2010-06-10 15:35 agriffa * [r655] capturing_parameter.php: Add pixel size computation from CCD camera for multipoint confocal 2010-06-16 15:30 danielsevilla * [r656] calculate_bp_pinhole.php: 2010-07-09 12:15 danielsevilla * [r657] inc/Fileserver.inc, inc/Util.inc, inc/hrm_config.inc.sample: Enable file size limitation for uploads less dependent on php.ini 2010-07-09 15:56 aarpon * [r658] home.php, images/system.png, inc/Database.inc, inc/Util.inc, stylesheets/default.css: Added system summary page for the administrator that will show versions, relevant php.ini settings and configuration values. Currently, only some have been implemented. More to come. 2010-07-12 11:03 aarpon * [r659] system.php: Added system.php file (forgotten in previous commit). 2010-07-12 16:54 aarpon * [r660] inc/System.inc, inc/Util.inc, stylesheets/default.css, system.php: Added a new static class System that can be used to query for system versions, php.ini and hrm configuration variable values. The page system.php (accessible from the admin home page) uses it to display all information. 2010-07-14 15:58 aarpon * [r661] inc/System.inc, inc/versions.inc: (1) Added formatting options in the System class; (2) increased HRM version in trunk to 1.3.0. 2010-07-15 12:16 aarpon * [r662] inc/System.inc, stylesheets/default.css, system.php: Added operating system and machine info reporting to the System class. 2010-07-15 12:28 aarpon * [r663] inc/System.inc: Changed uname parameters in System.inc to be portable between GNU/Linux and MacOSX. 2010-07-15 14:07 aarpon * [r664] inc/hrm_config.inc, inc/hrm_config.inc.sample: Moved two obsolete variables from hrm_config.inc.sample to hrm_config.inc, where they are set to the only acceptable values they can take. Later we will remove them completely (and remove dependences from the code as well). 2010-07-15 14:54 aarpon * [r665] resources/check.php, user_management.php: (1) Since Outlook does not follow the standards, implemented a simple workaround to support sending emails to distribution list in Outlook vs. every other email client. (2) Extended the resources/check.php script to be more reliable in checking hrm configuration files. 2010-07-16 09:37 aarpon * [r666] resources/checkConfig.php: Renamed resources/check.php into resources/checkConfig.php. 2010-07-16 11:22 aarpon * [r667] inc/hrm_config.inc.sample, resources/check.php, resources/checkConfig.php, user_management.php: (1) Renamed resources/check.php into resources/checkConfig.php; (2) Added option in hrm_config.inc.sample to specify the separator for e-mail address lists to cope with the fact that Microsoft outlook does not follow the standards. 2010-07-21 13:29 aarpon * [r668] account.php, capturing_parameter.php, footer.inc.php, home.php, inc/Database.inc, inc/System.inc, inc/hrm_config.inc, inc/hrm_config.inc.sample, login.php, resources/checkConfig.php, select_task_settings.php, setup/dbupdate.php, system.php, task_parameter.php, update.php, user_management.php: (1) Cleaned inc/hrm_config.inc from processing and dependences on other classes; (2) removed $enable_code_for_huygens variable from the configuration files since this is now handled through the database; (3) Additional cleanups. 2010-09-13 13:45 danielsevilla * [r669] scripts/hucore.tcl: Added access to new SNR estimator from HuCore version 3.6.1 on. 2010-09-13 13:53 danielsevilla * [r670] scripts/hucore.tcl: Corrected tiny blank to keep better edition. 2010-10-04 08:39 aarpon * [r671] ., inc/AccountingDatabase.inc, inc/Database.inc, inc/extern/adodb5, inc/extern/adodb5/adodb-active-record.inc.php, inc/extern/adodb5/adodb-active-recordx.inc.php, inc/extern/adodb5/adodb-csvlib.inc.php, inc/extern/adodb5/adodb-datadict.inc.php, inc/extern/adodb5/adodb-error.inc.php, inc/extern/adodb5/adodb-errorhandler.inc.php, inc/extern/adodb5/adodb-errorpear.inc.php, inc/extern/adodb5/adodb-exceptions.inc.php, inc/extern/adodb5/adodb-iterator.inc.php, inc/extern/adodb5/adodb-lib.inc.php, inc/extern/adodb5/adodb-memcache.lib.inc.php, inc/extern/adodb5/adodb-pager.inc.php, inc/extern/adodb5/adodb-pear.inc.php, inc/extern/adodb5/adodb-perf.inc.php, inc/extern/adodb5/adodb-php4.inc.php, inc/extern/adodb5/adodb-time.inc.php, inc/extern/adodb5/adodb-xmlschema.inc.php, inc/extern/adodb5/adodb-xmlschema03.inc.php, inc/extern/adodb5/adodb.inc.php, inc/extern/adodb5/contrib, inc/extern/adodb5/contrib/toxmlrpc.inc.php, inc/extern/adodb5/cute_icons_for_site, inc/extern/adodb5/cute_icons_for_site/adodb.gif, inc/extern/adodb5/cute_icons_for_site/adodb2.gif, inc/extern/adodb5/datadict, inc/extern/adodb5/datadict/datadict-access.inc.php, inc/extern/adodb5/datadict/datadict-db2.inc.php, inc/extern/adodb5/datadict/datadict-firebird.inc.php, inc/extern/adodb5/datadict/datadict-generic.inc.php, inc/extern/adodb5/datadict/datadict-ibase.inc.php, inc/extern/adodb5/datadict/datadict-informix.inc.php, inc/extern/adodb5/datadict/datadict-mssql.inc.php, inc/extern/adodb5/datadict/datadict-mssqlnative.inc.php, inc/extern/adodb5/datadict/datadict-mysql.inc.php, inc/extern/adodb5/datadict/datadict-oci8.inc.php, inc/extern/adodb5/datadict/datadict-postgres.inc.php, inc/extern/adodb5/datadict/datadict-sapdb.inc.php, inc/extern/adodb5/datadict/datadict-sqlite.inc.php, inc/extern/adodb5/datadict/datadict-sybase.inc.php, inc/extern/adodb5/docs, inc/extern/adodb5/docs/docs-active-record.htm, inc/extern/adodb5/docs/docs-adodb.htm, inc/extern/adodb5/docs/docs-datadict.htm, inc/extern/adodb5/docs/docs-oracle.htm, inc/extern/adodb5/docs/docs-perf.htm, inc/extern/adodb5/docs/docs-session.htm, inc/extern/adodb5/docs/docs-session.old.htm, inc/extern/adodb5/docs/old-changelog.htm, inc/extern/adodb5/docs/readme.htm, inc/extern/adodb5/docs/tips_portable_sql.htm, inc/extern/adodb5/docs/tute.htm, inc/extern/adodb5/drivers, inc/extern/adodb5/drivers/adodb-access.inc.php, inc/extern/adodb5/drivers/adodb-ado.inc.php, inc/extern/adodb5/drivers/adodb-ado5.inc.php, inc/extern/adodb5/drivers/adodb-ado_access.inc.php, inc/extern/adodb5/drivers/adodb-ado_mssql.inc.php, inc/extern/adodb5/drivers/adodb-ads.inc.php, inc/extern/adodb5/drivers/adodb-borland_ibase.inc.php, inc/extern/adodb5/drivers/adodb-csv.inc.php, inc/extern/adodb5/drivers/adodb-db2.inc.php, inc/extern/adodb5/drivers/adodb-db2oci.inc.php, inc/extern/adodb5/drivers/adodb-db2ora.inc.php, inc/extern/adodb5/drivers/adodb-fbsql.inc.php, inc/extern/adodb5/drivers/adodb-firebird.inc.php, inc/extern/adodb5/drivers/adodb-ibase.inc.php, inc/extern/adodb5/drivers/adodb-informix.inc.php, inc/extern/adodb5/drivers/adodb-informix72.inc.php, inc/extern/adodb5/drivers/adodb-ldap.inc.php, inc/extern/adodb5/drivers/adodb-mssql.inc.php, inc/extern/adodb5/drivers/adodb-mssql_n.inc.php, inc/extern/adodb5/drivers/adodb-mssqlnative.inc.php, inc/extern/adodb5/drivers/adodb-mssqlpo.inc.php, inc/extern/adodb5/drivers/adodb-mysql.inc.php, inc/extern/adodb5/drivers/adodb-mysqli.inc.php, inc/extern/adodb5/drivers/adodb-mysqlpo.inc.php, inc/extern/adodb5/drivers/adodb-mysqlt.inc.php, inc/extern/adodb5/drivers/adodb-netezza.inc.php, inc/extern/adodb5/drivers/adodb-oci8.inc.php, inc/extern/adodb5/drivers/adodb-oci805.inc.php, inc/extern/adodb5/drivers/adodb-oci8po.inc.php, inc/extern/adodb5/drivers/adodb-odbc.inc.php, inc/extern/adodb5/drivers/adodb-odbc_db2.inc.php, inc/extern/adodb5/drivers/adodb-odbc_mssql.inc.php, inc/extern/adodb5/drivers/adodb-odbc_oracle.inc.php, inc/extern/adodb5/drivers/adodb-odbtp.inc.php, inc/extern/adodb5/drivers/adodb-odbtp_unicode.inc.php, inc/extern/adodb5/drivers/adodb-oracle.inc.php, inc/extern/adodb5/drivers/adodb-pdo.inc.php, inc/extern/adodb5/drivers/adodb-pdo_mssql.inc.php, inc/extern/adodb5/drivers/adodb-pdo_mysql.inc.php, inc/extern/adodb5/drivers/adodb-pdo_oci.inc.php, inc/extern/adodb5/drivers/adodb-pdo_pgsql.inc.php, inc/extern/adodb5/drivers/adodb-pdo_sqlite.inc.php, inc/extern/adodb5/drivers/adodb-postgres.inc.php, inc/extern/adodb5/drivers/adodb-postgres64.inc.php, inc/extern/adodb5/drivers/adodb-postgres7.inc.php, inc/extern/adodb5/drivers/adodb-postgres8.inc.php, inc/extern/adodb5/drivers/adodb-proxy.inc.php, inc/extern/adodb5/drivers/adodb-sapdb.inc.php, inc/extern/adodb5/drivers/adodb-sqlanywhere.inc.php, inc/extern/adodb5/drivers/adodb-sqlite.inc.php, inc/extern/adodb5/drivers/adodb-sqlitepo.inc.php, inc/extern/adodb5/drivers/adodb-sybase.inc.php, inc/extern/adodb5/drivers/adodb-sybase_ase.inc.php, inc/extern/adodb5/drivers/adodb-vfp.inc.php, inc/extern/adodb5/lang, inc/extern/adodb5/lang/adodb-ar.inc.php, inc/extern/adodb5/lang/adodb-bg.inc.php, inc/extern/adodb5/lang/adodb-bgutf8.inc.php, inc/extern/adodb5/lang/adodb-ca.inc.php, inc/extern/adodb5/lang/adodb-cn.inc.php, inc/extern/adodb5/lang/adodb-cz.inc.php, inc/extern/adodb5/lang/adodb-da.inc.php, inc/extern/adodb5/lang/adodb-de.inc.php, inc/extern/adodb5/lang/adodb-en.inc.php, inc/extern/adodb5/lang/adodb-es.inc.php, inc/extern/adodb5/lang/adodb-esperanto.inc.php, inc/extern/adodb5/lang/adodb-fa.inc.php, inc/extern/adodb5/lang/adodb-fr.inc.php, inc/extern/adodb5/lang/adodb-hu.inc.php, inc/extern/adodb5/lang/adodb-it.inc.php, inc/extern/adodb5/lang/adodb-nl.inc.php, inc/extern/adodb5/lang/adodb-pl.inc.php, inc/extern/adodb5/lang/adodb-pt-br.inc.php, inc/extern/adodb5/lang/adodb-ro.inc.php, inc/extern/adodb5/lang/adodb-ru1251.inc.php, inc/extern/adodb5/lang/adodb-sv.inc.php, inc/extern/adodb5/lang/adodb-uk1251.inc.php, inc/extern/adodb5/lang/adodb_th.inc.php, inc/extern/adodb5/license.txt, inc/extern/adodb5/pear, inc/extern/adodb5/pear/Auth, inc/extern/adodb5/pear/Auth/Container, inc/extern/adodb5/pear/Auth/Container/ADOdb.php, inc/extern/adodb5/pear/readme.Auth.txt, inc/extern/adodb5/perf, inc/extern/adodb5/perf/perf-db2.inc.php, inc/extern/adodb5/perf/perf-informix.inc.php, inc/extern/adodb5/perf/perf-mssql.inc.php, inc/extern/adodb5/perf/perf-mssqlnative.inc.php, inc/extern/adodb5/perf/perf-mysql.inc.php, inc/extern/adodb5/perf/perf-oci8.inc.php, inc/extern/adodb5/perf/perf-postgres.inc.php, inc/extern/adodb5/pivottable.inc.php, inc/extern/adodb5/readme.txt, inc/extern/adodb5/rsfilter.inc.php, inc/extern/adodb5/server.php, inc/extern/adodb5/session, inc/extern/adodb5/session/adodb-compress-bzip2.php, inc/extern/adodb5/session/adodb-compress-gzip.php, inc/extern/adodb5/session/adodb-cryptsession.php, inc/extern/adodb5/session/adodb-cryptsession2.php, inc/extern/adodb5/session/adodb-encrypt-mcrypt.php, inc/extern/adodb5/session/adodb-encrypt-md5.php, inc/extern/adodb5/session/adodb-encrypt-secret.php, inc/extern/adodb5/session/adodb-encrypt-sha1.php, inc/extern/adodb5/session/adodb-sess.txt, inc/extern/adodb5/session/adodb-session-clob.php, inc/extern/adodb5/session/adodb-session-clob2.php, inc/extern/adodb5/session/adodb-session.php, inc/extern/adodb5/session/adodb-session2.php, inc/extern/adodb5/session/adodb-sessions.mysql.sql, inc/extern/adodb5/session/adodb-sessions.oracle.clob.sql, inc/extern/adodb5/session/adodb-sessions.oracle.sql, inc/extern/adodb5/session/crypt.inc.php, inc/extern/adodb5/session/old, inc/extern/adodb5/session/old/adodb-cryptsession.php, inc/extern/adodb5/session/old/adodb-session-clob.php, inc/extern/adodb5/session/old/adodb-session.php, inc/extern/adodb5/session/old/crypt.inc.php, inc/extern/adodb5/session/session_schema.xml, inc/extern/adodb5/session/session_schema2.xml, inc/extern/adodb5/tests, inc/extern/adodb5/tests/benchmark.php, inc/extern/adodb5/tests/client.php, inc/extern/adodb5/tests/pdo.php, inc/extern/adodb5/tests/test-active-record.php, inc/extern/adodb5/tests/test-active-recs2.php, inc/extern/adodb5/tests/test-active-relations.php, inc/extern/adodb5/tests/test-active-relationsx.php, inc/extern/adodb5/tests/test-datadict.php, inc/extern/adodb5/tests/test-perf.php, inc/extern/adodb5/tests/test-pgblob.php, inc/extern/adodb5/tests/test-php5.php, inc/extern/adodb5/tests/test-xmlschema.php, inc/extern/adodb5/tests/test.php, inc/extern/adodb5/tests/test2.php, inc/extern/adodb5/tests/test3.php, inc/extern/adodb5/tests/test4.php, inc/extern/adodb5/tests/test5.php, inc/extern/adodb5/tests/test_rs_array.php, inc/extern/adodb5/tests/testcache.php, inc/extern/adodb5/tests/testdatabases.inc.php, inc/extern/adodb5/tests/testgenid.php, inc/extern/adodb5/tests/testmssql.php, inc/extern/adodb5/tests/testoci8.php, inc/extern/adodb5/tests/testoci8cursor.php, inc/extern/adodb5/tests/testpaging.php, inc/extern/adodb5/tests/testpear.php, inc/extern/adodb5/tests/testsessions.php, inc/extern/adodb5/tests/time.php, inc/extern/adodb5/tests/tmssql.php, inc/extern/adodb5/tests/xmlschema-mssql.xml, inc/extern/adodb5/tests/xmlschema.xml, inc/extern/adodb5/toexport.inc.php, inc/extern/adodb5/tohtml.inc.php, inc/extern/adodb5/xmlschema.dtd, inc/extern/adodb5/xmlschema03.dtd, inc/extern/adodb5/xsl, inc/extern/adodb5/xsl/convert-0.1-0.2.xsl, inc/extern/adodb5/xsl/convert-0.1-0.3.xsl, inc/extern/adodb5/xsl/convert-0.2-0.1.xsl, inc/extern/adodb5/xsl/convert-0.2-0.3.xsl, inc/extern/adodb5/xsl/remove-0.2.xsl, inc/extern/adodb5/xsl/remove-0.3.xsl: Added ADOdb version 5.11 (in parallel to the old version 4). The new version is enabled. Please check. 2010-10-26 11:11 aarpon * [r672] inc/extern/adLDAP/CHANGELOG.txt, inc/extern/adLDAP/README.txt, inc/extern/adLDAP/adLDAP.php, inc/extern/adLDAP/examples, inc/extern/adLDAP/examples/authenticate.php, inc/extern/adLDAP/examples/examples.php, inc/extern/adLDAP/examples/menu.htm: Updated adLDAP library to version 3.3.2 (bug fixes). 2010-10-26 11:55 aarpon * [r673] login.php: Corrected comment. 2010-10-26 15:18 aarpon * [r674] inc/accounting_db_config.inc, inc/accounting_db_config.inc.sample: Removed inc/accounting_db_config.inc and created inc/accounting_db_config.inc.sample. 2010-11-05 08:53 aarpon * [r675] home.php, inc/Mail.inc, login.php, registration.php: (1) Added missing require (Util.inc) in registration.php; (2) Added checks for inclusion of CreditOwner.inc only if the accounting system is enabled; (3) fixed the header of emails in Mail::send(). 2010-11-05 13:47 aarpon * [r676] inc/Mail.inc, registration.php: Added some more error checking/reporting on mail sending. 2010-11-05 17:32 aarpon * [r677] inc/Validator.inc, registration.php: Added a new static class Validator that checks user input for validity (in particular user name, password, email) before they are used in SQL queries. The registration.php page now already makes use of the new Validator (moreover, it was refactored). Next, the login and the add user pages should use the Validator. The Validator could also implement generic checks for parameters (just the type). 2010-11-08 17:32 aarpon * [r678] account.php, add_user_popup.php, inc/Database.inc, inc/User.inc, inc/Validator.inc, login.php, registration.php, user_management.php: (1) Heavily refactored the user class and the way it is used throughout the code. (2) Moved some user handling to the Database class. (3) A validator is taking care of checing user input at least wherever there are login forms and user creation/edition. (4) Started removing references to the Montpellier RIO accounting system (that was still in for historical reasons only).This will be completed in the next commits. 2010-11-09 12:52 aarpon * [r679] login.php: Added additional controls for the validity of user name and passwords in login.php. 2010-11-09 15:37 aarpon * [r680] login.php: Bug fix in how post data is checked (or not checked...). 