High ResolutionToF-AMS Analysis Toolkit v1.10H 2011 Spring Users Meeting Release Update since ToF-AMS HR Analysis Toolkit v1.10C Notes by Donna Sueper 2 Jun 2011 * Fixed small display bug with HR_peakHeights_gr. * Removed traces of HR_frag_pCO2 - this is now replaces with more sensible HR_frag_organic[{CO2}] notation. * Fixed other smallish bugs. Update since ToF-AMS HR Analysis Toolkit v1.10B Notes by Donna Sueper 14 Apr 2011 * Fixed smallish non-niceties so that now families can be redefined after pika sticks have been generated. This means that any family and HR species can be modified quickly, easily. * Fixed some isotopic abundance values so that all are consistent. The only HR ion isotopic abundance that changed significantly are the Br ions. * Fixed a small bug the incorrectly displayed peak width values in the peak shape tab as zeros. * Changed the default left & right side peak shape parameters. * Changed the default list of ions to fit at 28 and 32 so that only the major air peak is fit. * Removed the use of PCO2 (particulate CO2, not gas phase CO2) from the HR frag table, as it was too confusing. Update since ToF-AMS HR Analysis Toolkit v1.10 Notes by Donna Sueper 19 Mar 2011 * Enabled the ability to do time-varying peak width. * Fixed various small bugs, including HR sticks that weren't stacked correctly in the HR_peakHeights_gr when an average of a todo was selected for one run. Update since ToF-AMS HR Analysis Toolkit v1.09G Notes by Donna Sueper 24 Feb 2011 * Fixed a bug that had to do with ion counting errors. Previously calculated errors were incorrect. If used in a PMF analysis, the higher masses were given an incorretly low error value. * Ion Counting errors now include baseline errors. The name of the data set is now HRTotalOMinusCIonCountErr (the bad, old errors were named HROMinusCIonCountErr). * There is a new button in step 4 for the calculation of these new errors. Users do not have to recalculate their HR sticks, but they must have already recalculated their unit resolution sticks with the baseline option checked. * Added functionality to the batch table to allow Org43, and OrgCO2 entries. Users are encouraged to follow these examples to create new batch entries is needed. * Removed old, obsolete options and cleaned up some tabs. * Added functionality in the HR ion query tab of the mass calculator to find and optionally select/deselect to fit related HR ions. * Added an option to create an itx of all pertinent waves for a PMF analysis. ------- PK_elemAnal.ipf------- Modified Functions: * HR_calc_EAMassSpec Now returns a string of the waves that were created. * HR_plot_EAAvgMassSpec Moved the normalization code elsewhere for modularity. ------- PK_Backbone.ipf------- New Functions: * PK_TotalCountingErrors Now includes unit resolution baseline sticksin the calculation of errors. * PK_getHRPeakWidths A helper function that puts the peak width parameter values used in the HR fits of a todo wave. * HR_ExpandUMR2HR A helper function that takes 2d matricies where the columns represent unit res and 'expands' them so that the columns match the list of HR ions that were fit for a todo wave. * gen_TextWavesTheSame A general purpose function that checks to see that 2 text waves have the same values. * HR_butt_totalIonCountErr A new button in the HR fit many runs tab that allows the correct calculation of the HR ion counting errors. * PK_TotalCountErr_CheckFor Checks to see if the squirrel baseline sticks have been calculated - if not calculate them and calculate the total ion counting error. * sq_UMRBaselineSticks A method for calculating the squirrel baseline stick values if they haven't already been found. Modified Functions: * HR_MakeRawSpectra Removed the option for uses to do HR on raw spectra without the baseline removed. * HR_CalculateSticksSQ_prep Added HR sticks for the pika (found sticks) to sit atop of the baseline. * HR_CalculateSticksSQ Changed the code so that we never calculate or use 'pete's' baselines, and we calculate the peak heights for squirrel baseline sticks. * HR_CalcSticksOneRun Removed the option for uses to do HR on raw spectra without the baseline removed. * HR_SticksOneRun_prep Removed the option for uses to do HR on raw spectra without the baseline removed. * PK_CreateElementWaves Expanded to include elemental isotopic parents for calculation. * PK_checkMassWithChemFormula Minor bug fix for the wave inVorWnameTemp * PK_duplicate_FitTodoWaves Now also saves which isotopes were constrained. * PK_FindHRResultsWavesFitTodo Now also retrieves which isotopes were constrained. * PK_CopyHRIonWavesFitTodo Now also saves which isotopes were constrained. ------- PK_frag.ipf------- New Functions: * pk_ConvertPartialFrags Added code for the conversion of 'partial frags' like HROrg44, etc. Modified Functions: * HR_generateFinalFrags Modified code so that a message about ion not fit is not printed so often. * HR_fragList_pass Now calls pk_ConvertPartialFrags. * HR_getParamStr Now handles partial frags like HROrg44 etc. * HR_fragTable Now handles partial frags like HROrg44 etc. * HR_SQvsPK_calcWaves Adds a sanity check so that it never normalizes spectra. * HR_populate_SQvsPkMSCorrGraph Fixed bug where old code a one to one line many times. * HR_populate_SQvsPkTSCorrGraph Fixed bug where old code a one to one line many times. * gen_removeTracesFromGraph Got rid of old kludge for removing multiple traces. ------- PK_gr_table.ipf------- New Functions: * HR_DisplayHRFailWins New function for making a table of runs and m/zs that didn't converge to a fit. * PK_FindMassFromFormula Given a string such as "C3H6O2" determines the mass * HR_butt_FindIsoDiscrepancy Checks the isotopic ratio in the table with a calculated value. * PK_ProbIsoTable Displays a table of HR ions whose isotopic ratio in the table is different from that calculated. * PK_ProbMassTable Displays a table of all the HR ions for which the mass in the table is different from that calculated. * HR_butt_TableHRIonsTodoFit Button for displayin the ions that were fit in a todo wave. * HR_butt_HRSpeciesFitTodoTable Button for displayin the ions that were fit and those identified in a species wave in a todo wave. * HR_GenerateFamilyExceptionLists Returns two strings exceptionFamilyList, exceptionMassList from the HR batch table. * HR_returnGrouping For a given fragment, return the family the algorithm wants to put it in * HR_CalcPlot_MSAvgSpeciesGrouped Calls HR_Calc_MSAvgSpeciesGrouped and HR_plot_MSAvgSpeciesGrouped * HR_Calc_MSAvgSpeciesGrouped For a given species, calculates the average mass spectra, then groups the HR ions into family-like categories. * HR_plot_MSAvgSpeciesGrouped Plots the results of HR_Calc_MSAvgSpeciesGrouped * UM_SumHRSpeciestoGroupsUMR When the user wants a family grouped species, allows for summing to UMR * HR_CalcPlot_5PanelHRSpecies Calls HR_Calc_5PanelHRSpecies and HR_plot_5PanelHRSpecies * HR_Calc_5PanelHRSpecies Calcs the 5 axis plot but only with fitted HR ions, not HR species * HR_plot_5PanelHRSpecies Plots the results of HR_Calc_5PanelHRSpecies. * sq_NormalizeSpectra Users can now normalize spectra. * HR_massCalcGlobals Separate function for the big & improved HR ion calculator. * HR_findIsotopesToFit Finds isotopic children from parents that have a minimum isotopic abundance. * HR_oneHRIonElementalComp Breaks down an HR ion name ("C4H3O2") and sets several waves for later use * HR_findIsotopes_Tolerance Using waves set in