README.md

In chz31/SlicerMorphR: Import SlicerMorph data into R

SlicerMorphR

R convenience functions for importing SlicerMorph dataset

install via devtools

devtools::install_github('SlicerMorph/SlicerMorphR')

Usage

• read.markups.fcsv : Reads the 3D Slicer Markups file saved in fcsv format
• read.markups.json: Reads the 3D Slicer Markups file saved in json format (the default format)
• write.markups.fcsv: Writes a matrix of 3D LM coordinates in 3D Slicer's Markups format as fcsv. By default LM coordinates are written with LPS (Left-Posterior-SUperior) coordinate system header, which is default in Slicer.
• parser : Reads and parses the analysis.log file as output by the SlicerMorph's GPA module.

> library(SlicerMorphR)
# point out to the analysis.log file created by the SlicerMorph's GPA function. 
> SM.output=parser(file.choose(), forceLPS = TRUE)
#For details of the forceLPS parameter, please see the example of read.markup.fcsv() below and its associated help file
Warning message:
In readLines(file) :
  incomplete final line found on 'C:\Users\murat\Desktop\2021-08-09_14_17_38\analysis.log'
> SM.output
$input.path
[1] "C:/Semi_LM_paper/landmark sets/Gorilla/sphere"

$output.path
[1] "C:/Users/murat/Desktop/2021-08-09_14_17_38"

$files
 [1] "USNM174715-Cranium.vtk_SL_warped.fcsv"         
 [2] "USNM174722-Cranium.vtk_SL_warped.fcsv"         
 [3] "USNM176209-Cranium.vtk_SL_warped.fcsv"         
 [4] "USNM176211-Cranium.vtk_SL_warped.fcsv"         
 [5] "USNM176216-Cranium.vtk_SL_warped.fcsv"         
 [6] "USNM176217-Cranium.vtk_SL_warped.fcsv"         
 [7] "USNM220060-Cranium.vtk_SL_warped.fcsv"         
 [8] "USNM220324-Cranium.vtk_SL_warped.fcsv"         
 [9] "USNM252575-Cranium.vtk_SL_warped.fcsv"         
[10] "USNM252577-Cranium.vtk_SL_warped.fcsv"         
[11] "USNM252578-Cranium.vtk_SL_warped.fcsv"         
[12] "USNM252580-Cranium.vtk_SL_warped.fcsv"         
[13] "USNM297857-Cranium.vtk_SL_warped.fcsv"         
[14] "USNM582726-Cranium.vtk_SL_warped.fcsv"         
[15] "USNM590942_CRANIUM.vtk_SL_warped.fcsv"         
[16] "USNM590947_CRANIUM.vtk_SL_warped.fcsv"         
[17] "USNM590951_CRANIUM.vtk_SL_warped.fcsv"         
[18] "USNM590953_CRANIUM.vtk_SL_warped.fcsv"         
[19] "USNM590954_CRANIUM.vtk_SL_warped.fcsv"         
[20] "USNM599165_CRANIUM_MANDIBLE.vtk_SL_warped.fcsv"
[21] "USNM599166_CRANIUM.vtk_SL_warped.fcsv"         
[22] "USNM599167_CRANIUM.vtk_SL_warped.fcsv"         

$format
[1] ".fcsv"

$no.LM
[1] 2304

$skipped
[1] FALSE

$semi
[1] TRUE

$semiLMs
[1] " "

$scale
[1] TRUE

$MeanShape
[1] "MeanShape.csv"

$eigenvalues
[1] "eigenvalues.csv"

$eigenvectors
[1] "eigenvectors.csv"

$OutputData
[1] "OutputData.csv"

$pcScores
[1] "pcScores.csv"

$ID
 [1] "USNM174715-Cranium.vtk_SL_warped"          "USNM174722-Cranium.vtk_SL_warped"         
 [3] "USNM176209-Cranium.vtk_SL_warped"          "USNM176211-Cranium.vtk_SL_warped"         
 [5] "USNM176216-Cranium.vtk_SL_warped"          "USNM176217-Cranium.vtk_SL_warped"         
 [7] "USNM220060-Cranium.vtk_SL_warped"          "USNM220324-Cranium.vtk_SL_warped"         
 [9] "USNM252575-Cranium.vtk_SL_warped"          "USNM252577-Cranium.vtk_SL_warped"         
[11] "USNM252578-Cranium.vtk_SL_warped"          "USNM252580-Cranium.vtk_SL_warped"         
[13] "USNM297857-Cranium.vtk_SL_warped"          "USNM582726-Cranium.vtk_SL_warped"         
[15] "USNM590942_CRANIUM.vtk_SL_warped"          "USNM590947_CRANIUM.vtk_SL_warped"         
[17] "USNM590951_CRANIUM.vtk_SL_warped"          "USNM590953_CRANIUM.vtk_SL_warped"         
[19] "USNM590954_CRANIUM.vtk_SL_warped"          "USNM599165_CRANIUM_MANDIBLE.vtk_SL_warped"
[21] "USNM599166_CRANIUM.vtk_SL_warped"          "USNM599167_CRANIUM.vtk_SL_warped"         

$LM
, , USNM174715-Cranium.vtk_SL_warped

             x        y          z
1    113.57322 289.4062  -47.68592
2    108.90213 289.2997  -48.16833
3    111.90668 292.8073  -46.45086
4    107.57013 293.4006  -46.32930
5    104.77066 290.7697  -47.70352
6    105.19183 287.0535  -48.59508
7    108.95377 285.2464  -48.92385
8     93.12697 315.0776 -146.69631
9     91.10847 326.3815 -130.82622
10    78.21323 327.9392 -126.33089
11    73.24375 307.2772 -116.18021
12   104.85556 301.4360 -103.32111
13   118.44697 289.5207  -46.93095
14   123.72807 289.7841  -46.25342
15   129.60968 290.5058  -46.02137


#An example of using read.markups.fcsv() with the forceLPS parameter
#forceLPS = FALSE
> file = "https://raw.githubusercontent.com/SlicerMorph/SampleData/master/Gorilla_template_LM1.fcsv"
> lms = read.markups.fcsv(file = file, forceLPS = FALSE) #default setting for forceLPS
#Return a 41x3 matrix that stores raw landmark coordinates from the fcsv files; rownames = labels in the FCSV file; colnames = "x", "y", "z"
> lms[1:3, ]
                             X       Y         Z
Gorilla_template_LM1-1 111.987 312.757 -148.0780
Gorilla_template_LM1-2 114.785 381.650 -128.2390
Gorilla_template_LM1-3 109.137 294.534  -97.4347

#forceLPS = TRUE
> file = "https://raw.githubusercontent.com/SlicerMorph/SampleData/master/Gorilla_template_LM1.fcsv"
> lms = read.markups.fcsv(file = file, forceLPS = TRUE)
#Because forceLPS = TRUE, the function will read the "coordinateSystem" in the 2nd line of the fcsv to see if it is "LPS"
> x <- readLines(file, n = 2)
> x[[2]]
[1] "# CoordinateSystem = 0"
#The coordinateSystem is not "LPS", so the signs of x, y coordinates are reversed to be consistent with the LPS coordinate system.
> lms[1:3, ]
                           [,1]     [,2]      [,3]
Gorilla_template_LM1-1 -111.987 -312.757 -148.0780
Gorilla_template_LM1-2 -114.785 -381.650 -128.2390
Gorilla_template_LM1-3 -109.137 -294.534  -97.4347

...

chz31/SlicerMorphR documentation built on Feb. 10, 2023, 11:56 p.m.