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HIPE Owner`s Guide - Herschel

1. Figure 21 The Observation Viewer All the features of the Product Viewer also work in the Observation Viewer In addition note the following e The Summary section may include a thumbnail image Click on the thumbnail to enlarge it Click again to go back to the Observation Viewer The thumbnail does not open in the HIPE image viewer e Red entries in the left area of the Data section have not been loaded into memory HIPE does not load an entire observation at once to save time and memory space Click on a red entry to load it into memory and display it 15 3 Inspecting datasets 25 HIPE Owner s Guide Build 13 0 5130 HIPE data inside products come in tabular form and are packaged in datasets Datasets are automat ically shown within the Product Viewer and the Observation Viewer You can also open a dataset separately by right clicking on its name and choosing Open With Dataset Viewer The Dataset Viewer shows the metadata associated with a dataset and the tabular data itself E obsid_1342 1Table4 x Meta Data 2009 05 14T 16 54 52 TA First product time keyin da 2009 05 14T23 30 04 TAI Last product key within data LAGRANGE interpDegree 8 Table Data Index recordTime onBoard orbitPos orbitvel es f 2 1599 162101 SALER in neoe 1572 162101134 1621011 48489 2 1544 162101137 1621011 48552 _ 2 1515 162101
2. 14 Managing calibration sources The Herschel calibration source database contains all the information on celestial sources used for calibration both primary and secondary calibrators These sources are planets notably Uranus and Neptune bright stars that are still bright at far infrared wavelengths and asteroids The Herschel 20 HIPE Owner s Guide Build 13 0 5130 instrument calibration scheme uses this set of stellar planet and asteroid calibrators and models for determining the overall calibration of the photometers and spectrometers on board the spacecraft Planets Physical modelling of planetary atmospheres has lead to the formulation of very accurate predictive models of order 1 across the Herschel bandwidth Currently calibration uses models updated with Herschel spectroscopic data that has constrained the fluxes for the giant planets Models 2 and 3 for Neptune are used by SPIRE and PACS respectively from R Moreno Stars Stellar models are based on the work of Dehaes et al 2011 A and A 533 107 Stellar atmosphere models provide the prime flux calibrators for PACS Primary stellar calibrators which have such models are the following e alpha Boo e alpha Cet e alpha Tau e beta And e beta Peg e beta Umi excess noted at SPIRE wavelengths dropped as a calibrator standard e gamma Dra e Sirius PACS calibration also uses a set of faint secondary stellar calibrators Asteroids Asteroids need careful modell
3. Table 2 Mouse clicks in HIPE Mouse click Windows Linux with two Mac with two Mac_ with one button mouse button mouse button mouse Left click click Left click click Leftclick click Leftclick click Click a click a left click an E left click n left click click Right click Right click Right click Ctrl left click Ctrl click Three button mice work as expected on all supported operating systems The Mac five button mouse can be configured via the Mouse utility in the Mac System Preference Pane as a standard three button mouse Different HIPE tools may associate different actions to the same mouse gesture For details refer to the documentation of each tool in the Data Analysis Guide 20 2 Keyboard shortcuts The following table lists a selection of shortcuts available in the Console view and in the Editor view when working on scripts and other text files For a complete list issue the help command in the Console view Note The keyboard shortcuts shown in the following table are for Windows and Linux comput ers For Mac computers note the following The equivalent of the Ctrl key is Cmd the db key 41 HIPE Owner s Guide Build 13 0 5130 e Some Apple keyboards have one Delete key corresponding to Backspace on PC key boards Other Apple keyboards have a second Delete key called forward delete cor responding to Delete on PC keyboards References to Delete in HIPE documentation are to
4. Performs common cosmological calculations e Herschel Quick Look Accesses Herschel quick look data products For more information on using plug ins see the user s manual of the plug in framework on the Herschel public TWiki Note The plug ins on the download page are provided as is without any warranty The Her schel Science Centre does not provide support for third party plug ins To learn more about plug in development see the author s manual on the Herschel public TWiki 7 Managing memory Setting the amount of memory available to HIPE You can set this value during installation To change it afterwards choose Edit Preferences go to Startup amp Shutdown and change the Maximum memory value Restart HIPE for the change to take effect Monitoring used memory The memory bar in the HIPE status bar shows the amount of memory used by HIPE see Figure 14 The bar goes from green to orange and then to red as the amount of used memory increases A vertical line in the bar shows the highest memory consumption during the session You can reset this value to the current memory consumption by hovering your mouse pointer on the memory bar and clicking Reset in the tooltip that appears The maximum memory available to HIPE can vary slightly over time This is reflected in the value shown by the memory bar The maximum memory value is not expected to vary more than 10 from the value defined at installation or in the P
5. arithmetics commands 45 basic commands 43 data import export commands 44 plot commands 44 installed properties file 8 Installing 2 developer builds 3 J Javadoc 12 Jobs monitoring 14 stopping 14 47 Build 13 0 5130 HIPE Owner s Guide K Keyboard shortcuts 41 L Log levels changing 18 saving to file 18 Log messages 18 Log view 32 Memory freeing 13 monitoring 13 setting maximum value 13 Memory bar 14 Monospaced font 42 Mouse behaviour 41 N Navigator view 33 O Observation viewer 25 Outline view 33 P PACS Calibration Products plug in 12 PACS Simple Aperture Photometry plug in 12 Perspectives 37 customising 39 PlotXY properties view 37 Plug ins 12 use with batch mode hipe 16 Preferences 6 Product Browser perspective 37 Product Browser view 29 Product Tree view 29 Product viewer 24 Prompt 31 Properties 6 Proxy server 4 R Resetting a perspective 39 Restoring variables and sessions 19 S Save Products to Pool view 30 Saving variables and sessions 19 ScanAmorphos plug in 12 Scripts editing 17 opening 14 48 Build 13 0 5130 HIPE Owner s Guide running 15 outside HIPE 15 remotely 17 Sessions saving and restoring 19 SPIA plug in 12 T Tasks help in User s Reference Manual 35 running 35 viewing source 35 Tasks view 34 Throbber 14 Toolbar 5 Traceback 32 U Undocking a view 39 Uninstalling
6. about ths Chick here fara Help System Analysis Tana quick intraduction Halp an Halp D Coa Ariolpais Guide 0 Seetpling Guce Leam how in get data from the Herschel Archiwa HIF Phe AIF Daa Reducen Grice Leam abul PACS dala SEA Leam aout HFI dala e ai Dia Learn about SPIRE dale i PHI Pipalins Specilicatiar HIF photometry an 3 oa SPIRE Daia knoe issues ae E ee r Gata known issues PS SPIRE Date Reduction Guire P SPIRE Fipelne Epecinoation Manwal a PACS fe z i PACS Daa Aectuchon Guna Spectromspy i T 7 l d See a listof all the H PP ACK Date Asctaslion Guide Pholarely HIPE kesh is skes Find out what s pew N awa il able manuals PACS Public Documents Fo Deterrence HESSU ers Reference Maral Hm Users Plstsrense Manual Watch won Fall ow Us on E i PACS Usar Heterence Manual Figure 9 The HIPE Help System home page As shown in Figure 9 the HIPE Help System window contains three components e A toolbar at the top of the screen e An area on the left hand side containing the Table of Contents TOC the search facility and the glossary More advanced material appears towards the bottom of the Table of Contents In the Table of Contents manuals are grouped into categories and represented by a folder icon next to a plus sign Click on the plus sign to view the contents of a manual You can do the same with manual sections containing subsections Click on any entry to d
7. and the state of advancement is shown in the progress bar see Figure 15 If you are running a script the progress bar also shows the line being executed m Stopping jobs To stop a running job click the icon in the HIPE toolbar or in the running jobs pane see Figure 15 where you can choose whether to stop a single job or all running jobs A job may not stop immediately when you click the stop icon For example tasks that do not check frequently enough for the stop signal sent by HIPE may keep running even after you click the stop icon Cancel all jobs Job 1 Running jobs icon Cancel button Progress bar Throbber Figure 15 The running jobs pane memory bar and throbber icon in the HIPE status bar 9 Opening and running scripts Opening scripts You can open a Jython script in the Editor view in the following ways Choose File Open File e Double click on the script in the Navigator view HIPE Owner s Guide Build 13 0 5130 If you opened the file in a previous HIPE session choose it from File Open Recent Running scripts from the Editor view You can run scripts with the following four icons in the toolbar Ez gt Run runs either a single statement of your script the one indicated by the arrow or all the selected statements at once BE bP Run all runs the entire script B PEE Stop stops execution of the script The current statement of the script will be completed before t
8. documentation A progress bar tells you how close HIPE is to completing the operation After the index has been built subsequent searches take a negligible time Tip Q When you click on a search result HIPE opens the corresponding page at the top not at the location of the word you searched for You can reach the word quickly with your browser s search function However 1f there are many search results it is likely that your browser s search will first find all the occurrences of the word in the list of results before finding it in the documentation page To avoid this problem you can switch to another tab such as TOC or Glossary to hide the list of search results 10 HIPE Owner s Guide Build 13 0 5130 5 2 Limiting the search scope To limit your search to one or more manuals or categories for instance Analysis Tools follow these Steps 1 Click Filter in the search interface The Search Options pop up window opens see Figure 11 2 Click on any manuals or categories you want to be included in the search Clicking on more manuals and categories adds to the current selection it does not replace it Alternatively click Search all except developer s manuals to include all manuals except those in the Developer Reference category To clear the current selection click any of the first two options 3 Click OK The pop up window closes The selection you made will be used in all the following searches Sear
9. install Java on Mac OS is available here If you are using a developer build of HIPE you must install a compatible Java version separately irrespective of the operating system you are running Note K HIPE only supports the Oracle Java platform To see if your Java installation is supported choose Help Check Java platform in HIPE Memory requirements The minimum amount of memory needed is two GBytes Four GBytes are the highly recommended minimum for data processing more may be needed in some cases such as large PACS maps You can set the maximum amount of memory available to HIPE during installation To change the maximum available memory afterwards choose Edit Preferences and change the value in the Startup amp Shutdown section of the preferences window HIPE Owner s Guide Build 13 0 5130 Versant database You can also specify the name and location of a Versant database during instal lation Only advanced users and calibration scientists should need to specify a database If you are unsure about this option you can safely skip it 2 1 Upgrading and uninstalling To uninstall HIPE follow the usual uninstallation procedure for your operating system or execute the uninstall_hipe command in the uninstall_hipe directory located in the HIPE installation directory It is possible to install different HIPE versions alongside each other To upgrade HIPE to a new version you do not need to uninstall the previous ver
10. tab of your default web browser The help contents are installed on your computer so you do not need to be connected to the Internet However if you are not connected some advanced features will not be available such as the comments box at the bottom of each page 7 Help Contents Working in HIPE What s Mew Video Tutorials Data Reduction Help on Editor view Fz Online Help HS Helpdesk Give Feedback Tip of the Day Software Updates Check Java platform a o el l Figure 8 Accessing the HIPE Help System The following are some of the entries available in the Help menu e Help Contents opens the offline Help System see Figure 9 e Working in HIPE opens this manual HIPE Owner s Guide Build 13 0 5130 e What s New opens the What s New page on the Herschel public Wiki e Data Reduction opens a submenu from which you can access the data reduction guides for HIFI PACS and SPIRE e Help on Editor view opens a help page about the active view the Editor view in this case This entry is visible only when a view is active e Online Help opens the online Help System The contents are mostly the same as the offline version except that it contains the most recent updates Text Fant Giannry i fot tocla lslaqo hese 100 2279 Introductory ee Welcome to the Herschel Interactive Processing Environment Help System akk Stet Guide HIRE cevners Guide i PF Prequentiy Asked Guectone E Hew im HIPF Leam
