameters step, the edition by the administrator of the corresponding templates resulted in an error. The administrator's templates will be created for general file formats, with no confidence levels. Thus, the administrator will have to enter values for all the parameters. 2012-08-22 15:34 danielsevilla * [r1325] /branches/newWorkflow/home.php: Rearranged icons at the admin panel. 2012-08-23 08:59 danielsevilla * [r1326] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php: Fixed a couple UI flaws: (1) the backward/forward buttons of the image settings page were not aligned with the same buttons of the subsequent pages; (2) The text areas of the create job page had no padding on the right side. 2012-08-23 15:23 danielsevilla * [r1327] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/inc/Job.inc.php: Finish working on the parsing functions of the Job class to be able to report all the (types of) scaling factors. This class and its parsing functions are growing too much. This commit will be followed by some corrections and clean-up. 2012-08-23 16:21 danielsevilla * [r1328] /branches/newWorkflow/inc/Job.inc.php: Clean-up in the parsing functions of the Job class. 2012-08-26 13:05 aarpon * [r1329] /branches/newWorkflow/aberration_correction.php, /branches/newWorkflow/account.php, /branches/newWorkflow/calculate_pixel_size.php, /branches/newWorkflow/capturing_parameter.php, /branches/newWorkflow/create_job.php, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/footer.inc.php, /branches/newWorkflow/header.inc.php, /branches/newWorkflow/image_format.php, /branches/newWorkflow/inc/Setting.inc.php, /branches/newWorkflow/job_queue.php, /branches/newWorkflow/microscope_parameter.php, /branches/newWorkflow/scripts/jquery-1.7.2.min.js, /branches/newWorkflow/scripts/jquery-1.8.0.min.js, /branches/newWorkflow/scripts/jquery.qtip-1.0.0-rc3.min.js, /branches/newWorkflow/scripts/wz_tooltip, /branches/newWorkflow/scripts/wz_tooltip/.htaccess, /branches/newWorkflow/scripts/wz_tooltip/tip_centerwindow.js, /branches/newWorkflow/scripts/wz_tooltip/tip_followscroll.js, /branches/newWorkflow/scripts/wz_tooltip/wz_tooltip.js, /branches/newWorkflow/select_analysis_settings.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_psf.php, /branches/newWorkflow/select_task_settings.php, /branches/newWorkflow/task_parameter.php: (1) Restored the old tooltip library. (2) The (ajax) report of restoration parameters is now correctly filtered by number of channels. (3) Updated jQuery to version 1.8.0. 2012-08-27 06:45 aarpon * [r1330] /branches/newWorkflow/scripts/common.js, /branches/newWorkflow/scripts/settings.js, /branches/newWorkflow/select_images.php: Corrected some Javascript errors. 2012-08-28 09:04 aarpon * [r1331] /branches/newWorkflow/ajax/ajax.php, /branches/newWorkflow/home.php, /branches/newWorkflow/job_queue.php, /branches/newWorkflow/scripts/ajax_utils.js, /branches/newWorkflow/select_analysis_settings.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php: (1) Added prefix (ajax) to all AJAX-based JS functions. (2) Partial implementation of setting the image file format via AJAX calls. 2012-08-29 12:52 danielsevilla * [r1332] /branches/newWorkflow/create_job.php, /branches/newWorkflow/inc/Job.inc.php, /branches/newWorkflow/select_parameter_settings.php: The last commits that reset the tooltips to a previous state also rolled back to old buttons, and button layouts, which is some cases looked crooked. 2012-08-29 14:19 danielsevilla * [r1333] /branches/newWorkflow/select_analysis_settings.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php: Fixed glitch in the template previews. The javascript code was called upon a template change but not upon a template click. The preview was not shown if there was only one template once it one time was selected. 2012-08-29 14:55 danielsevilla * [r1334] /branches/newWorkflow/ajax/ajax.php: Fixed template preview for the analysis parameters. 2012-08-29 15:46 danielsevilla * [r1335] /branches/newWorkflow/select_analysis_settings.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php: Several 'onchange' events were replaced with 'onclick' events in a previous commit. The 'onchange' events should als be present along with 'onclick' so that the event is triggered from both the keyboard and the mouse. 2012-08-29 16:02 danielsevilla * [r1336] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/login.php: The "Welcome" message at the login page was accidentaly changed due to css conflicts. A new css type "welcome" has been added. 2012-08-29 16:22 danielsevilla * [r1337] /branches/newWorkflow/create_job.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php: Corrected several Quick Help texts. 2012-08-30 09:24 danielsevilla * [r1338] /branches/newWorkflow/inc/Setting.inc.php, /branches/newWorkflow/select_images.php: Fixed an important issue in the image selection: some selections fell back to other values upon posting the selection. This is now handled via the new javascript function "storeFileFormatSelection". Moreover the "ImageFileFormat" parameter had to be removed from the "chechPostImageParameters" which reset the value of the file format. 2012-08-30 10:04 danielsevilla * [r1339] /branches/newWorkflow/ajax/ajax.php, /branches/newWorkflow/select_images.php: Switch to the Ajax functions to clean up the user image selection whenever the file format choice is changed. 2012-08-30 15:41 danielsevilla * [r1340] /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/select_images.php: The user file selection and the file server were out of sync. There was a proposal to handle this via jQuery. For the time being this has been fixed with PHP as the out of sync problem happened whit POST, i.e., in relation with the server. 2012-08-31 14:55 danielsevilla * [r1341] /branches/newWorkflow/ajax/ajax.php, /branches/newWorkflow/inc/Fileserver.inc.php: (1) Added check on existing 'setting' to the File Server. (2) Formatted the parameter preview strings to make them clearer and more understandable. The formatting coded has been added to the 'getParameters' function of the ajax.php file. We might want to do this differently. (3) Tried unsuccessfully to add PHP file series filters to the image selection. The existing File Server code is strongly based on the old features, it doesn't seem to work this around. 2012-08-31 15:47 danielsevilla * [r1342] /branches/newWorkflow/inc/Parameter.inc.php: The coloc parameters did not have specific 'displayString' functions yet. Starting to implement them. 2012-09-03 09:03 danielsevilla * [r1343] /branches/newWorkflow/inc/Parameter.inc.php: Finished implementing 'displayString' functions for the colocalization parameters. 2012-09-03 09:31 danielsevilla * [r1344] /branches/newWorkflow/inc/Setting.inc.php: Changes on the 'displayString' at the setting level are were also necessary for the coloc parameters. The setting summary does not show the coloc parameter details if coloc is skipped. 2012-09-03 09:44 danielsevilla * [r1345] /branches/newWorkflow/inc/QueueManager.inc.php: If the job finishes in an error, a parameter summary is reported to the administrator. Attach the analysis parameters to this report as well. 2012-09-03 13:46 danielsevilla * [r1346] /branches/newWorkflow/create_job.php, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/select_analysis_settings.php: If the user chose one channel in the image settings then there's nothing to do at the analysis stage, as the only analysis parameters refer to colocalization analysis, which needs at least two channels. In that case, gray out and disable most parts of the analysis settings page. 2012-09-03 14:52 danielsevilla * [r1347] /branches/newWorkflow/select_analysis_settings.php: The analysis page is now able to continue to "create job" without selecting any settings if there's only one channel to process. 2012-09-03 15:15 danielsevilla * [r1348] /branches/newWorkflow/select_analysis_settings.php: Improvements on recently committed code. 2012-09-04 08:38 danielsevilla * [r1349] /branches/newWorkflow/inc/Fileserver.inc.php: It does no longer make sense to generate previews with customized sampling sizes and wavelengths. There exist no such data at the image selection stage now. 2012-09-04 11:55 danielsevilla * [r1350] /branches/newWorkflow/inc/QueueManager.inc.php, /branches/newWorkflow/inc/Shell.inc.php: Added checks and close+return on failure to several Shell functions which seemed to produce a seldom error in which when the OS can't provide more pipes (or other resources) the Queue Manager ends up writing lots of stuff to the HRM logs. Apparently this error could be caused by a number of pipes not being properly closed by the Queue Manager. 2012-09-04 14:17 danielsevilla * [r1351] /branches/newWorkflow/inc/Shell.inc.php: Commented out obsolete code. A number of revisions back to r1 have been checked to look for the use of function "isJobWithPidRunning". No use has been found in the current or past code. 2012-09-05 10:22 danielsevilla * [r1352] /branches/newWorkflow/inc/Shell.inc.php: (1) 'proc_open' does not return handlers to open files but handlers to newly created files and handlers to created, "ready" pipes. Thus, fclose won't work with the file handlers as they are not open. This produced PHP warnings and notices since a long time ago. Commit 586 got rid of the warnings and notices by pre-appending '@' symbols before the fclose statements. This is now fixed. (2) Added a destructor to the Shell class which works from PHP 5 on and which will release the pipe/file handlers if there exist no further instances of the object. This way the seldom problem by which some installations run out of resources should be fixed. 2012-09-05 15:18 danielsevilla * [r1353] /branches/newWorkflow/scripts/settings.js: Minor: removed blank from javascript code. This seemed to produce a glitch in the coloc parameter editor when upgrading from HRM 2.1.2 to HRM 2.2. 2012-09-06 15:45 danielsevilla * [r1354] /branches/newWorkflow/css/default.css, /branches/newWorkflow/select_images.php: Starting the implementation of a 'file series' flag in the form of a checkbox in the image selecion page. This flag should activate a mechanism to be able to toggle the deconvolution of one single file of a file series or the whole file series. 