HR_oneHRIonElementalComp, finds isotopic children. * HR_extractHRIonNamePart Returns part of HRIonName with element X removed. * sq_inTextWave1InTextWave2 Given two text waves returns a wave of indicies where one is in the other. * HR_populate_IsotopChildrenTable Puts waves in iso. children table. * HR_findIsotopAbund For a given HRIonStr, returns an abundance based on the ratio of it's parent * HR_findIsotopParent For a given HRIonStr, returns it's isotopic parent. * HR_addWavesToAll Adds HR ions in certain waves to the *_all waves. *HR_change2FitHRIon For a given wave of HR ions, changes the mask wave to fit. * HR_butt_AddListToAll Button for HR_addWavesToAll. * HR_butt_FindIsoChildrenForAll Button on mass calculator for finding all isotopic children. * HR_IsotopeSubset Code used to reduce the list of displayed isotopic children based on inclusion into ions that were chosen, etc. * sq_KillWavesInList Generic function for killing all waves in a given list. * HR_getAllIsotopicChildren Does the work of HR_butt_FindIsoChildrenForAll * gen_partialstringfromList Used for the management of many family waves, such as when we perform a family-colored avg mass spec. HR_butt_ShowPkHtsGr * New button for bringing to the front the Peak Heights graph. * HR_SqVsPk_OneRun_Panel A modified version of the SQ vs PK panel for todos. Shows spectra and correlations. * HR_plotSqVsPk1RunGrs Handles the 4 plots for the SQ vs Pk one run panel. * SqVsPkOneRunTabProc Tab function for the SQ_VS_PK for one run. * HR_populate_SQvsPk1MSGraph For the SQ vs Pk one run panel. * HR_populate_SQvsPk1MSCorrGraph For the SQ vs Pk one run panel. * HR_SqvsPk_CheckProc_leftAxisLog For the SQ vs Pk one run panel. * HR_SqvsPk_CheckProc_allAxisLog For the SQ vs Pk one run panel. * gen_RemoveNaNs Generic procedure for getting rid of nans in a 1D wave. * HR_FindRelatedHRIonSuffix Finds all HR ions that are related by a C, CH, or CH2 fragment for a given HR ion. * HR_MassCalcQueryHRionTab Tab function for the new and improved mass calculator. * HR_populate_QueryTable Makes table for mass calculator. * HR_ChemFormFind Finds HR ions that have x many Cs, y many Os, etc. * HR_RemoveHRIonsOfNumElem generic function for finding elements such as C but not Cu, Ca, etc. * HR_QueryCheckType Checkbox procedure for indicating what kind of HR ion search to perform. * HR_checkProc_massCalc Checkbox control for indicating what subset of HR ions to search for. * gen_TextWave2List Returns a list of elements in a text wave. * gen_List2textWave Overwrites a wave with the items in a list. * gen_SameInBothLists Returns a string with common list entries. * gen_InListANotListB Obvious. * HR_butt_SetHRChoices2Todo New button that allows a user to 'reset' the list of ions to choose from a list of HR ions that were fit from todo wave. * HR_butt_QueryHRionChemForm Button on mass calculator. * HR_butt_Add2ListOrChange2Fit Button on mass calculator. Modified Functions: *HR_getHRwin Changed to also display squirrel panel so no error is generated when the pika panel sets todo wave. * HR_globals Various new global strings, variables. * HR_Analysis_Panel_Create Tried to declutter. Big change to Ion Groups tab. * HR_panel_credits Changed affiliations for Pete, Allison. * HR_butt_CreditsURLPetePaper Changed url to pdf. * HR_butt_CreditsURLAllison1Paper Changed url to pdf. * HR_butt_CreditsURLAllison2Paper Changed url to pdf. * HR_butt_CreateMSDiffp Removed the option of using raw spectra without the baseline removed. * HR_butt_CalcSticksForThisRun Now calculated Pika baseline peak heights for use in display. * HR_butt_CalcExactMassSticksTodo Removed the option of using raw spectra without the baseline removed. * HR_calc_TSeriesMSMatricies Added code for the creation of a PMF itx for export. * HR_calc_5PanelSummary Added the ability to normalize spectra. * HR_plot_5PanelSummary Added awareness of normalized spectra. * HR_plotPeakHeightsOneRun Added pika baselin peak heights. Got rid of older bits. * HR_addThisMass Now returns a string of the newly added mass. Fixed a bug whereby HR name got capitalized. * HR_butt_AddThisMass Button for HR_addThisMass on PeakHeights_gr * HR_butt_AddThisHRIon Button in mass calculator panel for adding an HR ion to the all wave. * HR_reCenterAmu Got rid of mass spectra insets checkbox. * HR_calcGausFitWaves Pika peak heights not sit on top of the pika baseline peak heights. * HR_butt_setResultsList Small bug fix for correctly clearing HR ions list. * HR_populate_IsotopesTable Fixed bug whereby users weren't allow to not constrain an isotope. * HR_tabProc Got rid of APES pic because it was too squished. Boo hoo. * HR_butt_ViewHRIntegerSpectra Button for HR_SqVsPk_OneRun_Panel() * HR_populate_ChemFormTable For the mass calculator panel. * UMR_plot5GraphSummary Changed axis label from Inorganic to hopefully avoid folks from thinking the frag table has been applied. * HR_butt_MakeExactMassWaves A function that it calls, UM_generateAxByMaskWaves, now requires a wave. * HR_ck_ChemFormFind Updated options for finding subset of ion that were chosen, etc. * HR_plotAllHRGrpPlots All HR ion table now takes upmost of the space on the Ion Groups tab. * HR_populate_ChosenMassesTableX A function that it calls, UM_generateAxByMaskWaves, now requires a wave. * HR_butt_MS_Calc Added an option for normalizing spectra. * PK_exportForDataBase Adds minimum ion error to other waves that were saved. * HR_butt_HRFitFailTodo Fixed bugs whereby it only checked the Open data set, not closed also. * HR_butt_CalcMassOneHRIon Really overhauled the functionality of the mass calculator. * HR_butt_massCheckAllIons Really overhauled the functionality of the mass calculator. * HR_butt_IonMassCalculator Really overhauled the functionality of the mass calculator. ------- PK_PartitionAvg------- No change. ------- PK_peakShape------- Modified Functions: * GF_butt_GFsTodo No longer allows using raw spectra without the baseline removed. * PW_NewGlobals No longer allows using raw spectra without the baseline removed. * PW_PeakWidthShapePanel Fixed a typo. * PW_butt_showPWOneRun No longer allows using raw spectra without the baseline removed. * PS_butt_PeakShapeAllMassTodo Added a sanity check for bad m/z parameters. * PS_PeakShapeAllMassTodo No longer allows using raw spectra without the baseline removed. ------- PK_UnitMassSpec ------- Modified Functions: * UM_DoAllCalcsForIntMassSpectrum A function that it calls, UM_generateAxByMaskWaves, now requires a wave. * UM_GenerateAxByMaskWaves Now requires that the wave of HR ion names be given as a parameter. Update since ToF-AMS HR Analysis Toolkit v1.09G Notes by Donna Sueper 14 Jan 2011 * smallish bug fixes for peak heights panel. Updated All mass list values and added new entries in the HRfrag table for CO2. Added new functionality for mass calculator and HR frag waves. Update since ToF-AMS HR Analysis Toolkit v1.09F Notes by Donna Sueper 22 Nov 2010 * Updated squirrel panel ipf to 1.50F. Updated the element ion waves, the mass calculator, the HR Results tab, HRfrag waves to include j13CO. Notes by Donna Sueper 15 Sept 2010 ----------Begin In a Nutshell---------- * Rearranged, grouped, renamed controls in HR Results tab * Modified code such that if raw spectra does not exist and is detected during an HR pika fit of a todo wave, an error is printed to the history instead of aborting mid-execution. * Upgraded SQ_AMSPanel ipf to 1.50A due to a bug which prevented the calcs of average raw spectra that crept