Sq pk programming

APES

To Do

• Fold the whole thing into Pika?
• Delphine wanted to spit out the elemental mass spectra without normalizing them all to average total mass.
• Get and incorporate Jose's read me to the wiki
• Add the ability to apply the AB correction factor, if it exists.
• Allow users to select HR spectra from non-root data folders
• Create some documentation on the web!

Done

• Ken had an issue when he chose the tag wave instead of the text wave as the chemical mass formula wave. Perhaps there should be a warning that appears when x number of mass fragments are flagged as having issues instead of simply printing them to history. (done in 1.02)
• Add a new table on the web page for downloading ipf (done in 1.01)
• Add ability to not require the fit of CO and/or CO2 (done in 1.01)
• Add the ability to do the analysis on user selected HR spectra, such ans PMF results (done in 1.01)

Pika

To Do Priority

• Begin to implement the HR frag table. W need to introduce the concept of species. For example CO2 would belong partially to an HR-Organic and partially to the HR_air species. This also involves the use of an HR batch table, In this HR batch table users also their own RIE, CE. Note that this is a similar but slightly different concept than the family groupings.

• Change default behavior so that we have two HR difference sticks one which is found by fitting the raw diff spectra (called HRDiff), and an OpenMinusClosed which is simply the open HR sticks - closed HR sticks.
  • Change the default behavior from fitting difference spectra to only fitting open and closed. James' point at the user's mtg is that we should always be looking at the HR_OpenSticks - HR_ClosedSticks.
  • Jose, 4-Apr-09: disagree with not fitting the diff, I think we should keep fitting it as for some peaks it is much more useful. However we should also show the open-closed fits (not just sticks) in the PIKA window. User should be able disable fitting the diff, and to use the diff results, even if the default it to use the open-closed results.

• In HR_peakHeights_gr, change the color of the residuals to be different from the red, orange, brown. Also add squirrel integration regions. Also, add a checkbox to add remove black lines between raw data points.

Final Peak Shape

• We may want to allow a 'smoothly varying' peak width.

Other

• Change all peak shape candidates to have a 0 entry in the left- and right-most value so that 'peak-shape type baselines' dont' get extended beyond +- 7 PW values.

• In the Graph 5 summaries, include one 'bar' type graph showing the fraction of each family to the total. Also, we may want to redo the addition of HR fragments to force the child isotopes to go with their parents.

• A plot of the Residual Errors vs Counting errors (for one m/z and for chosen species)

• m/z calibration and masses - We need to subtract the mass of an electron from all our masses.

• Begin to automatically create uncertainty values generated from peak shape and/or m/z calibration knowledge.

• Generate 'Neil's graph' whereby we plot as sticks from zero amount of C and H mass as a function of number of Oxygens. Do a similar thing for the number of C's (the amount of H and Os and a function of number of Cs).

• Checkbox for truncating sticks to zero in stacked graphs.

• Many parameters panel
  • 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

• 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).

To Do (Less Urgent)

• Pika on PToF spectra (gasp!)

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

• 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.

• 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).
• Incorporate some of Mike Q's functions that deal with sq frag vs pika sticks (Donna: Mike Q's July 2008 email) Also think about NH4 measure vs predicted and RIE for NH4 (Donna: Jose's July 2008 email).
• Make clear what limitations there are about the total number of masses that can be fit at any m/z value.

To Discuss

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

Done in latest release

• Rami found a small bug in HR_peakHeights_gr that has to do with the display of the very first HR fragment. It is a display issue only and does not effect sticks generation or calculation. Done in 1.06

• Need to redo PW fitting function so it weighs the inverse of the errors. Done in 1.06

• In PeakShape panel, make confirm todo wave choice a gold button. Done in 1.06

• In the peakHeights graph, show squirrel baseline region. Done in 1.06

• Allow identification of peak width parameters/peak shape for certain runs. Done in 1.04P

• Doug wants the green sticks in the HR_PeakHeights_gr to be colored by family. Done in 1.04P

• Currently some CS species get lumped into the CH species. make a new family? Done 1.04P

• Changed default behavior so that all pika operations are done on the raw spectra with the squirrel-calculated baselines removed. (1.04M)

• Overhauled Peak Width/Shape panel. Too many changes to mention! (1.04M)

• In final peak shape graph add ability to:
  • truncate at 3.5 sigma
  • trim wings to ensure monotonicity
• In final peak shape algorithm remove/modify final peak shape smoothing and/or make it user editable

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

• In the peak shape panel, include a string that indicates what species are used but not displayed.(done in 1.04J)

• Make the pop button work for examining one spectra.(done in 1.04J)

• In HR One Spectra plot, when different open/closed m/z fitting parameters are used, use these parameters in displaying raw data in HR_peakHeights graph (done in 1.04J)

• In HR One Spectra plot, when different open/closed m/z fitting parameters are used, calculate and display sensible 'blue lines, or fits' for the difference spectra in HR_PeakHeights graph (done in 1.04J)

• Deal with CO tag (Cobalt in usage in tags) and (C2HN?) (done in 1.04J)
• Change the error that says "no can do!" to something more specific (done in 1.04H at least)
• In the tables that indicate pthalate279 use the formula C16H23O4 (done in 1.04H at least)
• In Peak shape panel and "live update" button similar to the one in the m/z calibration panel. Similarly, don't clear all previous fits when one presses the 'begin peak width' button. (done in 1.04H at least)
• In Peak Heights graph, the x axis should be centered on the gray area. (done in 1.04H at least)
• In peak shape panel, add the ability to plot real data onto final peak shape graph (show scatter of real points on 'wings') (done in 1.04H at least)
• In peak width/shape panel, if todo wave is v mode and user selects a w mode peak shape, an error message should pop up right away. (done in 1.04H at least)
• Add the ability to plot residuals on the raw spectra axes in the HR_peakHeights graph (not only on the top axis). (done in 1.04H at least)
• In final peak width/shape add ability to subtract sq baseline from peak shape algorithm (instead of baselines being constant) done in 1.04H at least)
• In Samara test case the redo fit button on the peak heights graph wasn't working. (it went to get the raw spectra) (done in 1.04J at least)

Done

• 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”? (Done in 1.04)
• 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

Extreme Priority

• Rework the entire m/z calibration fitting routine so that we fit all plausible peaks (getting peak centers and widths) at the beginning. Then we only need to select which masses to use for the m/z calibration equation.