2010-11-10 14:21 aarpon * [r681] create_job.php, header.inc.php, home.php, inc/AccountingDatabase.inc, inc/CreditOwner.inc, inc/Database.inc, inc/JobDescription.inc, inc/JobQueue.inc, inc/QueueManager.inc, inc/User.inc, inc/Versions.inc, inc/accounting_db_config.inc.sample, inc/hrm_config.inc, inc/versions.inc, login.php, scripts/settings.js, select_credit.php, setup/dbupdate.php, stylesheets/default.css: (1) Removed the unused accounting system (that was probably no longer working and was anyways only usable at Montpellier RIO imaging). (2) Fixed bug 3105425: Missing stopping criteria when qmle is chosen. (3) Changed the background color of the header ;-) 2010-11-10 16:01 aarpon * [r682] config, config/samples, config/samples/hrm_client_config.inc.sample, config/samples/hrm_server_config.inc.sample: Created the config subdirectory that from the next release will host the configuration files of the HRM and the config/samples subdirectory that will host the sample configuration files. 2010-11-10 16:08 aarpon * [r683] config/samples/active_directory_config.inc.sample, config/samples/hrm.conf.sample, config/samples/ldap_config.inc.sample, inc/active_directory_config.inc.sample, inc/hrm_config.inc.sample, inc/ldap_config.inc.sample, inc/reservation_config.inc, resources/hrm.conf.sample: Moved the sample configuration files from inc/ and resources/ to config/samples. 2010-11-10 16:17 aarpon * [r684] config: Added ignore option for the configuration files. 2010-11-10 16:44 aarpon * [r685] inc/ActiveDirectory.inc, inc/Database.inc, inc/Ldap.inc, inc/Util.inc, inc/hrm_config.inc, resources/checkConfig.php: Moved all references rto configuration files to $HRM_ROOT/config. 2010-11-10 17:00 aarpon * [r686] setup/dbupdate.php: Cleaned dbupdate.php. 2010-11-10 17:38 aarpon * [r687] inc/extern/adodb: Removed ADOdb version 4.x. 2010-11-11 07:54 aarpon * [r688] config/.htaccess, config/samples/.htaccess: Added .htaccess file to config and config/samples. 2010-11-11 14:30 aarpon * [r689] header.inc.php, statistics.php: Added a mechanism to add an array of javascript includes in header.inc.php which also allowed to remove the HighChart Javascript library inclusions. So far those libraries were included in ALL files, and not only in statistics.php (which is now the case). 2010-11-11 14:47 aarpon * [r690] image_format.php, scripts/quickhelp, scripts/quickhelp/imageformatHelp.js: Added a new Javascript-only mechanism to get dynamic help on pages (as was introduced only for the restoration settings in HRM 1.2 but with a hybrid PHP-Javascript way that will be replaced by the new one). Only one page (image_format.php) has been changed to implement the new method so far. The others will come over the next commits. 2010-11-17 16:32 aarpon * [r691] aberration_correction.php, capturing_parameter.php, image_format.php, microscope_parameter.php, scripts/quickhelp/aberrationCorrectionHelp.js, scripts/quickhelp/capturingParameterHelp.js, scripts/quickhelp/help.js, scripts/quickhelp/imageFormatHelp.js, scripts/quickhelp/imageformatHelp.js, scripts/quickhelp/microscopeParameterHelp.js, stylesheets/default.css: Added more dynamic help to a few more pages. 2010-11-18 15:46 aarpon * [r692] aberration_correction.php, capturing_parameter.php, image_format.php, microscope_parameter.php, scripts/quickhelp/aberrationCorrectionHelp.js, scripts/quickhelp/capturingParameterHelp.js, scripts/quickhelp/imageFormatHelp.js, scripts/quickhelp/microscopeParameterHelp.js, scripts/quickhelp/taskParameterHelp.js, scripts/settings.js, stylesheets/default.css, task_parameter.php: Added more dynamic help on pages. Cleaned some layout glitches. 2010-11-22 14:02 aarpon * [r693] aberration_correction.php, create_job.php, footer.inc.php, header.inc.php, home.php, image_format.php, inc/QueueManager.inc, inc/System.inc, inc/User.inc, inc/Util.inc, inc/Versions.inc, login.php, setup/dbupdate.php, stylesheets/default.css, system.php, task_parameter.php: (1) Merged Version.inc into System.inc and cleaned the various ways to get the HuCore version. (2) Added more info to system.php. (3) Removed contact info for Alessandra. 2010-11-23 09:15 aarpon * [r694] create_job.php: Fixed typo. 2010-11-23 09:47 aarpon * [r695] inc/Database.inc, inc/QueueManager.inc, inc/System.inc: Moved last methods to query and store the HuCore version from and to the Database in the System class. 2010-11-24 11:38 aarpon * [r696] inc/Database.inc, job_queue.php: Added documentation to all functions in Database.inc. Started removing all direct SQL queries from UI (php) pages. 2010-11-25 08:57 aarpon * [r697] inc/ActiveDirectory.inc, inc/Database.inc, inc/FileBrowser.inc, inc/Fileserver.inc, inc/Job.inc, inc/JobDescription.inc, inc/JobQueue.inc, inc/Ldap.inc, inc/Mail.inc, inc/Parameter.inc, inc/QueueManager.inc, inc/Setting.inc, inc/SettingEditor.inc, inc/Shell.inc, inc/Stats.inc, inc/System.inc, inc/User.inc, inc/Util.inc, inc/Validator.inc: Started effort to properly document all code for doxygen. 2010-11-25 16:21 aarpon * [r698] inc/ActiveDirectory.inc, inc/Database.inc, inc/FileBrowser.inc, inc/Fileserver.inc, inc/JobDescription.inc, inc/Ldap.inc, inc/Parameter.inc, inc/QueueManager.inc, inc/Setting.inc, inc/SettingEditor.inc, inc/Stats.inc, inc/User.inc, inc/Util.inc: Documented, cleaned and reorganized more files. 2010-11-25 20:21 aarpon * [r699] inc/Job.inc, inc/JobQueue.inc: Documented Job.inc and partially JobQueue.inc. 2010-11-26 17:06 aarpon * [r700] inc/Database.inc, inc/FileBrowser.inc, inc/Fileserver.inc, inc/Job.inc, inc/JobDescription.inc, inc/JobQueue.inc, inc/Ldap.inc, inc/Mail.inc, inc/Shell.inc: Documented, cleaned, and reorganized more code. 2010-11-30 14:41 aarpon * [r701] inc/Job.inc, inc/User.inc, select_task_settings.php, update.php, user_management.php: (1) Removed automatic admin login from two pages: update.php (where it was not needed at all) and user_management.php (where the usual redirect to login and back mechanism was implemented). (2) Commented, cleaned and reorganized User.inc (classes Owner and User). 2010-11-30 15:35 aarpon * [r702] account.php, estimate_snr_from_image.php, home.php, job_queue.php, login.php, registration.php, select_parameter_settings.php, select_task_settings.php, system.php, task_parameter.php, user_management.php: (1) Cleaned login.php. The user must be registered with the session ONLY if login was successful, otherwise all checks in the other pages can get VERY confused. (2) Removed hard-coded admin name from pages. 2010-11-30 16:10 aarpon * [r703] home.php, inc/User.inc, user_management.php: Removed more direct SQL queries from the UI pages. 2010-12-02 15:05 aarpon * [r704] aberration_correction.php, home.php, inc/Database.inc, inc/Fileserver.inc, inc/JobDescription.inc, inc/Parameter.inc, inc/Setting.inc, setup/dbupdate.php, update.php: (1) Completely commented Parameter.inc. (2) Several minor cleaning efforts. 2010-12-02 16:15 aarpon * [r705] inc/Parameter.inc: Rewritten all class constructors in Parameter.inc to use PHP 5 syntax. 2010-12-04 21:29 aarpon * [r706] inc/Parameter.inc, task_parameter.php: (1) Added a new class NumericalArrayParameter for those Parameters that store a numerical value per channel. (2) Forced the original NumericalParameter to accept only scalars. (3) Bug fix: minor change in task_parameter.php to completely disable any hiding of the stopping criteria for now. 2010-12-06 14:28 danielsevilla * [r707] inc/JobTranslation.inc: Initial work towards a new job description. The jobs will be translated into nested lists compliant with HuCore templates. HuCore will then execute the deconvolution jobs from these lists. Improvements on the code of this file are coming. 2010-12-08 08:21 aarpon * [r708] aberration_correction.php, capturing_parameter.php, image_format.php, inc/Database.inc, inc/Parameter.inc, inc/Setting.inc, inc/SettingEditor.inc, microscope_parameter.php, select_parameter_settings.php, task_parameter.php: Documented and refactored SettingEditor plus several additional minor changes. 