High ResolutionToF-AMS Analysis Toolkit v1.08CB1 Update since ToF-AMS HR Analysis Toolkit v1.08C Notes by Donna Sueper 1 JUn 2010 Version 1.08CB1 has the "1.08C"version of Pika and the "1.49B1" version of Squirrel. There was small bugs in 1.49 (but not previous versions) whereby the species correction factor was no applied. 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.