• Add Doug's threshholding diagnostics and correction factor.

• Incorporate John S's method for improving m/z calibration using PFT (or PFK).

• Redo the Frag Corrections section to have just one big panel with pop-able grahs.

To Do Priority

• In the modify SI table, perhaps include the TofTypeVKey and TofTYpeWKey waves to help folks know that they are available for use.

• In m/z calibration panel, add vertical red lines for gaussian peak centers. Change black lines to gray. When saving a copy of the m/z calibration settings, write a message to the history window.

• Tim O wants the capability to write the frag matricies for import into the DAQ.

• Manjula had the fantastic idea of including a > and < button when looking at individual m/z calibration peaks (could also be used for individual peak width peaks).

• In m/z calibration window, include ability to nan parameters only in runs in a todo wave.

• In m/z calibration window, for individual peak graphs, add red vertical line for peak center from gaussian fit.

• Heringa Maarten brought up the issue about smoothing the AB correction factor when users are doing V/W mode switching. The current code does not smooth across V mode runs when users alternate between v and w mode. Some code was inserted in the squirrel panel 1.46D, but has not been implemented into the panel. There needs to be a new field in the AB corrections section of the panel to prevent smoothing across i.e. V-mode runs when adjacent V mode runs are too far apart in time space.

• The save interval section near the get index should perhaps be removed.

• Tim O really want to have PToF min and max size regions for PToF operations.

• Add some sort of pre-compiler directive that helps users that don't have the hdf5 xop loaded.

• Incorporate the CE algorithms as identified by Tim O, Roya, etc

• Mike's pcurser in todo wave names

• 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

• 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

• 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 m/z calibration panel, think about the ability to tweak settings in conditions of high loadings (Mike C).

• Add somewhere in the help/faq something about the averaging of raw spectra and the units conversion (Donna - see James email of 11/2007).

• Doug wants the diagnostic of Closed/Diff sticks. Anything that sticks out as being very high has a different source (CO2, O, K, C).

• In Tim's Ron Brown data set the m/z calibration panel updates so slow (91,000) runs because the right side plots update also.

• In Tim's Ron Brown data it might be good to write MSSDiff_p matrix to memory to free up memory - make this an option?

• Allow for m/z fitting of PToF data

• Add a note to the help web site that tells what the blue/red progress bars mean.

To Do (Less Urgent)

• Users may often run into out of memory issues when performing the Export Matricies in the PToF tab, because results will be #runs * #mz * #sizebins big. Perhaps there should be an option for exporting these matricies, but cutting things off a a max m/z value (150ish?)

• Some want the ability to 'shut off' the automatic coloring that happens with a MS time series graph, for example.

• Add the ability to do weekday/weekend diurnal time series plots (Folks can do this right now by making todo waves that reflect weekday/weekend periods. Still, it would be a convenience.

• Include Frank D's method for deriving detection limit for CToFs? http://direct.sref.org/amt/2009-2-33

• Deal with the popup menus that deal with long strings by using 'reflection'.

• Doug wants to rename 'AB reference runs' to something else.

• 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 distribution 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.

• 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” (Donna can't reproduce this)

• For DC marker corrections, Manjula wants to be able to enter nitrate, and then have squirrel figure out what m/zs this corresponds to.

• Re-look at IE/AB calculations (Donna - see Tim O's email of Jan 2008).

• 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.

• Review todo wave name length limitations.

• 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.

• Update squirrel web site.

• 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.

• Create Frag table default fragment text waves (Donna would be good for the manual)

• 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 the todo graph.... add checkboxes to remove todo waves?

• Add code that calculates the mean/median for size distributions (Manjula)

• Add an upper limit to when we generate normalization factors (current usage is to have user's create custom size interval).

• Suggestion from Tim O: Since everyone needs to do size calibrations, can we get the fitting function into the squirrel code for use? Ideally, we would have two functions, one to fit velocity vs dva data (typical process for getting size calibration parameters) and one that takes the parameters and calculates the dva from velocity (i.e. same equation, just solved for dva rather than velocity). I can provide you with both, if you wish. I keep finding myself going back to either retype these in all of the time or copying for older *.pxp files.

• Achim wants the ability to calculate sticks beyond 1000m/z for SP2. (It is a simple code change; Achim knows how to do it. It is not clear how this could be incorporated into squirrel for other users.)

• Add a button to the misc tab for dumping MSSDiff_p to intermediate files (Tim O Ron Brown data).

To Discuss

• 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

• Change frag_organics as per Allison's paper

• Should we allow users to enter a negative value for the PToF vl parameter? (Liz, John J)

• Should I add PAH to the default list of species (i.e. in the MS average graphs)

Time Trace

Not Urgent

• Make the quick view program instructions more clear.

LS

To Do

Wait for requests and updates from Eben, Tim, Jay, etc.

EC

Priority

• Wait for request from Delphine - nothing to do yet.