in in 1.50 * Very slight modification of HR_frag_pCO2 entries: 0.01112*HR_frag_pco2[{CO2}] is now 0.01081570*HR_frag_pco2[{CO2}] 0.004*HR_frag_pco2[{CO2}] is now 0.00410998*HR_frag_pco2[{CO2}] Update since ToF-AMS HR Analysis Toolkit v1.09 Notes by Donna Sueper 8 Sept 2010 * Fixed a few small bugs discovered at the users mtg. * Added a family-colored UMR single HR species button (useful for the HRorg species) High ResolutionToF-AMS Analysis Toolkit v1.09 (2010 Users Meeting Release) Update since ToF-AMS HR Analysis Toolkit v1.08C Notes by Donna Sueper 16 Aug 2010 ----------Begin In a Nutshell---------- * Added the ability to retain a copy of all the HR ions that were fit for a todo wave. This means that one can 'play', can edit the list of ions to fit for a single spectra (step 4) and not have to worry about having to redo the time-consuming step of fitting all HR ions again for a todo. * Added the ability to find and check the exact mass values of any or all HR ions from their formula. * Added the ability to export the root:HR:ExactMassWave_all etc waves from an experiment for easy import into another experiment (to assure that one is fitting the same set of HR ions). * The list of ions to fit be default has changed such that only N2 is fit at 28, only O2 is fit at 32. Added HR ions CH5O,CHO2, j13CC2H7O2 to the list of all ions. ------- PK_Backbone_1_09.ipf------- New Functions: * PK_CreateElementWaves Uses waves compiled by Qi Chen to create elemental mass waves. These waves are used to caluclate exact mass values from their (pika-formatted) formulas. * PK_recalc_IonMasses Does the work of HR_butt_massCheckAllIons. Recalculates the masses of all the ions in the "ExactMassText_all" waves. Warnings in the history appear when the mass calculated from its formula is different from the given mass. * PK_checkMassWithChemFormula Does the work of HR_butt_massCheckAllIons * PK_duplicate_FitTodoWaves Makes copies of important waves after the HR fitting of a todo wave has been completed. Duplicated waves are in the HR_Sticks folder and have a _FitTodo suffix. * PK_FindHRResultsWavesFitTodo Given a todo wave, find the copies of the ExactMassText, etc waves that were copied from a previous HR fit of a todo wave. * PK_IndexHRResultsWavesFitTodo() Create and saves root:index:HRstick_series, root:index:HRstick_seriesKey waves which keep track of which runs were fit with which todo waves. * PK_WavesForHRResults When the user requests any kind of HR product, we need to copy the ExactMassWave, etc waves last used for the fit for this todo wave to their proper place in the HR_sticks folder. * PK_CopyHRIonWavesFitTodo Does the work of making copies of the HR ions that were fit and to put the copies in folder were they can be retrieved later, as in a call from PK_WavesForHRResults. Modified Functions: * PK_MS_concentration Replaced waves with their _fitTodo counterparts where needed. * HR_CalculateSticksSQ_prep Redid the sequence of the creation of some waves to hopefully be more streamlined. Added a parameter to count the number of times a peak fit failed. * HR_CalculateSticksSQ Added a parameter to count the number of times a peak fit failed. Saves FailedFit matrix to hdf. * HR_SticksOneRun_prep Moved the creation of UM_make3DColorWave and OneRunDisplayVertGrid to this function because it makes more sense. * PK_GetErrors Replaced waves with their _fitTodo counterparts where needed. * PK_CountingErrors New scheme finds and saves counting errors for Open, Closed, and OMinusC data sets. ------- PK_elemAnal_1_09.ipf------- No changes. ------- PK_frag_1_09.ipf------- Modified Functions: * HR_generateFinalFrags Replaced waves with their _fitTodo counterparts where needed. * HR_createTempSpeciesMask Replaced waves with their _fitTodo counterparts where needed. Made root:Int_sticks:mask_family_FitTodoWaves. * HR_getListNewHRAlgebraMass Replaced waves with their _fitTodo counterparts where needed. * HR_getParamStr Tidied up a bit. Fixed a non-existed fragStr value with a default of 1. * HR_CheckListForHRSpecies Replaced waves with their _fitTodo counterparts where needed. ------- PK_gr_table_1_09.ipf------- Deleted Functions: * HR_butt_ChosenMassesTable This code was moved to the Chose Ions tab in 1.07/1.08. New Functions: * HR_addThisMass Function called by both HR_butt_AddThisMass (called from the HR_PeakHeights_gr) and the HR_butt_AddThisHRIon (called from the main panel). * HR_butt_AddThisHRIon New button in HR Ion Groups tab that adds a new HR ion (its chemical formula and it's mass) that was previously calculated in the panel to the ExactMassWave_all etc waves. Similar to the functionality in the HR_PeakHeights_gr but only from the main panel. * SticksGr_check_showResidErrors New checkbox in HR_PeakHeights_gr to optionally show the old ReisdualFit errors. * HR_ck_FitFailOption Radio buttons in the HRFits for Many Runs for selecting Open, Closed Diff pika fit error image plot. * HR_butt_ChosenMassFitTodo New function for displaying the waves of HR ions fit the last time a todo wave was HR fitted. * HR_populate_ChosenMassesTableX New function that does the work of HR_butt_ChosenMassFitTodo and the other button for the currently chosen list of ions (for one spectra) * pk_butt_ExportExactMassAll New button on panel that allows one to easily export the waves root:HR:ExactMassWave_all AND the integration mask waves into an itx (for possible later importing into another experiment). * HR_butt_HRFitFailTodo New button on panel allows user to create a table of the last todo wave and an image plot of all the places where the HR fit failed (in m/z and run number dimensions). * HR_ButtonCalcMassOneHRIon New button from the main HR panel that allows a user to calculate the mass from a pika formatted chemical formula. * HR_butt_massCheckAllIons New button from the main HR panel that allows a user to calculate the mass from all the HR ions in the "ExactMassText_all" wave. * HR_butt_IonMassCalculator Displays the HR ion mass calculator tool. * HR_butt_TableHRIonsTodoFit For any todo wave, finds the copy of the "root:HR_sticks:HRIonWaveCopies: folder containing the exactmassText_fitTodo, etc waves. HR_butt_HRSpeciesFitTodoTable Displays the list of ions that go in to the species calculations (which may include some ions that were not fit, such as CO). Modified Functions: * HR_globals Added a few new global strings and variables. Added creation of ElementalIon waves. * HR_MakeIntegrationMaskWave Removed some code that sorted waves unneccessarily and moved code that dealt with OneRunDisplayVertGrid waves to a more sensible function. * HR_Analysis_Panel_Create Added section detailing info about last time a todo wave was fit. * HR_SetVar_RunModeStr Added code to automatically choose the one run options (instead of an average of a todo wave) when a user enters a run number. * HR_butt_CalcSticksForThisRun Reorganized to streamline things. Added code to keep track of fit fails. Added code to find, save pika counting errors for open, closed diff. * HR_butt_CalcExactMassSticksTodo Added code to keep track of fit fails. Added code to duplicate current ExactMassWave etc and append a _fitTodo suffix, and basic info about finished todo wave fit. * HR_plot_MSAvg Replaced waves with their _fitTodo counterparts where needed. * HR_calc_TSeriesMSMatricies Fixed error about product types in 1.08C * HR_calc_5PanelSummary Fixed bug where the waves incorrectly retained a _temp suffix. * HR_plot_5PanelSummary