11. to solve this problem You can also use other software such as 7 Zip In case of any other problems during installation check the Known Issues page or contact the Herschel Helpdesk via the Herschel Science Centre website You can download HIPE from the Herschel Science Centre on this page please open this link in a new window tab Installation instructions and a list of supported platforms are provided on the page Developer builds Development builds are available via the Continuous Integration system These builds are untested and potentially unstable and are meant only for Herschel software developers If you are not a software developer but you still want to get access to these developer s builds for any particular reason see Section 2 2 Java HIPE needs the Java SE Runtime Environment version 6 version 7 for HIPE 12 or later Windows and Linux installers come with an integrated Java environment If you are using a Mac you can check which Java version is installed by running Applications gt Utilities gt Java gt Java Preferences Make sure to select the same Java version as recommended in the HIPE download page or a newer one To update your Java version use the Mac OS software update feature Note Since Mac OS 10 7 Apple no longer provides Java Java 7 requires Mac OS 10 7 3 or later and should be downloaded from Oracle Java page please open this link in a new window tab More information on how to
12. user area is a named link to a directory so that you can reach its contents with a single click from the Navigator view See for example the My scripts user area in Figure 29 i gt Navigator x S amp S gt Lak My scripts ja IsSolarsystemPlugin amp scripts P Basket py Colne pen Crea m Open With Aa creg Ji Delete Delete P creg Exa E Run Script E Run in Background A exa P FitFr a FitFringeExample py P fixcws checkout py P FixedMaskTest py kj ka Figure 29 The Navigator view showing the options available for a Jython script in the My scripts user area 17 13 Outline This view displays information about selected items in HIPE such as the following 33 HIPE Owner s Guide Build 13 0 5130 e Variables in the Variables view see Section 17 15 If more than one variable is selected informa tion is displayed about the first selected variable Common information displayed is the variable name type class and package in which the variable type is defined see for instance Figure 30 e Tasks in the Tasks view see Section 17 14 You can see information on the task parameters e Files in the Navigator view A preview is shown for FITS or other image files You cannot edit the contents of this view a Variables X xo i Tz Outline x Class Doubleld rank 1 Figure 30 Outline of a variable in the Outline view 17 14 Tasks This view lists all the tasks pi
13. you release the mouse button e Undocking views Undocking a view means turning it into an independent window separate from the main HIPE window To undock a view right click on its title and choose Undock Alternatively click on its title and drag it away A small rectangle under the mouse pointer see Figure 40 with no black outline anywhere in the HIPE window means that the view will be undocked when you release the mouse button You cannot undock the Editor view Navigator X Aes User areas a fy Home Folder G BM File System ly My scripts Lal My table files Figure 40 A view being undocked e Docking views After you have undocked a view see previous point you can dock it again by clicking on the tab with the view title and dragging it on the main HIPE window A black outline appears showing where the docked view will be placed To dock the view in the same position it occupied before being undocked right click on the tab and choose Dock from the context menu If you undocked a window from inside the Editor view such as a viewer see Section 15 or a task see Section 17 14 1 the context menu is not available To dock the window click on the tab and drag it inside the Editor view A black outline appears showing where the docked window will be placed If you drag the tab close to other existing tabs the black outline disappears and the tab appears next to the others e Moving through
14. 0arayvanis0 These are external resources that you may find useful e IDL to Python e Jython homepage HIPE is based on Jython 2 5 External examples for different Jython Python versions might not always work Index Symbols clear 31 help 31 history 31 hess d 3 A Autocompletion 31 B Batch processing 15 Buffer size 31 C Calibration Sets view 31 Calibration sources database 20 Calibrators view 30 CASSIS plug in 12 CIB installer 3 options 3 Console view 31 configuring 31 ConsoleHandler 18 Convolution plug in 12 Cosmology plug in 12 Crash log files 27 Crash logs see Crash log files D Data Access perspective 38 Dataset viewer 25 Debugging mode 15 Developer builds 2 3 Docking a view 39 DP Data Processing 1 46 HIPE Owner s Guide Dump files creating 28 28 locating 28 E Editor configuring 17 Editor view 31 Export Herschel data from HIPE view 29 External tools 6 Feedback 26 FileHandler 18 Fonts monspaced 42 G Garbage collector 14 Glossary 9 H handler log messages 18 HCSS 1 Help system 8 navigating 11 searching 9 grouping results 10 jumping to results 10 starting outside HIPE 12 Helpdesk 26 Herschel Science Archive view 29 hipe batch command 15 graphical interfaces 16 plots 17 remote execution 17 hipe props file 8 hipe_help command 12 History size 31 History view 32 IDL equivalents 43
15. 140 1621011 48615 1487 162101143 1621011 48678 2 1458 Figure 22 The Dataset Viewer Note the pop up option to display numbers in hexadecimal Changing the column ordering Click a column header to sort the table rows according to the values in that column Click a second time to reverse the sorting order Click a third time to restore the default order Changing the format of integer numbers To display integer numbers types int and long in hexadecimal right click on a cell with an integer number and choose Display numbers in hexadecimal To return to the decimal display right click on a cell with a hexadecimal value and choose Display numbers in decimal These settings apply to all the integer values in a table Changing the format of dates To display dates such as the startDate and endDate fields in the metadata in International Atomic Time TAD right click on a cell with a date value and choose Display dates in TAI To return to the display in Coordinated Universal Time UTC right click on a cell with a date value and choose Display dates in UTC These settings apply to all the date values in a table For more information on TAI and UTC see the Scripting Guide Section 9 1 in Scripting Guide Editing values To edit values in a dataset right click on any cell and choose Allow editing You can then double click on any cell to edit its contents All the changes you m
16. 2236341E 6 1 0996288364399719E 5 8 27485558447085 7E 5 5 889840434918457E 5 948649778012E 4 6 341803652531793E 5 5 34595570120495 4E 5 3 2039449803074625E 5 28077304599E 5 9 306429727304372E 5 3 436425371269879E 5 2 9722932248687952E 5 423942517604E 5 5 7912238424038295E 5 1 2899266778258274E S_ 4 4993452910787854E 5 4 Figure 20 The Product Viewer 24 HIPE Owner s Guide The Data section is divided into two areas The left area shows a hierarchy of the product contents Click on an item to open it in the right area in its default viewer You can maximise the viewer by clicking the cal icon Above the viewer there is a reference you can use in the Console view to extract the data and assign it to a variable Click the icon to copy the reference to the clipboard In the case shown in Figure 20 you would assign the data to a variable with this command HIPE gt myImage myProduct image Right click on an item in the left area to open a menu with the following options e Open opens the item in its default viewer in a new tab inside the Editor view e Open With allows you to choose the viewer for opening the item e Send to sends the item to a FITS file a text file or to a Virtual Observatory enabled application e Create Variable creates a variable referring to the item much like you can do manually by copying and pasting the item reference to the Console view Tip Another way to cre
17. 3 Upgrading 3 User areas 33 user props file 8 userlogging properties file 18 V Variables saving and restoring 19 Variables view 36 Views 29 customising 39 W Welcome screen 5 Workbench perspective 38 49 Build 13 0 5130
18. Build 13 0 5130 HIPE Owner s Guide 1 Welcome Welcome to HIPE the Herschel Interactive Processing Environment This guide contains everything you need to know about the main software tool for the analysis of Herschel data Here is what the next pages have in store for you Section 2 Installing HIPE and performing basic configuration Section 3 Basic concepts about HIPE Section 4 Fine tuning every aspect of HIPE with the Preferences dialogue window Section 5 The Help System and its browsing and search features Section 6 Extending HIPE with plug ins Section 7 Managing memory Section 8 Managing running jobs Section 9 Opening and running scripts Section 10 Running scripts outside HIPE Section 11 Editing scripts and configuring the editor Section 12 Managing log messages Section 13 Saving and restoring variables and sessions Section 14 Managing calibration sources Section 15 Viewing data products and observations Section 16 Giving feedback about HIPE Section 17 HIPE views Section 18 HIPE perspectives Section 19 Customising views and perspectives Section 20 Mouse click behaviours and keyboard shortcuts Section 21 Managing monospaced fonts Section 22 Comparison tables to translate the most used IDL commands into HIPE There is much more to HIPE than is contai
19. Original file can be found at ftp hcalsg ftp sciops esa int asteroids O019_Fortuna Comments s Figure 17 Detailed information on a calibration source Several tabs give access to more specific information on the calibration objects Some tabs allow you to save tabular information to FITS by pressing Save Table or to copy text information to the clipboard by pressing Copy to clipboard Note Not all tabs have complete sets of information Although information will be increased in this database over time it is not yet a complete repository Flux tab Provides fluxes and errors in Jansky for reference measurements in the Herschel wave length range None are provided for planets or asteroids since these vary over the course of the mis sion as the distance between Herschel and object changes The articles referenced are listed under the Articles tab Note that these information are not used in the overall calibration of Herschel unless it is indicated under the General tab that the object is a primary or faint secondary standard star Full calibration information for primary calibrators used by Herschel instruments are stored as SEDs see SED tab Transition tab A few objects have some limited molecular transition ground measurements which are included in the database Articles tab Provides full reference information to particularly relevant calibration information on the object 22 HIPE Owne
20. UI version HIPE and the command line version hipe several expressions are used to explicitly refer to the command line version e hipe batch command e hipe as a batch processor e hipe as a script interpreter e batch version of hipe e batch mode hipe hipe in batch mode 15 HIPE Owner s Guide Build 13 0 5130 You can now run scripts from a command line window outside HIPE using hipe executable as a batch processor hipe myscript py The graphical UI of HIPE does not need to be in execution for you to use the hipe batch command All the modules automatically imported by HIPE in a GUI session are also imported by hipe when ran as batch processor so you do not have to add extra import statements to your scripts The batch version of hipe takes the same amount of time to start as the GUI version The hipe executable is the same file you use to launch a graphical session of HIPE so it is located in the apps directory in your HIPE installation As a command line script interpreter hipe accepts the following options help Displays the options of the hipe batch command same as in this list properties Sets values for one or more properties A property and its value are separated by a sign Property value pairs are separated by a colon Example hipe properties hess foo database my_database hcss foo instrument PACS myscript py Properties set on the command line override the same properties de fined in the hipe prop
