Rachel GUI

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(How to get the Rachel package: change to version 1.1)
(Changed installation to include forking the git repo.)
 
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[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]
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For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]
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For a demo of Rachel's capabilities, watch [http://youtu.be/moVVC-GODzQ The Rachel Video on Youtube], or [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html Download the mp4 (9MB)].
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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 it has ''not'' been tested under Windows.
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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.  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.  A Windows version is not planned.
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A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines.  The release-candidate version, expected in the September 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.   
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A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines.  Versions 1.* have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations.   
[[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 of matrix elements.  For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values.  This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.
[[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 of matrix elements.  For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values.  This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.
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==How to get the Rachel package==
==How to get the Rachel package==
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Release version 1.1 is now available.  This version does not read beta-version files, but level schemes and matrices can be ported following the instructions in the 2012 version of the Gosia manual.  Refer to the [[gui_release_notes | release notes]] for the change in this version and known issues.
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Get the latest release version from the [[Gosia#Downloads | Downloads section on the Main Page]].
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[http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.0.tar Rachel 1.0 download]
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==Version notes==
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The [[Gui_release_notes | version notes page]] gives a history of Rachel updates. Known issues are given for each version, as well as the current version.
==Installation notes==
==Installation notes==
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===General===
===General===
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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.)
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A script was added by Mitch Allmond that compiles and sets up Rachel, Gosia and Elast in one step.  First, un-tar the distribution, or pull the git repo from the [[Gosia#Downloads | Downloads section on the Main Page]].  Please fork it and make pull requests if you have anything to contribute.
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<pre>
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% tar -xvf rachel_distribution_1.3.0.tar
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</pre>
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or similar for the correct version number.  Move into the new Rachel directory and run compile-all.sh:
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<pre>
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% cd rachel_distribution_1.3.0
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% ./compile-all.sh
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</pre>
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You will be prompted if any previous setup information needs to be overwritten.
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Rachel has been installed successfully on a number of Linux and OS X systems.  Most problems are related to the level scheme graphics.  Refer to [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends] for remedies.  You can view or submit detailed installation notes for any particular operating system.  (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:
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:
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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.
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.
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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.
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When changing to version 1.0 or later, 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. Subsequent versions will have the automatic upgrading reinstated.
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==Graphics Issues==
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If you do not see a level scheme diagram after loading a level scheme or a saved session, click "Examine fig. window" once.  The level scheme should then appear.
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If it does not, or if the level scheme window buttons (zoom, pan, etc.) do not work, you may need to change the graphics back-end.  The matplotlib graphics library used for the level scheme and particle detector layout comes with several choices of back-ends. 
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*On OS X machines, "macosx" may work best.
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*On Ubuntu, GTKAgg works best, but the user must click "Examine fig. window" 'once' after loading a level scheme or saved session.
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The back-end is in the matplotlibrc file in the .matplotlib directory, or will be, after you start Rachel for the first time.
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<pre>
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hayes@Sobchak:~$ cd .matplotlib/
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hayes@Sobchak:~/.matplotlib$ ll
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total 116K
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drwxr-xr-x  3 hayes hayes 4.0K Nov  5 12:30 ./
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drwxr-xr-x 125 hayes hayes  12K Nov  5 12:53 ../
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-rw-r--r--  1 hayes hayes  92K Oct 27 13:13 fontList.cache
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-rw-r--r--  1 hayes hayes  17 Aug 19 02:09 matplotlibrc
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drwxrwxr-x  2 hayes hayes 4.0K Oct 27 13:13 tex.cache/
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hayes@Sobchak:~/.matplotlib$ cat matplotlibrc
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backend : GTKAgg
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hayes@Sobchak:~/.matplotlib$
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</pre>
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Change the backend line as desired.  The choices are found
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In the release versions, automatic upgrading of saved sessions will be reinstated.
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==Capabilities of version 1==
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==Beta version capabilities==
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Note that there are major simplifications in the Ge detector array setup and data loading.
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* Human-readable data files that are robust for changes in the experimental setup and level scheme
* Azimuthally symmetric particle detection
* Azimuthally symmetric particle detection
* Partitioning particle-detector data by azimuthal angle
* Partitioning particle-detector data by azimuthal angle
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* Normal or inverse kinematics experiments
* Normal or inverse kinematics experiments
* A user-expandable library of standard Ge crystals e.g. Gammasphere
* A user-expandable library of standard Ge crystals e.g. Gammasphere
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* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)
* Data from summed 4pi arrays
* Data from summed 4pi arrays
* Efficiency-corrected gamma-ray data only
* Efficiency-corrected gamma-ray data only
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* Accuracy testing to determine if Gosia will be appropriate for a planned experiment
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment
* Fitting and correlated error estimations
* Fitting and correlated error estimations
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* Reading level schemes and gamma-ray data from Radware AGS files and including
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* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including
** Branching ratio data
** Branching ratio data
** Previously measured EM matrix elements, including the measured phases
** Previously measured EM matrix elements, including the measured phases
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* 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.]]
* 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
* Automated generation of stopping power and internal conversion input for Gosia
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* Push-button controls
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* Push-button controls, optional pop-up guidance and guided prompts
* A searchable help function
* A searchable help function
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* Saving the entire session to a file
 
