#!/usr/bin/env python3

'''
Created on Wed Jun 10 14:15:02 2015

@author: suciud
'''
'''
Copyright (c) 2015 Computational Biomechanics (CoBi) Core, Department of
Biomedical Engineering, Cleveland Clinic

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to permit
persons to whom the Software is furnished to do so, subject to the
following conditions:

The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
-------------------

csv_filereader.py

DESCRIPTION:

Python script to read a csv file and output matrixes and aritmetic values.

REQUIREMENTS:

Python (http://www.python.org)
nptdms (https://pypi.python.org/pypi/npTDMS/)

DEVELOPERS:

Ahmet Erdemir
Computational Biomodeling (CoBi) Core
Department of Biomedical Engineering
Lerner Research Institute
Cleveland Clinic
Cleveland, OH
erdemira@ccf.org

'''

import sys
import csv
import numpy
import scipy
from numpy import array
import os
numpy.seterr(divide='ignore', invalid='ignore')
                            
#Check that passing argument has a file and the program to run                            
def USAGE(argv):             
    print('\n')
    print('USAGE: ', argv[0], ' <csv file>')
    print('\n')
    return "null"

#function that reads through the file and extract all frames, average them together, then scale them.
def csv_filereader(filename):
    file = open(filename,'r')
    lines = file.readlines()
    found_first = False    
    index = 0
    findindex =0
    scalefactor = 0.0
    current_array=[[]]
    accum_array=numpy.zeros(shape=(44,44))
    line=0
    count=0
    current_lists = []
    x=0
    #while the index is less than the total number of lines, and that the line is not a new line, or the end of the file
    while index<len(lines) and (line!='\n' or line!='@@\n'): 
        #store all lines
        line = lines[index]
        
        #if the first 12 characters of a line is 'SCALE_FACTOR' extract the next value and convert it into a float
        if line[:12]=='SCALE_FACTOR':  			
            str = "MPa / raw" 
            findindex = line.find(str)
            scale = line[14:findindex-1]
            #store the scaleing factor
            scalefactor = float(scale)  
            
        #if the first 4 characters of line is 'ROWS', and extract the next value and convert it to an integer  
        if line[:4]=='ROWS':  			
            str = "\n" 
            findindex = line.find(str)
            row = line[4:findindex]
            #store the value of rows
            rownums = int(row)			

        #if the first 5 characters of the line is "Frame" , get the next line, and count how the instances of "Frame"         
        if line[:5]=='Frame':
            #increase the index
            index += 1
            #reset the counter, that will be used to count the number of rows for the matrix
            count=0
            #reset the current list(where the next matrix will be stored)
            current_lists=list()
            #holds the index of where the new matrix starts
            line = lines[index]
            #counts the instances of 'Frame'
            x+=1
        
            #while the count is less the the number of rows
            while count<rownums: 
                #set the line to the index where the matrix starts                           
                line=lines[index]
                #convert each line of strings into an array of floats
                linenew=[float(k) for k in line.split(',')]
                #append each new array into the blank array making a matrix
                current_lists.append(linenew)
                #incrament index and count
                index+=1
                count+=1

        #if none of the above, while still reading through the file
        else:
            #incrament index
            index+=1
            #for the range of the matrix
            for i in range(len(current_lists)):
	       # iterate through columns 44 and 44 rows
                for j in range(len(current_lists[0])):
                    #add each matrix to a summation matrix
                    accum_array[i][j] = accum_array[i][j] + current_lists[i][j]

            
    #average this matrix by the number of matrixes, thenmultiply by the scaling factor
    accum_array=(accum_array/x)*scalefactor
    #return the averaged and scaled matrix
    return accum_array    

#find the maximum pressure in the found matrix
def max_pressure(filename):
    #get the matrix from the matrix reader
    matrix=filename
    x=[]
    for row in matrix:
        for value in row:
            #append the all of the values of the matrix into a list
            x.append(value)
    #return themaximum value
    return max(x)