2012-09-07 14:53 danielsevilla * [r1355] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/select_images.php: First attempt to implement a different approach for the handling of file series. This approach includes a simple checkbox in the image selection page. The checkbox refers to whether the file series should or should not be read in automatically. Pretty much in the same fashion as the Huygens Batch Processor. If ticked the user will only see the first file of the series. Selecting this file will then imply deconvolving the series. If unticked, all the files of the series can be deconvolved independently. 2012-09-07 15:21 danielsevilla * [r1356] /branches/newWorkflow/inc/FileBrowser.inc.php: Shortened a couple of tooltips to go the point. 2012-09-07 15:39 danielsevilla * [r1357] /branches/newWorkflow/scripts/common.js: Adapted one more tooltip to stress the relevance of the previews. Hopefully, this will catch a bit more of the attention of the users. 2012-09-11 11:21 danielsevilla * [r1358] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css: Expanded reserved room for the coloc results. More and more coloc coefficients have been added lately, so this is needed in order to show a clear coefficients table. 2012-09-11 11:28 danielsevilla * [r1359] /branches/newWorkflow/select_parameter_settings.php: Creating a new setting without providing a name for it ended up in an error: fixed. 2012-09-17 12:14 aarpon * [r1360] /branches/newWorkflow/aberration_correction.php, /branches/newWorkflow/account.php, /branches/newWorkflow/calculate_pixel_size.php, /branches/newWorkflow/capturing_parameter.php, /branches/newWorkflow/create_job.php, /branches/newWorkflow/job_queue.php: Several HTML corrections. 2012-09-17 12:30 aarpon * [r1361] /branches/newWorkflow/scripts/ajax_utils.js: Added some more description to the Ajax php functions. 2012-10-02 15:15 danielsevilla * [r1362] /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/select_images.php: Added more javascript code to filter out those files part of a series. Only the first file of the series is displayed. 2012-10-02 15:50 danielsevilla * [r1363] /branches/newWorkflow/select_images.php: Small html addition to keep the "Automatically load file series" checkbox ticked after posting. 2012-10-03 15:33 danielsevilla * [r1364] /branches/newWorkflow/select_images.php: Fixed glitch in the file series filter. More corrections should come, though it would be helpful to know whether we really want to go in this directions. 2012-10-05 10:13 danielsevilla * [r1365] /trunk/inc/HuygensTemplate.inc.php: Fixed bug: when using a measured PSF the deconvolution job could result in an error if the PSF and the raw data were located in different folders. 2012-10-08 15:07 danielsevilla * [r1366] /branches/newWorkflow/ajax/ajax.php, /branches/newWorkflow/create_job.php, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/inc/Database.inc.php, /branches/newWorkflow/inc/HuygensTemplate.inc.php, /branches/newWorkflow/inc/JobDescription.inc.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/setup/dbupdate.php: Save the 'automatically load file series' mode into the database along with the job files. This option is now functional. The javascript of the image selection can be further improved to fix some hiccups. The image geometry input field (which presented a problem for already quite some time) could eventually be removed. 2012-10-10 09:28 aarpon * [r1367] /branches/newWorkflow/ajax/ajax.php, /branches/newWorkflow/inc/Database.inc.php, /branches/newWorkflow/inc/User.inc.php, /branches/newWorkflow/setup/dbupdate.php: (1) Fixed a problem with the ajax calls to display the number of jobs in the queue. (2) Made dbupdate.php more robust against adding columns to tables if they already exist. 2012-10-10 15:40 aarpon * [r1368] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/images/logo_bsse.png, /branches/newWorkflow/images/logo_epfl.png, /branches/newWorkflow/images/logo_svi.png, /branches/newWorkflow/login.php: Added BSSE and SVI logos and redesigned the login page slightly. 2012-10-10 16:07 aarpon * [r1369] /branches/newWorkflow/images/results.png: Added tentative results icon for the home page. 2012-10-10 17:32 aarpon * [r1370] /branches/newWorkflow/scripts/jquery-1.8.0.min.js, /branches/newWorkflow/scripts/jquery-1.8.2.min.js: Updated jQuery to version 1.8.2. 2012-10-10 18:55 aarpon * [r1371] /branches/newWorkflow/create_job.php, /branches/newWorkflow/file_management.php, /branches/newWorkflow/file_manager.php, /branches/newWorkflow/header.inc.php, /branches/newWorkflow/home.php, /branches/newWorkflow/images/deconvolved.png, /branches/newWorkflow/images/filemanager_title.png, /branches/newWorkflow/images/raw.png, /branches/newWorkflow/images/results_title.png, /branches/newWorkflow/inc/FileBrowser.inc.php, /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/select_analysis_settings.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php: Removed file_manager.php and separated the raw data from the deconvolved data views, that now have independent icons in the home page. 2012-10-11 07:18 aarpon * [r1372] /branches/newWorkflow/account.php, /branches/newWorkflow/home.php, /branches/newWorkflow/images/account_title.png, /branches/newWorkflow/images/queue_title.png, /branches/newWorkflow/job_queue.php: Uniformed title layouts. 2012-10-11 15:31 aarpon * [r1373] /branches/newWorkflow/inc/Util.inc.php: Added a check for successful file opening in the report() function. 2012-10-11 15:35 aarpon * [r1374] /branches/newWorkflow/ajax/ajax.php: Fixed bug in posting the id of jobs to kill in ajax.php (from job_queue.php). 2012-10-12 08:53 aarpon * [r1375] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/select_images.php: Moved the autoseries checkbox to the "Images available on server" fieldset. 2012-10-29 09:27 aarpon * [r1376] /branches/newWorkflow/calculate_bp_pinhole.php, /branches/newWorkflow/images/system_title.png, /branches/newWorkflow/system.php: (1) Added title image for the system summary page. (2) Minor fix in calculate_bp_pinhole.php. 2012-10-29 13:18 danielsevilla * [r1377] /branches/newWorkflow/ajax/ajax.php, /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/select_images.php: Fixed a number of errors logged by Apache as undefined variables. 2012-10-29 13:37 danielsevilla * [r1378] /branches/newWorkflow/select_images.php: According to the old select_images architecture the raw images should be inserted into an array. The insertion was missing, whereas other access to the array was still present. 2012-10-29 13:49 aarpon * [r1379] /branches/newWorkflow/select_images.php: Fixed some bugs in select_images.php. 2012-10-29 13:49 aarpon * [r1380] /branches/newWorkflow/ajax/ajax.php, /branches/newWorkflow/inc/Fileserver.inc.php: Committed forgotten files. 2012-10-29 15:32 aarpon * [r1381] /branches/newWorkflow/create_job.php, /branches/newWorkflow/inc/Setting.inc.php: Hidden output file name from the restoration parameter table (string). 2012-11-01 12:12 danielsevilla * [r1382] /branches/hrmOmero/bin/ome_hrm, /branches/hrmOmero/css/default.css, /branches/hrmOmero/css/default_ie.css, /branches/hrmOmero/file_management.php, /branches/hrmOmero/header.inc.php, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/Fileserver.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php, /branches/hrmOmero/scripts/common.js, /branches/hrmOmero/scripts/jqTree, /branches/hrmOmero/scripts/jqTree/.travis.yml, /branches/hrmOmero/scripts/jqTree/LICENSE, /branches/hrmOmero/scripts/jqTree/README.rst, /branches/hrmOmero/scripts/jqTree/build, /branches/hrmOmero/scripts/jqTree/docs_src, /branches/hrmOmero/scripts/jqTree/docs_src/base.tmpl, /branches/hrmOmero/scripts/jqTree/docs_src/example1.tmpl, /branches/hrmOmero/scripts/jqTree/docs_src/example2.tmpl, /branches/hrmOmero/scripts/jqTree/docs_src/example3.tmpl, /branches/hrmOmero/scripts/jqTree/docs_src/example4.tmpl, /branches/hrmOmero/scripts/jqTree/docs_src/example5.tmpl, /branches/hrmOmero/scripts/jqTree/docs_src/example6.tmpl, /branches/hrmOmero/scripts/jqTree/docs_src/generate.py, /branches/hrmOmero/scripts/jqTree/docs_src/requirements.txt, /branches/hrmOmero/scripts/jqTree/examples, /branches/hrmOmero/scripts/jqTree/examples/example.css, /branches/hrmOmero/scripts/jqTree/examples/example1.html, /branches/hrmOmero/scripts/jqTree/examples/example2.html, /branches/hrmOmero/scripts/jqTree/examples/example3.html, /branches/hrmOmero/scripts/jqTree/examples/example4.html, /branches/hrmOmero/scripts/jqTree/examples/example5.html, /branches/hrmOmero/scripts/jqTree/examples/example6.html, /branches/hrmOmero/scripts/jqTree/examples/spinner.gif, /branches/hrmOmero/scripts/jqTree/extra, /branches/hrmOmero/scripts/jqTree/extra/css, /branches/hrmOmero/scripts/jqTree/extra/css/documentation.css, /branches/hrmOmero/scripts/jqTree/extra/css/gridless.css, /branches/hrmOmero/scripts/jqTree/extra/example_data.js, /branches/hrmOmero/scripts/jqTree/extra/js, /branches/hrmOmero/scripts/jqTree/extra/js/jquery-1.8.2.min.js, /branches/hrmOmero/scripts/jqTree/extra/js/jquery.cookie.js, /branches/hrmOmero/scripts/jqTree/extra/js/jquery.mockjax.js, /branches/hrmOmero/scripts/jqTree/extra/prism, /branches/hrmOmero/scripts/jqTree/extra/prism/prism.css, /branches/hrmOmero/scripts/jqTree/extra/prism/prism.js, /branches/hrmOmero/scripts/jqTree/extra/qunit, /branches/hrmOmero/scripts/jqTree/extra/qunit/qunit.css, /branches/hrmOmero/scripts/jqTree/extra/qunit/qunit.js, /branches/hrmOmero/scripts/jqTree/index.html, /branches/hrmOmero/scripts/jqTree/jqtree-circle.png, /branches/hrmOmero/scripts/jqTree/jqtree.css, /branches/hrmOmero/scripts/jqTree/mouse.widget.coffee, /branches/hrmOmero/scripts/jqTree/phantomjs, /branches/hrmOmero/scripts/jqTree/phantomjs/run-qunit.js, /branches/hrmOmero/scripts/jqTree/phantomjs/server.js, /branches/hrmOmero/scripts/jqTree/simple.widget.coffee, /branches/hrmOmero/scripts/jqTree/test, /branches/hrmOmero/scripts/jqTree/test/test.html, /branches/hrmOmero/scripts/jqTree/test/test.js, /branches/hrmOmero/scripts/jqTree/tree.jquery.coffee, /branches/hrmOmero/scripts/jqTree/tree.jquery.js, /branches/hrmOmero/scripts/jqTree/tree_logo.png: More work on the Omero branch. Many files are added or changed in this commit to include a JQuery/JSon tree view of the Omero data. Also, we no longer use the Omero Java client but the Omero Command Line Interpreter where we can retrieve information, import and export data by invoking Omero commands. 2012-11-01 14:59 danielsevilla * [r1383] /branches/hrmOmero/bin/ome_hrm, /branches/hrmOmero/config/samples/hrm_client_config.inc.sample, /branches/hrmOmero/file_management.php: The 'in-between' bash Omero script is now more focused on the elements id's rather than on the elements names. 