BUG GUI Fix grid when converting overlayed window to a grid window. Wasn't retaining the dataset dims. For example, if spectra in single window had dim 1 on x and dim 3 on y, the overlay would have dim1 on x and dim 2 ony
BUG CMD Generating simulated relaxation experiments was working, but they weren't picking up the x values correctly.
IMPROVE CMD Fix dispatchnv so .py scripts can be run with arguments
NEW GUI Add normalization and controls to peak graph. Useful for displaying meaasured peaks from releaxation experiments where one typically normalizes the values by dividing by the first point, and possibly also by taking the log of the normalized value (as in CPMG experiments).
NEW GUI Update to 10.2.15
BUG GUI When making simulated peak list name from dataset remove the ".nv" Peaklist names shouldn't have a "." in them. Peak lists with "." characters can be problematic when the code is figuring out the list name and peak number from a specifier like noesy.3.
NEW GUI Don't add Simulate tab in processor (only useful in Analyst)
NEW CMD Initial addition of script generator and auto execution from command line. Use via "auto" subcommand. This allows generating a processing script from the command line. The processed script can be executed immediately or just saved to a file.
NEW CMD Add new command-line scripting methods for creating a dataset, creating a dataset with fewer dimensions than original dataset, and getting a vector from dataset.
BUG CMD The DPHASE command should not auto-phase dimensions (when using dim=0 arg) if they are not frequency mode.
NEW CMD Read in fq3list files when opening Bruker files. Useful for CEST datasets.
IMPROVE GUI Added ability to edit a table of parameter values for dataset dimensions that are not frequency dimensions.
IMPROVE CMD Code for merging datasets (used from Scanner tool) only worked for 1D files. Now you can merge a series of 2D datasets into a pseudo-3D. Useful for non-interleaved relaxation experiments.
IMPROVE CMD Save peak lists "slidable" state to star file.
IMPROVE GUI Allow loading yaml file for window to create new stage. This allows saving multi-window states to a project.
NEW CMD Write a STAR file out to a new star directory in project.
IMPROVE CMD Read and write peak dim Frozen value to star file
BUG CMD Fix reading .xpk files. Wasn't parsing bracketed fields properly as original .xpk reader was based on reading Tcl list format.
NEW GUI Add mkinst.sh to generate simple installer that generates an archive file with code and Java JVM.
NEW CMD Add quick parser for getting shifts from bmrb file
NEW CMD Add assignAtomLabels. Uses bipartite matcher to assign peaks shift list
IMPROVE GUI Allow displaying peaks where the labels don't agree, but the nuclei do
IMPROVE CMD Allow using sf,sw pars from nmrPipe file.
IMPROVE CMD Add nusfile support to NMRPipeData
BUG CMD BCSINE was using old style parameters Was failing because it was calling the Java code with too many args
IMPROVE CMD Improvements in baseline correction In window methods now make the window a little wider to encompass regions on each side of detected signal regions (as they may not qualify as signal regions, but still have elevated intensities that shouldn't be considered baseline. Add cwtdf in which you specify the fraction of spectrum that should be baseline.
BUG CMD Clear annotation data in VecRef op. Makes sure that apodization is no longer displayed in GUI when you remove the apodization op.
BUG CMD Sample schedule wan't being recreated when number of points changed. Caused by renaming some variables in earlier commit.
IMPROVE CMD NESTANMR now returns silently if no schedule present. Useful in doing demo in GUI when we turn schedule on/off
IMPROVE CMD Allow complex vectors to be bucketed and use method in Vec for op code
IMPROVE CMD tdSize should get set in VecRef. Windows were not getting calculated properly in demo modes because tdSize wasn't changing when vector size was changed
IMPROVE CMD Add offset arg to Blackman and Kaiser.
IMPROVE GUI Allow peak navigator to zoom to specified width around peak. Adds choice box with set of scales
BUG GUI Fix getting rows/cols of spectra. Was calculating rather than existing. .yaml file was not getting correct grid values.
IMPROVE GUI First addition of a Reference Menu. Currently only has an entry for adjusting reference of experiments with diagonal so the diagonal has same shift for each of the two dimensions.
IMPROVE GUI Add ability to freeze/thaw all peaks regardless of condition. Holding down Alt key while clicking freeze or thaw will apply to all linkded dimensions even if they are in a peak list with condition different than selected peak. Also Tweak/Freeze applys to peaks that are linked in all dimensions to the selected peak.