Replaced waves with their _fitTodo counterparts where needed. * HR_plotPeakHeightsOneRun Added a checkbox fo optionally displayiing the peak fit residual errors. * HR_butt_AddThisMass Significantly overhauled to streamline the addition of HR ions either through the main panel or the HR_PeakHeights_gr. * HR_butt_ResidvsTime Added a modifyGraph gaps command *UMR_plot5GraphSummary Changed bottom m/z axis to automatically go from 100 to 120 m/z. * pk_butt_5FamilyMSGraph In the plotting of Doug's 5 axis HR mass spec for one run, I removed the residual noise error bars - they are not that helpful. * HR_butt_MakeExactMassWaves Modified this very important function to reduce duplication and streamline things. * HR_populate_ChosenMassesTable Now calls HR_populate_ChosenMassesTableX("") which can be use for _fitTodo chosen mass waves. *HR_MSCalc_Diurnals Changed the destination waves of the HR_calc_MSVsTime function to have a temporary "_temp" suffix so early plots, waves would not be inadvertantly overwritten. * HR_MSplot_DiurnalBoxPlot Bottom axis is now correctly labeled diurnal hour. * PK_exportSaveFileDB() Modified so that signal descriptor is appended to wave names (i.e. MSSD_*_hexane. * PK_exportForDataBase() Modified so that signal descriptor is appended to wave names (i.e. MSSD_*_hexane. ------- PK_partitionAvg_1_09.ipf------- No changes. ------- PK_peakShape_1_09.ipf------- * GF_makeMassWaves Changed in 1.08D so that if a user edits the GF table, the waves are not overwritten (Puneet's issue). * PW_PeakWidthShapePanel Changed the wording in a button from "Update plot" to "Recreate plot" *PS_createGlobals Changed defaults for PS_enforceMonotonicity and PS_enforceNotGTGauss to USE * PS_butt_updatePSGraph Tweaked so that this is updated nicely with hiding/showing items in panel. ------- PK_UnitMassSpec_1_09.ipf------- Deleted Functions: * UM_makeChosenMassFamText code is now folded into UM_GenerateAxByMaskWaves() Modified Functions: * UM_DoAllCalcsForIntMassSpectrum Added UM_DoAllCalcsForIntMSOMinusC() at the end * UM_GenerateAxByMaskWaves Added code from UM_makeChosenMassFamText * UM_MakeIntResolutionSticks Added code to prevent errors if upgrading from 1.06 Removed unneccessary call to HR_MakeHRFamilyBatch * HR_SortIsotopicValues The function call to HR_MakeIsotopePairings was changed slightly. * HR_MakeIsotopePairings Changed function to work on entire wave instead of one chemical formula at a time for efficiency. * UM_SumHRtoUMR Replaced waves with their _fitTodo counterparts where needed. High ResolutionToF-AMS Analysis Toolkit v1.08C (2010 Clinic Release) Update since ToF-AMS HR Analysis Toolkit v1.08A Notes by Donna Sueper 24 Mar 2010 Small bugs were fixed. * The isotopic abundances of j13CO2 and Cj18OO for HR_frag_pCO2 were incorrect by a very small amount. Old values were: HR_frag_pCO2[j13CO2] = 0.01112 // correct value is 0.01081570 HR_frag_pCO2[Cj18OO] = 0.004 // correct value is 0.00410998 * The formula for the Ion Counting Statistics error had an error - the duty cycle correction was inadvertantly applied twice. It is now fixed. * There was an obvious bug in the code that generated a 2D Time Series Mass Spectra wave. The bad code only filled the HR sticks for one column; this has been fixed. * The squirrel unit resolution frag wave for organics and orgLessPAH were reversed. This has been fixed. Update since ToF-AMS HR Analysis Toolkit v1.08A Notes by Donna Sueper 25 Feb 2010 * A small bug was found that prevented default user defined families from being retained after a Pika fit was found. Update since ToF-AMS HR Analysis Toolkit v1.08 Notes by Donna Sueper 21 Feb 2010 ----------Begin In a Nutshell---------- * New master list of all ions! Now has air 'camels'' and 'dromedaries' that are listed as i.e. N2inV. List also changed the notation for the deuterium ion from D to the more standard j2H. The list of default ions to fit goes out to 115 m/z. Many more isotopes are fit by default (users should still typically constrain them) * Added code to simplify the creation of average spectra for export as .itx files into the HR AMS data base. * Changed the code for averaging in the time dimension. The old code simply used as a time weight the difference in time between consecutive runs. The new code looks to DAQ values of time spent in different modes (open, closed, fast) for a more accurate time weight. * Corrected a small bug having to do with changing duty cycle and peak width vaules for parent and child isotopes. ------- PK_Backbone_1_08.ipf------- * PK_MS_concentration Added waves TimeMSOpen, TimeMSClosed, TimePToFSec, FastModeAvgTimeSec in the declaration for later possible use in the time-weighting functionality. Added timeweight_op flag for new time-weighting functionality. ------- PK_elemAnal_1_08.ipf------- * HR_plot_EAAvgMassSpec Fixed a small bug thathad to do with plotting EA average mass spectra against the correct x-axis (m/z wave) * HR_EAextractIsotopicElements Added the ability to decipher masses with j2H ------- PK_frag_1_08.ipf------- * HR_CheckListForHRSpecies Added the ability to figure out that the 'all' 'species' really means that we want all HR sticks. ------- PK_gr_table_1_08.ipf------- New Functions: *HR_checkDuplicatesAllMasses Checks both the name of new ions and the mass values to ensure there are no duplicates. *pk_exportSaveFileDB Creates the file that users will submit to the database. *pk_exportForDataBase Does any pika averaging in preparation for saving to the database itx file. Modified Functions: * HR_globals Bug fix! Added the creation of root:HR_ms_mats here to avoid future confusion. * HR_Analysis_Panel_Create Added a button for the export into the HR AMS data base. * HR_butt_CalcSticksForThisRun Silly typo - When one did a fit on an average mass spectra, the open m/z parameters were being used to fit the closed! This had no bearing on final pika stick calcs. * HR_calc_MSAvg Added the ability to average all pika sticks (if the HR list is blank, just as in squirrel). * HR_butt_MakeExactMassWaves Added a call to HR_checkDuplicatesAllMasses() * HR_populate_ChosenMassesTable Fixed small bug found by Mike Q - the full path to the wave is needed. *HR_butt_MS_Calc Added the updated time weighting functionality. ------- PK_gr_table_1_08.ipf------- No change. ------- PK_peakShape_1_08.ipf------- No change. ------- PK_UnitMassSpec_1_08.ipf------- UM_GenerateAxByMaskWaves Small bug found by Paul W. Some Si masses were being grouped into the SO family. This has now been fixed. Update since ToF-AMS HR Analysis Toolkit v1.07A Notes by Donna Sueper 6 Nov 2009 * A small bug was found that prevented default Gaussian peak fitting and PW analysis. The HR ion 'OH' has been renamed to 'HO' in the master list of all HR ions. It has been fixed in 1.07B. Update since ToF-AMS HR Analysis Toolkit v1.06 Notes by Donna Sueper 4 Nov 2009 ----------Begin In a Nutshell---------- * Pika is now considered to be fully functional with the addition of Squirrel-like batch and frag tables for HR ions. * In addition, there is now a more clear distinction between HR sticks obtained by fitting the raw difference spectra, and the HR sticks obtained by subtraction the Open HR sticks from the Closed HR sticks. The first data set is called Diff (D), the second is called OMinusC (M). * New HR ion list, compiles by Puneet et al, has been imported. * A new data folder, HR_frag, and default values has been created. * A brand new "all" list of HR ions