2012-11-01 17:20 danielsevilla * [r1384] /branches/hrmOmero/bin/ome_hrm, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php: The Omero tree stores now the id's of projects, datasets and images, which is much more practical to import/export data. 2012-11-01 17:21 danielsevilla * [r1385] /branches/hrmOmero/inc/OmeroConnection.inc.php: Removed privated data. :S 2012-11-06 14:24 danielsevilla * [r1386] /branches/hrmOmero/bin/ome_hrm, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/Fileserver.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php, /branches/hrmOmero/inc/QueueManager.inc.php: The user can now import data from the Omero server. The Omero data structure can first be visually inspected via the tree view. Later on, the images can be selected and imported individually. 2012-11-07 10:37 aarpon * [r1387] /branches/newWorkflow/capturing_parameter.php, /branches/newWorkflow/create_job.php, /branches/newWorkflow/estimate_snr_from_image.php, /branches/newWorkflow/estimate_snr_from_image_beta.php, /branches/newWorkflow/image_format.php, /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/inc/Setting.inc.php, /branches/newWorkflow/inc/Stats.inc.php, /branches/newWorkflow/scripts/quickhelp/capturingParameterHelp.js, /branches/newWorkflow/statistics.php: Removed image geometry. 2012-11-07 10:38 aarpon * [r1388] /branches/newWorkflow/inc/FileBrowser.inc.php: Change forgotten in previous commit. 2012-11-07 11:37 danielsevilla * [r1389] /branches/hrmOmero/bin/ome_hrm, /branches/hrmOmero/file_management.php, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/Fileserver.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php: User can now export deconvolved data to Omero as well. 2012-11-07 12:43 aarpon * [r1390] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css: Minor layout change. 2012-11-07 13:23 danielsevilla * [r1391] /branches/hrmOmero/css/default.css, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/scripts/common.js: Better behaviour of the Omero control buttons. 2012-11-07 15:46 aarpon * [r1392] /branches/newWorkflow/inc/extern/adLDAP4, /branches/newWorkflow/inc/extern/adodb5: Removed old versions of adLDAP and ADOdb. 2012-11-07 15:51 aarpon * [r1393] /branches/newWorkflow/inc/extern/adLDAP4, /branches/newWorkflow/inc/extern/adLDAP4/CHANGELOG.txt, /branches/newWorkflow/inc/extern/adLDAP4/LICENCE.txt, /branches/newWorkflow/inc/extern/adLDAP4/README.txt, /branches/newWorkflow/inc/extern/adLDAP4/examples, /branches/newWorkflow/inc/extern/adLDAP4/examples/authenticate.php, /branches/newWorkflow/inc/extern/adLDAP4/examples/examples.php, /branches/newWorkflow/inc/extern/adLDAP4/examples/groupCollection.php, /branches/newWorkflow/inc/extern/adLDAP4/examples/menu.php, /branches/newWorkflow/inc/extern/adLDAP4/examples/userCollection.php, /branches/newWorkflow/inc/extern/adLDAP4/src, /branches/newWorkflow/inc/extern/adLDAP4/src/adLDAP.php, /branches/newWorkflow/inc/extern/adLDAP4/src/classes, /branches/newWorkflow/inc/extern/adLDAP4/src/classes/adLDAPComputers.php, /branches/newWorkflow/inc/extern/adLDAP4/src/classes/adLDAPContacts.php, /branches/newWorkflow/inc/extern/adLDAP4/src/classes/adLDAPExchange.php, /branches/newWorkflow/inc/extern/adLDAP4/src/classes/adLDAPFolders.php, /branches/newWorkflow/inc/extern/adLDAP4/src/classes/adLDAPGroups.php, /branches/newWorkflow/inc/extern/adLDAP4/src/classes/adLDAPUsers.php, /branches/newWorkflow/inc/extern/adLDAP4/src/classes/adLDAPUtils.php, /branches/newWorkflow/inc/extern/adLDAP4/src/collections, /branches/newWorkflow/inc/extern/adLDAP4/src/collections/adLDAPCollection.php, /branches/newWorkflow/inc/extern/adLDAP4/src/collections/adLDAPComputerCollection.php, /branches/newWorkflow/inc/extern/adLDAP4/src/collections/adLDAPContactCollection.php, /branches/newWorkflow/inc/extern/adLDAP4/src/collections/adLDAPGroupCollection.php, /branches/newWorkflow/inc/extern/adLDAP4/src/collections/adLDAPUserCollection.php, /branches/newWorkflow/inc/extern/adodb5, /branches/newWorkflow/inc/extern/adodb5/adodb-active-record.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-active-recordx.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-csvlib.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-datadict.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-error.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-errorhandler.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-errorpear.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-exceptions.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-iterator.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-lib.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-memcache.lib.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-pager.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-pear.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-perf.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-php4.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-time.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-xmlschema.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb-xmlschema03.inc.php, /branches/newWorkflow/inc/extern/adodb5/adodb.inc.php, /branches/newWorkflow/inc/extern/adodb5/contrib, /branches/newWorkflow/inc/extern/adodb5/contrib/toxmlrpc.inc.php, /branches/newWorkflow/inc/extern/adodb5/cute_icons_for_site, /branches/newWorkflow/inc/extern/adodb5/cute_icons_for_site/adodb.gif, /branches/newWorkflow/inc/extern/adodb5/cute_icons_for_site/adodb2.gif, /branches/newWorkflow/inc/extern/adodb5/datadict, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-access.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-db2.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-firebird.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-generic.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-ibase.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-informix.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-mssql.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-mssqlnative.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-mysql.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-oci8.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-postgres.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-sapdb.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-sqlite.inc.php, /branches/newWorkflow/inc/extern/adodb5/datadict/datadict-sybase.inc.php, /branches/newWorkflow/inc/extern/adodb5/docs, /branches/newWorkflow/inc/extern/adodb5/docs/docs-active-record.htm, /branches/newWorkflow/inc/extern/adodb5/docs/docs-adodb.htm, /branches/newWorkflow/inc/extern/adodb5/docs/docs-datadict.htm, /branches/newWorkflow/inc/extern/adodb5/docs/docs-oracle.htm, /branches/newWorkflow/inc/extern/adodb5/docs/docs-perf.htm, /branches/newWorkflow/inc/extern/adodb5/docs/docs-session.htm, /branches/newWorkflow/inc/extern/adodb5/docs/docs-session.old.htm, /branches/newWorkflow/inc/extern/adodb5/docs/old-changelog.htm, /branches/newWorkflow/inc/extern/adodb5/docs/readme.htm, /branches/newWorkflow/inc/extern/adodb5/docs/tips_portable_sql.htm, /branches/newWorkflow/inc/extern/adodb5/docs/tute.htm, /branches/newWorkflow/inc/extern/adodb5/drivers, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-access.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-ado.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-ado5.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-ado_access.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-ado_mssql.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-ads.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-borland_ibase.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-csv.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-db2.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-db2oci.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-db2ora.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-fbsql.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-firebird.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-ibase.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-informix.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-informix72.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-ldap.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-mssql.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-mssql_n.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-mssqlnative.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-mssqlpo.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-mysql.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-mysqli.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-mysqlpo.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-mysqlt.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-netezza.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-oci8.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-oci805.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-oci8po.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-odbc.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-odbc_db2.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-odbc_mssql.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-odbc_oracle.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-odbtp.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-odbtp_unicode.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-oracle.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-pdo.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-pdo_mssql.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-pdo_mysql.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-pdo_oci.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-pdo_pgsql.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-pdo_sqlite.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-postgres.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-postgres64.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-postgres7.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-postgres8.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-postgres9.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-proxy.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-sapdb.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-sqlanywhere.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-sqlite.