High ResolutionToF-AMS Analysis Toolkit v1.05 (2009 HR Clinic Release) 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.