2010-12-09 15:59 aarpon * [r709] capturing_parameter.php: Started a big refactoring of Setting.inc and Parameter.inc and their use in the user interface. The Parameters should take care of checking their own validity, whereas this was mostly done by the Setting class and partially in the user interface. The part concerning the image parameters is done. The restoration parameters come next. 2010-12-09 16:00 aarpon * [r710] aberration_correction.php, calculate_pixel_size.php, image_format.php, inc/Database.inc, inc/Parameter.inc, inc/Setting.inc, inc/SettingEditor.inc, microscope_parameter.php: Completing partial commit. 2010-12-09 16:49 aarpon * [r711] inc/Parameter.inc, select_psf.php, select_psf_popup.php: (1) Made the VariableChannelsParameter inherit from NumericalArrayParameter and the PSF parameter from VariableChannelsParameter. (2) Updated select_psf.php to use the new PSF parameter. 2010-12-10 15:30 danielsevilla * [r712] inc/Job.inc, inc/JobDescription.inc, inc/JobTranslation.inc, scripts/hrmJob2huCore.tcl: Added the basics for a job deconvolution based on HuCore templates. This functionality can work already and produce deconvolution results, although more improvements included code revisions are coming. Also added the functions to produce thumbnails with the deconvolution jobs. 2010-12-13 15:24 aarpon * [r713] aberration_correction.php, calculate_pixel_size.php, capturing_parameter.php, create_job.php, image_format.php, inc/Database.inc, inc/JobDescription.inc, inc/Parameter.inc, inc/Setting.inc, microscope_parameter.php, select_parameter_settings.php, select_task_settings.php, task_parameter.php: (1) All Parameter objects are now responsible for performing their own checks; this also means that many methods in the Setting classes were removed. (2) RangeParameters were removed. (3) Unused Parameters were removed. 2010-12-14 13:36 aarpon * [r714] inc/Database.inc, inc/Parameter.inc, inc/QueueManager.inc, inc/Shell.inc, inc/Stats.inc, inc/System.inc, scripts/highcharts/excanvas.compiled.js, scripts/highcharts/highcharts.js, scripts/highcharts/jquery.min.js, statistics.php: (1) Documented Queuemanager.inc, Shell.inc and Stats.inc. (2) Updated Highcharts library to version 2.1.1 and JQuery to 1.4.4. 2010-12-14 15:34 aarpon * [r715] inc/Parameter.inc, inc/Setting.inc, inc/Shell.inc: (1) Documented and cleaned JobParameterSetting and JobTaskSetting. (2) Several minor changes and fixes. 2010-12-14 17:43 aarpon * [r716] image_format.php, inc/Parameter.inc, inc/Setting.inc: (1) Every Parameter has its own overloaded displayString() method to take care of the correct display of name and value(s). (2) In image_format.php, after the Parameter check and the redirection to the new page, the $numberOfChannels variable of all VariableChannel Parameters is updated to ensure consistency. 2010-12-15 09:51 aarpon * [r717] inc/Job.inc, inc/hrm_config.inc: The HRM now runs the old Jobs if HuCore is older than 3.7.0 and the new template-based Jobs for HuCore version 3.7.0 and above. In case of problems, it is still possible to force the use of the old Jobs even for new HuCores by setting the variable $useHuScriptVersion to 0 in inc/hrm_config.inc. Should this be in the standard configuration files? 2010-12-16 08:34 aarpon * [r718] inc/Job.inc: Typo in the minimum HuCore version required to use new template-based jobs. 2010-12-22 15:44 danielsevilla * [r719] inc/JobTranslation.inc, scripts/hrmJob2huCore.tcl: Improved template-based tcl script. Adapted the JobTranslation to be able to use several cores when running jobs. 2011-01-03 13:17 aarpon * [r720] inc/System.inc, job_queue.php, setup/dbupdate.php, system.php: Added two changes to the database for the upcoming revision 8. 2011-01-03 16:07 danielsevilla * [r721] inc/Shell.inc: Fixed the kill job action in the new template-based job schema. 2011-01-07 13:17 danielsevilla * [r735] inc/JobTranslation.inc: Expanded comments in the class and its atributes and methods. 2011-01-07 15:42 danielsevilla * [r736] scripts/hrmJob2huCore.tcl: Fixed a problem with thumbnails. They were not properly created with the execution of the deconvolution job. 2011-01-07 16:24 danielsevilla * [r737] scripts/hrmJob2huCore.tcl: Added Z and time slices to the list of thumbnails. TODO: Adjust the thumbnail size to the image size. Log properly. 2011-01-10 11:45 danielsevilla * [r738] scripts/hrmJob2huCore.tcl: Log properly 2011-01-10 13:46 danielsevilla * [r739] inc/JobTranslation.inc, scripts/hrmJob2huCore.tcl: (1) More understandable variable names. (2) Deactivate zdrift correction until available in the GUI. 2011-01-10 15:16 aarpon * [r740] ., inc/Job.inc, inc/JobDescription.inc, inc/Setting.inc, inc/hrm_config.inc: Started commenting out deprecated code. After thorough testing, the commented code will be removed definitively. 2011-01-10 17:05 danielsevilla * [r741] inc/Job.inc, scripts/hrmJob2huCore.tcl: Added control over the thumbnail creation, SFP creation, thumbnail comparison size and movie size, as it used to work in older deconvolution job scripts. 2011-01-11 12:17 danielsevilla * [r742] scripts/hrmJob2huCore.tcl: (1) Added two missin raw image thumbnails. (2) Better variable naming. 2011-01-11 15:32 danielsevilla * [r743] scripts/hrmJob2huCore.tcl: Fixed writing permissions problem. The same thumbnail can now be overwritten. 2011-01-11 16:36 danielsevilla * [r744] registration.php: Fixed faulty password registration. 2011-01-13 10:21 aarpon * [r745] inc/Fileserver.inc: Bug fix in FileServer::previewPage(): the case where some previews were disabled in the configuration files was not handled correctly. 2011-01-13 11:36 aarpon * [r746] inc/Fileserver.inc: Some more cleaning in FileServer::previewPage(). 2011-02-02 12:38 danielsevilla * [r747] inc/Job.inc, inc/JobTranslation.inc, inc/QueueManager.inc, inc/Shell.inc, scripts/hrmJob2huCore.tcl: Removed Tcl code. No scripts are to be executed in HuCore to carry out the deconvolution jobs. This is now purely based on templates. 2011-02-02 17:22 aarpon * [r748] image_format.php, images/paramMissing.png, images/paramProvide.png, images/paramTrusted.png, images/paramUntrusted.png, inc/Mail.inc, registration.php, stylesheets/default.css, user_management.php: (1) Added fifth parameter (additional_parameters) to the mail() function in the Mail class. (2) Made it clearer (in the subject) that the emails sent in response to user registration/acceptance/refusal come from the HRM. (3) Added one page with design example for the new runtime parameters handling in the GUI. 2011-02-03 11:24 danielsevilla * [r749] inc/JobTranslation.inc: Further improved JobTranslation code. Expanded comments. 2011-02-03 13:42 danielsevilla * [r750] inc/JobTranslation.inc: Further improvements and code cleaning. 2011-02-03 14:03 danielsevilla * [r751] inc/JobTranslation.inc: Adapted the visibility of some properties and methods. 2011-02-03 14:12 danielsevilla * [r752] inc/JobTranslation.inc: Minor change on template names. 2011-02-03 17:22 aarpon * [r753] inc/System.inc, login.php: Added minimum Hucore version needed to run current HRM version (in System.inc) and corresponding check (in login.php). 2011-02-08 10:24 aarpon * [r754] inc/Database.inc: Added stub function in inc/Database.inc to simulate querying the database for the confidence level of parameters. 2011-02-09 12:18 aarpon * [r755] inc/Setting.inc: Handled geometry properly in case one of the 'single' file formats are chosen. 2011-02-09 14:08 aarpon * [r756] inc/Setting.inc: More changes in the handling of the ImageGeometry parameter for the 'single' file formats. 2011-02-10 17:54 danielsevilla * [r757] inc/JobTranslation.inc: Added thumbnail making to the template-based jobs. It is now purely based on templates. Still needed: clean up and extended comments. 2011-02-11 13:15 danielsevilla * [r758] inc/JobTranslation.inc: Improved comments. Cleaned up. 2011-02-14 09:32 danielsevilla * [r759] inc/QueueManager.inc: Minor: Word 'Script' becomes 'Template'. 