and a new list of HR ions to be fit by default, thanks to Puneet Chhabra, Delphine Farmer, Qi Chen, and Niall Robinson. There are two new ipfs: **PK_elemAnal_1_07, which took code and functionality from APES version 1.03. ** PK_frag_1_07, which contains code for all the HR batch and frag table items. ------- PK_Backbone_1_07.ipf------- * HR_MakeRawSpectra Now kills MSClosedDup which is no longer needed. * HR_CalculateSticksSQ Added a spectraType flag in the fetch parameter string. Cleaner way of accessing the 4 different stick data sets, Diff, Open, Closed, OMinusC and writing to intermediate files. *pk_CountingErrors Now uses a dest flag in the fetch parameter string. This data set used to be called HRCountErrorDiff, but are now called HROMinusCIonCountErr. * PK_MS_concentration Significant changes to accommodate HR species. ------- PK_gr_table_1_07.ipf ------- New functions: * HR_butt_CreditsURLPetePaper A simple button on the credits tab going to Pete's paper. * HR_butt_CreditsURLAllison1Paper A simple button on the credits tab going to Allison's paper. * HR_butt_CreditsURLAllison2Paper A simple button on the credits tab going to Allison's other paper. * HR_calcPlot_MSVsTime Mirrors the calcPlot function in squirrel for time series calculations. Simply calls HR_calc_MSVsTime and HR_plot_MSVsTime. * HR_calc_MSVsTime Mirrors the calc function in squirrel for time series calculations. * HR_plot_MSVsTime Mirrors the plot function in squirrel for time series calculations. * HR_calcPlot_MSAvg Mirrors the calcPlot function in squirrel for time series calculations, however, we need to be mindful of two other things summing to UMR and possibly different x-axis waves for HR species. Simply calls HR_calc_MSAvg and HR_plot_MSAvg. * HR_calc_MSAvg Mirrors the calc function in squirrel for the average mass calculations, with the possible UMR and HR species complications. * HR_plot_MSAvg Mirrors the plot function in squirrel for the average mass calculations, with the possible UMR and HR species complications. * HR_calc_TSeriesMSMatricies Was called HR_butt_ExportMatrix but now mirrors the squirrel usage. * HR_calcPlot_5PanelSummary Wanted to keep the pattern of small and separate calc and plot functions for major products. * HR_calc_5PanelSummary You can probably guess what this does. * HR_plot_5PanelSummary You can probably guess what this does. * HR_butt_setResultsList A more generic button function for appending familes, HR ions in families, species, etc to the results list. * HR_butt_ConvertedFrags A hidden feature for those wishing to see the squirrel-like converted frag waves. * HR_butt_displayQueryHRIonPanel A small stand-alone panel for identifying HR ions of certain chemical formulas. * HR_ck_ChemFormFind The button in the QueryHRIonPanel that makes things go. * HR_plotAllHRGrpPlots This generates the tables in the HR ion groups tab. * HR_populate_ChosenMassesTable This table is now on the main Pika panel, HR ion groups tab. * HR_butt_MS_Calc A one stop shop for all your HR calc needs. Is similar to the monster sq_butt_MS_calc function. * HR_MSCalcPlot_Diurnal Was easy enough to port from squirrel to pika so I did it. * HR_MSCalc_Diurnals You can probably guess what this does. * HR_MSplot_DiurnalBoxPlot You can probably guess what this does. * HR_butt_viewEAtable Similar to the APES Elemental Fraction table, but is now on the HR Results tab of the main Pika panel. * PkAPESlogo Small apes picture for the Pika panel, HR results tab. New constants: DOUG5GRAPH_SPECLIST that has all the families in the 5 panel graph. DOUG5GRAPH_AXISLIST that lists the paired axes for the families in the 5 panel graph. Old functions that have been reorganized, made modular for HR species, and thus no longer exist: * HR_butt_CreditsURL See HR_butt_CreditsURLxxx * HR_ChooseMassesPanel Instead of a panel, there is a HR ion grouping tab which contains this functionality. * HR_butt_MSVsTime Now see HR_calc_MSVsTime andHR_plot_MSVsTime * HR_butt_MSVsMz Now see HR_calc_MSAvg and HR_plot_MSAvg * HR_ck_TimeSeriesOption Now a drop down menu in the HR Results tab for all the kinds of HR stick data sets. * HR_enterMassList Now merged with other controls that add things to the results list in teh HR results tab. * HR_IsotopesTable Now merged in the HR ion groups tab. * HR_butt_ChooseMassPanelEnd There is no more ChooseMass Panel. * HR_butt_ChooseMassesPanel There is no more ChooseMass Panel. * HR_butt_defaultHRMS We now have separate buttons for all the families, all the HR species. * HR_butt_ExportMatrix Now see HR_calc_TSeriesMSMatricies * HR_butt_5PanelSummary Now see HR_calc_5PanelSummary and HR_plot_5PanelSummary * HR_5PanelErr Functionality is now folded in with every other error data set usage. Modified functions: * HR_globals Added new variable for the checkbox indicating to do the gauss fits in preparation for the peak width/shape calculations. * HR_Analysis_Panel_Create The HR ion groups tab is new and the HR Results tab has been significantly overhauled. * HR_panel_credits Added Allison's work to credits because APES has been mergedinto Pika. * HR_butt_CreateMSDiffp Will now also perform gaussian peak fits in anticipation of Peak Width, shape analysis. * HR_populate_AllMassesTable This table is now on the main pika page. * HR_butt_ChosenMassesTable This table is now on the main pika page. * HR_SetVar_RunModeStr Now adds ionization type to the simple v/w info about a particular run. * HR_butt_CalcExactMassSticksTodo Now is careful with the distinction between Diff and OMinus C data sets. * HR_SpeciesList_prep Now looks out for HR species names. * HR_butt_AddThisMass Puneet requested that we have the ability to add ions > 300. It now squawks if you try to add an HR ion >= 1000 m/z. * HR_calcGausFitWaves Changed default behavior to add squirrel baseline spectra in HR_PeakHEights_gr plot by default. * HR_butt_familyTable Name of the popup menu for the families has changed because it moved to the main Pika panel. * HR_populate_IsotopesTable This is now in the HR ion groups tab in the main pika panel. * HR_tabProc Added an HR ion groups tab. * HR_butt_url_FAQs Now points to the wiki instead of the old empty web pages. * HR_popMenu_FamilyList There are now two places for popup menus with families. One in the HR ion groups tab, one in the results tab. * HR_populate_ChemFormTable Minor cosmetic change. * HR_butt_ChemFormFind Now allows for searching the entire HR ion list or the chosen HR ion list. * Pk_graphTweaks Now plots species colors, along with family colors. * UMR_plot5GraphSummary We now have a Cx family. * HR_butt_MakeExactMassWaves Now prints a message to the history window whenever someone chooses masses to fit. * HR_butt_CheckIsotopeMask A clearer message to the history window is printed when this has been successful. ----------PK_UnitMassSpec_1_07.ipf---------- New Functions: * UM_makeChosenMassFamText This function creates a text wave that indicates the family to which an HR ion has been assigned. Modified Functions: * UM_GenerateAxByMaskWaves We now assign S and HS and all their isotopes to the SO family; they were in the other family. * HR_MakeHRFamilyBatch New Cx family. * UM_SumHRtoUMR This function has a new parameter sent to it, to indicate whether or not one needs to deal with HR species. ------- PK_peakShape_1_07.ipf------ New Functions: * PW_ck_OneRunOpenClosed Allows users to look at either open or closed raw spectra gaussian fits. * GR_butt_setAllMaskTo0 Sets