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-sqlite3.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-sqlitepo.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-sybase.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-sybase_ase.inc.php, /branches/newWorkflow/inc/extern/adodb5/drivers/adodb-vfp.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-ar.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-bg.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-bgutf8.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-ca.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-cn.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-cz.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-da.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-de.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-en.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-es.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-esperanto.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-fa.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-fr.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-hu.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-it.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-nl.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-pl.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-pt-br.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-ro.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-ru1251.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-sv.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb-uk1251.inc.php, /branches/newWorkflow/inc/extern/adodb5/lang/adodb_th.inc.php, /branches/newWorkflow/inc/extern/adodb5/license.txt, /branches/newWorkflow/inc/extern/adodb5/pear, /branches/newWorkflow/inc/extern/adodb5/pear/Auth, /branches/newWorkflow/inc/extern/adodb5/pear/Auth/Container, /branches/newWorkflow/inc/extern/adodb5/pear/Auth/Container/ADOdb.php, /branches/newWorkflow/inc/extern/adodb5/pear/readme.Auth.txt, /branches/newWorkflow/inc/extern/adodb5/perf, /branches/newWorkflow/inc/extern/adodb5/perf/perf-db2.inc.php, /branches/newWorkflow/inc/extern/adodb5/perf/perf-informix.inc.php, /branches/newWorkflow/inc/extern/adodb5/perf/perf-mssql.inc.php, /branches/newWorkflow/inc/extern/adodb5/perf/perf-mssqlnative.inc.php, /branches/newWorkflow/inc/extern/adodb5/perf/perf-mysql.inc.php, /branches/newWorkflow/inc/extern/adodb5/perf/perf-oci8.inc.php, /branches/newWorkflow/inc/extern/adodb5/perf/perf-postgres.inc.php, /branches/newWorkflow/inc/extern/adodb5/pivottable.inc.php, /branches/newWorkflow/inc/extern/adodb5/readme.txt, /branches/newWorkflow/inc/extern/adodb5/rsfilter.inc.php, /branches/newWorkflow/inc/extern/adodb5/server.php, /branches/newWorkflow/inc/extern/adodb5/session, /branches/newWorkflow/inc/extern/adodb5/session/adodb-compress-bzip2.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-compress-gzip.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-cryptsession.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-cryptsession2.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-encrypt-mcrypt.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-encrypt-md5.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-encrypt-secret.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-encrypt-sha1.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-sess.txt, /branches/newWorkflow/inc/extern/adodb5/session/adodb-session-clob.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-session-clob2.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-session.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-session2.php, /branches/newWorkflow/inc/extern/adodb5/session/adodb-sessions.mysql.sql, /branches/newWorkflow/inc/extern/adodb5/session/adodb-sessions.oracle.clob.sql, /branches/newWorkflow/inc/extern/adodb5/session/adodb-sessions.oracle.sql, /branches/newWorkflow/inc/extern/adodb5/session/crypt.inc.php, /branches/newWorkflow/inc/extern/adodb5/session/old, /branches/newWorkflow/inc/extern/adodb5/session/old/adodb-cryptsession.php, /branches/newWorkflow/inc/extern/adodb5/session/old/adodb-session-clob.php, /branches/newWorkflow/inc/extern/adodb5/session/old/adodb-session.php, /branches/newWorkflow/inc/extern/adodb5/session/old/crypt.inc.php, /branches/newWorkflow/inc/extern/adodb5/session/session_schema.xml, /branches/newWorkflow/inc/extern/adodb5/session/session_schema2.xml, /branches/newWorkflow/inc/extern/adodb5/tests, /branches/newWorkflow/inc/extern/adodb5/tests/benchmark.php, /branches/newWorkflow/inc/extern/adodb5/tests/client.php, /branches/newWorkflow/inc/extern/adodb5/tests/pdo.php, /branches/newWorkflow/inc/extern/adodb5/tests/test-active-record.php, /branches/newWorkflow/inc/extern/adodb5/tests/test-active-recs2.php, /branches/newWorkflow/inc/extern/adodb5/tests/test-active-relations.php, /branches/newWorkflow/inc/extern/adodb5/tests/test-active-relationsx.php, /branches/newWorkflow/inc/extern/adodb5/tests/test-datadict.php, /branches/newWorkflow/inc/extern/adodb5/tests/test-perf.php, /branches/newWorkflow/inc/extern/adodb5/tests/test-pgblob.php, /branches/newWorkflow/inc/extern/adodb5/tests/test-php5.php, /branches/newWorkflow/inc/extern/adodb5/tests/test-xmlschema.php, /branches/newWorkflow/inc/extern/adodb5/tests/test.php, /branches/newWorkflow/inc/extern/adodb5/tests/test2.php, /branches/newWorkflow/inc/extern/adodb5/tests/test3.php, /branches/newWorkflow/inc/extern/adodb5/tests/test4.php, /branches/newWorkflow/inc/extern/adodb5/tests/test5.php, /branches/newWorkflow/inc/extern/adodb5/tests/test_rs_array.php, /branches/newWorkflow/inc/extern/adodb5/tests/testcache.php, /branches/newWorkflow/inc/extern/adodb5/tests/testdatabases.inc.php, /branches/newWorkflow/inc/extern/adodb5/tests/testgenid.php, /branches/newWorkflow/inc/extern/adodb5/tests/testmssql.php, /branches/newWorkflow/inc/extern/adodb5/tests/testoci8.php, /branches/newWorkflow/inc/extern/adodb5/tests/testoci8cursor.php, /branches/newWorkflow/inc/extern/adodb5/tests/testpaging.php, /branches/newWorkflow/inc/extern/adodb5/tests/testpear.php, /branches/newWorkflow/inc/extern/adodb5/tests/testsessions.php, /branches/newWorkflow/inc/extern/adodb5/tests/time.php, /branches/newWorkflow/inc/extern/adodb5/tests/tmssql.php, /branches/newWorkflow/inc/extern/adodb5/tests/xmlschema-mssql.xml, /branches/newWorkflow/inc/extern/adodb5/tests/xmlschema.xml, /branches/newWorkflow/inc/extern/adodb5/toexport.inc.php, /branches/newWorkflow/inc/extern/adodb5/tohtml.inc.php, /branches/newWorkflow/inc/extern/adodb5/xmlschema.dtd, /branches/newWorkflow/inc/extern/adodb5/xmlschema03.dtd, /branches/newWorkflow/inc/extern/adodb5/xsl, /branches/newWorkflow/inc/extern/adodb5/xsl/convert-0.1-0.2.xsl, /branches/newWorkflow/inc/extern/adodb5/xsl/convert-0.1-0.3.xsl, /branches/newWorkflow/inc/extern/adodb5/xsl/convert-0.2-0.1.xsl, /branches/newWorkflow/inc/extern/adodb5/xsl/convert-0.2-0.3.xsl, /branches/newWorkflow/inc/extern/adodb5/xsl/remove-0.2.xsl, /branches/newWorkflow/inc/extern/adodb5/xsl/remove-0.3.xsl: Updated adLDAP to version 4.0.4 and ADOdb to version 5.18a. 2012-11-07 16:03 danielsevilla * [r1394] /branches/hrmOmero/capturing_parameter.php, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/scripts/jquery-1.7.1.min.js, /branches/hrmOmero/scripts/jquery-1.8.2.min.js, /branches/hrmOmero/task_parameter.php: Updated jQuery version: 1.7.1 -> 1.8.2. 2012-11-07 17:04 danielsevilla * [r1395] /branches/hrmOmero/header.inc.php, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/scripts/jquery-ui, /branches/hrmOmero/scripts/jquery-ui/jquery-ui-1.9.1.custom.css, /branches/hrmOmero/scripts/jquery-ui/jquery-ui-1.9.1.custom.js, /branches/hrmOmero/scripts/jquery-ui/jquery.bgiframe-2.1.2.js: First version of an embedded dialog to ask for the Omero login credentials. 2012-11-09 11:09 danielsevilla * [r1396] /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php, /branches/hrmOmero/scripts/jquery-ui/images, /branches/hrmOmero/scripts/jquery-ui/images/ui-bg_diagonals-thick_18_b81900_40x40.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-bg_diagonals-thick_20_666666_40x40.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-bg_flat_10_000000_40x100.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-bg_glass_100_f6f6f6_1x400.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-bg_glass_100_fdf5ce_1x400.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-bg_glass_65_ffffff_1x400.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-bg_gloss-wave_35_f6a828_500x100.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-bg_highlight-soft_100_eeeeee_1x100.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-bg_highlight-soft_75_ffe45c_1x100.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-icons_222222_256x240.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-icons_228ef1_256x240.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-icons_ef8c08_256x240.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-icons_ffd27a_256x240.png, /branches/hrmOmero/scripts/jquery-ui/images/ui-icons_ffffff_256x240.png: Partial implementation of the javascript dialog to ask for the Omero credentials. Work in progress. 2012-11-09 13:46 danielsevilla * [r1397] /branches/hrmOmero/file_management.php, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php: More work on the Omero login process. To be finished. 2012-11-09 15:29 danielsevilla * [r1398] /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php: The code added for the Omero connection needs further polishing. Still in progress. 2012-11-09 15:57 danielsevilla * [r1399] /branches/hrmOmero/header.inc.php, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/scripts/omero.js: (1) Bound the 'Enter' key to the 'Submit' button of the floating credentials dialog. (2) Moved javascript code to a new, dedicated omero.js. 2012-11-12 11:43 danielsevilla * [r1400] /branches/hrmOmero/bin/ome_hrm, /branches/hrmOmero/inc/OmeroConnection.inc.php: No Omero tree should be built if the user/password weren't correct. Added more work in this direction, still to be finished. 2012-11-12 14:58 danielsevilla * [r1401] /branches/hrmOmero/css/default.css, /branches/hrmOmero/file_management.php, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php: A few code improvements. 2012-11-12 16:06 danielsevilla * [r1402] /branches/hrmOmero/css/default.css, /branches/hrmOmero/css/default_ie.css, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/Fileserver.