Sq pk programming

APES

To Do Priority

• Get and incorporate Jose's read me

• Allow users to select HR spectra from data folders instead of assuming Pika usage.

• Add a new table on the web page for downloading ipf

Pika

To Do Priority

• Deal with Cobalt (in usage in tags)

• Create other methods for the user to select masses to fit beyond the simple default option.

• The legend for the peak width graph doesn't update when defaults are changed.

• Checkbox for truncating sticks to zero in stacked graphs.

• Param graph
  • add small raw spectra insets to left and right
  • add graph showing spectra-like data with window highlighting where you are
  • have run numbers update with cursor move

• In final peak shape graph add ability to:
  • truncate at 3.5 sigma
  • trim wings to ensure monotonicity

• In final peak width/shape add ability to subtract sq baseline from peak shape algorithm

• In Peak shape panel the first run number of index should be put into “run number” field (it defaults to 0)

To Do (Less Urgent)

• Step 4 of pika: maybe rather than two options (one run or Todo wave) and one button, we could just have two buttons? Something like “Calculate HR Sticks for averaged Todo wave” and “Calculate HR Sticks for one run”?

• Add ability to duplicate PeakHeights graph and functionality
• In the m/z calibration panel, currently the width and accuracy vs m/z graphs don't show a summary of all the runs. E.g. the summary of all the peak widths for all the runs with error bars in the peak shape panel very nicely summarizes this information.
  • (Jose) This could be done with a radio button on top of the graph that selects SR/AR (meaning single run / all runs)
• We need to add camels, dromedaries, and vw "bug" ions to the lists. We need some notation for these ions, let me suggest vw28, vw23, d28, d32, and c28, c32, with the comment column describing what they are. It is important that those are lowercase letters, so people don't confuse these ions with vanadium (V), tungsten (W), and deuterium (D).
• There is a need to consolidate the three sets of m/z lists that exist into a single one. We currently have the list of m/z possibly used in fits,(1) ones actually selected for HR sticks (2) list of m/z used for m/z calibration, and (3) the list of isolated ions. Each list is a subset of the previous one, and we can work with a single big list, and a series of masks to select / deselect the various m/z for the different purposes.
• change the field analysis to warn users to check for large CO influence in ab correction; provide a sample pre and post AB correction from Tim to demonstrate
• change frag_organics as per Allison's paper
• change frag_sulphate as per Ann M's paper
• change the error that says "no can do!" to something more specific
• If user only does the m/z calibration and does not play with the HR panel, the code calculating the HR sticks may go awry (maybe - I need to check).

To Discuss

• Change saving of the HR sicks matrix from masses that were selected to fit to all known masses.

Done

• Change in step 4 options, test for peak height to be less than 0 to be less than user defined value (done in 1.03D)
• Warn clearly that changing selected masses is done globally (done in 1.03D)
• Add a button in PeakHeights graph to redo pika fits (Keep all user settings from step 4) (done in 1.03D)
• Partition Avg ability for todo waves (especially v only, for Qi Chen - done in 1.03A)

• In Param graph add radio buttons for raw and percent (done in 1.03D)
• In Param graph add print all cursors (done in 1.03D)
• Add button for web link in credits panel. (done in 1.03E)
• In the graph for one spectra HR fit, move the redo fits button so it is farther away than the arrows. (done in 1.03E)
• Double check m/z parameters (so they are not nan) before trying to fit (done in 1.03E)
• Alex had an issue with the show inset button being clicked on, but the insets weren't showing up. Make sure that this toggle value keeps up with the display. (done in 1.03E)