2011-02-14 13:20 danielsevilla * [r760] inc/JobTranslation.inc: Fixed thumbnail creation for lif images. 2011-02-14 15:28 danielsevilla * [r761] inc/JobTranslation.inc: Added special lif thumbnails cases: image and subimage stored at the raw data folder. 2011-02-15 10:00 danielsevilla * [r762] inc/JobTranslation.inc: Improved treatment of Lif files. 2011-02-15 15:54 danielsevilla * [r763] inc/Shell.inc: Minor: keep stdout and stderr separated. 2011-02-16 17:00 aarpon * [r764] aberration_correction.php, capturing_parameter.php, image_format.php, images/paramMissing.png, images/paramProvide.png, images/paramTrusted.png, images/paramUntrusted.png, inc/Setting.inc, microscope_parameter.php, stylesheets/default.css: Additional changes to add support for parameter confidence levels in the UI. 2011-02-17 13:40 danielsevilla * [r765] inc/JobTranslation.inc: Minor: typo in parameter. 2011-02-17 14:53 danielsevilla * [r766] inc/JobTranslation.inc: Corrected pinhole spacing in templates. Nipkow disks should get this parameter, the other types shouldn't. 2011-02-17 16:05 aarpon * [r767] bin/hrmd_new: Added an experimental version of the hrmd deamon that will run the queue manager as the user set in /etc/hrm.conf even though the hrmd daemon is started by root. This will make it easier to launch the daemon at boot. 2011-02-22 14:57 aarpon * [r768] inc/Job.inc, inc/JobDescription.inc, inc/Setting.inc, scripts/quickhelp/taskParameterHelp.js: (1) Cleaned obsoleted code. (2) Updated quick help for the task parameters. 2011-02-23 09:51 aarpon * [r769] aberration_correction.php, capturing_parameter.php, image_format.php, inc/Parameter.inc, microscope_parameter.php, scripts/quickhelp/capturingParameterHelp.js: (1) Added the concept of confidenceLevel to the Parameters. (2) Added handling of Parameter confidence levels in the UI. (3) Refactored use of Parameters in the UI to increase robustness of the code. 2011-02-25 15:21 aarpon * [r770] aberration_correction.php, calculate_pixel_size.php, capturing_parameter.php, image_format.php, inc/Database.inc, inc/Parameter.inc, inc/Setting.inc, microscope_parameter.php, scripts/quickhelp/microscopeParameterHelp.js, select_psf.php: More implementation steps toward run-time parameters. 2011-02-25 17:12 aarpon * [r771] inc/Parameter.inc, inc/SettingEditor.inc, inc/User.inc: Removed/changed a few todos and comments in the code. 2011-02-28 11:52 aarpon * [r772] inc/Database.inc: Temporarily set all variable confidence levels to Missing. 2011-03-02 10:20 aarpon * [r773] account.php, inc/Database.inc: Fixed a bug in the user management. 2011-03-02 10:33 aarpon * [r774] inc/User.inc: Fixed logging of log-in time if the embedded user management system is used. 2011-03-02 12:51 aarpon * [r775] aberration_correction.php, account.php, calculate_pixel_size.php, capturing_parameter.php, create_job.php, file_management.php, home.php, image_format.php, job_queue.php, login.php, microscope_parameter.php, registration.php, select_images.php, select_parameter_settings.php, select_psf.php, select_task_settings.php, statistics.php, task_parameter.php, update.php, user_management.php: Changed help links to point to the new help pages on http://www.svi.nl (bypassing the redirections). 2011-03-02 13:50 aarpon * [r776] inc/Fileserver.inc: Bug fix: uploading zip files with blank spaces in the name would result in an error. 2011-03-02 16:25 danielsevilla * [r777] inc/JobTranslation.inc: Fixed bug: the deconvolution failed on files with blanks on their names. 2011-03-02 16:33 aarpon * [r778] estimate_snr_from_image.php: Bug fix in estimate_snr_from_image.php. When simply refreshing the file list, the estimation would be launched if one of the files was selected in the browser. 2011-03-02 16:46 danielsevilla * [r779] inc/JobTranslation.inc: Make sure the deconvolution does not fail as a consequence of blanks in the psf file name. 2011-03-02 18:06 aarpon * [r780] inc/QueueManager.inc, inc/User.inc, inc/Util.inc: (1) Added logging of user logins to the hrm log. (2) Fixed several issues with reporting by email. 2011-03-02 18:07 aarpon * [r781] images/title_bkg.png, images/valid-css21.png, images/valid-xhtml10.png, images/validation_bkg.png, stylesheets/default.css: Changes to the graphical layout. 2011-03-03 15:54 aarpon * [r782] inc/QueueManager.inc: Clearer email subject. 2011-03-03 17:10 danielsevilla * [r783] inc/JobTranslation.inc: Fixed bug: the brick mode was missing when there was no refractive index mismatch. 2011-03-04 09:28 danielsevilla * [r784] inc/Fileserver.inc: Replace blanks with underscores in file names. 2011-03-04 12:01 danielsevilla * [r785] inc/JobTranslation.inc: Removed double (repeated) extension from the deconvolved image. 2011-03-04 17:59 aarpon * [r786] images/title_bkg.png, images/validation_bkg.png: Changed color in header and footer. 2011-03-07 13:09 aarpon * [r787] images/title_bkg.png, images/validation_bkg.png, stylesheets/default.css: Test CSS3 multiple-background support to create a title image that adapts to any window size. 2011-03-07 13:20 danielsevilla * [r788] inc/JobTranslation.inc: If the output format is Tiff, save the deconvolved image in a single file rather than one per slice. 2011-03-07 14:19 aarpon * [r789] header.inc.php, inc/Fileserver.inc, stylesheets/default.css: Since IE does not support multiple backgrounds, implemented workaround with multiple divs layered on top of each other. 2011-03-07 15:10 danielsevilla * [r790] inc/JobTranslation.inc: Make a distinction between the file type and the file extension. Since the generated previews contained the file type instead of the file extension the comparison site would not show even when the previews had been generated properly. 2011-03-08 13:36 aarpon * [r791] stylesheets/default.css: Changed color of title. 2011-03-08 14:38 aarpon * [r792] inc/JobDescription.inc: One missing replacement for blank spaces with underscores for output file names. 2011-03-09 10:20 danielsevilla * [r793] scripts/hucore.tcl: Added new HuCore tool: getFormatInfo. 2011-03-09 10:32 danielsevilla * [r794] scripts/hucore.tcl: Corrected reportFormatInfo call. 2011-03-09 10:35 danielsevilla * [r795] scripts/hucore.tcl: Corrected reportFormatInfo call (2). 2011-03-09 16:13 aarpon * [r796] inc/Database.inc, inc/QueueManager.inc, setup/dbupdate.php: Implemented requesting confidence levels from hucore and parsing. The dbupdate.php function already creates the required table. Still missing: actual storing of the confidence levels in the database. 2011-03-09 20:35 aarpon * [r797] inc/Database.inc, inc/QueueManager.inc: Confidence levels provided by hucore are now stored (INSERTed or UPDATEd) in the confidence_levels table when the queue manager is started (to be tested!). 2011-03-10 08:33 aarpon * [r798] inc/Database.inc, inc/QueueManager.inc, setup/dbupdate.php: Fixed and finished inserting and updating confidence levels. 2011-03-10 09:49 aarpon * [r799] setup/dbupdate.php: Added mapping between HRM file formats and Hucore to the database. 2011-03-10 11:01 aarpon * [r800] aberration_correction.php, capturing_parameter.php, inc/Database.inc, microscope_parameter.php, setup/dbupdate.php: The UI now uses the confidence levels returned from the database. 2011-03-10 11:22 danielsevilla * [r801] inc/Job.inc: Rename Huygens default output file. Not yet available for multiserver configurations. 2011-03-10 13:19 aarpon * [r802] inc/Database.inc: Added handling of Parameters that have a common confidence in the HRM but two independent confidences in hucore (the lower confidence is used). 2011-03-10 13:32 danielsevilla * [r803] inc/JobTranslation.inc: Fixed bug: lif subimages would not be opened. 2011-03-10 13:33 aarpon * [r804] inc/Database.inc: Bug fixes in the handling of the Parameter confidences. 