PMF Evaluation Panel v2.03
	Nov. 9, 2009

Update since PMF-AMS Analysis v2.02
Notes by Ingrid Ulbrich  8th Nov. 2009

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IMPORTANT CHANGES YOU SHOULD KNOW ABOUT
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* No changes should interfere with old experiments.  To upgrade, replace old .ipfs with new .ipfs and remake the main panel from the PMF pull-down menu. 

* Error preparation functions are now available in functions
   * pmf_ErrPrep_Q-AMS_OneIonEquiv_v2.3.ipf  or  pmf_ErrPrep_ToF-AMS_OneIonEquiv_v2.3.ipf
   * pmf_ErrPrep_AMS_v2_3.ipf

* Convergence criteria for the PMF calculation can be set proportional to Q/Qexp using flags in the header of PMF_Execution_v2.03.ipf

* Default SEED and FPEAK can be changed in the headers of PMF_Execution_v2.03.ipf

* Alternate PMF executable file can be selected in the headers of PMF_Execution_v2.03.ipf
   * Download the updated version of mypmft.ini

* Deleting NaNs from matrices has been made much faster.  Changes made are backwards compatible with previous versions.

* A new option has been added for viewing factor time series overlayed and mass spectra separately.  Use Select Factor = -2.

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DETAILED CHANGES
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----- PMF_Execution_v2.03.ipf -----

* Significantly improved the efficiency of pmf_ams_DeleteNaNs_mxWvs.  NaNsLists are now stored as 2D NaNsWvs.
   * Created pmf_ams_NaNsList_2_NaNsWv for backward compatibility with old NaNsLists
   * Updated all pmf_ams_DeleteNaNs and pmf_ams_insertNaNs functions to use NaNsWvs

*Changed the calculation of Qexp (for Qmx2d and Chi2NoDownwtMx2d) to be correct (mn-p(m+n))
     (for Resid_as_TseriesFactors) to be correct (m-p) or (n-p) and for model error to be applied in these calcs

*  Correctly applied user-specified ModelError to calculation of Q-contribution time series/mass spectrum

* Fixed SEED when running in Exploration Mode and changing FPEAK

* Fixed problems with paths for Vista machines

* Added a new strconstant line for choosing PMF executable file as pmf2wopt.exe; requires change to mypmft.ini!

* Added constants DEFAULT_SEED and DEFAULT_FPEAK so that one can run e.g., a range of fpeaks at DEFAULT_SEED=2 

* If PMF executable not found in PMF path, warning text is red

* In View PMF Results Selection panel, pulldown menus for row and column waves only include waves with dimensions that match matrix size

* Implemented James' bug fixes for bootstrap factor reordering

* In Bootstrapping, if noNaNs_amus and noNaNs_t_series do not exist for plotting average factors, user is prompted for waves to use

* In Bootstrapping, correlations between bootstrap cases and base case are made with uncentered correlation (instead of Pearson R) at recommendation of James Allan


----- PMF_ViewResults_v2.03.ipf -----

* Save Sol'n Space Waves button now creates subfolder Diurnals and save factor, total Resid, Q/Qexp diurnals

* for Factor Profile plots, changed left axes to cross bottom at 0 instead of 10, narrowed bottom axis
   * made a global variable minY_Log_Profiles which the user can set with a min Y axis in log view;  max in log view now = 1

* for Total Residual plots, changed left axes to cross bottom at left edge, narrowed bottom axis, changed axis label for Q-contribution to include /Qexp

* for Credits, updated paper info to ACP 2009 version
   * added button to link to PMF-AMS Analysis wiki

* for plots of species TS, total signal TS, resid TS, resid ratio TS, both axes of RR plot, make y-axis go from 0 or full scale if min values is negative

* Factor Profile plots, y-axes cross the left axis at 0 (was at 10, a problem for non-AMS users who might start the indexes for their data at 0.

* for species reconstruction and total reconstruction plots, put reconstructed trace on top of measured data trace 

* for TS overlay, made new option Select Factor = -2: TSS are overlayed, MS are plotted separately


----- PMF_Scatter_v2.03.ipf -----
* Updated scat_make_noNaNs_ms_OR_ts_DF to use NaNsWvs instead of NaNsLists.  For compatibility with previous versions, if no NaNsWv is found, looks for NaNsList and converts it to a NaNsWv