IMPROVE GUI Add ability to freeze/thaw all peaks regardless of condition. Holding down Alt key while clicking freeze or thaw will apply to all linkded dimensions even if they are in a peak list with condition different than selected peak. Also Tweak/Freeze applys to peaks that are linked in all dimensions to the selected peak.
IMPROVE CMD Change Kaiser and Blackman apod to work on single, specified dim . In matrix mode, these windows were applying the apodization to all dimensions of the extracted matrices. Now they apply to a specified dimension, allowing different parameters and windows for each dim.
IMPROVE CMD Locating position of dataset maxima now uses extreme rather than max. This allows searching for plane with negative intensity in the GUIs max plane menu item.
IMPROVE CMD Allow Blackman to work as matrix op
NEW CMD Add mkinst.sh script for packaging simple .tar package with Java Useful for a distribution where you just want to unpack tar file and not use any GUI.
NEW CMD Add toPipe method to dscript.py
NEW CMD Set dataset header temperature field when processing
NEW CMD Store temperature in NMRViewJ format file header
NEW CMD Add changes for exporting a Dataset in nmrPipe format
IMPROVE CMD Add threshold to NESTA.
IMPROVE CMD Allow Kaiser window to work on matrices. This allows its use prior to nD NUS operations so each one doesn't need to support apodization.
NEW GUI Add Kaiser and BLACKMAN apodization windows as operations in operation menu
NEW CMD Add simfid.py. Code for generating simulated 2D fids
IMPROVE GUI Add support for displaying NMRView file format FIDs in GUI.
NEW GUI Add peakList condition selector to peak inspector display
IMPROVE CMD Add properties map to PeakList to store arbitrary data in. Useful for RNA Peak tools
IMPROVE CMD Changes to .xpk2 file format. Different mode for flags, add scale field
BUG GUI Peak picking from keyboard should use existing list if present. Was always using list with name based on dataset even if another list linked to dataset was present.
IMPROVE CMD Add type column to .xpk2 files Type stores the type of peak
IMPROVE CMD Store solvent and temperature in dataset header
NEW GUI Add undo/redo for spectrum display.
NEW GUI Add project menus to nmrfxprocessorgui
BUG GUI Shouldn't move crosshair when control-button down. Fix append peak. Control-click is used for menu display wasn't working. Add warning about no open datasets.
IMPROVE CMD Add condition field to peaklist values in .xpk2 file
IMPROVE GUI Allow moving cross hair with meta-key down. Add checkbox for slice1. In selector mode you can now move crosshairs by dragging mouse with the meta-key . Cleaned up slice controls
IMPROVE GUI Allow dragging out a region on spectrum in selector mode. With shift down it selects peaks. With alt down it expands to selected region.
NEW GUI Add Dataset List with drag/drop and move Attributes to a popover. The Open button is replaced by a Dataset button which shows a list of currently open datasets. They can be dragged onto spectra. The attributes button now shows the Spectrum Attributes in a popover. The popover can be detached so it stays around like old one. When not detached there toolbar is not shown.
IMPROVE GUI Add a slice for second crosshair and make the slice colors (optionally) that of dataset.
NEW GUI Add Peak Selector to Spectrum Attributes dialog to allow specifying what peak list(s) is to be displayed.
NEW GUI Add simulate peak tab and code to call python methods
IMPROVE CMD Add read/write of frozen and color to peak .xpk2 files
IMPROVE GUI More work on Project. Keep list of open projects and a ref to active project. Provide getter to get active project
IMPROVE GUI Always write .mpk2 file when writing .xpk2 file
IMPROVE CMD When saving peak lists to project delete files that already exist, but don't have a peak list in memory
NEW GUI Add button for linking peaks in slider and activate/deactivate buttons based on number of peaks selected
NEW GUI Draw lines between linked peaks when slider active
NEW GUI Add ability to specify a search pattern in textfield of peak navigator
NEW GUI Initial add of peak navigator to bottom bar of chart window
NEW GUI Add aa and as keyboard bindings for peak add. Fix update of dataset name in peak reference inspector
NEW GUI Add Peak Reference tab
NEW GUI Implement PeakListener in PolyChart so the peaks move in response to changes in values.
NEW GUI Prompt for search dim string when doing cluster without search dim already set.