21. ake are echoed to the Console view To stop editing values right click on any cell and choose Stop editing For more information on datasets see the following sections of the Scripting Guide e Section 2 3 in Scripting Guide e Section 2 4 in Scripting Guide e Section 2 5 in Scripting Guide 16 Giving feedback You can send feedback about HIPE in the following ways Opening a Helpdesk ticket Choose Help HSC Helpdesk The Helpdesk page opens in your default browser Use this method to contact the official support service Sending feedback on HIPE Choose Help Give Feedback A new email message opens in your default email client Use this method to send informal feedback to HIPE developers 26 HIPE Owner s Guide Build 13 0 5130 e Sending feedback on the documentation Leave a comment using the comment box at the bottom of any documentation page You must be connected to the Internet to send and read comments Alternatively click the 4 icon at the top of the help page A new email message opens in your default email client Use this method to send private informal feedback to the Herschel Editorial Board e Sending information on HIPE crashes You can send information about crashes to HIPE devel opers To enable this feature choose Edit Preferences then go to Startup amp Shutdown and tick the checkbox labelled Show dialogue box when a crash dump file is created When you restart HIPE after a cr
22. anual 17 14 1 Running tasks When you double click on a task its dialogue window opens in the Editor view 2 meanSmoothing x image amp myimage width gt Execution Status ready status progress Source Help Clear Accept Figure 32 Task dialogue window A standard task dialogue window has three sections Inputs and Outputs containing the task param eters and Execution Status containing status and progress information You can expand or collapse each section by clicking the small triangle left of the section title The names of task parameters are formatted according to these rules e The primary input parameter is in bold e All the mandatory parameters have an asterisk following their name for example image in Fig ure 32 Note that the asterisk is not part of the parameter name e All other parameter names are written in plain text Each input parameter has a small circle next to it You can drag a variable from the Variables view onto the circle to set it as parameter value The circle becomes green if the parameter value is valid red otherwise usually because the variable is of the wrong type Right click on a parameter name to display a menu with the following entries e Reset to default Resets the parameter to its default value e List valid variables Prints a message to the Console view listing all the existing variables that are compatible with this parameter C
23. ash a dialogue box asks you whether to send open or delete a crash dump file see Figure 23 A crash dump file contains useful information to help developers diagnose the problem If you click Send a new email message opens in your default email client with the crash dump file attached You can add your own text and then send the message Note that there are two main types of dump files and HIPE does not create one in all situations For more information see the next section rJ Dump due to abnormal exit HIPE had an abnormal exit on 2011 Aug 17 at 10 52 16 The dump file home hcssfapps fhipe dumps hipe_dump_ _20110817_105216 txt contains information about that event You can send this file to Helpdesk if you want it to be analyzed Do you like to send open or delete it _j Don t show this message again Open Delete Close Figure 23 The dialogue box shown when HIPE is restarted after a crash 16 1 Types and locations of crash log files There are two main types of crash log files e Sometimes HIPE crashes because the underlying Java Virtual Machine has crashed In this case the JVM produces a log file called hs_err_pid log where is the process identification number This log file is created in the directory HIPE was started from These log files do not trigger the dialogue box shown in Figure 23 e When you kill HIPE manually a log file called hipe_dump_ yyyymmdd_hhmmss txt is create
24. ata in Data Analysis Guide and spectrum viewing in Data Analysis Guide The next sections introduce the generic data product viewer the observation viewer and the dataset viewer 15 1 Inspecting products All Herschel data come packaged as products The Product Viewer shown in Figure 20 gives you a summary of the product and lists the metadata and data it contains E myProduct x Meta Data Degrees WCS Unit axis 1 default Degrees WCS Unit axis 2 default 2 777777777778E 4 WCS Pixel scale axis 1 unit Angle 2 777777777777778E 4 WCS Pixel scale axis 2 unit Angle RA TAN WCS Projection type axis 1 default LINEAR DEC TAN WCS Projection type axis 2 default LINEAR 27 0 The Rotation angle 1446 S myProduct nyProduct image B A DRE 4U 5245 003b 4 L 2YS DU4DOBSYBIOZE 4 4 42 UbSYYUOZ LE gt gt SOD BZY4U4D YBSPE D error 653416208374E 4 9 847727014748225E 5 5 1681025399935616E 5 2 7976010323588536E 5 coverage 067216975223E 4 9 398568406697252E 5 8 170102473677037E 5 7 48005 2665455011E 6 s a History 5842 1623978E 4 1 52668007541373 9E 4 1 2064753267520535E 4 1 2818966964259359E 5 967172205243E 4 9 859580413793097E 5 7 723 194246083 423E S 1 771911115880420S5E 5 7555740042094E 5 2 4112647623600309E 5 15 507940191108301E 5 6 95483 454846571E 5 346625432908E 5 9 207340971734303E 5 1 5596839043856923E 5 6 546658326220348E 5 66283
25. ate a variable is to drag the item to the Variables view 15 2 Inspecting observations An observation is packaged as an observation context a kind of product containing other products so it is not surprising that the Observation Viewer shown in Figure 21 is very similar to the Product Viewer Q obsid_1342231981 x Build 13 0 5130 Meta Data type OBS ObservationContext for SPIRE data of observation 1342231981 AOR labeli Calibration_cycle52_1 SpireSpec R Rep4 Bright highBias DarkSky Instrument SPIRE Obs ID 1342231981 Object Dark Sky Obs Date 2011 11 07T10 28 512 AOT Spectrometer Obs Mode Single Painting RA Nominal 17h 40m 12s Dec Nominal 69 0 0 SPG Version SPG v7 3 0 Operational Day 907 Resolution CR Map Sampling sparse description Product Type Identification Generator of this product Creation date of this product Name of this product linstrument attached to this product Model name attached to this product endDate 2011 11 07T 10 43 062 creator ISPG v7 3 0 creationDate 2011 11 07T22 45 272 description ObservationContext for SPIRE data of observatio instrument SPIRE modelName FLIGHT startDate 2011 11 07T10 28 512 Start date of this product End date of this product obsid_1342231981 obsid_1342231981 amp browseProduct calibration S leveld amp level0_5 amp levell S level2
26. ava 1ang Pi laegalarqunenteyception Ath 0 and AeA 0 WUST D gt at Jawa at nage Sanplehodel Sempl ehadal Java 108 at java at i nage ConponentSang l elodel ConponentSang skodel jaw at Javak tedi a 14 lonmponentsarpleHode l JAL Lonponents amp eHode l at jawas media jal ResterFactory createbandecSanpledodel Raster dt jawan media jai RasterFactory Crealebandecsanpledodel Raster srar heli Hoe page Anet rarT ThagevanipylarionTask gets Figure 27 Traceback of an error from the History view The following icons control the behaviour of the History view Di Activate recording of commands Deactivate recording of commands Ek Clear list of recorded commands You can copy and save to file not just the traceback but any cell of the Command Error and Trace columns of the History view You can do so in the following ways e Right click on a cell From the context menu choose Copy to copy the cell contents to the clipboard or Save to save them to file e Click and drag the mouse pointer to select multiple cells Press Ctrl C Cmd C on a Mac to copy the contents to the clipboard e Click the header of the Command Error or Trace column to select the entire column Press Ctrl C Cmd C on a Mac to copy the contents to the clipboard Note that when using this method with the Command column HIPE only copies the successful commands to the clipboard e Double click on any
27. bove variables Save ab ser a bo Save all varciables save all ser a Weise ellbJk ween sellers miareull tcl a b c None prime a oy He IRESSCOREeS Ellon resvroret Vall ser print a ec Note K Use the extension ser when saving variables to file If you use another extension HIPE shows a warning message Saving and restoring full HIPE sessions Use the File Session menu to export the current HIPE session to file or to import a saved session You can export one or more variables preferences the ones you set via Edit Preferences and configuration properties stored in props files such as hipe props For more information on preferences and properties see Section 4 Warning 3 The file format of variables exported with File Session gt Export has changed from HIPE 10 This means that HIPE 10 or higher will not be able to read session variables exported with HIPE 9 and vice versa If you exported variables with HIPE 9 or a previous version follow this workaround to read them in HIPE 10 or higher I Open HIPE 9 and import the exported variables with File Session Import Set Save variables on exit in the Preferences dialogue window under General Start up amp Shutdown 3 Exit HIPE 9 4 Open HIPE 10 The variables shall be restored in the Variables view 5 Export the variables with the new format of HIPE 10 with File gt Session gt Export
28. cell to copy the contents to a file called History clipping txt HIPE asks you whether to create the file if it does not already exist and opens it in the Editor view If the file already exists its contents are erased 17 11 Log 32 HIPE Owner s Guide Build 13 0 5130 This view lists all the commands that have been executed like the History view but also any output and warning generated by the system You can filter messages according to their severity level click the arrow at the upper right corner of the view to reveal the menu shown in Figure 28 Log x 18 Jan 2011 10 51 52 65 INFO Command image Simplelmagen Show all 18 Jan 2011 10 51 58 408 INFO Full Call rotatetimage descripti tory None mandatory Tap few ENE 18 Jan 2011 10 51 58 413 INFO Command result rotatefirage 2 ter lewe Filter level INFO Filter lewel WARRING Filter jewel SEVERE Figure 28 Filtering messages in the Log view The following icons control the behaviour of the Log view gt Activate logging of messages Deactivate logging of messages Ek Clear list of logged messages 17 12 Navigator The Navigator view provides access to the files and directories on your computer Right click on any item to display a context menu with the available actions see for instance Figure 29 Double click on an item to open it in HIPE with the default tool Ja User areas Click the icon to add or remove user areas A
29. ch Options Select manuals to search Search all manuals Search all except developer s manuals Introductory Welcome welcome Quick Start Guide quickstart HIPE Owner s Guide hipeowner Frequently Asked Questions faq Analysis Tools Herschel Data Analysis Guide howtos Scripting and Data Mining um HIFI The HIFI Data Reduction Guide hifi_um HIFI Pipeline Specification hifi_pipeline E cor OK Cancel Figure 11 The search interface 5 3 Navigating the help You can move around help pages create bookmarks and access PDF versions of manuals via the toolbar at the top of the HIPE help window shown in Figure 12 Tite page show permanent link Home page Next page About Yajahs Previous page send feedback Up one level synchronise TOC Figure 12 The toolbar of the HIPE Help System e The Previous page and Next page icons lead to the previous and next page in the manual you are viewing They let you move through a manual not through your browsing history For that use the Back and Forward buttons of your browser 1 HIPE Owner s Guide Build 13 0 5130 e The Show permanent link icon gives you the full address of the page you are viewing This is useful if you want to add the page to your browser s favourites or share the address with others e The Synchronise TOC icon will show the current page in the Table of Contents pane for example by expanding the nodes leading to it e Ya
30. d where yyyymmdd_hhmms s are the date and time of creation Depending on how you kill HIPE the log file may or may not be created The following table shows the various cases for each supported operating system Log files are created in a hcss apps hipe dumps directory in your home directory See the last column of the table to locate your home directory Table 1 Where and when HIPE creates a log file Operating system Log file created Log file not created Home directory loca tion Ctrl C kill or Force kill 9 Users username Quit Windows taskkill or Task Man taskkill f or Task C Documents and ager Applications Manager Processes SEtt ings oe name Windows XP Ce Users user 27 HIPE Owner s Guide Build 13 0 5130 Operating system Log file created Log file not created Home directory loca tion name Windows Vista 7 16 2 Crash dumps automatically generated by the op erating system Crash log files only contain limited information about the machine loaded classes and the faulted process Each of the operating systems supported by Java and HIPE has a different mechanism for creating a more complete snapshot of the process when it fails There are resources at Oracle s website on how to create or collect Java crash dumps for further analysis usually loading them in a debugger but it is outside the scope of this section Please check Troubleshooting Guide for Java SE 6 with HotSpot VM pleas