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php, /branches/hrmOmero/scripts/omero.js: Although this commit introduces some regressions it also includes several advantages and improvements. 2012-11-13 11:41 danielsevilla * [r1403] /branches/hrmOmero/bin/ome_hrm, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php: Only report data that has been previously 'archived' in Omero. This means, that the originals are stored as such in the Omero server, no need to covert them. 2012-11-13 14:41 danielsevilla * [r1404] /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php, /branches/hrmOmero/scripts/omero.js: (1) Improvements on which nodes must be selected in each case for the Omero transfers to work. (2) There where no archived Omero data exists we'll show it in the Omero tree view. 2012-11-13 15:16 danielsevilla * [r1405] /branches/hrmOmero/bin/ome_hrm, /branches/hrmOmero/config/samples/hrm.conf.sample: Replaced hardcoded paths with configuration options. 2012-11-13 15:38 danielsevilla * [r1406] /branches/hrmOmero/config/samples/hrm_server_config.inc.sample: Added Omero options to the 'hrm_server_config' file. 2012-11-14 11:23 danielsevilla * [r1407] /branches/hrmOmero/bin/ome_hrm, /branches/hrmOmero/inc/OmeroConnection.inc.php, /branches/hrmOmero/scripts/omero.js: (1) Fix a mistake in the javascript code which prevented the user from exporting data to Omero even when the destination dataset was selected. (2) Committing unfinished code to add annotations to the Omero exports. 2012-11-14 14:25 danielsevilla * [r1408] /branches/hrmOmero/bin/ome_hrm, /branches/hrmOmero/inc/OmeroConnection.inc.php: Long annotation texts can now be exported to Omero along with the deconvolved image. Work in progress. 2012-11-14 17:53 danielsevilla * [r1409] /branches/hrmOmero/inc/OmeroConnection.inc.php: A first version of an annotation parser for Omero. To be improved. 2012-11-15 13:21 danielsevilla * [r1410] /branches/hrmOmero/inc/OmeroConnection.inc.php: Better code in the OmeroConnection class. Work in progress. 2012-11-15 15:13 danielsevilla * [r1411] /branches/hrmOmero/inc/OmeroConnection.inc.php: Further improved the code of the OmeroConnection class. Still in progress. 2012-11-15 16:06 danielsevilla * [r1412] /branches/hrmOmero/file_management.php, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php: (1) Removed serialize/unserialize commands from the Omero enviroment. (2) Getting ready to add an update omero tree icon and action. 2012-11-15 16:25 danielsevilla * [r1413] /branches/hrmOmero/inc/FileBrowser.inc.php: (1) Added refresh button to the Omero section. (2) Fixed tooltips on the Omero buttons. 2012-11-15 16:29 danielsevilla * [r1414] /branches/hrmOmero/config/samples/hrm_client_config.inc.sample, /branches/hrmOmero/config/samples/hrm_server_config.inc.sample: Removed obsolete 'omero_port' option from the configuration files. 2012-11-15 17:08 danielsevilla * [r1415] /branches/hrmOmero/inc/Fileserver.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php, /branches/hrmOmero/scripts/common.js, /branches/hrmOmero/scripts/omero.js: Added comments and fixed a few more issues. 2012-11-16 09:09 danielsevilla * [r1416] /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroConnection.inc.php: Adapted the export command so that we don't export the image with the HRM suffix but just the raw image name. 2012-11-28 11:09 danielsevilla * [r1417] /branches/hrmOmero/file_management.php, /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroTransfers.inc.php, /branches/hrmOmero/omero_transfers.php: Created new files to hold code for the connection with Omero. This way we can keep a clearer picture. 2012-11-30 15:57 danielsevilla * [r1418] /branches/hrmOmero/inc/FileBrowser.inc.php, /branches/hrmOmero/inc/OmeroTransfers.inc.php, /branches/hrmOmero/omero_UI.php: Putting all the Omero code in one single file with simple functions is still not that straightforward. Let's first try to rename and relocate the UI file. More ideas may come up... 2012-11-30 16:01 danielsevilla * [r1419] /branches/hrmOmero/file_management.php, /branches/hrmOmero/omero_actions.php, /branches/hrmOmero/omero_transfers.php: Renamed one of the omero files for the sake of clarity. 2012-12-03 11:15 danielsevilla * [r1420] /branches/newWorkflow/login.php: Little change to render the collaborator icons at the login page with smaller blank spaces between them. 2012-12-03 15:28 danielsevilla * [r1421] /branches/newWorkflow/inc/Database.inc.php, /branches/newWorkflow/inc/QueueManager.inc.php, /branches/newWorkflow/scripts/hucore.tcl, /branches/newWorkflow/setup/dbupdate.php: Added functions to retrieve the license details from HuCore when the Queue Manager is started. The details are then stored in the database for later reference. 2012-12-03 16:42 danielsevilla * [r1422] /branches/newWorkflow/inc/Database.inc.php, /branches/newWorkflow/inc/Util.inc.php, /branches/newWorkflow/select_task_settings.php: (1) Added check function for specific license features. (2) Re-route to the job creation page if the license supports no colocalization, i.e., the analysis stage will be skipped. 2012-12-04 10:49 danielsevilla * [r1423] /branches/newWorkflow/login.php, /branches/newWorkflow/select_task_settings.php: Rearranged the collaborator icons so that the space of the login page is better distributed. There are two icons which deserve more vertical space because of the long links shown below them: BSSE and FMI. Therefore, these two have been brought to the lowest row. 2012-12-04 10:53 danielsevilla * [r1424] /branches/newWorkflow/login.php: To finish rearranging the collaborator icons move the SVI icon away from a central position. It otherwise seems to claim prominence. 2012-12-04 13:24 danielsevilla * [r1425] /branches/newWorkflow/account.php, /branches/newWorkflow/home.php, /branches/newWorkflow/images/account_huygens.png, /branches/newWorkflow/images/account_title_huygens.png, /branches/newWorkflow/images/users_huygens.png: Committing new user icons consisting of coloured versions of the Huygens icon. These are meant to replace the current KDE user icon, though this is just an idea. Please, roll back to the previous revision in case there's no agreement to use the new icons. 2012-12-04 14:05 aarpon * [r1426] /branches/newWorkflow/login.php: Swapped logo captions. 2012-12-04 16:54 danielsevilla * [r1427] /branches/newWorkflow/inc/QueueManager.inc.php, /branches/newWorkflow/inc/Util.inc.php: (1) Added call to the 'release' method of the 'Shell' class in the Queue Manager, where the class was being instantiated in a loop to 'ping' the server. Now the object is destructed after pinging. (2) Minor: added comment to the 'report' function. 2012-12-05 10:29 danielsevilla * [r1428] /branches/newWorkflow/inc/Job.inc.php, /branches/newWorkflow/inc/JobQueue.inc.php, /branches/newWorkflow/inc/QueueManager.inc.php, /branches/newWorkflow/inc/Shell.inc.php: Please review: (1) Added more checks to parts of the Queue Manager that may be leaving processes open. (2) Re-formatted some code for better readability. 2012-12-05 12:16 danielsevilla * [r1429] /branches/newWorkflow/inc/QueueManager.inc.php: Created a function to check whether the processing server/s is reachable. We'll use this function in the Queue Manager instead of repeating the same code several times. 2012-12-06 14:45 danielsevilla * [r1430] /branches/newWorkflow/inc/Fileserver.inc.php: Improved the colocalization code of the Fileserver class. Work in progress. 2012-12-06 15:08 danielsevilla * [r1431] /branches/newWorkflow/inc/Fileserver.inc.php: Fixed a few issues in the colocalization previews. 2012-12-06 16:05 danielsevilla * [r1432] /branches/newWorkflow/inc/Fileserver.inc.php: Improved some more colocalization code in the Fileserver class. 2012-12-07 10:25 danielsevilla * [r1433] /branches/newWorkflow/inc/Fileserver.inc.php: Found a more appropriate icon for the 'Back' action (previews page). 2012-12-07 10:58 danielsevilla * [r1434] /branches/newWorkflow/images/image_parameters.png, /branches/newWorkflow/images/image_parameters2.png: Added a new 'image parameters' icon. The "old" one has not been removed but renamed. 2012-12-10 10:47 danielsevilla * [r1435] /branches/newWorkflow/inc/Setting.inc.php, /branches/newWorkflow/select_parameter_settings.php: More work on the image parameter templates, which should take the file format selected at stage 1. Work in progress. 2012-12-10 11:58 danielsevilla * [r1436] /branches/newWorkflow/inc/Setting.inc.php: The 'Image parameters' page checks now whether the selected setting is compatible with the selected image format. Among other this will have the great advantage of not having to create different settings for different image formats. Error messages still need further improvements. 2012-12-10 17:28 danielsevilla * [r1437] /branches/newWorkflow/inc/Setting.inc.php: Better code and extra comments for when a parameter set misses values. 2012-12-11 10:25 danielsevilla * [r1438] /branches/newWorkflow/account.php, /branches/newWorkflow/home.php, /branches/newWorkflow/inc/Fileserver.inc.php: (1) Roll back to the old account icon. The Huygens icon clearly belongs to a different sort of style. (2) Fixed bug in the job previews: the coloc maps of different jobs could be displayed simulatenously. 2012-12-11 12:49 danielsevilla * [r1439] /branches/newWorkflow/home.php, /branches/newWorkflow/images/filemanager_tmp.png, /branches/newWorkflow/images/results_tmp.png: Added a proposal for the "raw data" and "results" icons. 2012-12-11 13:26 danielsevilla * [r1440] /branches/newWorkflow/images/filemanager_title_tmp.png, /branches/newWorkflow/images/results_title_tmp.png, /branches/newWorkflow/inc/FileBrowser.inc.php: Added thumbnails of the new icons for the FileBrowser page. 2012-12-11 14:39 danielsevilla * [r1441] /branches/newWorkflow/inc/Database.inc.php: Several cases have been encountered of stalled queue managers which logged a warning of an empty array which could not be passed as argument to a foreach. Added a check on the corresponding place. 2012-12-18 14:05 aarpon * [r1442] /branches/newWorkflow/login.php: Replaced hard-coded "bin/hrm" in login.php with $userManager (issue #56). 2012-12-18 14:13 aarpon * [r1443] /branches/newWorkflow/inc/Database.inc.php, /branches/newWorkflow/inc/Util.inc.php: Added header documentation to the hasFeature() methods. The SQL query was changed from "... feature = '$feature'" to "... feature LIKE '$feature'" so that SQL wildcards can be used. 2012-12-18 14:43 aarpon * [r1444] /branches/newWorkflow/estimate_snr_from_image.php, /branches/newWorkflow/estimate_snr_from_image_beta.php, /branches/newWorkflow/inc/FileBrowser.inc.php: Added missing title icons to the SNR estimators (issue #54). 