2011-03-10 14:24 aarpon * [r805] inc/Parameter.inc: Added a method to the Parameter class that returns the confidence level to be used in the template. Mind that this confidence level is a function of the original confidence level and the actions taken by the user. 2011-03-10 14:51 danielsevilla * [r806] inc/Job.inc: Rename Huygens default output file in multiserver configurations. 2011-03-10 17:02 aarpon * [r807] inc/Parameter.inc: Updated the Parameter::displayString() method to show when a Parameter value was not set. 2011-03-10 17:06 aarpon * [r808] task_parameter.php: Added graphical layout for Parameters to be provided also for task parameters. 2011-03-11 08:05 aarpon * [r809] footer.inc.php, scripts/common.js, select_parameter_settings.php, select_task_settings.php, user_management.php: (1) Added confirmation when deleting parameter sets. (2) Updated copyright notice in footer.inc.php. 2011-03-11 08:28 danielsevilla * [r810] inc/Database.inc: Inserted missing dollar sign. 2011-03-11 08:45 aarpon * [r811] scripts/common.js, select_parameter_settings.php, select_task_settings.php: (1) Bug fix: when clicking the Delete icon if no setting is selected the question dialog no longer appears. (2) Added some more explanatory text in the select settings pages. 2011-03-11 08:55 danielsevilla * [r812] inc/Parameter.inc: The default confidence level per parameter and file format returned empty. Query the database to fix this. 2011-03-11 10:41 danielsevilla * [r813] inc/JobTranslation.inc: Adapted the confidence levels of the backprojected pinhole radius so that they are read from the database when needed. 2011-03-11 13:00 danielsevilla * [r814] inc/JobTranslation.inc: Adapted the confidence levels of the microscope type so that they are read from the database when needed. 2011-03-11 13:18 danielsevilla * [r815] inc/JobTranslation.inc: Adapted the confidence levels of the lens refractive index so that they are read from the database when needed. 2011-03-11 13:46 danielsevilla * [r816] inc/JobTranslation.inc: (1) Adapted the confidence levels of the numerical aperture so that they are read from the database when needed. (2) Fixed bug in qmle. 2011-03-11 13:55 aarpon * [r817] inc/Parameter.inc: Restored changes in revision 807 that got lost in revision 812. More cleaning. 2011-03-11 14:18 danielsevilla * [r818] inc/JobTranslation.inc: Adapted the confidence levels of the pinhole spacing so that they are read from the database when needed. 2011-03-11 14:33 danielsevilla * [r819] inc/JobTranslation.inc: Fixed bug: An error occured if the numerical aperture was empty. 2011-03-11 14:42 danielsevilla * [r820] inc/JobTranslation.inc: Adapted the confidence levels of the objective quality so that they are read from the database when needed. 2011-03-11 14:48 danielsevilla * [r821] inc/JobTranslation.inc: Adapted the confidence levels of the excitation photon count so that they are read from the database when needed. 2011-03-11 14:53 danielsevilla * [r822] inc/JobTranslation.inc: Adapted the confidence levels of the excitation wavelength so that they are read from the database when needed. 2011-03-11 14:56 danielsevilla * [r823] inc/JobTranslation.inc: Adapted the confidence levels of the excitation beam factor so that they are read from the database when needed. 2011-03-11 15:01 danielsevilla * [r824] inc/JobTranslation.inc: Adapted the confidence levels of the emission wavelength so that they are read from the database when needed. 2011-03-11 15:50 aarpon * [r825] create_job.php: For multi-channel datasets, saving to 8- or 16-bit TIFF is disabled. 2011-03-11 15:53 aarpon * [r826] capturing_parameter.php: If any of the refractive indices are not set, the aberration correction cannot currently be selected. This cleans the behavior a bit. Later support for the aberration correction should be restored and extended. 2011-03-11 15:55 aarpon * [r827] bin/hrmd, bin/hrmd_new: The new hrmd daemon uses the SUSER variable defined in /etc/hrm.conf also to start the queue manager. This makes it possible to start the hrmd at boot and still run the queue manager as the apache user. 2011-03-11 18:49 aarpon * [r828] aberration_correction.php, capturing_parameter.php, image_format.php, images/textMissing.png, images/textProvide.png, images/textTrusted.png, images/textUntrusted.png, microscope_parameter.php, nbproject, select_psf.php, stylesheets/default.css, task_parameter.php: Added explanation to the Parameter confidence levels to the user interface. Since IE does not follow standards, images had to be used instead of simple css elements... 2011-03-11 18:51 aarpon * [r829] nbproject: Removed folder added by mistake. 2011-03-12 11:04 aarpon * [r830] stylesheets/default.css: Updated license notice on default.css. 2011-03-14 13:38 danielsevilla * [r831] inc/JobTranslation.inc: Adapted the confidence levels of the remaining parameters (except sampling sizes) so that they are read from the database when needed. 2011-03-14 14:00 aarpon * [r832] config/samples/hrm.conf.sample, file_management.php, inc/Fileserver.inc: Added display of the used parameters in the advanced view of the file browser. 2011-03-14 14:40 aarpon * [r833] inc/Fileserver.inc: Added hint in the slicer view mouseover() in Fileserver.inc that displaying it could take several seconds. 2011-03-14 15:30 danielsevilla * [r834] inc/JobTranslation.inc: Adapted the confidence levels of the sampling sizes so that they are read from the database when needed. 2011-03-14 15:30 aarpon * [r835] file_management.php, inc/FileBrowser.inc: Cleaned up the file manager to make view and explanations clearer and more consistent. 2011-03-14 17:47 aarpon * [r836] capturing_parameter.php, stylesheets/default.css: If at least one of the refractive indices is not known, we cannot calculate whether an aberration correction is necessary and we leave the decision to the user in the aberration_correction.php page. 2011-03-14 17:56 aarpon * [r837] inc/QueueManager.inc: Added code to report the file (both by mail and in the file manager) with the template paramters returned by hucore. 2011-03-15 09:51 aarpon * [r838] images/textTrusted.png: Modified text for the "trusted" parameters. 2011-03-15 14:46 danielsevilla * [r839] inc/QueueManager.inc: The destFolder was not defined whenever yhe error mail had to be sent. 2011-03-15 16:12 aarpon * [r840] images/textMissing.png, images/textTrusted.png, inc/Database.inc, inc/System.inc, stylesheets/default.css: (1) Reduced the HRM confidences to 2: 'verified', 'reported' and 'estimated' map to 'trusted'; 'default' maps to 'missing'. Enhanced the explanation in the UI. (2) Increased HRM version to 2.0. 2011-03-16 09:18 aarpon * [r841] inc/JobDescription.inc, inc/QueueManager.inc, inc/System.inc, inc/hrm_config.inc, login.php, resources/checkConfig.php: (1) Updated release number to 2.0. (2) Removed reference and usage of $resultImagesRenamed. 2011-03-16 13:40 aarpon * [r842] inc/Fileserver.inc, stylesheets/default.css: Some layout tweaks. 2011-03-17 10:08 danielsevilla * [r843] inc/Fileserver.inc: Corrected the name of the parameters file. 2011-03-17 13:54 danielsevilla * [r844] inc/Job.inc: Added temporary (draft) code for the creation of a parameter summary file. 2011-03-17 16:22 danielsevilla * [r845] inc/Job.inc: (1) Created basic html (temporary) table to show the job parameters. (2) Improved the file layout. 2011-03-17 17:19 danielsevilla * [r846] inc/Job.inc: (1) Extended comments. (2) Improved file layout. 2011-03-18 11:34 danielsevilla * [r847] inc/JobTranslation.inc: Set all the confidence levels to verified. HuCore will compare the input template to the metadata and make a selection according to an extra user choice. 