the spectra type (open, closed, don't use) to 0. * GF_butt_addMass A way to add a new HR ion to the list of ions in the Gauss Fit HR ion table. * GF_ck_showGFdetails A checkbox meant to shield details from most users. New constants: DEFAULTPWLIST = string list of default PW ions to use; will likely change with more user input. GFMASSLIST = = string list of default HR ions to do gaussian fits on; will likely change with more user input. Modified Functions: * GF_createGlobals Added a new global variable for showing GF details. Changed some explanatory text to make things more clear. * GF_makeMasswaves cleaned up this code via use of list of ions intead of identifying all from scratch. * GF_butt_GFsTodo Now prevents any hiccup due to nans in the mask wave. Hopefully redimensions things so folks don't get a "can't fit cuz the waves are of different sizes" error. * GF_GausFitPrelims Cleaned up old code. * GF_fetch_GetGausCoefs Now allows for gaussian fitting of open (and diff) spectra instead of only the closed. * GF_GausFitOneRun Now passes a spectra type as a parameter. * GF_dumpCoeffs Now passes a spectra type as a parameter. * GF_plotAllGFplots Added code for optional seeing of details. * GF_butt_SetGFDefaults Added a call to PW_SetDefaults to initialize things better. * GF_populate_MassTable Added v or w mode indicators, made pretty. * PW_NewGlobals Created a few new globals. * PW_makePeakWidthWaves Changed the PW power constraint wave so that that power parameter is betwenn .3 and .7 * PW_PeakWidthShapePanel Cleaned things up, now optionally displays Gauss Fit details. * PW_populate_MassTable Calls GF_populate_MassTable to ensure that they are the same between the two tabs. * PW_populate_PeakWidthGraph Again refers back to the list of HR ions in the GF table. * PWPSTabProc Checkbox for showing and hiding GF details. * PW_butt_FitPWAvgs Added some flags to ensure that a curve fit call has converged to a solution. * PW_HideChosenPSMass This had to get lots more complicated because we can use Open, Closed or Diff spectra. * PW_butt_RemoveTheseRuns Changed the code to try to handle cases where the user has inserted a new ion to the GF ion table. *PW_findFitsOneRun Added a /G flag to the curve fit operations so that it would have good starting guesses. * PW_butt_showPWOneRun Redimensioned waves in case the user added a new HR ion. * PW_individualMassFitGraphs Now scales from 0. * PW_butt_RecalcPWAvgs Now considers different specta type (open closed, diff) * PW_SetDefaults Uses string constant DEFAULTPWLIST now. * PW_makeColorMx Made this matrix bigger. * PS_butt_PeakShapeAllMassTodo Cleaned up. * PS_PeakShapeAllMassTodo Uses the GFMask to indicate which spectra type to use. *PS_fetch_PeakShapeAllMassTodo Got lots more complicated with the option of using any spectra type. ------- PK_PartitionAvg_1_07.ipf------- No changes. Update since ToF-AMS Analysis Toolkit v1.06A Notes by Donna Sueper 23th July 2009 There was a small bug that had to do with the generation of peak shape candidates using selected masses for the left-and right-side. Pika 1.06 returned the peak shape candidate using only the last mass in the list, not the entire list. Update since ToF-AMS Analysis Toolkit v1.05 Notes by Donna Sueper 19th June 2009 ----------Begin In a Nutshell---------- A bug in the calculation of some "Graph5 summary" plots was found and corrected. Several minor bugs were fixed. Most had to do with graph displays. Several sanity checks were added. This will be the last relase until the User's meeting in October, when a version with an HR frag table will be debuted. ----------End In a Nutshell---------- -------PK_gr_table_1_05.ipf------- New functions: * HR_InitializeHRtodowave A small function called on the recreation of the pika panel to set the todo wave to the same wave as the squirrel panel. * Sticksgr_disableBaselineChks Function that diables, enables the plotting of squirrel-subtracted raw spectra if pika baselines are used. * SticksGr_check_ShowPikplusSqBa A new checkbox in the HR_PeakHts_gr that allows plotting the the fitted peaks 'on top' of the squirrel baseline and the plotting of the raw spectra with without the squirrel baseline . Modified Functions: * HR_globals Added a few new global strings and variables fo clarity. * HR_Analysis_Panel_Create Added a function to initialize todo wave properly * HR_butt_CreateMSDiffp Added sanity checks * HR_butt_CalcSticksForThisRun Minor change to display run number nicely * HR_butt_MSVsTime Added sanity checks * HR_butt_MSVsMz Added sanity checks * HR_plotPeakHeightsOneRun Added a variable to display raw spectra without the baseline subtracted. * HR_reCenterAmu Changed the y-axis for HR_PeakHeights graph to display the min residual or the -10% of the max stick * HR_calcGausFitWaves Added code to allow the optional plotting the the peak fits on top of the squirrel baseline for the HR_PeakHeights graph * SticksGr_SetResidAxis When displaying the residuals as a percent in the HR_PeakHeights graph, the min and max are now fixed at 10%, and changed the formatting to see the numerical values easier. * SticksGr_check_DisplaySQBase Now executes instead of does nothing (now un-italicized) * HR_butt_updateMaskWave Removed the annoying alert message that wanted you to verify that you wanted to change the set of masses to fit from the HR_PeakHeights graph * HR_butt_5PanelSummary Sanity checks added *UMR_plot5GraphSummary Changed code to search for the existence of windows instead of creating them new each time. * pk_butt_5FamilyMSGraph Changed code to search for the existence of windows instead of creating them new each time. -------PK_peakShape_1_05.ipf------- Modified Functions: *HR_PeakWidthSanity Added code to display a bad run number formatted nicely. * HR_CalculateSticksSQ_prep Added a line so that the first integer mass gets displayed nicely in the HR_PeakHts_gr. * HR_SticksOneRun_prep Added new waves to be fetched in anticipation of display on the HR_PeakHts_gr - OneRunRawSpectraOpenp, etc. so that users can plot the raw spectra without the baseline removed (Jose's request). Changed the way the squirrel baseline wave is retrieved in anticipation of dispaly on HR_PeakHts_gr. * PK_MS_concentration Killed a temporary wave at the end of the function to clean up nicely. -------PK_peakShape_1_05.ipf------- Modified Functions: * GF_createGlobals Eliminated the redundant global root:GaussFits:GF_UseSqBaseline * GF_butt_GFsTodo Now uses the variable set in the HR panel, root:HR_panel:HR_UseSQBaseline * GF_fetch_GetGausCoefs Added code to display a bad run number formatted nicely * PW_PeakWidthShapePanel Modified todo wave popup window so that it initializes to the same todo wave currently selected in the Squirrel panel. * PW_butt_FitPWAvgs Fixed, the curve fit to find the peak width as a function of mass. We now use the weighting as the receiprical of the std dev (not the std dev). * PW_butt_PWSet1 Added code to nan out averages when resetting to a new todo wave * PS_CalcPSCandidateFromList A fix for Igor 6.10, found by U Hawaii folks, dealing with the concatenate command. * PS_populate_PeakShapeGraph Changed code to ensure that the appropriate window was identified before waves were appended. * PS_populate_FinalPSGraph Changed code to ensure that the appropriate window was identified before waves were appended. -------PK_UnitMassSpec_1_05.ipf------- Modified Functions: * UM_SumHRtoUMR Fixed a bug that had to do with counting from 