Squirrel

To Do Priority

• Make clear the errors are in units of Hz.
• Add the LS diagnostics to the set of waves that get loaded. (This is finished in 1.43I but needs to be tested using new DAQ)
• Manjula thought that when the user puts more hdf files in the data folder, and presses the Get Index button, that the code does not handle new v/w switching and mode changes well. (For example, at first the DAQ is set up to do all v then does v/w switching.) Donna's comment: Right now I cannot reproduce this problem but there was a problem with the diagnostic plot not updating correctly, and this was fixed in 1.43F.
• Make the quick view program instructions more clear.
• Mike's pcurser in todo wave names
• Mike Q's issue with m/z calibration with fast mode data
• Pre-process: when recalculating sticks with new m/z parameters, the error related to some m/z parameters being NaNs often shows up. A few times at the beginning, and then halfway through. Is there any way to deal with this more effectively?
• In the baseline subpanel, make the mass defect default values more clear.
• In some data sets, many small intermediate files get written instead of a few big ones. (Some of Mike C's Arctas)
• In the preprocess step, make clear the distinction between using DAQ sticks and recalcing sticks
• Add Doug's threshholding diagnostics and correction factor.
• In the modify SI table, also include ionization and tof type waves so users can more easily see how to change SI values.
• Deal with Helsinki/Doug's unique PToF data (grouping last 3 of 4 choppers).
• In average mass spec plots, review how negative values can be 'hidden' by other traces.
• In average mass spec plots, a better system for expanding/shrinking is needed.
• We have problems with averaging PToF runs when the PToF settings change between runs. Have squirrel automatically create different todo waves for each PToF setting.
• Bug found with Sanna: when using a user defined time base but minutes = 0, we get an out of memory error.
• Review existing code that deals with fast mode data.

To Do (Less Urgent)

• Write intermediate files as compressed HDF files? Check to see if/how this is best done for updating experiments.
• The 'resolution' parameters for determining peak integration area need to be printed to the history window whenever we recalc sticks.
• Doug wants to rename 'AB reference runs' to something else.
• Load in menu information from DAQ hdfs and make menu info more readily available to user.
• Make squirrel handle situations whereby the sEI is not really sEI but a different menu.
• In frag check tab we need a button to update plots instead of replotting every time.
• In frag diagnostic plots we need to change the 'display gaps' setting.
• In Dva popped table we should also see run numbers and whether or not a run has PToF data.
• In m/z calibration panel we need a readout that tells ionization type (sEI, EI) as well as ToF type (v/w)
• In baseline panel we need a readout that tells ionization type (sEI, EI) as well as ToF type (v/w)
• Heikki had out-of-memory issues with the organic matricies.
• Make more consistent the todo wave creation scheme whereby users can input "todowave and not 1xxx and not 2yyy" for the todo wave formula
• Change PToF code so that users have an option to plot the legend (for size distrib graphs).
• For PToF size distributions, often the size range extends to smaller values than are useful. Add controls so that user can quickly zoom in and out of interested size ranges.
• In the baseline panel allow uses to go higher than m/z 500.
• Should we allow users to enter a negative value for the PToF vl parameter?
• Add the ability to calculate diameter mean and median in PToF data (Manjula).
• Occasionally after preprocessing, the status bar ends saying “Estimating space requirements” rather than “Done”
• For DC marker corrections, Manjula wants to be able to enter nitrate, and then have squirrel figure out what m/zs this corresponds to.
• In average mass spec graph, when checking linear scale have the default go to 0.
• In average mass spec graph, check the display of negative values. (Doug thought that it wasn't working right.)
• In average mass spec graph, perhaps add a 'magnification' drop down menu - x 2, x 10, x 25, etc.
• Doug really likes for tables to have columns be the minimum width that is sensible.
• Re-look at IE/AB calculations.
• Doug really likes to have time series graphs be such that grids are on midnight of every day, and labels have day of week inserted.
• In the diagnostic plots, perhaps the PToF airbeam wave should be nanned whenever the run doesn't have PToF data.
• In m/z calibration panel, check the possible bug when interpolating across a todo wave.
• Ask user to save experiment before blacklisting and/or indicate how to unblacklist
• In diagnostic plots, change legends that give integer m/z values to molecular species.
• We need to be able to select some ions to be used in m/z cal and peak shape for V or W only.
• Review todo wave name length limitations.
• When doing an m/z cal fitting, put runs with bad fits into a separate todo wave.
• In the m/z calibration panel, make more clear what the nan param button does.
• From Tim O:During manual (F3) saves, the mass spectral data (e.g. MSOpen_V, MSSOpen_V, etc.) are saved as simple data arrays with the m/z in the rows direction. During autosaving, even if only for one run, these waves are always saved with the m/z in the column (run number in the row dimesion). It turns out that Squirrel can read and process either, just not at the same time. Thus, while he can process the data separately, he cannot ask Squirrel to load and process autosaved data with nonautosaved data interspersed.
• Incorporate some peak finding code as per Jesse's request.
• Deal with Fast runs not finishing a fast mode cycle.
• Update squirrel web site.
• From Ken: In the baseline fitting panel make the main plot in the popped window automatically scale the x axis to that in the main window.
• From Ken: In the baseline fitting panel, when scrolling through the baseline fits for all runs in a todo list, add the ability to pause on a chosen run. It would also be great to select the direction in which the run baselines are scrolled - forward or backward.
• In the m/z calibration panel, think about the ability to tweak settings in conditions of high loadings (Mike C).
• Allow users to go > 500m/z.
• Create Frag table default fragment text waves (Donna)
• When a user enters runs and the first is > than the last, 45-40, a better error message should be generated.
• Tim O's issue with somehow getting the squirrel_index matrix messed up and getting the stick matrix data set being as wide (columns) as the raw spectra matricies. (Donna - is this replicable?)
• Review the use of t_series_old
• Review the use of custom time series - are sanity checks in place?
• Review the use of the todo graph.... add checkboxes to remove todo waves?
• Add code that calculates the mean/median for size distributions (Manjula)
• Add code that somehow simply tells the user whether the sticks were recalced or not, and if recalced, the parameters used.
• Add somewhere in the help/faq something about the averaging of raw spectra and the units conversion (Donna - see James email of 11/2007).