* Undo/Redo of most functions and crash recovery
* Undo/Redo of most functions and crash recovery
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===Planned upgrades===
===Planned upgrades===
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There are a number of planned upgrades, ''some'' of which will be incorporated in the first [[rachel_release_candidate | release candidate] version.  The upgrade plan and priorities will be changed based on user feedback and bug reports.   
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There are a number of planned upgrades, many of which have already been added to versions 1.0 and later.  The upgrade plan and priorities will be changed based on user feedback and bug reports.   
# More accurate stopping power calculations for low-Z beams.
# More accurate stopping power calculations for low-Z beams.
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[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0.  These will be much shorter and more focused than the old videos.
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0.  These will be much shorter and more focused than the old videos.
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You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes.  General procedures are similar.
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You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes.  General procedures are similar.  These old videos contain more topics per video, so some are quite long.
===The manual===
===The manual===
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===Experiment planning and accuracy testing tools===
===Experiment planning and accuracy testing tools===
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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:
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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 looks like the following:
<pre>
<pre>
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Experiment 1 Detector  2
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Experiment 1
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                                      Raw                    Count  Gamma  **Est. intr.  "Corrected"               
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Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.
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Band       Spin   Band   Spin    *Counts        Error   Rate(Hz)  E(keV)    effic.(1)   ***Counts        Error     
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Detector 1
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----------------------------------------------------------------------------------------------------------------
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Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.
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    gsb   18.0    gsb    16.0        864          29 0.002001    686.0       0.271        3266          198
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This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia.     
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     gsb    16.0     gsb   14.0     21056          145 0.048741    658.7       0.277        78074        3941
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      Transition            |  Gammas incident      |                    Fraction of |        Observed Counts       
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     gsb    14.0     gsb    12.0    400895          633  0.927999    626.6       0.284     1360201        68044
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                              |  on Ge detectors      | Gamma               Incident    |                               
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    gsb   12.0     gsb    10.0    5914064        2432 13.689963    579.7        0.296     21145020      1057287
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  Initial        Final        |                      | Energy **Detector  Gammas      |                               
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    gsb    10.0     gsb    8.0  65755367        8109 152.21149    512.4       0.315    211214415    10560753
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    Band Spin     Band Spin   | Counts   *Error     | (keV)   Efficiency  Detected   | Rate(Hz)   Counts  ***Error     
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    gsb     8.0     gsb    6.0 527950313        22977 1222.1072    426.3        0.343  1470121661     73506111
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-------------------------------------------------------------------------------------------------------------------------
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    gsb    6.0     gsb    4.0 2866371774        53539 6635.1198    325.6        0.379  7435917854    371795919
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    gsb 1.5      gsb  0.5     4.662e+06 2.332e+05    100.0 0.00049     0.09962      1.075e+00  4.644e+05  6.815e+02
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    gsb    4.0    gsb    2.0 8174712130       90414 18922.944    213.5       0.382 21045773464  1052288699
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    gsb 2.5     gsb 0.5    1.570e+07  7.848e+05     200.0 0.00179     0.36853      1.339e+01  5.784e+06  2.405e+03
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    gsb    2.0    gsb    0.0  706191594        26574 1634.7027     93.3       0.078  8631491935    431574719
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       a  2.5     gsb 0.5     1.079e+04  5.647e+02    250.0.00189     0.38907      9.719e-03  4.199e+03  6.480e+01
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      a  2.5      gsb 1.5     9.816e+02 7.705e+01    150.0.00135     0.27823      6.322e-04  2.731e+02  1.653e+01
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      a  2.5       b  3.5     4.689e+05 2.376e+04      75.0  0.00015     0.0312        3.387e-02  1.463e+04  1.210e+02
</pre>
</pre>
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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.
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The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user.  The "Detector Efficiency" <math>\epsilon</math> is the usual definition.  Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.

Latest revision as of 13:07, 17 May 2013

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