0. -------PK_PartitionAvg_1_05.ipf------- No change Update since ToF-AMS Analysis Toolkit v1.04 Notes by Donna Sueper 3rd June 2009 ----------Begin In a Nutshell---------- Peak Width and Shape functionality completely overhauled. Over 100 changes to the entire list of HR mass fragments, and >50 masses eliminated from default fitting settings. Some error estimates are calculated. The use of squirrel baselines instead of pika-generated baselines is encouraged. The ability to average HR spectra has been added. See the HR clinic notes on the ToFAMS web site (linked via Jose Jimenez web site) for more details. ----------End In a Nutshell---------- Update since ToF-AMS Analysis Toolkit v1.03 Notes by Donna Sueper 3rd Sept 2008 ----------Begin In a Nutshell---------- Several new helpful features and a few important bug fixes. Fixed a small bug whereby the very last HR mass would not fi fit properly because the last integer m/z value to fit was 1 less than it needed to be. ----------End In a Nutshell---------- -------HR folder ------- The master list of all available species to select for fitting has approximately 200 yes 200 changes. All Deuterium fragments were removed. Many fragments > 100 were added. The default list of species has been changed to only fit masses < 100. In particular, the pthalate 149 and 279 are no longer fit by default. Users are still encouraged to fit masses > 100 when appropriate, however, and to continue to contribute mass fragments to the 'master' list. When upgrading experiments, users can elect to retain their mass choices through the 'import' button in step 3. -------PK_Backbone_1_04.ipf------- Modified Functions: * HR_CalculateSticksSQ_prep Fixed a small bug whereby the very last integer HR mass would not fi fit properly. * HR_MakeUnitMassWave Fixed a small bug whereby the very last integer HR mass would not fi fit properly. * HR_CalculateSticksSQ Added the ability to calculate the squirrel baseline (background) raw spectra for possible display in HR_PeakHeight_graph. * HR_CalcSticksOneRun Added ability to retry to fit when first try of Igor fit gives negative values. -------PK_gr_table_1_04.ipf------- New Functions: * HR_butt_CreditsURL Added button to take users to url. * HR_butt_AddThisMass Added button in HR_PeakHeight_Gr to allow users to add a mass to the master list of all known fragments. * SticksGr_AppendChosenMassTags Isolated this feature for modularity - code is the same, it is just it's own function now. * PK_calcSQBaselineFit New feature to calculate the squirrel baseline for display in HR_PeakHeights_gr. * SticksGr_check_DisplaySQBase Function for new checkbox in HR_PeakHeights_gr to display raw squirrel baseline spectra. * HR_CreatePeakHtsListBox New functionality in HR_PeakHeights_gr for selecting which masses to fit at any integer m/z. * HR_butt_updateMaskWave New functionality in HR_PeakHeights_gr for changing the entries in the mask_stick_integration wave to reflect changes in list box. * HR_butt_reDoFit Handy function for redoing HR fit for one spectra in HR_PeakHeights_gr. * sq_check_NansInWaveList General purpose function for checking if values are nans in the waves at runs in the todo wave. (for use when m/z fitting not good or not found). Modified Functions: * HR_globals Many changes due to panel reorganization and new features. * HR_Analysis_Panel_Create Many changes due to panel reorganization and new features. * HR_panel_credits Updated. * HR_butt_CalcSticksForThisRun Added some sanity checks regarding peak shape variable. Added checks for non-nan values in m/z fitting parameters for selected todo wave. Changed the calculations so that Pika will automatically retrieve the squirrel sticks for possible later display (in step 4 diagnostics). * HR_butt_CalcExactMassSticksTodo Added checks for non-nan values in m/z fitting parameters for selected todo wave. * HR_setSpecies Code changed to allow for user-defined families. * HR_plotMassesVsTime_prep Code changed to allow for user-defined families. * HR_plotMassesVsTime Slight code change for Igor 6.03 update. Code cleanup. * HR_plotPeakHeightsOneRun Small bug fix dealing with whether insets were plotted or not. * HR_reCenterAmu Fixed small bug whereby the y axis sometimes did not scale correctly. * SticksGr_check_ShowAllTags Changed to use global variable to set this, instead of simply inspecting the checkbox. * SticksGr_check_ShowHorGrid Changed to use global variable to set this, instead of simply inspecting the checkbox. * SticksGr_check_DisplayInsets Disabled old-school legend for families. * SticksGr_SetResidAxis Fixed small bug whereby the y axis sometimes did not scale correctly. * HR_butt_familyTable Fixed small bug having to do with the user defined families. * HR_tabProc 3 tabs instead of 2! * HR_butt_MakeExactMassWaves Removed unneccessary print statement to history window. * HR_OneRunHRSticksTable_Create Made prettier. * HR_ViewFamilyTable Fixed small bug having to do with the user defined families. -------PK_gr_table_1_04.ipf------- New Functions: * UM_ExtractSQMassSpectra Extracts the Squirrel stick for comparison with Pika * HR_makeHRFamilyLegend Gives each family a color, and allows for users to add their own families. * PK_SetUpParamPanel New globals, etc for panel for many parameters panel * PK_ConvertParam Changes units to percent or not. * PK_ExtractParamSum Squirrel fetch function to simply extract data for display in many parameter panel. * PK_CreateHRParamPanel Creates many parameter panel. * PK_AddLabelsToAxis Adds axis labels to many parameter panel. * PK_butt_delta10 Button control on many parameter panel for increasing the m/z values by 10. * PK_setVar_changeMz Set variable control on many parameter panel for increasing the m/z values by 1. * PK_setVar_changeCsrPt Set variable control on many parameter panel for increasing the cursors by 1. * PK_ck_ParamSpectraType Checkbox control on many parameter panel for changing the spectra type (diff, open, closed) * PK_ck_ParamDataType Checkbox control on many parameter panel for changing the data type ( Pika, Squirrel baselines, etc) * PK_ck_ParamDataMath Checkbox control on many parameter panel for changing original or percentaget data. * PK_Param_PrintCursorVals Button control on many parameter panel for changing the data type * UM_butt_ManyParam Button on Pika panel for pulling up the many parameter panel Modified Functions: * UM_PlotIntMassSpectra Slightly rearranged. * HR_MakeHRFamilyBatch Added a simple check for the existence of the table. -------PK_peakShape__1_04.ipf------- * HR_PeakShapeAllMassAllRuns Importnat indexing bug fix. -------PK_partitionAvg__1_04.ipf------- * Essentially no change. This ipf is somewhat obsolete and may likely be removed in future versions. High ResolutionToF-AMS Analysis Toolkit v1.03 (Major Bug Fix - don't use versions previous to 1.03) Update since ToF-AMS Analysis Toolkit v1.02 Notes by Donna Sueper 30th Mar 2008 ----------Begin In a Nutshell---------- Important bug fix. A mathematical mistake has been found in the Pika code. When finding the high-resolution peak fits for a todo wave (step 5), the results are in units of peak height (the entity solved for in the fits) instead of peak area. The peak area is the value to be used to compare results between different species. For more information, please refer to the email sent out with the notice of this release, or email Donna at donna.sueper@colorado.edu. One new useful feature is the ability