From 4eef435b6828109b1e1389d89641a398afb30a2e Mon Sep 17 00:00:00 2001 From: = Date: Thu, 21 Jan 2021 13:32:21 +0200 Subject: [PATCH] update readme --- README.md | 52 ++++++++++++++++++++++------------------------------ 1 file changed, 22 insertions(+), 30 deletions(-) diff --git a/README.md b/README.md index 2bbeafc..729f7b1 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,9 @@ # Ear-measures -This series of R scripts calculates various 3D distance, angle, and surface areas from 3D coordinate input in the form of *.fcsv (Slicer) or *.pp (MeshLab) files. +This series of R scripts calculates various 3D distance, angle, and surface areas from 3D coordinate input in the form of *.fcsv (from 3D Slicer) or *.pp (from MeshLab) files. -The inputs are a set of five *.fcsv files from 3D slicer and picked point files (*pp) from Meshlab. Specifically, the inputs are 5 files the tympanic membrane (TM), extracolumella (EC), round window (RW), cochlear aqueduct (CA) and columella footplate (FP): +## Data inputs +The inputs are a set of four *.fcsv files from 3D slicer and one picked point files (*pp) from Meshlab. Specifically, there are separate coordinates files for tympanic membrane (TM), extracolumella (EC), round window (RW), cochlear aqueduct (CA) and columella footplate (FP): 1) a *.fcsv file outlining the perimeter of the tympanic membrane with > 20 points 2) a *.fcsv file with 5 coordinates outlining the following landmarks, in this order: @@ -15,13 +16,13 @@ The inputs are a set of five *.fcsv files from 3D slicer and picked point files 4) a *.fcsv file outlining the perimeter of the round window with > 20 points 5) a *.fcsv file outlining the perimeter of the cochlear aqueduct with > 20 points -Example input coordinates are in the 'Input' folder. +> Example input coordinates are in the 'Input' folder. - -The outputs are: - -3 csv files with -(1) the computed values, (2) tympanic membrane angles, and (3) the coordinates used for calculations. +## Data outputs +The outputs are 3 csv files with +(1) the computed values, +(2) tympanic membrane angles, and +(3) the coordinates used for calculations. **Computed values:** 1) Height of tympanic membrane protrusion (Middle ear), @@ -39,46 +40,37 @@ The outputs are: In addition, there are scripts to plot wireframe diagrams based on the coordinates using the ‘rgl’ package. -(4) wireframe plots -(4) fcsv and stle files of the wireframe plots - +## Scripts Script for importing the coordinates and running the calculation scripts: > Import, calculate and export MASTER.R This script calls the following calculation scripts: -> 1_Tympanic membrane area, EC object coltip 2nd position.R - calculations of tympanic membrane area - -> 2_Footplate area.R - calculation of footplate area - -> 3_Cochlear aqueduct area.R - calculation of cochlear aqueduct area - -> 4_Round window area.R - calculation of round window area - -> 5_3D planes of best fit and angles between.R - calculation of planes of best fit for the base of the tympanic membrane and the columella footplate, and the angle between these two planes - -> 6_Euclid_dist to plane_ EC length_ col length.R - various 3D distance measurements - -> 7_Plotting the shortest distance from point to plane - calculations for plotting the shortest distance form a point to a plane - -> 8_TM angles and EC_col angle - calculation of angles of the tympanic membrane +> 1_Tympanic membrane area, EC object coltip 2nd position.R - calculations of tympanic membrane area +2_Footplate area.R - calculation of footplate area +3_Cochlear aqueduct area.R - calculation of cochlear aqueduct area +4_Round window area.R - calculation of round window area +5_3D planes of best fit and angles between.R - calculation of planes of best fit for the base of the tympanic membrane and the columella footplate, and the angle between these two planes +6_Euclid_dist to plane_ EC length_ col length.R - various 3D distance measurements +7_Plotting the shortest distance from point to plane - calculations for plotting the shortest distance form a point to a plane +8_TM angles and EC_col angle - calculation of angles of the tympanic membrane -File for plotting the planes and coordinates as a wireframe diagram: +It also calls a script for plotting the planes and coordinates of the values as a wireframe diagram: > plotearauto.R ![alt text](Capture.png) -File for combining all measurements and exporting as csv: +It also calls an export script, which exports the data in different formats: > outputs.R -The for each specimen, the output scripts puts data, with each file name unique for each specimen, into the following 5 folders: +For each specimen, the output scripts creates a unique set of data files, into the following 5 folders: 1) Coordinates - X,Y,Z coordinates of all points in a single csv file 2) FCSV - has fcsv points of all measurements for visualizing the wireframe plots in 3D Slicer 3) Single values - the computed values (these values used for the dataset) 4) STL files of the wireframe plots -5) TM angles - files with angles for each 16 perimeter points \ No newline at end of file +5) TM angles - files with the tympanic membrane angles for each 16 perimeter points \ No newline at end of file