31. dcol file csv t asciiTableReader file csv text file file csv DELIMITER Read a image FITS file im Sere fits fitsReader file image fits Display an image tvcsl im right click on im and Open with Image Viewer 44 HIPE Owner s Guide Build 13 0 5130 Data import export com IDL HIPE equivalent mands Read a cube FITS file Display a cube Read a spectrum FITS file sp mrdfits spec fits cube mrdfits cube fits im fitsReader file cube fits right click on cube and Open with CubeAnalysisToolbox sp fitsReader file spec fits Display a spectrum plot wave flux right click on sp and Open with SpectrumExplorer Write to FITS Write a text table csv by default get_lun u Arithmetics commands Add Multiply Powers Absolute value Arc cosine Natural logarithm Base 10 logarithm Arc sine Arc tangent Ceil Conjugate Cosine Hyperbolic cosine Exponential Floor Invert matrix Bit shift operations Sine Hyperbolic sine Square root Tangent Hyperbolic tangent Random 0 1 generator Reverse array a simpleFitsWriter product im age file 1mage fits mwrfits image image fits asciiTableWriter table t file file csv openw u file csv printf u a b close u free_lun u 45 HIPE Owner s Guide Build 13 0 5130 Arithmetics commands HIPE equivalent Number of elements len sizeQ Number of parameters len args ape
32. deleting and adding views and by moving resizing and rearrang ing existing views You can also undock views from the main HIPE window and dock them back The following actions are available e Closing minimising and maximising views Each view has the usual icons for closing next to the view title minimising and maximising in the small tab on the right hand side Minimised views appear at the bottom of the workspace above the status bar Note that views organised as tabs can only be minimised and maximised together like the History Log and Console views in the next figure i gt Navigator xX History Log Console X Figure 38 Minimised views at the bottom of the HIPE window e Resizing views Click and drag the borders of a view e Customising tabs If you right click on the title of a view a context menu appears With the Tab Orientation and Tab Direction submenus you can change the position and orientation of title tabs Experiment with the various options until you find what works best for you a Undack Dock Restore iL Minimize e E File Sv5 x Close a My scri al My tab x Close Others Move to Window Bar he Tab Orientation Up Down 4 Left Figure 39 Customising tabs in a HIPE view 39 HIPE Owner s Guide Build 13 0 5130 e Moving views To move a view within the main HIPE window click on the view title and drag it around A black outline box shows where the view will be placed when
33. e Down Yes Yes O Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes O Yes O O O O O O Yes Yes Yes Yes Yes O Yes Yes Yes Yes Yes Yes es 21 Managing monospaced fonts In some occasions HIPE may show a dialogue window asking you to change your monospaced font In a monospaced font every letter occupies the same space on a line of text HIPE uses the default monospaced font defined by Java to show text in the editors for Jython scripts and other text files 42 HIPE Owner s Guide Build 13 0 5130 Sometimes the font selected as default monospaced is not really monospaced This can lead to display problems in the editors for example the arrow indicating the next line to be executed might point to the wrong line This problem may occur if you are running a HIPE session from a remote server and the local and remote font configurations are different The recommended solution is to let HIPE use an alternative font for the editors To change the font at a later time choose Edit gt Preferences and go to General Appearance Fonts Select your preferred monospaced font from the drop down list and click Apply You can also deactivate the check for a proper monospaced font by unticking the Check monospaced font checkbox If you are comfortable modifying configuration files you can change the default monospaced font used by Java See the following pages for de
34. e of the instrument calibration programs then look at its date follow the above instructions to display the operational day information then select the day of your observation by clicking on it in the list displayed Then click View Seds This opens a window similar to that obtained under the SED tab for planets and stars Click on the SED wanted for the obsid you are working with You can then plot and save it as described in the SED tab paragraph 15 Inspecting data Any item appearing in the Variables or Outline views with a green dot to its left can be opened with one of HIPE viewers See Section 17 15 for how to display the contents of a variable with the default tool or with another available tool An example is shown for a SimpleImage A right click on a variable of this type in the Variables view shows there are three viewers see Figure 19 The Product Viewer shows associated metadata and array values see following section the Wcs explorer shows WCS settings the Standard Image Viewer displays the image Variables X x iin E Open With gt Wes explorer for Images Standard Image Viewer Show methods Rename Delete Help in URM F1 Help in DRM Figure 19 Available viewers are shown with a right click See the Data Analysis Guide for information on viewers in HIPE in particular the sections on data display of the Data Analysis Guide that is image in Data Analysis Guide product metad
35. e open this link in a new window tab or Troubleshooting Guide for Java SE 7 Desktop Technologies for more information In the next section you can find a platform independent method for creating partial memory dumps using only Java tools 16 3 Advanced Creating dump files manually You can copy portions of memory to file while HIPE is executing This is useful if HIPE has frozen or if you suspect a memory leak memory useage constantly increasing due to a bug To create a memory dump you need the Java Development Kit JDK for your system To see if the JDK is already installed open a terminal window and issue this command javac version You should get the version number for example 1 6 0_33 If you do not have the JDK installed follow these steps to install it e Windows and Linux go to Oracle s Java for developers homepage please open this link in a new tab window and click the Download button inside the box Java Platform Standard Edition below the label JDK or click the Download button with the Java logo just above the box Follow the instructions on the website to download and install e Mac the JDK is provided by Apple Install it via Software Update Note From Mac OS 10 7 and Java 7 Apple does not provide any Java component To install the JDK on Mac OS you should download it from the page mentioned above Once you have the JDK installed follow these steps to create a memory dump file 1 Find the process
36. ers e The predefined colours for keywords comments numbers and other language elements high lighting Warning X In the case of very long scripts nearing the maximum of Jython script size the high lighting refresh can slow down text edition In that case you can disable highlighting altogether to improve performance To do that uncheck the Apply syntax highlighting checkbox For a selection of keyboard shortcuts available when working on scripts in the Editor view see Sec tion 20 2 Tip Q To quickly write a variable name in the Editor or Console view drag and drop the variable from the Variables view and HIPE will paste its name You can also drag and drop any selected text between the Editor and Console views 12 Managing log messages HIPE components send log messages about their activities You can see these log messages in the Log view described in Section 17 11 If you started HIPE from a command line window you can also see the log messages in that window This section explains how to fine tune the amount of log messages shown in the command line win dow and how to save log messages to file Note that these instructions do not apply to the Log view Log levels Any log message belong to one of these levels e SEVERE indicating a serious failure e WARNING indicating a potential problem e INFO indicating an information message e CONFIG indicating a configuration message e FINE FINER and FINEST
37. es in gt HIPE see Section 18 The default workbench is shown in Figure 37 This is the HIPE Owner s Guide Build 13 0 5130 Icon Description Workbench main work area for doing data analysis Here you can look at data values plot spectra and images create scripts for batch processing and run analysis tools The contents of the workbench can be updated with various views available un der the Window menu see Section 17 on available views Opens a window with four more icons providing access to data held either lo cally or at a remote site for example the Herschel Science Archive It also al lows the import of FITS and text table files For more information on these features see the Data input output in Data Anal ysis Guide chapter of the Data Analysis Guide Opens the HIPE Help System in your default Web browser For more information see Section 5 Documentation Opens the Preferences dialogue window For more information see Section 4 Preferences Checks if a new user release is available The same feature 1s available by choos ing Help gt Software Updates This feature only works with user releases It does not work with developer builds Updates Shows a set of icons linking to Virtual Observatory tools including Topcat Al adin SPLAT VO and VOSpec Clicking on any of the icons launches the exter nal VO tool Help with these tools is not provided within HIPE documentation except for the HSA b
38. he script stops running This can lead to a delay before the script stops Running scripts in debugging mode This mode allows you to pause the script at certain locations and inspect and change the value of any variable This is useful for finding the cause of problems in the script See the Scripting Guide for details Section 1 37 in Scripting Guide Running scripts without opening them To run a script without opening it right click on it in the Navigator view and choose one of the following options e Run Script HIPE runs the script Variables generated by the script appear in the Variables view This corresponds to the following command where path to myscript py is the path to the script exectile path to myscriot sOy e Run in Background HIPE runs the script Variables generated by the script do not appear This corresponds to the following command where path to myscript py is the path to the script OG SRSCI 1S paca co smyscmiipr py Running a script in the background can be useful for example when you have a script that generates a complicated plot You want the plot to appear but without the related variables populating the Vari ables view 10 Running scripts outside HIPE HIPE s main executable hipe file substitutes from HIPE 12 0 the jylaunch standalone script inter preter Note Please note that in this section and to avoid the ambiguity of only changing the case between the G
39. indicating progressively more fine grained messages about the run ning of the software You can manage how log messages are sent to the console and to file With console we mean the command line prompt from which you started HIPE not the Console view in HIPE If you started HIPE by double clicking an icon you will not see a console To manage log messages create a file called userlogging properties inthe hcss directory within your home directory and copy the following lines into the file handlers java util logging ConsoleHandler java util logging FileHandler level WARNING java util logging FileHandler pattern h java u log jaya til logging Filenancdler limit 50000 jaya u util logging Filenancler count 1 java util logging FileHandler append false 18 HIPE Owner s Guide Build 13 0 5130 java util logging FileHandler formatter herschel share log api StandardFormatter java util logging ConsoleHandler level INFO Java ube loggaung Conse lehandler formatter herschel share log api StandardFormatter For your changes to take effect restart HIPE after creating or modifying this file e The first line of the file lists the handlers of log messages separated by commas This example lists the ConsoleHandler and FileHandler which means that log messages will be sent to the console and to file If you do not want log messages to be sent to the console or to file delete the corresponding handler from thi
