update readme

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
+5) TM angles - files with the tympanic membrane angles for each 16 perimeter points