for users to define their own groups of ions any way they please (a group is called a 'family'). ----------End In a Nutshell---------- -------HR folder ------- The master list of all available species to select for fitting has approximately 20 changes. Some duplicates were removed, three species that were incorrectly labled with a zero instead of a "O" for oxygen were corrected, and species that were not in monotonically increasing order were moved to their rightful position, at least 4 new species between m/z 70 and 100 were added. Users do not have to change or modify the master list of species when they upgrade Pika versions. -------PK_Backbone_1_03.ipf------- New Functions: * PK_ConvertOldExactStickToArea A function to convert old (pre-1.03) HRDiffSticks that were saved as peak heights instead of peak areas. * PK_HeightToAreaMatrix Does the work of PK_ConvertOldExactStickToArea * PK_convertUnitSigmaToEachSpecie A general function for creating waves that have the peak width for each species. Modified Functions: * HR_CalculateSticksSQ_prep Added sanity check, the creation of more global variables if needed, and a call to PK_convertUnitSigmaToEachSpecie. * HR_CalculateSticksSQ Fixed the HRDiffSticks so that they reflect areas, not peak heights. * HR_CalcSticksOneRun Added the creation of global waves specifically named HRPeakHeightsDiff, etc, to aid in the separation and calculation of HRSticksDiff Added a sanity check for values of peakShapeScalers. -------PK_gr_table_1_03.ipf------- Renamed Functions: * HR_plotPeakHeightsOneRun was HR_plotSticksOneRun to distinguish between the results displayed in step 4. HR_butt_UpdateNewExactMass was HR_UpdateWavesFromGoogle, reflecting a time in the past when things were updated via a private google spreadsheet account. New Functions: * HR_checkOrderOfAllMasses Added a sanity check for when users enter masses and they are not monotonically increasing. * HR_butt_ViewFamilyTable New button on main panel - it is intended for folks who want to define their own groups of ions ('families"). * HR_ViewFamilyTable Added the ability to view user-customized families as well as the traditional families of CH, CHO, etc. * HR_popMenu_FamilyList Added a Get List menu item that refreshes the list of families in case the user has defined a new family. Modified Functions: * HR_globals Added a verbose mode global variable for debugging. * HR_Analysis_Panel_Create Minor tweaking so that panel items don't appear squished. Added a button for family table * HR_ChooseMassesPanel Minor tweaking so that panel items don't appear squished. * HR_butt_CalcSticksForThisRun Added clarity for the sticks, peak heights calculations. * HR_butt_PlotMassesVsTime Added sanity check in case no masses were chosen. * HR_plotMassesVsTime Removed call to Sq_AddCntrl_RunsFromCsrs() that added annoying buttons and control bar to graph. * HR_reCenterAmu Minor change dealing with the peak height to peak area issue. * HR_ExactMassTagsAll Commented out unneccessary code. * HR_AppendExactMassTags Commented out unneccessary code. * HR_calcGausFitWaves Minor change dealing with the peak height to peak area issue. * HR_butt_UpdateNewExactMass Minor word change. * HR_butt_MakeExactMassWaves Added sanity check via function call to HR_CheckOrderOfAllMasses() * HR_OneRunHRSticksTable_Create Added PeakHeightWaves along with the usual Stick waves. -------PK_gr_table_1_03.ipf------- No change from version 1.02 -------PK_peakShape_1_03.ipf------- * HR_makePsMassWaves Added a tungsten family, mostly as an example for others to define their own families. * HR_CreatePeakWidthShape_Panel Minor tweaking so that panel items don't appear squished. -------PK_peakShape_1_03.ipf------- * UM_GenerateAxByMaskWaves Added functionality that checks if a species belongs to any user defined families before it gets sent to the default families (CH, CHO, CHON, Air, etc) * UM_MakeIntResolutionSticks Changed code to reflect the new reality of separate PeakHeight and Sticks (peak area) waves. * HR_MakeHRFamilyBatch Added the Tungsten family. Update since ToF-AMS Analysis Toolkit v1.1 // should be v. 1.01 Notes by Donna Sueper 22th Feb 2008 ----------Begin In a Nutshell---------- New ability to find high resolution sticks for the average spectra of a todo wave. Fixed a few small bugs having to do with the finding the index of runs. ----------End In a Nutshell---------- -------PK_Backbone_1_0.ipf------- * Renamed all constants to be all capital letters for easier identification. * Changed string constant FRAG_PANEL_LIST to reflect better ordering of frag waves Funtions removed: * HR_TenGauss() Obsolete. * HR_TenGaussWPS() Obsolete. Funtions added: Functions modified: * HR_MakeDiff() Simple change to use a matrixop for faster calculations. * HR_MakeHoldString() Doesn't force hold string to be of a fixed length. * HR_ManyGaussWPS() Doesn't force hold string to be of a fixed length. * HR_ManyGauss() Doesn't force hold string to be of a fixed length. * HR_CalculateSticksSQ_prep() Reorganized where global waves are created. Added extra globals for when fitting lots of peaks at one integer m/z. * HR_CalculateSticksSQ() Small bug fix for v and w mode switching. Added a "verobse" mode to spit out info in the history window when peaks don't fit. HR_CalcSticksOneRun() Small bug fix for v/w mode switching. Also, the code now allows variable number of peaks to fit. Also allows for a 'verbose' mode. HR_SticksOneRun_prep() Significantly changed to allow the use of a todo-wave averaged raw spectra. -------PK_peakShape_1_02.ipf------- * HR_PeakShapeOneMassAllRun() Inserted a small bug fix and some sanity checks. * PS_CleanUpPeakShapeThisRun() Fixed a bug that can creep up in non-standard cases. * PS_MakePSAvg() Fixed a bug that can make the 'wings' of the peak shape be constant. -------PK_UnitMassSpec_1_02.ipf------- * UM_GenerateAxByMaskWaves Slightly changed the algorythm to better group CHO and sulfur families. * UM_PlotIntMassSpectra() Can now accomodate comparing a unit resolution todo-averaged spectra with a grouped HR spectra found by averaging the raw spectra from a todo wave. -------PK_PartitionAvg_1_0.ipf------- * PA_CreateGlobals() Fixed small bug that presumes the existence of some waves. -------PK_gr_table_1_02.ipf------- New functions: * HR_ck_oneRunOrAvg() Checkbox control for signaling if one is finding HR sticks for one run or the average of a todo wave. * HR_butt_FindRunInTodo() Button that works both for the find next and find previous run in todo wave * HR_butt_url_latestVersion() Button on main panel that takes one to the web site to download the latest version. * HR_butt_url_FAQs() Button on main panel that takes one to the general Pika web site. * HR_butt_UpgradePika() Added functionality for upgrading Pika - Useful for Igor verions 6.10+ Modified functions: *HR_globals() Several new or modified globals on the main HR panel. * HR_Analysis_Panel_Create() Now includes the ability to do the HR fit on a todo-averaged raw spectra. * HR_panel_credits() Changed Peter DeCarlo's email address. * HR_SetVar_RunModeStr() Changed to show v or w mode designation. * HR_butt_CalcSticksForThisRun() Changed to allow the user to fit an todo-wave averaged raw spectra. * HR_setSpecies() Fixed a bug the arose when run index not in increasing order. * HR_plotMassesVsTime() Fixed a minor kbcolorizetrace call (Igor version 6.03) * HR_ExtractResidSum() Fixed a bug the arose when run index not in increasing order.