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 XCLI:
trendreconstruct.exe
in all platformsSynopsis
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 scripttrendreconstruct.exe
requires thattrendmain.exe
first be run with the--reconstruct
option turned on. Normallytrendmain.exe
will not save the files needed for PCA reconstruction unless the--reconst
option is used.- Note that each time when
trendmaingui
ortrendmain
launches it creates a temp directory to save temporary files fortrendplot
andtrendreconstruct
and deletes the old one (if it exists). This preparestrendreconstruct
to use the last run oftrendmain
ortrendmaingui
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 infile.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 intotrendmain.exe
. If input format ismovie
orpng
, the output format will be mp4 format movie clip. mp4 movie reconstructed frommovie
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 fortrendmain.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 thediff
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 oftrendmain.exe
will be stored. For example, iftrendmain.exe
was used with the-o example
option,--rmsd
option generates a file named asprefix-rmsd.txt
.-o [output prefix name]
-o
specifies the prefix of reconstructed files or images