Reconstruction script – Use the PCA results from the Main script to model the 2D measurements

• GUI and CLI programs

  GUI: trendreconstructgui.exe in Windows and Linux, trendreconstructgui.app in OS X

  CLI: trendreconstruct.exe in all platforms

• Synopsis

  trendreconstruct.exe -n [components] -m [1/2/3/4]] [-e] [-p] [-r] [-z] 
  [-d] [--rmsd] [--gif] [--dpi integral for dpi of output PNG files]
  

• Description

  • trendreconstruct.exe rebuilds the original 2D measurements using the first N principal components requested by the user. The script trendreconstruct.exe requires that trendmain.exe first be run with the --reconstruct option turned on. Normally trendmain.exe will not save the files needed for PCA reconstruction unless the --reconst option is used.
  • Note that each time when trendmaingui or trendmain launches it creates a temp directory to save temporary files for trendplot and trendreconstruct and deletes the old one (if it exists). This prepares trendreconstruct to use the last run of trendmain or trendmaingui performed with the --reconstruct option turned on.

• Options

  • -n component(s) selected for reconstruction
-n specifies principal components selected to use in rebuilding the original measurements. For example, -n 1 means reconstruct the 2D measurements using only the first component, while -n 3 uses the third component. To reconstruct individual, non-consecutive components, you can separate the page numbers with commas: e.g. -n 2,4,6 would reconstruct using the second, fourth, and sixth components. To reconstruct the range of components 1 to 3, use -n 1-3. Range and individual components can be selected together, e.g. -n 1,3-5,7 means reconstruction by components 1, 3, 4, 5, 7. Note space is not allowed between selected components unless quotation marks are used. i.e. -n '1, 3-5, 7'.
  • -m [1/2/3/4]Background: trendmain.exe reorganizes the measurements listed in file.index as a large 2D matrix, filters them, and scales them for PCA. The -m option specifies which stage of the process should be reconstructed. -m specifies which matrix will be reconstructed. The choices are:

matrix mode	meaning
1	This recovers the state right before doing PCA. The large 2D matrix is row (column) scaled, with unchanged rows and noisy regions filtered out
2	This differs from matrix mode 1 in that the rows (columns) are unscaled
3	This option also recovers the filtered, unchanged rows from matrix mode 2
4*	This option differs from matrix mode 3 in also recovering the low intensity regions filtered out from being below the threshold

* mode 4 is for Fourier-Transformed 2D NMR spectra where -r option was used in trendmain.exe to set the threshold for filtering low intensity regions.

• -e-e is optional. When it is on, the reconstructions of the measurements are exported in the same format as the original measurements read into trendmain.exe. If input format is movie or png, the output format will be mp4 format movie clip. mp4 movie reconstructed from movie shares the same time length as the input movie. mp4 movie reconstructed from a series of PNG images is set as 10 second long.
• -p-p is optional. When it is on, the reconstructed images are exported as images in PNG format.
• --gif
--gif is optional. When it is on, the reconstructed movies are exported as GIF animation just in case there is no appropriate media player to play .mp4 movie clip generated by -e. GIF animation is more compatible since most web browsers can play it, although it has larger size than mp4.
• --dpi
  When -p option is turned on, --dpi specifies the dots-per-inch resolution of the png files to be reconstructed. By default, this is set to 96. This option is not required.
• -z
-z option is used to recover rows that do not change and hence was filtered out before doing PCA.
• -r
-r is used only when reconstructing 2D Fourier-transformed NMR spectra. When doing PCA on 2D NMR spectra, a threshold can be set to filter out noisy regions using the -r option for trendmain.exe. The -r option can be used in reconstruction to recover those noisy regions in order to fully recover the original spectra. It is not required and is usually not necessary.
• -d or --diff
-d turns on the diff mode, exporting difference spectra instead of reconstructed spectra. It is used to visualize the difference between original and reconstructed spectra.
• --rmsd
--rmsd calculates the RMSD between the reconstructed and original data for all principal components. A file with suffix name as -rmsd.txt and prefix name specified by the -o option of trendmain.exe will be stored. For example, if trendmain.exe was used with the -o example option, --rmsd option generates a file named as prefix-rmsd.txt.
• -o [output prefix name]
-o specifies the prefix of reconstructed files or images