40. ing Window Show View Reference Calibrators After opening the Calibrators view you should connect to the Official database Select it from the drop down list and press Connect button Note K You can also choose Local to connect to a local database although you most probably will not need to The local database must be a local pool whose name is defined by the 21 HIPE Owner s Guide Build 13 0 5130 hess calibration 1local property with default value calsdb_test For more information on local pools see the Data Analysis Guide in Data Analysis Guide For more information on how to set properties see Section 4 Calibrators x _o Select database Clear cache Planets amp Moons Callisto Europa hanymede lo Jupiter Mars Neptune Saturn Figure 16 The Calibrators view after connecting to a database Once you connect to a database the view fills with the available calibrators see Figure 16 grouped into Planets amp Moons Asteroid and Fixed Targets stars Click on a source to display basic informa tion in the Outline view Double click on a source to display detailed information in the Editor view as shown in the following figure 19 Fortuna x Files Line Surveys Spectral Line Surveys General i Operational Days Articles Name 19 Fortuna Type Asteroid Characteristics Flux calibration Delivery by Th Mueller on 24 June 2008
41. ing to take care of the time variability due to for instance rotation Full asteroid light curve modelling together with Herschel and asteroid ephemerides allow for predictions of fluxes across the Herschel mission In addition specific models provide flux infor mation for asteroids measures taken for calibration purposes see Mueller and Lagerros 2002 A and A 381 324 14 1 What can I get from the database The database contains all the models and fluxes used in the flux calibration of Herschel You can also get asteroid flux predictions for the main asteroids including the main calibrators Plus models for the specific time and date of calibration observations made by PACS and SPIRE of asteroids HIFI does not use asteroids for calibration purposes General information and fluxes for calibration standards are available Calibration model spectra of planets asteroids stars can be displayed in a HIPE session or saved as FITS files to disk Celestial calibration sources are only part of the flux calibration of instruments For instance inter nal loads are used by HIFI and the telescope background itself can be used for PACS and SPIRE spectrometer calibration For full information on flux calibration of any of the instruments check the published instrument in flight calibration documents 14 2 Using the Calibration Source Database The Calibrators view is part of the Workbench perspective If you cannot see the view open it by choos
42. int a print a Create an array a 2 3 a Floatld 2 3 Create a list a 2 3 Create an automatic array a findgen 10 a Floatld range 10 Get info on array variable print a print a Get one element of array print a 1 print a 1 Define new 1D array of 10 ele a fltarr 10 a Floatld 10 ments 43 HIPE Owner s Guide Build 13 0 5130 Assign value inside an array a 4 219 a 4 219 Define new 2D array of 5 rows a fltarr 10 5 a Float2d 5 10 10 columns a Plot commands HIPE equivalent Open a plotting window p PlotX YQ Plot two numeric arrays a amp b p PlotX Y a b a 0 10 PlotX Y a b xy range 0 10 xy title lambda xy title lambda Overplot me oplotac p 1 LayerX Y a c a annotations xyouts 0 2 0 7 Label d addAnnotation Label 0 2 0 7 Save as postscript set_plot ps p saveAsEPS file ps device filename file ps device close set_plot X Save as JPG Re p saveAsJPG file jpg Save as PNG Re p saveAsPNG file png Save as PDF Re p saveAsPDF file pdf Further customisations right click on plot and select Properties Data import export com IDL HIPE equivalent mands Read a text table readcol file dat a b c t simpleAsciuTableReader file file dat Plot read data plot a b PlotXY t cO getData t c1 getData or right click on t and choose Open with TablePlotter Read a comma separated table rea
43. ipt with hipe as a script interpreter You can check this by running the following script 16 HIPE Owner s Guide Build 13 0 5130 PROM Javax Ewing inport myAnswer poSsitbleAnswers HmPIY PACS SPIRE No clue All three while myAnswer myAnswer JOptionPane showInputDialog None Favourite Herschel instrument Test JOptionPane QUESTION_MESSAGE None possibleAnswers possibleAnswers 4 if myAnswer None myAnswer print Your answer is myAnswer Plots and batch mode HIPE Plots are created and displayed normally when running a script with batch mode hipe However any plot window will disappear as soon as the script is completed To preserve the plot you can save it to file before the script ends For more information on saving plots to file see the Data Analysis Guide Section 3 8 in Data Analysis Guide 10 1 Remote execution of scripts A typical way in which batch mode hipe is used is to run scripts on a remote computer The following are some best practices for remote computing e Avoid graphical interfaces as much as possible e Edit and test scripts on a local computer using small test datasets e Create log files You can do so on Linux with the following command hipe myscript py amp gt Session EXE You can also redirect standard output to file from within your Jython script with this command Import SyS SVS Stout open myfile txt ow e Process yo
44. isplay the corresponding page e The main screen area where the documents appear When you start the Help System this area shows nine boxes with links to the most important topics Two buttons at the bottom lead to external YouTube and Twitter resources for learning more about HIPE 5 1 Searching the help system Click the Search tab to display the search interface TOG Search l Glossary a AND OR AND C OR Filter Wo filter A y Figure 10 The search interface HIPE Owner s Guide Build 13 0 5130 Enter your search keywords and press Enter or click the GO button to perform a search You can search for multiple terms and link them with AND and OR logical operators For more information on limiting the search to one or more manuals or categories see Section 5 2 Logical operators limited searches and other advanced features are also available by using the fol lowing syntax in each search box e Boolean operators herschel AND archive OR store archive NOT store archive store The boolean operator words must be upper case Note that when writing multiple search keywords in the same text box the default operator is OR If you want to find text where all your keywords are present you must link the keywords explicitly with AND e Wildcards te t maxim A question mark replaces a single character an asterisk replaces from zero to any number of characters e Boosting aterm herschel 4 archive The boos
45. ite 3 bd Jatan bo Wier weas D Hires Faito n A Phe Saar Tl valais x 0 O Contam C Hm og Secu 0 s Sare Pragucds te Poot t A Export tinsel daa Mem HPE b 2 xa paved o poor moane P nte Pneus Tags sera es S inlseve E weus aaa G asco ME B E Figure 36 The Data Access perspective As part of the toolbar and visible in all perspectives and views there is an icon mi to instantly launch the HSA user interface in the same way as with the Section 17 1 Herschel Science Archive view button 18 3 The Workbench perspective The Workbench perspective provides nine views for working with tasks variables scripts and com mand line inputs You can also navigate in your file system and check log messages and the command history 38 HIPE Owner s Guide Build 13 0 5130 J HIPE File Edit Run Pipelines Scripts Window Tools Help Gecen Epb h FAR LO E sa gt Navigator X AG 4b ee o Editor x ai Tasks X i ET Applicable BB R By Category k gt User areas FX gt 3 Home Folder File System gt G My scripts S 3 My table fles f Variables x x amp R Log console x i E Outline x No outline information available a Jython Interpreter 100 116 of 3052 MB Figure 37 The Workbench perspective 19 Customising views and perspectives You can customise a perspective by
46. jahs is the engine that powers the HIPE Help System The name stands for Yet Another JAva Help System 5 4 Help outside HIPE When you quit HIPE links in any help pages of the offline Help System will not work anymore Even if you restart HIPE you will have to open the Help System again This of course does not apply to the online help opened with Help Online Help To access the offline help outside HIPE you can use the hipe_help command found in the apps directory in your HIPE installation the bin directory if you are using a developer build This com mand starts the Help System and opens the following window Yet Another JAva Help System Configuration hcss iadocumentyajahs webapp fherschelfiaf document war yajahs war hcss iadocumentyajahs contentdir drizzo Software hcss 6 0 doc yajahs Controller ID of document to be displayed v Display Exit Figure 13 The standalone Help System The window stays open as long as the Help System is running Click the Display button whenever you want to display the help in a tab of your browser Click Exit to stop the Help System The other controls in this window are useful only to developers of the Help System 5 5 For advanced users accessing the Javadoc If you are comfortable with Javadoc documentation you can access it from the HIPE Help System by clicking on any of the developer reference manuals listed in the Developer Reference section at the bottom
47. lick Accept to run the task or Clear to reset all parameter values For information on how to run tasks see the Scripting Guide in Scripting Guide 35 HIPE Owner s Guide Build 13 0 5130 For information on how to develop tasks in Jython or Java see these tutorials e Creating your first Jython task e Creating your first Java task 17 15 Variables This view shows the variables available in your session Select a variable to obtain more information in the Outline view see Section 17 13 Double click on a variable to display its contents with the default tool Right click on a variable to display a context menu with some of the following options they depend on the variable data type e Open displays the contents of the variable with the default tool e Open With displays a submenu with a list of tools that can be used to display the contents of the variable e Send to displays a submenu with entries to save the variable to FITS file or to a local pool See the Data Analysis Guide in Data Analysis Guide for more information on local pools e Show contents prints to the Console view a text representation of the contents of the variable For binary data such as images and observations this is usually a description followed by a list of metadata and included datasets e Show methods prints to the Console view all the methods routines applicable to the variable This is useful if you are working on a script o
48. m Explorer Frames HifiProduct v Show dialogue box when a crash dump file is created HrsSpectrumDataset PacsCube _ Check if used Java platform is supported SimpleSpectrum SpectralLineList _ Check for HIPE updates SpectralsimpleCube SpireSpectrumid S wheSpectrumbatactt v Check for plug in updates SpectrumFitterGul TablePlotter L Zoom amp Pan Factors 3 Text Editor v Check lock files in local pools L Jython Editor General Appearance Console Fonts Debug External Tools Help amp Documentation Logging Navigator aotartup amp Shutdown meon nes Restore Defaults Apply Advanced Import Export OK Cancel C Ask which variables to restore at startup v Check lock files in cache directories Figure 6 The HIPE preferences window You can set preferences in the available categories and revert to the default values at any time You can also export import the values of the preferences to from an XML file Press the Advanced button to open the list of properties including configuration properties specific to Herschel software and system properties affecting your system as a whole Propertios Fier by progervname 0 Progeny name Satus Type Description Source file username String Yser timezone Detaul Europen adnia var Galabase devel Default it Huser namek hcss var database server Detabase rane verdatabase devel hersehel release cemns general xml var database
49. mation on managing calibration sources see Section 14 Calibrators x Select database Clear cache Planets amp Moons Callisto Europa hanymede lo jupiter Mars Neptune Saturn Figure 26 The Calibrators view 30 HIPE Owner s Guide Build 13 0 5130 17 7 Calibration sets This view is available only if you install the PACS specific components of HIPE With this view you can inspect the release notes and file list for all the installed PACS calibration sets Click on the number of the calibration set you want to examine and choose Release Notes for selected set or Calibration File list for selected set from the drop down list Release notes may be missing from older calibration sets 17 8 Console The Console view provides a command line interface to all HIPE commands and functions Most graphical tools within HIPE echo in the Console view the commands corresponding to the action being taken This is useful if you want to automate a certain procedure through a script Press the Up key to access previous commands This feature also works across sessions if you have just started HIPE pressing the Up key will show the last command of the previous session You can use the following special commands while in the Console view e clear clears the Console view e history displays a list of previously entered commands each preceded by a number Type his tory 1l r to obtain a short help te
