Rachel GUI

From GOSIA

==General description== [[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]] The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. It is currently undergoing beta-testing. The GUI ''optionally'' uses a modified Gosia version based on release 20081208.10, called 20081208.10.a. This modified Gosia source code is distributed with the Rachel package. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines, but is ''not'' Windows compatible. A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. The release-candidate version, expected in the summer of 2011, will have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. It is expected that the release candidate will make more use of push-button control panels and less input and output to the terminal. [[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the input definition considerably. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix. ==How to get the Rachel package== Version 2.0.8.beta is completely compatible with version 2.0.4.beta&mdash;2.0.7.beta and has the same backward-compatibility for session files older than 2.0.4.beta. Refer to the [[gui_release_notes | release notes]] for the change in this version. The Rachel tar archive of version 2.0.8.beta is available on a [http://www.pas.rochester.edu/~hayes/beta_rachel/rachel.2.0.8.beta.tar temporary download site]. This includes an ''extended'' version of Gosia that makes use of file number 99 for amplitude vs. time data [[File:Amplitudes.png|thumb|right|Excitation amplitude as a function of the time-like variable 'w' generated by Gosia via the Rachel GUI.]] and collision function output for optional plotting functions in the GUI. Except for these two functions, the GUI can be run with the current version of Gosia, 20081208.10. ==Installation notes== ===General=== Rachel has been installed successfully on the following systems. You can view or submit detailed installation notes for these or other systems. (Please link them to a separate Wiki page.) If the default python environment set in the rachel.py executable is not appropriate, the following error will appear: <pre> % [path].rachel.py /usr/bin/env: python2.6: No such file or directory % </pre> The correct Python environment can be invoked by typing instead: <pre> % [python] [path].rachel.py </pre> where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it. ===Installation notes for other Linux/Unix systems=== * [[rachel_installation_ubuntu | Ubuntu]] * [[rachel_installation_open_suse | OpenSuse]] * [[rachel_installation_fedora | Fedora]] * [[rachel_installation_mac_os_x | Mac OS X]] The final tests that all necessary libraries and codes are installed are usually the following: * Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads <pre> backend : [backend] </pre> where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]]. * After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt. ==GUI version backward compatibility== In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session. When the release candidate becomes available, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data. In the release versions, automatic upgrading of saved sessions will be reinstated. ==Beta version capabilities== * Azimuthally symmetric particle detection * Partitioning particle-detector data by azimuthal angle * Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]] * 4pi experiments (e.g. experiments with no particle detection) * Normal or inverse kinematics experiments * A user-expandable library of standard Ge crystals e.g. Gammasphere * Data from summed 4pi arrays * Efficiency-corrected gamma-ray data only * Experiment planning aids ** Generation of simulated data based on a proposed beam run ** Optional quasi-Gaussian random scatter in simulated data ** Estimated precision of the proposed measurement * Accuracy testing to determine if Gosia will be appropriate for a planned experiment * Fitting and correlated error estimations * Reading level schemes and gamma-ray data from Radware AGS files and including ** Branching ratio data ** Previously measured EM matrix elements, including the measured phases ** Lifetime data for ''excited states'' (not the ground state lifetime) ** Mixing ratios * Several supported data file formats ** [Radware] AGS format ** [[Rachel format nuclear data files]] ** Gosia format (experimental yield and fitted matrix element data) * Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]] * Automated generation of stopping power and internal conversion input for Gosia * Push-button controls * A searchable help function * Saving the entire session to a file * Undo/Redo of most functions and crash recovery Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia. ==Upgrade strategy== Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.'' This voting plan has not been implemented yet. In the meantime, a page of [[rachel_desired_upgrades | desired upgrades]] has been created. ===Planned upgrades=== There are a number of planned upgrades, some of which will be incorporated in the first [rachel release candidate] version. The upgrade plan and priorities will be changed based on user feedback and bug reports. Users are encouraged to suggest desired upgrades through the Forum to steer the software development. # More accurate stopping power calculations for low-Z beams. # Improved graphics including ## a transition from matplotlib graphics to pyGtk in the level scheme window ## clickable objects in the level scheme diagram # Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, etc.) # Plot functions to visualize fit conflicts in the data # Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set as the level scheme and matrix change. # Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user. # Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>. ==Tutorial videos and run-time help== The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. Tutorial videos generated with a pre-beta version are now available. While the GUI control panel and some user input and output formats have changed slightly, most of these changes should be obvious during operation. Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data. ===The basics=== ''Note that some of narration in the later tutorials is outdated. Prompts in the GUI terminal window should clarify these changes.'' # To install Rachel and get it running for the first time, watch [http://www.pas.rochester.edu/~hayes/beta_rachel/rachel_installation.html Rachel Installation]. # A short video on [http://www.pas.rochester.edu/~hayes/beta_rachel/undo_redo.html the undo/redo buttons]. # How to [http://www.pas.rochester.edu/~hayes/beta_rachel/crash_recovery.html recover data from a crashed session]. # First steps: [http://www.pas.rochester.edu/~hayes/beta_rachel/reading_level_schemes.html Reading level schemes.] # How to [http://www.pas.rochester.edu/~hayes/beta_rachel/add_matrix_non_collective.html add individual matrix elements]. This is most applicable to small, non-collective systems, such as the one in the sample file example2levels.txt file distributed with Rachel. # How to [http://www.pas.rochester.edu/~hayes/beta_rachel/add_matrix_collective.html add matrix elements systematically], i.e., for collective nuclei with rotational bands. # How to [http://www.pas.rochester.edu/~hayes/beta_rachel/setting_up_calculations.html define experiments, Ge detectors and calculate predicted yields]. This video will show how to define experimental detector setup, data partitions and make instant plots as well. Use the files fitting_example_levels.txt and fitting_example_matrix.txt included in the example files to quickly set up for this video. (The previous videos show how to load a level scheme and define or load a matrix.) Note also that the current beta version 2.0.5 ''does'' allow arbitrary particle detector shapes to be defined. The video narration has not been updated for all of the new detector options, and some prompts will be different from those in the video. # A [http://www.pas.rochester.edu/~hayes/beta_rachel/basic_fit_example.html very basic example of fitting] including a correlated error calculation. The entire video is about 30 minutes long. You can follow along using the GUI on your system and the example files shown in the video, which are included with your Rachel distribution in the .../example_files/ subdirectory. # More advanced selection of fit parameters are shown in this video on [http://www.pas.rochester.edu/~hayes/beta_rachel/experiment_planning_2.html experiment planning]. ===Experiment planning and accuracy testing tools=== The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format will look like the following: <pre> Experiment 1 Detector 1 Raw Sim. Measured Band Spin Band Spin Counts Error eps Counts Error ------------------------------------------------------------------------------- t 24.0 gsb 22.0 17 4 0.118 179 45 t 24.0 t 22.0 18 4 0.151 121 29 four 22.0 four 20.0 14 4 0.166 63 17 </pre> The "raw counts" are estimated from a typical efficiency curve for Gammasphere, and the estimated absolute efficiency <math>\epsilon</math> is given as "Sim. eps" for each transition. Possion counting errors are based on the raw counts, while additional error on the ''total'' (simulated) efficiency-corrected counts may be added by the user. # [http://www.pas.rochester.edu/~hayes/beta_rachel/accuracy_testing.html Testing the accuracy] of your Gosia calculations and the applicability of Gosia to a planned experiment. # Semiclassical Coulomb excitation codes have inherent adiabaticity and eccentricity limits. [http://www.pas.rochester.edu/~hayes/beta_rachel/adiabaticity_limit.html This video] shows how to test for these limits with an experiment that would ''not'' be appropriate for Gosia. # [http://www.pas.rochester.edu/~hayes/beta_rachel/experiment_planning.html Generating simulated data]. The errors in the simulated data are based on Poisson statistics and the expected number of days, beam current, etc. to estimate your ability to observe desired gamma-ray yields and to fit matrix elements to the observed yields. The present beta version applies ''optionally'' a quasi-gaussian random scatter of the predicted yield data [http://www.pas.rochester.edu/~hayes/beta_rachel/experiment_planning_2.html as demonstrated in this video] to better aid in predicting expected precision of fitted matrix elements. Watch this supplemental video to see how this works. You should also watch the [http://www.pas.rochester.edu/~hayes/beta_rachel/accuracy_testing.html accuracy testing video] to see if Gosia would be an appropriate analysis tool for your planned experiment. ===Troubleshooting=== For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left. ==Bug reports== Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions. Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible. ==Links== [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video] ==Notes== <references/>

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