#read the value of the area of one sensor square
def sesonrarea(filename):
    file = open(filename, "r")
    lines = file.readlines()
    index = 0
    findindex =0
    scalefactor = 0.0
    line=0
    x=0
    #while index is less than the length of the file and there is not a new line or end of the file
    while index<len(lines) and (line!='\n' or line!='@@\n'):
        #get the index of the line
        line = lines[index]
        # if the line starts with "SENSLE_AREA get the number value in that line
        if line[:11]=='SENSEL_AREA':
            str = "mm2"
            findindex = line.find(str)
            #extract the string, and convert it to a float
            area = line[12:findindex-1]
            senslearea = area
            #print('area one square: ', senslearea, "mm2")
            #incrament index
            index+=1
        #if parameter above is not found, incrament index
        else:
            index+=1
    #return the sensory area
    return float(senslearea)
  
#find the total area of pressure felt    
def pressure_area(filename):
    file = open(filename, "r")
    lines = file.readlines() 
    index = 0
    findindex =0
    scalefactor = 0.0
    line=0
    x=0
    sensor=0
    #while index is less than the length of the file and there is not a new line or end of the file
    while index<len(lines) and (line!='\n' or line!='@@\n'):
         #get the index of the line
        line = lines[index]
        # if the line starts with "SENSLE_AREA get the number value in that line        
        if line[:11]=='SENSEL_AREA':  			
            str = "mm2" 
            findindex = line.find(str)
            #extract the string, and convert it to a float
            area = line[12:findindex-1] 
            senslearea = area  
            #print('area one square: ',senslearea, "mm2")
            #incrament index
            index+=1
        #if parameter above is not found, incrament index    
        else:
            index+=1

    #get the matrix from the matrix reader       
    matrix=csv_filereader(filename)
    sensor=sesonrarea(filename)
    x=0
    for row in matrix:
        for value in row:
            if value>0:
                #how many squares have pressure data on them
                 x+=1
                 
    # the total area that pressure is taken from
    total_area=x*float(sensor)
    #the total are of the pressure pad
    possible_area=44*44*1.6129
    
    #Print the matrix into a text file
    text_file = open("Output.txt", "w")       ###see if this is correct
    text_file.write("\n Matrix:\n %s" % matrix)
    text_file.seek(0)
    text_file.close()
    #append the sensle area into a text file
    text_file = open("Output.txt", "a")       ###see if this is correct
    text_file.write("\n Sensle Area: %s" % sensor)
    text_file.close() 
    #append the pressure area into a text file
    text_file = open("Output.txt", "a")       ###see if this is correct
    text_file.write("\n Pressure Area: %s" % total_area)
    text_file.close()
    #print(total_area)
    return total_area

#get the equations and values of the integral
from scipy import integrate
def integral(x,a,b):
    return a*b
    
#solve the integral setup
def intsolve(filename):
    matrix=csv_filereader(filename)
    #the parameters of the integration are between the area and the maximum pressure
    args=(sesonrarea(filename),max_pressure(matrix))  
    maxp=max_pressure(matrix)   
    #append the maximum pressure into a text file
    text_file = open("Output.txt", "a")       ###see if this is correct'
    text_file.seek(0)
    text_file.write("\n Max Pressure: %s" % maxp)
    text_file.close()  
    #run the integral
    results = integrate.quad(integral,0, pressure_area,args)
    #append the output integral into a text file
    text_file = open("Output.txt", "a")      
    text_file.write("\n Integral: %s" %results[0])
    text_file.close()
    #return the result of the integral
    return results[0]

#make this script callable from the terminal, and run all of its functions
if __name__ == "__main__":
    data = csv_filereader(sys.argv[-1])
    max_pressures = max_pressure(data)
    data2=sesonrarea(sys.argv[-1])
    pressure_area=pressure_area(sys.argv[-1])
    intsolve=intsolve(sys.argv[-1])