2012-12-18 15:54 danielsevilla * [r1445] /branches/newWorkflow/inc/Job.inc.php: Removed calls to 'error_log' from regular, non-error messages. 2012-12-18 16:08 danielsevilla * [r1446] /branches/newWorkflow/inc/Database.inc.php: Added confidence level 'asIs' whose confidence is as high as that of the 'verified' level. 2012-12-18 16:14 aarpon * [r1447] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/system.php: Added license summary for the admin (initial implementation). 2012-12-19 09:00 aarpon * [r1448] /branches/newWorkflow/inc/Parameter.inc.php, /branches/newWorkflow/microscope_parameter.php: Added check for microscope license when displaying the microscope type in microscope_parameter.php. 2012-12-19 09:39 aarpon * [r1449] /branches/newWorkflow, /branches/newWorkflow/bin/ome_hrm, /branches/newWorkflow/config/samples/hrm.conf.sample, /branches/newWorkflow/config/samples/hrm_client_config.inc.sample, /branches/newWorkflow/config/samples/hrm_server_config.inc.sample, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/file_management.php, /branches/newWorkflow/header.inc.php, /branches/newWorkflow/inc/FileBrowser.inc.php, /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/inc/OmeroConnection.inc.php, /branches/newWorkflow/inc/QueueManager.inc.php, /branches/newWorkflow/omero_UI.php, /branches/newWorkflow/omero_actions.php, /branches/newWorkflow/scripts/common.js, /branches/newWorkflow/scripts/jqTree, /branches/newWorkflow/scripts/jquery-ui, /branches/newWorkflow/scripts/omero.js: Merged hrmOmero branch into newWorkflow. 2012-12-19 09:56 aarpon * [r1450] /branches/newWorkflow/resources/checkConfig.php: Updated checkConfig.php to version 2.2. 2012-12-19 11:58 aarpon * [r1451] /branches/newWorkflow/header.inc.php, /branches/newWorkflow/inc/FileBrowser.inc.php, /branches/newWorkflow/scripts/jquery-1.8.2.min.js, /branches/newWorkflow/scripts/jquery-1.8.3.min.js: Updated jQuery to version 1.8.3. 2012-12-19 13:17 aarpon * [r1452] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/estimate_snr_from_image.php, /branches/newWorkflow/estimate_snr_from_image_beta.php, /branches/newWorkflow/inc/FileBrowser.inc.php, /branches/newWorkflow/task_parameter.php: Merged the two SNR estimator pages. 2012-12-19 13:39 aarpon * [r1453] /branches/newWorkflow/estimate_snr_from_image.php: Fixed problem with selection of SNR estimation algorithm being forgotten after a post if no image was seelcted. 2012-12-19 14:29 aarpon * [r1454] /branches/newWorkflow/inc/Setting.inc.php, /branches/newWorkflow/select_parameter_settings.php: Fixed a bug in ParameterSetting::checkPostedAberrationCorrectionParameters(). If the aberration correction was disabled, the function still was expecting all of the aberration correction parameters to be defined and valid. How this never gave problems before I don't understand. 2012-12-20 08:10 aarpon * [r1455] /branches/newWorkflow/inc/Database.inc.php, /branches/newWorkflow/inc/Setting.inc.php: Added a check for the existence of parameters in the parameterNameDictionary in DatabaseConnection::huCoreConfidenceLevel() before they are accessed. 2012-12-20 13:48 aarpon * [r1456] /branches/newWorkflow/estimate_snr_from_image.php, /branches/newWorkflow/image_format.php, /branches/newWorkflow/inc/FileBrowser.inc.php, /branches/newWorkflow/inc/Setting.inc.php: Some more fixes for various errors appearing in the apache error log. 2012-12-20 13:56 danielsevilla * [r1457] /branches/newWorkflow/inc/FileBrowser.inc.php: Minor: moved global declaration to a code block where it better belongs. 2012-12-20 14:29 aarpon * [r1458] /branches/newWorkflow/inc/FileBrowser.inc.php: Changed FileBrowser.inc.php to work on a local copy of the Fileserver when estimating the SNR. 2012-12-20 15:24 aarpon * [r1459] /branches/newWorkflow/footer.inc.php: Changed Aaron's email in the footer. 2012-12-20 16:54 danielsevilla * [r1460] /branches/newWorkflow/inc/OmeroConnection.inc.php, /branches/newWorkflow/omero_actions.php: Uncoupled the POST array from the constructor of the 'OmeroConnection' class. 2012-12-20 17:18 danielsevilla * [r1461] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css: Changed colour of the Omero credentials dialog to the HRM 2.x colour theme. 2012-12-20 17:44 danielsevilla * [r1462] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/inc/FileBrowser.inc.php: Added icon for the 'OMERO Data' button. The text on the icon needs further work to improve readability. 2012-12-21 09:28 danielsevilla * [r1463] /branches/newWorkflow/images/omero_data.png: Forgot to add the new 'omero_data' icon. 2012-12-21 09:45 danielsevilla * [r1464] /branches/newWorkflow/images/omero_data.png: The 'omero_data' icon has been slightly improved. 2012-12-21 09:56 aarpon * [r1465] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/login.php: Proposal for new (main) login dialog. 2012-12-31 10:40 danielsevilla * [r1466] /branches/newWorkflow/scripts/hucore.tcl: Fixed issue with lif subimages. There was a mistake in the hucore.tcl script. 2013-01-03 10:51 danielsevilla * [r1467] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/login.php: Work on the collaborator icons. The login page is now better balanced with smaller collaborator icons. The previous version with larger icons took too much of the user attention. We could now add a little 'register' section more visible than the current link. 2013-01-03 11:35 danielsevilla * [r1468] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/login.php: Finished rearragenment of collaborator icons. Although the results looks fine the html and css code have become too complicated. Maybe there's a better way of doing this? 2013-01-03 15:56 danielsevilla * [r1469] /branches/newWorkflow/inc/Job.inc.php, /branches/newWorkflow/inc/JobDescription.inc.php: The SNR report of the parameters summary was faulty. Fixed. 2013-01-03 16:24 danielsevilla * [r1470] /branches/newWorkflow/inc/HuygensTemplate.inc.php, /branches/newWorkflow/scripts/hucore.tcl: Added checks to the 'reportImageDimensions' procedure so that we don't encounter missing variables in weird situations. 2013-01-04 09:48 danielsevilla * [r1471] /branches/newWorkflow/inc/Fileserver.inc.php: One of the latest code clean-ups introduced a bug in the colocalization maps layout of images with more than 2 channels. Fixed. 2013-01-04 11:49 danielsevilla * [r1472] /branches/newWorkflow/images/filemanager_title_tmp.png, /branches/newWorkflow/images/filemanager_tmp.png, /branches/newWorkflow/images/results_title_tmp.png, /branches/newWorkflow/images/results_tmp.png, /branches/newWorkflow/inc/Job.inc.php: (1) Yet one more propsal for the 'raw data' and 'results' icons. These icons are now fully finished. If the proposal is accepted more work can go in that direction to polish them a bit more. (2) Round the coloc coefficients to 3 decimal places instead of 4. (3) Catch negative colocalization coefficients. 2013-01-04 14:10 danielsevilla * [r1473] /branches/newWorkflow/images/filemanager_title_tmp.png, /branches/newWorkflow/images/filemanager_tmp.png, /branches/newWorkflow/images/omero_data.png, /branches/newWorkflow/images/results_title_tmp.png, /branches/newWorkflow/images/results_tmp.png: My last word on HRM icons for this version. 2013-01-04 15:24 danielsevilla * [r1474] /branches/newWorkflow/images/filemanager_title_tmp.png, /branches/newWorkflow/images/filemanager_tmp.png, /branches/newWorkflow/images/results_title_tmp.png, /branches/newWorkflow/images/results_tmp.png: Yet one more (almost imperceptible) change on the icons. 2013-01-04 16:21 danielsevilla * [r1475] /branches/newWorkflow/images/filemanager_title_tmp.png, /branches/newWorkflow/images/filemanager_tmp.png, /branches/newWorkflow/images/results_title_tmp.png, /branches/newWorkflow/images/results_tmp.png: The new icons include now shadows and round corners. 2013-01-07 09:52 aarpon * [r1476] /branches/newWorkflow/images/results.png, /branches/newWorkflow/images/results_title.png: Removed old results*.png files. 2013-01-07 10:18 aarpon * [r1477] /branches/newWorkflow/estimate_snr_from_image.php, /branches/newWorkflow/file_management.php, /branches/newWorkflow/home.php, /branches/newWorkflow/images/filemanager_title_tmp.png, /branches/newWorkflow/images/filemanager_tmp.png, /branches/newWorkflow/images/rawdata.png, /branches/newWorkflow/images/rawdata_small.png, /branches/newWorkflow/images/rawdata_title.png, /branches/newWorkflow/images/results.png, /branches/newWorkflow/images/results_small.png, /branches/newWorkflow/images/results_title.png, /branches/newWorkflow/images/results_title_tmp.png, /branches/newWorkflow/images/results_tmp.png, /branches/newWorkflow/images/users_huygens.png, /branches/newWorkflow/inc/FileBrowser.inc.php: Removed the old file manager icon, renamed the new raw data and results images and added the navigation links (with relative icons) between raw data and results in the file manager. 2013-01-07 10:20 aarpon * [r1478] /branches/newWorkflow/file_management.php: Corrected typo. 2013-01-07 10:35 aarpon * [r1479] /branches/newWorkflow/create_job.php, /branches/newWorkflow/images/filemanager.png, /branches/newWorkflow/images/filemanager_small.png, /branches/newWorkflow/images/filemanager_title.png, /branches/newWorkflow/images/rawdata_title.png, /branches/newWorkflow/images/results_title.png, /branches/newWorkflow/select_analysis_settings.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php: Some more work on the raw images and results icons. 2013-01-07 10:42 aarpon * [r1480] /branches/newWorkflow/scripts/common.js: Changed "Go to deconvolution result" to "Go to detailed results" in the results page. 2013-01-07 11:05 danielsevilla * [r1481] /branches/newWorkflow/images/results.png: Changed the colour of the results icon. 2013-01-07 11:09 danielsevilla * [r1482] /branches/newWorkflow/images/results.png: One more proposal for the colour of the 'results' icon. 2013-01-07 11:17 danielsevilla * [r1483] /branches/newWorkflow/images/results.png: Again, one more colour proposal for the 'results' icon. 2013-01-07 11:51 aarpon * [r1484] /branches/newWorkflow/images/results.png, /branches/newWorkflow/images/results_small.png, /branches/newWorkflow/images/results_title.png: Created all results icons from the proposed (yellow) image. 