2011-03-18 16:07 danielsevilla * [r848] inc/Job.inc, inc/JobTranslation.inc: Added user defined confidence level to pick parameters from the metadata. Added default values for those parameters that are missing in the HRM UI. 2011-03-18 16:39 aarpon * [r849] images/paramMissing.png, images/paramProvide.png, images/paramTrusted.png, images/paramUntrusted.png, images/param_default.png, images/param_estimated.png, images/param_provided.png, images/param_reported.png, images/param_verified.png, images/text_default.png, images/text_estimated.png, images/text_provided.png, images/text_reported.png, images/text_verified.png, inc/Database.inc, inc/Parameter.inc, inc/QueueManager.inc, stylesheets/default.css, task_parameter.php: (1) Replaced old HRM interpreted confidence levels with hucore native ones. (2) Fixed missing variable bug in AdvancedCorrectionOptions::displayString(). 2011-03-18 17:28 aarpon * [r850] image_format.php: Minor bug fix in image_format.php. 2011-03-22 12:24 aarpon * [r851] aberration_correction.php, capturing_parameter.php, inc/Database.inc, inc/Job.inc, inc/Parameter.inc, inc/Setting.inc, override_parameter.php, select_psf.php, setup/dbupdate.php, stylesheets/default.css: Added page in the parameter settings for the parameter override option. 2011-03-22 12:53 aarpon * [r852] image_format.php: Bug fix in image_format.php. 2011-03-22 13:03 aarpon * [r853] inc/Parameter.inc: Added customized displayString() method to the OverrideConfidence Parameter. 2011-03-22 13:12 aarpon * [r854] override_parameter.php: Update help links on override_parameter.php. 2011-03-22 16:29 danielsevilla * [r855] inc/JobTranslation.inc, inc/Parameter.inc: Inserted new overrideConfidence parameter in the job templates. 2011-03-22 17:29 danielsevilla * [r856] inc/Job.inc: Removed html tags from report table. 2011-03-22 17:36 aarpon * [r857] inc/QueueManager.inc: Actually used parameters are now combined with HRM template parameters in a file which is displayed in the file manager and is sent to the user by email. 2011-03-22 17:38 aarpon * [r858] inc/QueueManager.inc: Removed double greetings in the QueueManager::notifyWarning() function. 2011-03-22 18:13 aarpon * [r859] inc/QueueManager.inc: Replaced "TEMPLATE PARAMETERS" with "DECONVOLUTION PARAMETERS" in the parameter summaries. 2011-03-23 16:06 danielsevilla * [r860] inc/Job.inc: (1) Aligned parameter table. (2) Renamed "*_history.txt" file. 2011-03-23 17:30 danielsevilla * [r861] inc/Job.inc: (1) Added check to the rename file command. (2) Adapted names of the parameter table to the standard HRM parameter names. 2011-03-24 10:05 danielsevilla * [r862] inc/Job.inc: Interted scaling factor in the parameter table. 2011-03-24 13:15 danielsevilla * [r863] inc/Job.inc: Improved column alignment of the parameter table. 2011-03-24 17:21 danielsevilla * [r864] inc/Job.inc: Adapted parameter parsing to the new HuCore output. 2011-03-25 09:06 danielsevilla * [r865] inc/Job.inc: Fixed bug in te parameter parsing: the parameters common to all channels would not show up. 2011-03-25 10:26 danielsevilla * [r866] inc/JobTranslation.inc: Enabled time series processing depending on the image geometry. 2011-03-25 15:26 danielsevilla * [r867] inc/Job.inc: Forgot to add the pinhole spacing to the parameter table. 2011-03-28 09:56 aarpon * [r868] inc/Setting.inc, setup/dbupdate.php: (1) Fixed problems with handling single-plane formats. (2) Corrected mapping for the confidence levels of dv file formats (r3d in Huygens). 2011-03-28 11:25 aarpon * [r869] setup/dbupdate.php: Added support for DeltaVision r3d files. 2011-03-28 12:15 aarpon * [r870] inc/QueueManager.inc: Minor formatting change. 2011-03-28 13:49 aarpon * [r871] inc/Parameter.inc: Overloaded the base Parameter::formattedName() method to return a better understandable name (i.e. 'pixel size' instead of 'c c d captor size x') for the CCDCaptorSizeX Parameter. 2011-03-28 14:19 aarpon * [r872] inc/Fileserver.inc, select_images.php: Changed the way the FileServer filters STK series in case XYZ geometry is chosen: all files are shown and are treated individually. The behavior was not change in case a "- Time" geometry is chosen. 2011-03-28 15:18 danielsevilla * [r873] inc/Job.inc: Change ccd captor size for x pixel size, y pixel size. 2011-03-29 08:01 aarpon * [r874] inc/FileBrowser.inc, scripts/common.js: Fixed a xhtml-strict incompatibility. 2011-03-30 08:42 aarpon * [r875] estimate_snr_from_image_beta.php: Started implementing support to the SNR estimator beta. 2011-03-30 09:50 aarpon * [r876] estimate_snr_from_image_beta.php, images/newSNR.png, stylesheets/default.css, task_parameter.php: Completed support (in the UI) for the new SNR estimator. The back-end must now be implemented and the correct function call must replace estimateSnrFromFile() in estimate_snr_from_image_beta.php. 2011-03-31 10:26 danielsevilla * [r877] estimate_snr_from_image.php, estimate_snr_from_image_beta.php, scripts/hucore.tcl: Completed backend changes for the beta SNR estimator. 2011-03-31 12:19 aarpon * [r878] inc/System.inc: Set minimum hucore version needed to run the HRM to 3070100 (3.7.1-p0). 2011-03-31 12:40 aarpon * [r879] setup/dbupdate.php: Changed the translations of the OverrideConfidence possible values. 2011-03-31 13:17 danielsevilla * [r880] inc/Job.inc: Remove Huygens default output history file after the deconvolution job. 2011-03-31 16:10 danielsevilla * [r881] inc/JobTranslation.inc: Fixed bug with time series whose file extension is written with capital letters. 2011-04-01 06:35 danielsevilla * [r882] inc/Job.inc: (1) Removed incorrectly reported scaling factor. (2) Formatted mycroscope conflict warning. 2011-04-01 06:41 danielsevilla * [r883] inc/Job.inc: Added word "warning" to the microscope conflict message. 2011-04-01 15:03 aarpon * [r884] inc/System.inc: Set the minimum hucore version required to 3.7.1-p1. 2011-04-01 16:21 aarpon * [r885] inc/System.inc: Extended operating system information report in System class. 2011-04-04 15:43 danielsevilla * [r886] inc/Fileserver.inc: Fixed bug: the stack comparison didn't show properly for uncompressed images. 2011-04-05 11:11 aarpon * [r888] license.txt: Updated license.txt file. 2011-04-05 13:13 aarpon * [r889] inc/Database.inc: Added missing include in Database.inc. 2011-04-05 15:01 aarpon * [r890] inc/Setting.inc: Bug fix in the handling of the geometry and number of channels for the "numbered series" file format. 2011-04-05 16:56 aarpon * [r891] override_parameter.php: Cosmetic change in override_parameter.php. 2011-04-05 19:22 aarpon * [r892] setup/dbupdate.php: Bug fix in dbupdate.php for postgresql updates. 2011-04-06 08:23 aarpon * [r893] header.inc.php, scripts/highcharts/excanvas.compiled.js, statistics.php: Added excanvas.js library to support the highchart library in Internet Explorer. 2011-04-06 13:03 aarpon * [r894] inc/Fileserver.inc: Restored the trimming of stk series. 2011-04-06 13:10 aarpon * [r895] inc/Fileserver.inc: Restored missing function. 2011-04-07 08:08 aarpon * [r896] inc/Job.inc: Added quotation marks around full file names in several shell operations. 2011-04-07 08:39 aarpon * [r897] inc/JobDescription.inc: More corrections on path handling (underscores). 2011-04-12 15:12 danielsevilla * [r898] inc/FileBrowser.inc, inc/Fileserver.inc, inc/JobTranslation.inc, inc/QueueManager.inc: Implemented support for larger file names. The job previews are now only coded by the job id. The number of characters to be used on the raw image as risen from about 50 to about 100. To be tested. 2011-04-12 15:28 danielsevilla * [r899] inc/Fileserver.inc: Fixed bug from the latest commit. Deleting raw data was sometimes not possible. 2011-04-13 08:59 aarpon * [r900] inc/JobTranslation.inc: Fixed a bug with the handling of the PSF file path. 2011-04-13 11:28 aarpon * [r901] inc/Parameter.inc, inc/Setting.inc: Cleaned and homogenized the display of Parameters. 