50. ned in this manual If you want to learn more about graphical tools to download visualise and analyse your data check the Data Analysis Guide If you want to learn the scripting language used in HIPE and master the command line interface have a look at the Scripting Guide See the Welcome page of the HIPE Help System for links to our YouTube and Twitter channels HIPE Owner s Guide Build 13 0 5130 Tip What is the relationship between the HCSS HIPE and DP HCSS Herschel Com mon Science System encompasses all software for the Herschel Science Ground Segment Commanding Proposal handling Mission Planning etc in addition to the Data Process ing DP system The DP system includes Standard Product Generation SPG Quality Control Pipeline QCP Quick Look Analysis QLA and Interactive Analysis IA HIPE stands for Herschel Interactive Processing Environment and is the main gateway to the DP system 2 Installing HIPE Warning 3 Before installing HIPE make sure that your default file compression program can unzip FITS files without corrupting them Otherwise calibration files shipped with HIPE may be corrupted during installation Under Windows WinZip is known to cause this problem WinZip has an option called TAR file smart CR LF conversion in the Miscellaneous tab of the Configuration dialogue window at least up to version 15 0 that is enabled by default and causes the corruption Disable the option
51. number corresponding to HIPE Open a command line window and issue this command jps You should get a result like this one 10408 Launcher ier 1 ers 10423 HipeStarter The HipeStarter process is the one you are interested in In this case the process number is 10423 28 HIPE Owner s Guide Build 13 0 5130 2 Create the dump file There are two commands you can use according to the situation e If you suspect a memory leak Issue this command jmap dump format b file hipe heap bin 10423 This command creates a dump file hipe heap bin for process 10423 Remember to use the process number you found in the previous step You can choose any file name you want instead of hipe heap bin The dump file can be very large Do not send it by email but put it somewhere HIPE developers can download it from e If you suspect that HIPE got stuck in an infinite loop Issue this command Jectcack 10423 gt hipe stack TxE This command puts some information about process 10423 in the hipe stack txt file Re member to use the process number you found in the previous step You can use any file name you want instead of hipe stack txt The resulting file is small and can be sent via email 17 HIPE views A view is any window embedded in the main HIPE window The views available in HIPE are described in the following sections 17 1 Herschel Science Archive With this view you can log into the Herschel Science Archive HSA and open it
52. of the Table of Contents To obtain the traditional frame based Javadoc layout click on the FRAMES link on any Javadoc page To get back to the HIPE Help System layout use the Back button of your browser clicking on the NO FRAMES link will not work To have both layouts available open the Javadoc layout in a new tab or window of your browser by right clicking on the FRAMES link 6 Extending HIPE with plug ins You can extend HIPE with plug ins To manage plug ins choose Tools Plug ins A dialogue win dow opens where you can install new plug ins and inspect and uninstall existing ones Click Find more to visit a web page with a list of available plug ins Click Install new to install a plug in from the Web or from your hard disk Among the plug ins currently available on the HIPE plug ins page are the following e SPIRE Photometric Interactive Analysis SPIA Facilitates artifact removal and map making from SPIRE scan maps e PACS Calibration Products Loads the PACS calibration products from a web server and in stalls the files on your computer e PACS Simple Aperture Photometry Performs aperture photometry of unblended sources on single or multiple PACS frames 12 HIPE Owner s Guide Build 13 0 5130 e CASSIS Spectral analysis toolset e ScanAmorphos Imports data from the ScanAmorphos program into HIPE e Photometric and spectroscopic convolution Convolves images and line flux maps to the same PSF e Cosmology
53. oi Tasks x yanas x Figure 3 Active left and inactive right HIPE view Depending on which view is active you will see different icons on the HIPE toolbar see Figure 4 The icons on the right are related to perspectives and never change The icons on the left apart from the first two to create open a file may change or become deactivated when you switch to a different view Figure 4 shows the icons that appear when you work on a file in the Editor view If you cannot find an icon in the toolbar it is probably because the active view does not use it cile Edit Run Pipelines scripts Window Tools Heip mee VTS vwta4a35 nb p hp Figure 4 The HIPE toolbar For a list of available views see Section 17 For a list of available perspectives see Section 18 3 1 The HIPE Welcome screen When you start HIPE for the first time you are greeted by a Welcome screen with six icons as shown in Figure 5 Welcome X Welcome to Herschel Interactive Processing Environment Hover your mouse over one of the images below for more information Work Bench Access Data Documentation Preferences Updates External Tools Welcome Figure 5 The Welcome screen You can return to the Welcome screen at any time by clicking the is icon at the top right of the HIPE window The following table describes the icons in the Welcome screen Description Takes you to the Workbench perspective for information on perspectiv
54. ot all properties can be modified To reset a property to its default value right click on the corresponding row and choose Reset to default from the menu HIPE Owner s Guide Build 13 0 5130 HIPE reads properties from these files with home and install being your home directory and HIPE installation directory respectively l install installed properties 2 All the properties files in install config properties 3 home hcess user props These properties affect all Herschel software on your system 4 home hcss hipe props These properties affect all HIPE versions on your system HIPE reads files in the order above so for instance a property set in hipe props overrides the same property set in installed properties If you choose to modify property files directly you should only have to modify the last two files Restart HIPE for any change to take effect Warning 3 Property files are not encrypted If you store sensitive information in a property file set access permissions so that only you can read the file and avoid sharing it with other users See the documentation of your operating system for how to limit access permissions to files Tip If you want a list of all the properties in text format choose Help About click on the Config tab and press Copy to Clipboard You can then paste the list to a text editor 5 Accessing help Open the HIPE Help System by choosing Help Help Contents Help pages open in a new
55. peline steps data analysis routines and other tools available in HIPE The tasks are listed under three folders which you can open and close with a double click e Applicable this folder is populated only when you select a variable in the Variables view In this case it lists all the tasks whose primary input is compatible with that variable e By Category this folder has seven subfolders General Image Spectrum Cube Hifi Pacs and Spire listing general tasks and tasks relevant to a specific instrument or data type e All lists all the available tasks When one or more folders are open you can type a few letters to jump to any tasks whose names begin by those letters Double click on a task to open its dialogue window in the Editor view see Figure 32 for an example ald Tasks x 4 Applicable S By Category m accessDataFrame accessHkParam accessPacket accumulate Figure 31 The Tasks view Right click on a task to display a context menu with the following entries 34 HIPE Owner s Guide Build 13 0 5130 e Open and Open With opens the dialogue window of the task e View source displays the source code of the task This is useful if you want to inspect the algorithm used or if you plan to modify the task For this entry to work you must have selected the option to include the source code when you installed HIPE e Help in URM opens the help page for the task in the User s Reference M
56. r form To extract a data column into a one dimensional array issue a command like the following in the Console view b neptune_test_FITS get spectrum getData T_b This assumes that neptune_test_FITS is the name of the variable created after loading the FITS file The command creates a one dimensional array of the brightness temperature SED Spectrum 1A 10 1 610 1410 1 210 1010 4 0 10 6 0 10 40 i0 20 10 o 0 2 0 10 ELLE Li ELLEI 1 MMM 1 SUH ALLELE 2 HH frequency GHz El save Clear Figure 18 SED plot for alpha Boo Operational Days tab This tab is available only for asteroids Since the fluxes vary considerably due to rotation as well as relative satellite asteroid positions information for asteroids is provided for each day of the mission To view flux and SED information for asteroids open this tab and select a range of dates The fluxes plus other information including approximate position in various units and apparent diameter scroll window results to the right appear after you click the Search button 23 HIPE Owner s Guide Build 13 0 5130 Note that these fluxes are not good enough for final calibration purposes For specific operational days and observation ids more accurate models have been made with improved updated ephemeris and best model parameters that fit the precise time of the observations If you have a calibration observation of an asteroid taken as part of on
57. r issuing command line instructions involving the variable e Rename and Delete renames or deletes the variable e Help in URM opens the entry of the User s Reference Variable corresponding to the type of the variable This menu entry is not available for all variable types e Help in DRM opens the entry of the Developer s Reference Variable corresponding to the type of the variable Since this is developer documentation it may be difficult to understand if you do not have some programming experience ae Variables X xo Ek ajv No fitter Observations Wo filter Sobsid_ vls42191 Filter Product Other Data Filter Dataset x acms Filter Numeric C dochook horizons hsastore orbitEy pointing sparer timeline uplink Figure 33 Variables view with filtering menu The view has a toolbar with the following four icons 36 HIPE Owner s Guide Build 13 0 5130 Ps Removes the selected variables Se Removes all variables Ee Clears the current selection eo _ Toggles between the single panel view all variables are listed together and the two panels view observations are shown separately from other variables Click the menu at the upper right corner of the view to display a menu to filter variables according to their type see Figure 33 The available options are e No filter Variables are not filtered e Filter Products Products in Scripting Guide containing a set of metada
58. r s Guide Build 13 0 5130 Line Surveys tab Currently not used but intended to include references to spectral line informa tion Spectral Line Surveys tab Currently not used but intended to include information from line sur veys including on ground observations SED tab Provides links to planet and stellar SEDs for the primary and some other calibrators These are model SEDs which are believed to have systematic errors of order two per cent see Dehaes et al 2011 Moreno private communication e Plotting a SED Click to select the SED you want and press Plot at the bottom of the tab Note that this plot is only meant as a quick look and does not provide all the information stored including all header information If looking at several SEDs press the Clear button after you have finished with each one otherwise the plotting scales and labels could be corrupted e Saving a SED to FITS Click Download to save all the SED information to a FITS file It is much easier to read this file back into HIPE if you give ita fits extension This is not automatic e Loading a saved SED into HIPE Find the FITS file in the Navigator view and double click on it HIPE creates a new variable and show its contents in the Editor view Double click spectrum in the Data panel to open the spectrum with the default viewer in a new tab of the Editor view Right click and choose Open With to select a viewer Select Dataset Viewer to see the data in tabula
59. references window Freeing memory from unused data HIPE automatically frees memory from unused data when ever necessary This is known as garbage collecting You can also free memory manually as follows e Delete any unused variables e Run garbage collection manually by clicking the bin icon next to the memory bar see Figure 14 To do the same from the command line issue this command System gc e Check for tasks retaining data in their outputs Follow these steps l Choose Edit gt Preferences The Preferences dialogue window appears 2 Click on Tasks in the list on the left The General gt Tasks panel appears on the right hand side 3 Tick the Detect tasks that retain data checkbox 4 Click OK at the bottom of the dialogue window Each time you run garbage collection manually HIPE shows you any tasks that retain data in their output values You can then choose to clean the data from some or all of these tasks 13 HIPE Owner s Guide Build 13 0 5130 Highest memory level in session Garbage collector 284 of 2730 MB _ i Max memory used 638 MB Reset Memory bar Reset highest memory level Figure 14 The memory bar and garbage collector icon in the HIPE status bar 8 Managing running jobs A job is any operation that HIPE can carry out such as running a script or executing a task e Monitoring running jobs Whenever HIPE is running a job the throbber icon in the status bar becomes animated