2013-01-07 12:47 aarpon * [r1485] /branches/newWorkflow/inc/Setting.inc.php: Removed commented code (related to issue 76). 2013-01-07 13:44 danielsevilla * [r1486] /branches/newWorkflow/images/rawdata.png: Tuning the colours of the 'raw data' icon. 2013-01-07 14:01 aarpon * [r1487] /branches/newWorkflow/image_format.php, /branches/newWorkflow/images/rawdata_small.png, /branches/newWorkflow/images/rawdata_title.png: Created all raw images icon sizes from the new suggestion. 2013-01-07 14:11 danielsevilla * [r1488] /branches/newWorkflow/images/rawdata.png, /branches/newWorkflow/images/results.png: One last change on the 'raw images/results' icons: the border on the fake dataset is blue instead of black. 2013-01-07 15:19 danielsevilla * [r1489] /branches/newWorkflow/images/results.png: Changed colour on the file manager icons. 2013-01-07 15:31 danielsevilla * [r1490] /branches/newWorkflow/images/results.png: A bit more contrast. 2013-01-07 15:36 danielsevilla * [r1491] /branches/newWorkflow/images/results.png: Unbelievably, there was yet one more change for the icons. 2013-01-07 16:01 aarpon * [r1492] /branches/newWorkflow/inc/Parameter.inc.php, /branches/newWorkflow/inc/Setting.inc.php: More careful checks for partially set multi-value parameters. 2013-01-07 16:22 aarpon * [r1493] /branches/newWorkflow/images/account_huygens.png, /branches/newWorkflow/images/account_title_huygens.png, /branches/newWorkflow/images/image_parameters2.png, /branches/newWorkflow/images/rawdata_small.png, /branches/newWorkflow/images/rawdata_title.png, /branches/newWorkflow/images/results_small.png, /branches/newWorkflow/images/results_title.png: Updated images. 2013-01-07 16:28 aarpon * [r1494] /branches/newWorkflow/inc/Parameter.inc.php: Changed error message for incomplete parameter values as a function of the confidence level. 2013-01-07 17:28 aarpon * [r1495] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/images/registration.png, /branches/newWorkflow/login.php: Suggestion for a more obvious registration on login.php. 2013-01-08 08:24 aarpon * [r1496] /branches/newWorkflow/images/registration.png: Replaced registration icon. 2013-01-08 14:38 danielsevilla * [r1497] /branches/newWorkflow/images/registration.png: Another propsal for the registration icon. 2013-01-08 14:40 danielsevilla * [r1498] /branches/newWorkflow/images/registration.png: And one more proposal for the registration icon. 2013-01-08 15:51 danielsevilla * [r1499] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/login.php: The collaborator icons have now specified sizes each. 2013-01-08 18:55 aarpon * [r1500] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/login.php: Fixed several css issues. 2013-01-08 19:50 aarpon * [r1501] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/login.php: Some more tweaking of the logos layout. 2013-01-09 08:37 aarpon * [r1502] /branches/newWorkflow/images/param_estimated.png, /branches/newWorkflow/images/text_estimated.png: Changed the color of the estimated parameter text and vertical band. 2013-01-09 11:02 aarpon * [r1503] /tools/images/param_untrusted.xcf, /tools/images/text_untrusted_metadata.xcf: Changed the color for untrusted. 2013-01-09 11:27 aarpon * [r1504] /branches/newWorkflow/images/param_asis.png, /branches/newWorkflow/images/param_default.png, /branches/newWorkflow/images/text_asis.png, /branches/newWorkflow/images/text_default.png: Finished changing colors for missing confidence levels. 2013-01-09 11:34 aarpon * [r1505] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css: Fix in the css files. 2013-01-09 11:51 danielsevilla * [r1506] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/login.php: Made the registration icon clickable. 2013-01-09 12:34 aarpon * [r1507] /branches/newWorkflow/images/registration_title.png, /branches/newWorkflow/registration.php: Added title image to the registration page (issue 78). 2013-01-09 13:15 aarpon * [r1508] /branches/newWorkflow/select_task_settings.php: Corrected task parameter page quick help text that was still mentioning analysis steps. 2013-01-09 14:14 aarpon * [r1509] /branches/newWorkflow/coloc_analysis.php, /branches/newWorkflow/scripts/quickhelp/colocHelp.js: Added javascript quick help for the colocalization page. Text to be provided. 2013-01-09 14:41 aarpon * [r1510] /branches/newWorkflow/login.php: Fixed link to the registration help page. 2013-01-09 14:55 aarpon * [r1511] /branches/newWorkflow/inc/QueueManager.inc.php: Bug fix in the call to TaskSetting::displayString($numberOfChannels) in QueueManager::ParameterText($job). 2013-01-09 16:19 aarpon * [r1512] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/registration.php: Cleaner layout in the registration page. 2013-01-09 16:52 danielsevilla * [r1513] /branches/newWorkflow/scripts/quickhelp/colocHelp.js: Added quick help text to the analysis page. 2013-01-10 10:05 aarpon * [r1514] /branches/newWorkflow/resources/checkConfig.php: Removed the check for the 'omero_server' variable in checkConfig.php. 2013-01-10 13:53 aarpon * [r1515] /branches/newWorkflow/inc/System.inc.php, /branches/newWorkflow/inc/Util.inc.php, /branches/newWorkflow/login.php, /branches/newWorkflow/select_task_settings.php, /branches/newWorkflow/system.php: (1) Added a check for a valid HuCore license in System::hucoreHasValidLicense() (that currently simply returns true until the necessary info is stored in the database when the Queue Manager starts). This method is used in login.php. (2) Moved the hasLicense() method from Util.inc.php to System.inc.php (and made it static). 2013-01-10 14:04 aarpon * [r1516] /branches/newWorkflow/inc/Database.inc.php, /branches/newWorkflow/inc/System.inc.php: System::hucoreHasValidLicense() now queries the database. 2013-01-10 14:55 aarpon * [r1517] /branches/newWorkflow/inc/Database.inc.php, /branches/newWorkflow/inc/System.inc.php, /branches/newWorkflow/system.php: Added report on validity of the license file and server information to the system summary page. 2013-01-10 14:59 aarpon * [r1518] /branches/newWorkflow/phpinfo.php: Added title icon to phpinfo.php. 2013-01-10 15:55 aarpon * [r1519] /branches/newWorkflow/create_job.php: Restored TIFF 8-bit TIFF for 2- or 3-channel datasets. 2013-01-10 16:01 danielsevilla * [r1520] /branches/newWorkflow/inc/Database.inc.php: Be more specific about the license server option. 2013-01-10 16:23 aarpon * [r1521] /branches/newWorkflow/inc/Database.inc.php: Small corrections in Database::storeLicenseDetails(). 2013-01-10 16:41 aarpon * [r1522] /branches/newWorkflow/create_job.php: Hidden the TIFF 8-bit output file format again since it requires too much work to fix for the upcoming release. 2013-01-10 17:21 aarpon * [r1523] /branches/newWorkflow/create_job.php, /branches/newWorkflow/setup/dbupdate.php: Added RGB TIFF 8 bit output format. 2013-01-10 17:22 danielsevilla * [r1524] /branches/newWorkflow/inc/Parameter.inc.php: Added 'tiffrgb' as an extension to the OutputFileFormat class. 2013-01-10 17:53 aarpon * [r1525] /branches/newWorkflow/inc/Fileserver.inc.php: Replaced some text with icons in the navigation buttons of the detailed results view. 2013-01-11 08:55 aarpon * [r1526] /branches/newWorkflow/inc/Fileserver.inc.php: Fixed some tooltips. 2013-01-11 09:55 aarpon * [r1527] /branches/newWorkflow/setup/dbupdate.php: Removed lsm-single and tiff-single, add added generic tiff and ome-tiff. 2013-01-11 10:07 aarpon * [r1528] /branches/newWorkflow/setup/dbupdate.php: Removed tiff series. 2013-01-11 12:34 aarpon * [r1529] /branches/newWorkflow/account.php: Fixed layout glitch. 2013-01-11 12:56 aarpon * [r1530] /branches/newWorkflow/inc/System.inc.php: Increased HRM version to 3.0. 2013-01-11 14:12 aarpon * [r1531] /branches/newWorkflow/setup/dbupdate.php: Added code to change the number of characters allowed for extensions in the file_extension table. 2013-01-11 14:19 aarpon * [r1532] /branches/newWorkflow/setup/dbupdate.php: (1) Bug fix in the change table SQL code. (2) Added tif extension for the generic-tif file format. 2013-01-11 15:27 danielsevilla * [r1533] /branches/newWorkflow/bin/hrm, /branches/newWorkflow/inc/QueueManager.inc.php: (1) Added option '-p' to several 'mkdir' calls. (2) Replaced error_log call with report call. 2013-01-11 15:35 danielsevilla * [r1534] /branches/newWorkflow/inc/System.inc.php: Increased mininum HuCore version to 4.3.0p2. 2013-01-11 16:07 danielsevilla * [r1535] /branches/newWorkflow/estimate_snr_from_image.php: Added a word to the SNR results title so that it's clearly stated which algorithm was used in the estimation. 2013-01-11 16:25 aarpon * [r1536] /branches/newWorkflow/setup/dbupdate.php: dbupdate.php now recreates the file_extension table to allow repeated file_format entries (file_format was earlier the primary key of the table). 2013-01-11 17:36 aarpon * [r1537] /branches/newWorkflow/select_images.php, /branches/newWorkflow/setup/dbupdate.php: Changed the translations of a few file formats. Please delete following rows from the possible_values table and rerun the database update! "ImageFileFormat";"ome-tiff";"OME-TIFF";"f" "ImageFileFormat";"tiff-generic";"Generic TIFF";"f" 2013-01-13 11:58 aarpon * [r1538] /branches/newWorkflow/resources/checkConfig.php: Increased the HRM version in resources/checkConfig.php. 2013-01-14 10:01 aarpon * [r1539] /branches/newWorkflow/config/samples/hrm.conf.sample: Minor changes in hrm.conf.sample to better match the documentation. 2013-01-14 10:25 danielsevilla * [r1540] /branches/newWorkflow/inc/QueueManager.inc.php, /branches/newWorkflow/select_parameter_settings.php: (1) When the admin edits an image parameter setting, allow him/her to skip parameters as much as possible. This can be achieved by forcing the image file format to "hdf5". (2) An instance of the 'report' function missed the level argument. 2013-01-14 11:49 danielsevilla * [r1541] /branches/newWorkflow/aberration_correction.php, /branches/newWorkflow/capturing_parameter.php, /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css, /branches/newWorkflow/image_format.php, /branches/newWorkflow/microscope_parameter.php: Added permanent message to the steps of the image parameter settings. This message shows which file format is being used. The message is shown under the Quick Help which seems fine but it would be nicer if we could add a horizontal separator. 