To Discuss

• Changing frag table to reflect info in Allison's paper (in next release, coordinating with Jose for sending email to the users)
• Normalize w mode to v mode - One diagnostic:the ratio of v and w sticks with the x axis as m/z.
• Change frag table of sulfate according to suggestion from Ann
  • Current frag_sulphate -> frag_sulphate_old
  • New frag_sulphate doesn't depend on frag_SO3 and frag_H2SO4 (Ann will wori up this new table)
  • Frag_SO3 and H2SO4 are kept in Squirrel for reference and if someone wants to put them back to use, but not used by default

Done

• Check the labels for graphs generated using x vs tof and dxdlogdp (Done in 1.43I).
• Possibly rename the checks to be done before preprocessing as 'stick adjustments'. (Done in 1.43I)
• Change defaults in Frag checks tab to be 'all' and colored by timewave.
• Fix bug that pops up in Frag checks plots. (Done in 1.43I)
• Make sure that when doing DC marker corrections squirrel changes todo wave to be todo wave AND allPToF (Donna note: This was done primarily to avoid creation of blanks in the prepocess step but was also added in the corrections tab, done in 1.43I).
• Add checkbox in Misc - graphs section that sets the default displays to not show gaps. (Done in 1.43I)
• When preprocessing PToF sticks generate a todo wave that has only PToF runs in it instead of generating dire warning. (Done in 1.43I)
• Change the preprocess checkbox settings so that the default is to apply dc markers. (Done in 1.43I)
• An error pops up when trying to creat normalization factors for user defined species (As in Pb for Leah). (The normalization routine was overhauled in 1.43G and this error should no longer appear.)
• A general warning should pop up when users try to create todo wave names with > x characters. (Done in 1.43E)
• Add button to generate diagnostic plot if user killed it. (Done in 1.43I)
• Change default for average mass spec so that only sticks (not sticks + raw) are calculated. (Done in 1.43I)
• Bug found by Mike Q about checking modifications of all frag waves, not just species selected in average mass spec (fixed in 1.43C-ish)
• In the m/z calibration panel, make the live option checked automatically when viewing one run. (Done in 1.43I)
• Bug found by Carly whereby the MS time series for the species all can replace the 'all' todo wave (Done in 1.32I)
• For PToF size distributions, the total loading for each species should be displayed (somewhat similar to the legends that get displayed with average mass spec). (Total MS and normalization factors are now printed to history - Done in 1.43I)
• When an intermediate file was not accessed successfully change the code from the existing error message that gets printed to history, to an abort command (Manjula). Done in 1.43I