60. rent HIPE session The oldest log contents in java0 log 1 are deleted This rule does not apply if the append property is set to t rue see below e java util logging FileHandler append controls whether log messages from new HIPE sessions are appended to old messages rather than replacing them If set to t rue log mes sages are appended to the most recent log file 13 Saving and restoring variables and ses sions Saving and restoring variables automatically To enable automatic saving and restoring of vari ables across HIPE session choose Edit Preferences go to Startup amp Shutdown and tick the Save variables on exit checkbox If you tick the Ask which variables to restore at startup checkbox HIPE will offer you at each startup a choice of variables to restore Not all variable types can be saved and restored Among those that can be saved and restored are the following e Numbers and strings e Arrays metadata datasets and products e Observation contexts and other contexts Only loaded references are saved 19 HIPE Owner s Guide Build 13 0 5130 Warning 3 Saving and restoring large variables can slow down HIPE considerably Saving and restoring variables from the command line You can save and restore variables at any moment during a HIPE session by using the save and restore commands as shown by the following example Define three variables 1 l 2 3 Hello world Q O 0 s He Save two OL the a
61. ripts For example it can show detailed infor mation about data products and observations see Section 15 and is where the graphical interface of data analysis tasks is shown see Figure 32 for a typical example 31 HIPE Owner s Guide Build 13 0 5130 17 10 History The History view provides a list of the commands executed at the console and from Jython scripts It also shows whether the command was successful or not with the following icons K The command was successful The command caused an error The icon appears next to a failed command and indicates that the row can be expanded to reveal additional information In particular the Trace column will show a detailed traceback of the error see Figure 27 The traceback is a list of all the function calls that lead to the error location It will probably tell little to you but it is invaluable to a developer for investigating a problem If you think that the error was caused by a HIPE bug be sure to include the traceback in your Helpdesk report Right click on the traceback to copy it to the clipboard or save it to file EJ History x a Y S Line Status Torriani Error Trace k Fe inagp Sinplel mage 1 x result rotatecinage 2 jawa 1ang IegalArgunentEsceptionTraceback Cinnernost last File ling 1 I F gt Offending Lines Mo Line idenritied Java 1ang I 1egalargunentesception Width 0 and height g0 wust be gt 0 j
62. rowser interface which is described in the Data Analysis Guide in Data Analysis Guide External tools When you click on the icon of an external application it will be automatically downloaded and launched After the download you may see a security dialogue window telling you that the application s digital signature is missing or has an error For the applications shown in this window you can safely click the Run button You can check the Always trust content from this publisher checkbox to avoid being prompted again An external application is downloaded the first time you click on its icon and whenever a new version becomes available Note that the application will be downloaded even if you have a version already installed on your hard disk 4 Setting properties and preferences HIPE s behaviour is controlled by preferences and properties Preferences include the most common and frequently used settings Properties are more advanced settings which you should change only if you know what you are doing Choose Edit Preferences or press Alt Enter to open the Preferences dialogue window HIPE Owner s Guide Build 13 0 5130 rJ Preferences Data Access General gt Startup amp Shutdown Cache tr Maximum memory MB To be applied the next execution of HIPE Pacs Calibration Storages amp Pools v Show tips at startup Editors amp Viewers Image Viewer _j Save variables on exit Ploc viewer L Mouse gt Spectru
63. s and user props files Some proper ties such as java vm memory max can only be set ina file See Section 4 for more information on properties and property files settings Lists all the available properties and their values log Sets the log level of different components that is the amount of in formation written to the terminal while the script runs You can con figure different log levels for different software modules packages as in the following example hipe log herschel share OFF herschel cus INFO myscript py You can choose among the following levels SEVERE WARNING INFO CONFIG FINE FINER and FINEST Going from FINEST to SEVERE fewer and fewer messages are displayed leav ing only the most important ones You can also set the level to ALL to see all log messages or to OFF to see no messages See Section 12 for more information on managing logging levels version Displays the version of HIPE For example 8 0 2504 These are the same numbers you see when you choose Help About in the GUI version of HIPE Warning 3 Some HIPE plug ins such as Unit Conversion Tool Herschel Quick Look and Cassis do not initialise properly with hipe as a batch processor If you have scripts that use features of these plug ins they may not run correctly with batch mode hipe Graphical interfaces and hipe in batch mode If the script opens a graphical interface this will also work when running the scr
64. s graphical interface See the Data Analysis Guide in Data Analysis Guide for more information Herschel Science Archive x re Open HSA User Interface Figure 24 The Herschel Science Archive interface view 17 2 Export Herschel Data from HIPE With this view you can export Herschel data as loose files or as a compressed archive You can export a local pool whatever it contains or a full observation The observation is exported with the same directory structure found in the t ar files retrieved from the Herschel Science Archive For more information see the Data Analysis Guide Section 1 11 in Data Analysis Guide 17 3 Product Browser This view is the main component of the Product Browser perspective see Section 18 1 It allows you to query and browse products stored locally or remotely For more information see the Data Analysis Guide Section 1 7 in Data Analysis Guide 17 4 Product Tree 29 HIPE Owner s Guide Build 13 0 5130 Like the Product Browser view this view is also part of the Product Browser perspective When you select a product in the Variables view the Product Tree view gives you additional infor mation B Product Tree x MapContext for SPIRE products unt description SpireMapContext Product Type Identification SPG v2 1 0 Generator of this product io 2010 02 10T Creation date of this product i MapContext for Name of this product SPIRE Ins
65. s line e The level WARNING line defines the overall logging level Only messages of the same or higher level than the one on this line will be shown You can use ALL to show all log messages You are unlikely to need log messages on a more fine grained level than INFO unless you are trying to diagnose a problem with HIPE Individual handlers can override this global setting in the userlogging properties file shown above the ConsoleHandler defines a different level Warning X If you use a very fine grained log level with aFileHandler HIPE could slow down to the point of becoming unresponsive because of the high number of log messages to be written to file e java util logging FileHandler pattern defines the format of the log file name and location The default is to have files placed in your home directory with names such as java0 log See the FileHandler documentation for details on how to define the format e java util logging FileHandler limit is the maximum size in bytes of the log file e java util logging FileHandler count is the maximum number of log files that can be created For example setting this parameter to 2 means that there will be at most two files with names like java0 log 0 and java0 log 1 These are rotating files For example if you start a new HIPE session when the two files have already been created the contents of java0 log 0 are moved to java0 log 1 and java0 log 0 receives log messages from the cur
66. ser Detaut atri localhost Database Server war database server herschel sreleas Se eee Eee eral xml har hess ctadir Detaun Huser homely Hess Directory for configuration purposes sherschelfrelease oetnsygeneral wml Sirig fame Software hess 7 0 Builg Girectory var hiss ciry war hicss instrum i String NONE Instrument usediivar Aces instrament herschelsrelease cefns general mil Vanes workin String fhaie 2 OS tmp Scrateh directory tor heas 0an hes a veorkd home eS S O Ser ps JS ste St dir Detaun Siring Hvar hess dir Tes hamess directory ar hcsshest oiri hersihel reease dems general nml Default String rt war hess dir he ss dp hilprogertles Default String home data MPS top lewel data directonsiwar mps dataclir herschel release defns general xml Integer 3677 Port HUME rear rower port herschel release cetns general wml Figure 7 The HIPE advanced properties window Properties in bold are not set to their default values Click the column headers to change the ordering of the properties Write anything in the Filter by property name field to show only the properties whose name contains that text To modify a property double click in the Value field change the value and press Enter or click anywhere else to confirm The Source file field now shows the file where the custom value has been stored Note that n
67. sion first Note K Most files of a HIPE installation are stored into a hcss d directory within your home directory This directory is shared among all the HIPE installations on a computer which means that the uninstaller will not clean it up to avoid damaging other installations You can remove this directory manually after you have removed HIPE completely from your system Any HIPE installations left will stop working after removing this directory If you install and upgrade many HIPE versions over time the size of your hcss d directory can grow to several gigabytes To free this space follow these steps 1 Uninstall all the HIPE versions on your computer 2 Delete the hcss d directory 3 Reinstall all the HIPE versions you need 2 2 Installing developer builds To install developer builds follow these steps 1 Download the dedicated installer from _http herschel esac esa int hcss repository php item hcss installer zip_ 2 Unzip the installer file A new directory HcssInstaller is created 3 Open a command line prompt and go to the HcssInstaller directory 4 Execute the hess installer command on Linux and Mac or the hess installer bat command on Windows See the remainder of this section for the syntax of these commands Option Project Track Build hess installer Figure 1 The syntax of the developer builds installer e Command options are preceded by two dashes To see a list of all available op
68. ta entries and datasets are shown e Filter Dataset Array Datasets Table Datasets and Composite Datasets are shown datasets are described summarily in the Scripting Guide in Scripting Guide and the Product Definitions Document in Product Definitions Document e Filter Arrays Numeric Arrays in Scripting Guide are shown This does not include native Jython arrays 17 16 PlotXY properties This view displays the properties of any plot components highlighted in the Outline view as shown in Figure 34 S Outline x PlotXY properties x amp Plot Layout color WB black hie font Serif 0 14 Subtitle text Sample title Legend gt amp Subplot 0 visible v Margin position TOPCENTER gt amp Layer 0 pglid 0 location 294 461949110 Style x 294 461949110 Bx id 0 y 44 5584493 961 f y id 1 locationP 2 45579359266 x 2 45579359266 y 3 781673 17708 A a m on Ae aa 4 Figure 34 The PlotXY properties view showing title properties 18 HIPE perspectives A perspective is a collection of related views You can customise a perspective by adding deleting and moving views To save space you can also rearrange different views as tabs sharing the same screen area HIPE comes with four perspectives available in the Window Show Perspectives menu The Wel come perspective is described in Section 3 1 18 1 The Product Browser perspecti