2013-01-14 12:55 aarpon * [r1542] /branches/newWorkflow/config/samples/hrm_client_config.inc.sample, /branches/newWorkflow/config/samples/hrm_server_config.inc.sample: Removed $omero_server variable from the configuration samples since it is ignored in HRM 3.0. 2013-01-14 13:29 aarpon * [r1543] /branches/newWorkflow/css/default.css, /branches/newWorkflow/css/default_ie.css: Changed the style of the requirements class. 2013-01-14 16:04 aarpon * [r1544] /branches/newWorkflow/scripts/quickhelp/imageFormatHelp.js, /branches/newWorkflow/select_images.php: Extended the quick help for select_images.php and removed the unused quickhelp/imageFormatHelp.js script. 2013-01-14 16:11 danielsevilla * [r1545] /branches/newWorkflow/coloc_analysis.php, /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/scripts/common.js, /branches/newWorkflow/select_images.php: Trying to patch the image selection with a big hack. 2013-01-14 16:26 danielsevilla * [r1546] /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/scripts/common.js, /branches/newWorkflow/select_images.php: The hack includes now all the file types. 2013-01-14 16:28 aarpon * [r1547] /branches/newWorkflow/select_images.php: Removed call to changeQuickHelp(). 2013-01-15 15:07 danielsevilla * [r1548] /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/scripts/common.js, /branches/newWorkflow/select_images.php: Working on a new, hopefully more accurate approach to filter the images. Not yet finished. 2013-01-15 15:50 danielsevilla * [r1549] /branches/newWorkflow/scripts/common.js: Better javascript code. 2013-01-15 16:43 danielsevilla * [r1550] /branches/newWorkflow/image_format.php, /branches/newWorkflow/inc/Fileserver.inc.php, /branches/newWorkflow/scripts/common.js, /branches/newWorkflow/select_images.php: (1) Added the new file filter to the backend as well. (2) Removed called to recently deleted imageFormatHelp file. 2013-01-15 17:37 danielsevilla * [r1551] /branches/newWorkflow/create_job.php, /branches/newWorkflow/select_images.php, /branches/newWorkflow/select_parameter_settings.php, /branches/newWorkflow/select_task_settings.php: The step numbering and links were defaults for the case when there's a colocalization license. Without license the links and step numbers did not make sense. Added a rather simple but ugly mechanism to display the correct numbers and links depending on whether there's a colocalization license. 2013-01-16 10:07 danielsevilla * [r1552] /branches/newWorkflow/select_psf_popup.php: When using a measured psf, if the file format allows us to skip some microscopic parameters, the psf selector (pop-up) can raise a division by zero which thankfully is caught by Apache. Fixed. 2013-01-16 10:53 danielsevilla * [r1553] /branches/newWorkflow/select_psf_popup.php: When choosing a measured PSF the PSF pop-up sets the Fileserver instance to 'hdf5' and 'ics' files only. The reason for this is that these two file types are the only ones that support the Huygens 'pre_open' operation and therefore their metadata can be checked quickly (on the fly). This, however, caused the image selection page to lose track of the other existing files. Added a reset mechanism at the end of the pop-up page so that the image selection remains functional. 2013-01-16 14:10 danielsevilla * [r1554] /branches/newWorkflow/ajax/ajax.php, /branches/newWorkflow/select_images.php: The behaviour of the "automatically load file series" checkbox does not yet match what was intented at the initial implementation. For example, when the checkbox status is changed the file selection should be reset. This works now properly though more work is needed to polish the filtering of file series. 2013-01-16 15:32 danielsevilla * [r1555] /branches/newWorkflow/select_images.php: Trying to fix a glitch on the autoseries option when the form is posted. 2013-01-16 16:05 danielsevilla * [r1556] /branches/newWorkflow/select_images.php: A slightly faster and tidier version of the image selection. 2013-01-16 16:45 aarpon * [r1557] /branches/newWorkflow/inc/Fileserver.inc.php: Fixed a problem with the file list being cleared if any of the subfolders in src is not readable. 2013-01-16 16:58 aarpon * [r1558] /branches/newWorkflow/inc/Fileserver.inc.php: Built in more checks and cleaner handling of failing dir() calls. 2013-01-16 17:09 aarpon * [r1559] /branches/newWorkflow/inc/Fileserver.inc.php: More handling of cases where scanning directories (remotely) could fail. 2013-01-16 17:51 aarpon * [r1560] /branches/newWorkflow/inc/Setting.inc.php: The ImageFileFormat parameter should not be displayed in the preview of the image parameter sets. 2013-01-16 18:06 aarpon * [r1561] /branches/newWorkflow/ajax/ajax.php: Fixed a problem caused by Chrome firing the onclick event even when clicking on an empty area of an input field. 2013-01-16 18:18 danielsevilla * [r1562] /branches/newWorkflow/inc/Parameter.inc.php: The 'displayString' function of the 'BackgroundOffsetPercent' parameter missed the number of channels as argument. Fixed. 2013-01-16 18:42 aarpon * [r1563] /tools/bash/Doxyfile, /tools/bash/createChangelogTxt.sh: Updated scripts to create API and changelog for the HRM 3.0 release. 2013-01-17 08:37 aarpon * [r1564] /branches/hrmOmero: Removed branches/hrmOmero. 2013-01-17 13:00 aarpon * [r1565] /trunk/aberration_correction.php, /trunk/account.php, /trunk/ajax/ajax.php, /trunk/bin/hrm, /trunk/bin/ome_hrm, /trunk/calculate_bp_pinhole.php, /trunk/calculate_pixel_size.php, /trunk/capturing_parameter.php, /trunk/coloc_analysis.php, /trunk/config/samples/hrm.conf.sample, /trunk/config/samples/hrm_client_config.inc.sample, /trunk/config/samples/hrm_server_config.inc.sample, /trunk/create_job.php, /trunk/css/default.css, /trunk/css/default_ie.css, /trunk/estimate_snr_from_image.php, /trunk/estimate_snr_from_image_beta.php, /trunk/file_management.php, /trunk/file_manager.php, /trunk/footer.inc.php, /trunk/header.inc.php, /trunk/home.php, /trunk/image_format.php, /trunk/images/Thumbs.db, /trunk/images/account_title.png, /trunk/images/analysis.png, /trunk/images/deconvolved.png, /trunk/images/filemanager.png, /trunk/images/filemanager_small.png, /trunk/images/image_parameters.png, /trunk/images/launch.png, /trunk/images/launch_start.png, /trunk/images/logo_bsse.png, /trunk/images/logo_epfl.png, /trunk/images/logo_svi.png, /trunk/images/omero_data.png, /trunk/images/param_asis.png, /trunk/images/param_default.png, /trunk/images/param_estimated.png, /trunk/images/queue_title.png, /trunk/images/raw.png, /trunk/images/rawdata.png, /trunk/images/rawdata_small.png, /trunk/images/rawdata_title.png, /trunk/images/registration.png, /trunk/images/registration_title.png, /trunk/images/restoration.png, /trunk/images/results.png, /trunk/images/results_small.png, /trunk/images/results_title.png, /trunk/images/select_images.png, /trunk/images/system_title.png, /trunk/images/text_asis.png, /trunk/images/text_default.png, /trunk/images/text_estimated.png, /trunk/inc/Database.inc.php, /trunk/inc/FileBrowser.inc.php, /trunk/inc/Fileserver.inc.php, /trunk/inc/HuygensTemplate.inc.php, /trunk/inc/Job.inc.php, /trunk/inc/JobDescription.inc.php, /trunk/inc/JobQueue.inc.php, /trunk/inc/OmeroConnection.inc.php, /trunk/inc/Parameter.inc.php, /trunk/inc/QueueManager.inc.php, /trunk/inc/Setting.inc.php, /trunk/inc/SettingEditor.inc.php, /trunk/inc/Shell.inc.php, /trunk/inc/Stats.inc.php, /trunk/inc/System.inc.php, /trunk/inc/User.inc.php, /trunk/inc/Util.inc.php, /trunk/inc/extern/adLDAP4/CHANGELOG.txt, /trunk/inc/extern/adLDAP4/README.txt, /trunk/inc/extern/adLDAP4/src/adLDAP.php, /trunk/inc/extern/adLDAP4/src/classes/adLDAPComputers.php, /trunk/inc/extern/adLDAP4/src/classes/adLDAPContacts.php, /trunk/inc/extern/adLDAP4/src/classes/adLDAPExchange.php, /trunk/inc/extern/adLDAP4/src/classes/adLDAPFolders.php, /trunk/inc/extern/adLDAP4/src/classes/adLDAPGroups.php, /trunk/inc/extern/adLDAP4/src/classes/adLDAPUsers.php, /trunk/inc/extern/adLDAP4/src/classes/adLDAPUtils.php, /trunk/inc/extern/adLDAP4/src/collections/adLDAPCollection.php, /trunk/inc/extern/adLDAP4/src/collections/adLDAPComputerCollection.php, /trunk/inc/extern/adLDAP4/src/collections/adLDAPContactCollection.php, /trunk/inc/extern/adLDAP4/src/collections/adLDAPGroupCollection.php, /trunk/inc/extern/adLDAP4/src/collections/adLDAPUserCollection.php, /trunk/inc/extern/adodb5/.htaccess, /trunk/inc/extern/adodb5/adodb-active-record.inc.php, /trunk/inc/extern/adodb5/adodb-active-recordx.inc.php, /trunk/inc/extern/adodb5/adodb-csvlib.inc.php, /trunk/inc/extern/adodb5/adodb-datadict.inc.php, /trunk/inc/extern/adodb5/adodb-error.inc.php, /trunk/inc/extern/adodb5/adodb-errorhandler.inc.php, /trunk/inc/extern/adodb5/adodb-errorpear.inc.php, /trunk/inc/extern/adodb5/adodb-exceptions.inc.php, /trunk/inc/extern/adodb5/adodb-iterator.inc.php, /trunk/inc/extern/adodb5/adodb-lib.inc.php, /trunk/inc/extern/adodb5/adodb-memcache.lib.inc.php, /trunk/inc/extern/adodb5/adodb-pager.inc.php, /trunk/inc/extern/adodb5/adodb-pear.inc.php, /trunk/inc/extern/adodb5/adodb-perf.inc.php, /trunk/inc/extern/adodb5/adodb-php4.inc.php, /trunk/inc/extern/adodb5/adodb-time.inc.php, /trunk/inc/extern/adodb5/adodb.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-access.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-db2.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-firebird.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-generic.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-ibase.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-informix.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-mssql.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-mssqlnative.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-mysql.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-oci8.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-postgres.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-sapdb.inc.php, /trunk/inc/extern/adodb5/datadict/datadict-sqlite.inc.php, 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/trunk/select_task_settings.php, /trunk/setup/dbupdate.php, /trunk/statistics.php, /trunk/system.php, /trunk/task_parameter.php: Brought trunk to have the same content of the newWorkflow branch at revision 1563. 2013-01-17 13:19 aarpon * [r1566] /trunk/images/Thumbs.db: Removed Thumbs.db from images/. 2013-01-17 14:28 danielsevilla * [r1567] /branches/newWorkflow/inc/Job.inc.php: Fixed the signal/noise ratio values shown on the restoration parameters summary table, which was wrong when running a QMLE deconvolution on a multichannel image.