2011-04-13 13:24 aarpon * [r902] calculate_pixel_size.php, images/param_estimated.png, images/param_provided.png, images/param_reported.png, images/textMissing.png, images/textProvide.png, images/textTrusted.png, images/textUntrusted.png, images/text_default.png, images/text_estimated.png, images/text_provided.png, images/text_reported.png, override_parameter.php, select_psf.php, stylesheets/default.css: (1) Several changes on the representation of confidence levels in the HRM. More explanation text was added; the colors were changed to make reading easier. (2) Changed text for the pixel size in calculate_pixel_size.php to make it more consistent with the rest of the HRM. 2011-04-13 13:48 danielsevilla * [r903] inc/FileBrowser.inc: Fixed bug in the File Manager: files stored in subdirectories could not be previewed. Still to fix the download and delete operations for these files. 2011-04-13 15:41 danielsevilla * [r904] inc/FileBrowser.inc: Fixed bug from a previous commit: the previews of some images would not show. 2011-04-13 16:06 danielsevilla * [r905] inc/Fileserver.inc: Fixed bug: the download didnt work from the preview page in the case of images stored in subfolders. 2011-04-13 16:21 aarpon * [r906] images/param_default.png, images/param_estimated.png, images/param_provided.png, images/param_reported.png, images/text_default.png, images/text_estimated.png, images/text_provided.png, images/text_reported.png, override_parameter.php, stylesheets/default.css: Changed color scheme for confidence levels. 2011-04-13 16:43 aarpon * [r907] stylesheets/default.css: Typo. 2011-04-13 16:56 danielsevilla * [r908] inc/QueueManager.inc: Corrected the link sent with a successful job. It was wrong for images located in subfolders. 2011-04-14 08:41 danielsevilla * [r909] inc/JobTranslation.inc: Wrap the directory name between curly braces to avoid uneven templates in case the directory name contains blanks. 2011-04-14 09:05 danielsevilla * [r910] inc/JobTranslation.inc: All paths and file names are now wrapped with curly braces. 2011-04-14 09:57 danielsevilla * [r911] inc/Job.inc: Stick to the HuCore naming standard. Otherwise there will be an error notification if the folder contains blanks, even if the job finishes successfully. 2011-04-14 10:37 danielsevilla * [r912] inc/QueueManager.inc: More checks to avoid blanks on destination folders. 2011-04-14 14:15 danielsevilla * [r913] inc/Fileserver.inc: Added more cases to the new naming convention of the File server. 2011-04-14 16:30 danielsevilla * [r917] inc/FileBrowser.inc, inc/Fileserver.inc: Improved the file server. Almost done. 2011-04-14 17:08 danielsevilla * [r918] inc/Fileserver.inc: Fixed bug in the preview download of some images. 2011-04-14 17:20 danielsevilla * [r919] inc/Fileserver.inc: Finished with file server changes. 2011-04-15 08:16 danielsevilla * [r920] inc/Fileserver.inc: Fixed bug raised in very few backwards compatible scenarios. 2011-04-15 08:58 danielsevilla * [r921] inc/Fileserver.inc: The parameter and log files did not show up correctly. 2011-04-15 09:42 danielsevilla * [r922] inc/FileBrowser.inc: Making previews of raw data was faulty. This is now fixed but there is still a permission issue depending on the user that runs the Queue Manager. 2011-04-15 09:51 aarpon * [r923] images/text_default.png, images/text_estimated.png, images/text_provided.png, images/text_reported.png, images/text_verified.png, stylesheets/default.css: Modified confidence level messages. 2011-04-15 10:58 aarpon * [r925] override_parameter.php: Hopefully made the text in override_parameter.php clearer to the user. 2011-04-15 17:53 aarpon * [r926] select_parameter_settings.php, select_task_settings.php: Workaround for a strange behavior in Google Chrome that does not post element names in some circumstances where other browser would: this would not allow to delete parameter settings in Chrome. 2011-04-18 09:09 danielsevilla * [r927] inc/QueueManager.inc: Grant read/write permissions to job independent previews in order to avoid conflicts between the preview generation of the Queue Manager and the interactive preview generation probably run by another user. 2011-04-18 12:36 danielsevilla * [r928] inc/Fileserver.inc: Added TODO to a function that seldom produces a weird bug in the File Manager. 2011-04-18 15:45 danielsevilla * [r929] inc/QueueManager.inc, scripts/hucore.tcl: Added permissions checks to the preview generation. 2011-04-19 12:06 danielsevilla * [r930] inc/QueueManager.inc: Improved and widened the chmod treatment of the result images. This guarantees that operations such as the preview generation and the image delete will work better. 2011-04-19 16:44 danielsevilla * [r931] inc/Shell.inc: Fixed bug: the multiserver configuration would not execute the template due to a typo in the execute command. 2011-04-19 17:12 danielsevilla * [r932] inc/Job.inc: Replaced the old marker names with updated suffixes. The remote jobs do finish properly now. There is a number of new secondary errors logged, though. 2011-04-20 07:53 danielsevilla * [r933] inc/Job.inc: Pull the image previews properly in multiserver installations. 2011-04-20 08:01 danielsevilla * [r934] inc/Job.inc, inc/QueueManager.inc: (1) Commented out old multiserver-related code. (2) Inserted missing global variable declaration. 2011-04-20 09:09 danielsevilla * [r935] inc/Job.inc: Fixed bug: The .inf file was not properly created in the multiuser configuration. 2011-04-20 09:13 danielsevilla * [r936] inc/Job.inc: Fixed bug: the history file would not be removed in the multiserver configuration. 2011-04-20 09:55 danielsevilla * [r937] inc/Job.inc: Modified job marker so that the multiserver configuration can also work with images stored in subfolders. 2011-04-20 12:29 danielsevilla * [r938] inc/Job.inc, inc/QueueManager.inc: (1) Added option -p to several mkdir's. (2) Further improved the deconvolution pipeline in the multiserver configuration. 2011-04-20 12:40 danielsevilla * [r939] inc/QueueManager.inc: Removed option -p from some mkdir's. 2011-04-20 15:01 danielsevilla * [r940] inc/Job.inc, inc/QueueManager.inc: (1) Corrected faulty file pattern with which the multiserver configuration would not transfer some images. (2) Commented out old code related to the job estimated end time. 2011-04-20 15:27 danielsevilla * [r941] inc/JobTranslation.inc: Fixed bug: The lif images were not properly opened. This was done to a curly brace too many. 2011-04-20 16:05 danielsevilla * [r942] inc/Job.inc: The rename and remove commands are now written to be compatible with the single-server and multiserver configurations. 2011-04-20 17:08 danielsevilla * [r943] inc/Job.inc, inc/QueueManager.inc: Added a new function to the Queue Manager to get rid of debris from previously failed jobs. This is important so that the parameter tables from upcoming jobs don't get merged with the debris. TODO: Move to Shell.inc, along with many other functions that execute shell commands out of the Shell classes. 2011-04-22 16:00 aarpon * [r944] aberration_correction.php, account.php, calculate_bp_pinhole.php, calculate_pixel_size.php, capturing_parameter.php, create_job.php, estimate_snr_from_image.php, estimate_snr_from_image_beta.php, file_management.php, home.php, image_format.php, images/manual.png, images/user.png, job_queue.php, microscope_parameter.php, override_parameter.php, select_images.php, select_parameter_settings.php, select_psf.php, select_task_settings.php, statistics.php, system.php, task_parameter.php, update.php, user_management.php: (1) Added link to the user manual to the navigation bar of the home page. (2) Added user icon in the navigation bar next to the user name. 2011-04-26 07:46 aarpon * [r946] inc/System.inc: Set the minimum required version of HuCore for HRM 2.0 final to 3070102 (3.7.1-p2).