69. tabs Ifa window is too narrow to display all its tabs three new controls appear two arrows to cycle through the tabs and one more downward arrow to get the list of tabs see Figure 41 i gt Navigator x amp Ky g User areas fs Home Folder t E File System al My scripts al My table files ae Variables g Tasks amp Navigator B Calibrators Figure 41 Moving through tabs 40 HIPE Owner s Guide Build 13 0 5130 Adding views To add a view to a perspective select it from the Window Show View menu If a view is already in a perspective it is not added again e Resetting a perspective Any change you make to a perspective is kept in future HIPE sessions To restore a perspective to its original settings choose Window Reset perspective or click the arrow icon on the toolbar next to the perspectives icons see Figure 42 You can also right click on the icon of the modified perspective and choose Reset perspective from the context menu Figure 42 The icon to reset a perspective 20 Mouse and keyboard shortcuts 20 1 Mouse clicks in HIPE The following table shows how left middle and right mouse clicks are simulated on different plat forms Note K It is assumed that the standard model of mouse is a three button mouse even if the middle button is a scrollwheel that allows clicking The table below explains how to simulate clicks using mice with less buttons
70. tails e For Java 6 http download oracle com javase 6 docs technotes guides intl fontconfig html e For Java 7 http download oracle com javase 7 docs technotes guides intl fontconfig html 22 IDL to HIPE command mapping The following tables contain the HIPE equivalents of the most common IDL commands and functions Warning X HIPE uses row column as notation for two dimensional arrays while IDL uses column row In addition HIPE uses row major ordering when allocating array elements into memory elements in the first row are allocated first followed by elements in the second row and so on IDL uses column major ordering instead This difference also holds for arrays of more than two dimensions This means that IDL scripts involving loops on large arrays will suffer big performance penalties unless they are adapted to row major ordering Write your loops so that elements are accessed in the same order they are located in memory x Z sly 14 5 6 Two rows chree columns Order of elements in memory 1 2 3 4 5 6 Correct way of looping for i in range 2 Loop ON TOWS for J J in range 3 s3 4 LOOP on columns printe xiliga You should also use array operations instead of loops whenever possible Look here for more information Section 2 2 10 in Scripting Guide Basic commands IDL HIPE equivalent Create a variable a 5 Get info on a variable type help a print a __class__ Print value of variable pr
71. ted term is considered more relevant which influences the ordering of results The default boost level is one e Proximity searches the string herschel archive 10 searches for herschel and archive within ten words from each other e Fuzzy search herschel herschel 0 6 Finds words with similar spelling You can specify a fuzziness level between zero and one the default is 0 5 Lower values of the fuzziness parameter mean that greater spelling variations are considered e Limit search to one manual manual hipeowner AND herschel manual hipeowner OR manual quickstart AND herschel Fora list of identification strings for the man uals see the drop down list Each string is listed next to the manual name for instance Quick Start Guide quickstart Some strings like howtos for the Data Analysis Guide do not resemble the name of the manual for historical reasons Grouping search results By default search results in the glossary are displayed first Click the cog icon to set how the other results are grouped You can choose to group results by manual or by category or not to group results at all The default is to group search results by category You can dynamically change the grouping of results without having to repeat the search Note When you use the search feature for the first time HIPE must build the search index This can take up to a few minutes depending on the speed of your system and on the amount of installed
72. the PC keyboard key See this Boot Camp page for information on mapping between Apple and PC keyboards Boot Camp information on keyboard shortcuts please open this link in anew window tab Action Shortcut Editor Incremental search Matching words are found as Ctrl I Shift Ctrl I you type Autocomplete command In case of ambiguity re Tab N turns a list of possible command starting with the letters you have typed N N N N N N N Console N Toggle text direction between left to right and Shift Ctrl O right to left Get first entry in command history Ctrl Home Get last entry in command history Ctrl End Get previous entry in command history Up Get next entry in command history Get previous entry in command history matching Ctrl Up what you have typed Get next entry in command history matching what Ctrl Down you have typed No Loa Mo Get command history CH JN Remove selection CA Yrs Select previous character Shift Left Yes Select next character Shift Right Yes Select to beginning of line Shift Ctrl Home Yes oe ee ie Select to beginning of line excluding command Shift Home prompt Select to end of line Select previous word Select next word Select to same position on previous line Yes Select to same position on following line Shift Down Yes Select to end of text Shift Ctr End Yes Select previous page Shift PageUp Yes Select next page Shift Pag
73. tions run the com mand with the he lp option Two useful options are the following e doc Controls whether to install documentation default is yes Use as doc yes or doc no If no documentation is installed locally HIPE automatically falls back to the online documentation e src Controls whether to install the source code default is no Use as src yes or src no You can run HIPE without installing its source code but you will not be able to use the Source button in task dialogue windows HIPE Owner s Guide Build 13 0 5130 e The project is the part of HIPE you want to install Use hcss to install everything hess dp core to install only the core system without instrument specific software hcess dp hifi to install core software plus HIFI specific software and hcss dp pacs or hcess dp spire to install core software plus PACS or SPIRE specific software respectively Specifying a project is mandatory e Tre track correspond to a major HIPE version and its minor versions For example use track 9 0 to download a developer build leading to HIPE 9 0 or to a 9 x version Specifying a track number is mandatory e The build number indicates the specific HIPE build you want to install If you omit this number the latest available build is downloaded The developer build is installed in a subdirectory of the directory from which you launched the in staller To uninstall the developer build delete its direc
74. tory However note that developer builds store software in the hcss d directory just like user releases For more information on the developer build installer see http herschel esac esa int hcss install php 2 3 Configuring HIPE for a proxy server You can configure HIPE for use with a proxy server during installation To change proxy settings after installation add or edit the following entry in the installed properties file within the HIPE installation directory java vm options Dhttp proxySet true Dhttp proxyHost proxyserver myinstitute com Dhttp proxyPort 8888 All the above properties must be on the same line of text Since HIPE connects to the Herschel Science Archive via the ht tps protocol you must also configure the proxy for this protocol by adding the same three properties with Dht tps instead of Dhttp If the proxy requires authentication add the following two properties Dhttp proxyUser myUserName Dhttp proxyPassword myPassword 3 HIPE basic concepts The building blocks of HIPE are views windows embedded in the main HIPE interface organised into perspectives HIPE also offers viewers to visualise many types of data such as images and spectra Figure 2 The components of HIPE HIPE Owner s Guide Build 13 0 5130 Click a view title to make the view active When a view is active its title tab is highlighted see Figure 3 There can be only one active view at any time
75. trument attached to this product Unknown Model name attached to this prod 2009 11 30T Start date of this product 2009 11 30T End date of this product C herschel spire ia dataset cd4urn hsa hersc outputDataset P JPP herschel spire ia ci gt D Datasets 2 2 Bib History herschel i HY outputDataset he Figure 25 The Product Tree view The top area shows the metadata associated with the product The lower left area shows a tree structure of all the inner products and datasets contained in the product This is especially useful for exploring entire observations which have an onion structure made of several layers The lower right area shows the unique identifier for any product selected in the lower left pane This identifier is useful if you want to manage the product via the command line Click the icon to the right of the identifier to copy the string to the clipboard This layout is also used in the product and observation viewers described in Section 15 17 5 Save Products to Pool In this view you can save data products from your session into a pool See the Data Analysis Guide for examples Section 1 9 in Data Analysis Guide This section describes the Save Products Tool which looks the same as the Save Products to Pool view 17 6 Calibrators With this view you can browse and retrieve products from the database of Herschel calibration sources For more infor
76. ur data in stages Save intermediate results wherever appropriate e If you want to examine images save them as JPG files 11 Editing scripts and configuring the editor You can edit Jython scripts and other text files in the Editor view When you open a Jython script or a text file a set of editing commands becomes available under the Edit menu and as icons in the HIPE toolbar To configure the editor choose Edit Preferences and go to Text Editor under Editors amp Viewers Here you can configure the following e Whether to enable autosave to save open files automatically at regular intervals e Whether to show a vertical bar at a given column This is useful if you want to keep all lines below a certain length e Whether to show line numbers e Whether to highlight the current line that is the line the cursor is at To configure specific options for the Jython editor choose Edit Preferences and go to Jython Editor under Text Editor Here you can configure the following e By how many spaces to shift a line when using the Shift left and Shift right commands e The size in spaces of the tab character 17 HIPE Owner s Guide Build 13 0 5130 e Whether to indent code automatically e Whether to close brackets automatically Whenever you type a or character the corre sponding closing character is added automatically e Whether to show hidden characters like spaces shown with a dot or end of line charact
77. ve With the Product Browser perspective you can search for and view data from databases and data stores both local and remote 37 HIPE Owner s Guide Build 13 0 5130 For more information see the Data Analysis Guide in Data Analysis Guide J HIPE File Edit Run Pipelines Scripts Window Tools Help icu Epp gt Produa Browser x a 22 variables BA Observations Products Meadaia Free Metadata x k BR Data Source Search parameters A myHsa a Show all versions On line Off line Observation Id obsid C Local Pools Instrument instrument 1342180456 Operational Day o Nurmber 1342231722 A 1342238244 No results found odNumber S Outline x No outline information available El console x p 198 of 3051 MB 0 Figure 35 The Product Browser perspective 18 2 The Data Access perspective With the Data Access perspective you can query and obtain data from the Herschel Science Archive HSA Login is now done using the status bar at the bottom of the screen For more information see the Data Analysis Guide in Data Analysis Guide Hk Bal Puy Motnes Somes Widow Tons Hep nen sr oa an Cae x Lae 5 d Mad homie t Oonan TF 2 li Z Oper HSA User Imerfare Coser mows Weractete Free Weractetn Daa Sauce earl par amiter Umyaa hya wl ernces L J a Of Aprono 0 pd N m Local P pok heraren ese 7 Operatora Day pam
78. xt on the syntax of this command e n copies from history the command identified by number n The command is not executed auto matically For that you have to press Enter e help displays a short help text about these commands and a list of keyboard shortcuts Many of these shortcuts are also available in the Editor view Autocompletion If you write some letters and press the Tab key HIPE shows you a list of all commands and variables whose names start with those letters If there is only one match HIPE com pletes the word automatically Configuration To configure the Console view choose Edit gt Preferences and go to Console under the General Appearance category Here you can configure the following e Buffer size The maximum number of characters than the Console view can hold e History size The maximum number of lines held in the history e Prompt The prompt shown before each new line Further information For a selection of keyboard shortcuts available in the Console view see Sec tion 20 2 For more information on the scripting language used by HIPE see the Scripting Guide in Scripting Guide 17 9 Editor Use the Editor view to display and edit scripts and other files For more information on running Jython scripts in HIPE see Section 9 For information on editing text files and Jython scripts and on configuring the editor see Section 11 The Editor view is used for much more than editing sc

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