#Jeff Hardin, Dept. of Integrative Biology
#Univ. of Wisconsin-Madison
#jdhardin@wisc.edu

#Additional colors (see also https://htmlcolorcodes.com/color-picker/)
#Green = #32a852
#Purple = #7132a8
#Dark red = #9C2005
#Dark brown = #754F04
#Light brown = #9C6905

#This script imports data from one or more CSV files in the form x[i],y[i] as paired columns
#using the ImageJ's built-in support for importing CSV files in a ResultsTable
#and ImageJ's built-in  Plot functions.

#Currently uses the hard-wired colors built into ImageJ's Plot class
#Could be expanded to a nicer color palette using hexadecimal colors.
#Use the PlotWindow "More >> " button to change range, line thickness, colors, etc.

#Ideally, one could open the CSV using a parser without opening a data window.
#Using JFreeChart would also be great, since JFreeChart can export
#as an editable SVG file.

from org.jfree.chart import ChartFactory, ChartPanel, JFreeChart  
from org.jfree.chart.plot import PlotOrientation, XYPlot
from org.jfree.data.xy import XYDataset, XYSeries, XYSeriesCollection
from org.jfree.chart.plot import PlotOrientation, XYPlot
from org.jfree.data.xy import XYDataset, XYSeries, XYSeriesCollection
from org.jfree.data.category import DefaultCategoryDataset
from org.jfree.chart.ui import RectangleEdge
from javax.swing import JFrame  
import java.awt.Color as Color
from java.awt import Dimension, BasicStroke
import java.awt.Frame as Frame
import java.awt.Window as Window
from java.io import File as File
from java.lang import System as System
from ij import WindowManager as WindowManager
from ij.plugin.frame import RoiManager as RoiManager
from ij.process import ImageStatistics as ImageStatistics
from ij.measure import Measurements as Measurements
from ij import IJ as IJ
from ij.measure import CurveFitter as CurveFitter
from ij.gui import Plot as Plot
from ij.gui import PlotWindow as PlotWindow
from ij.gui import ImageWindow as ImageWindow
from ij.gui import GenericDialog
from ij import ImagePlus as ImagePlus
from ij.io import FileInfo as FileInfo
from ij.measure import ResultsTable as ResultsTable
from ij import WindowManager as WindowManager
import math
import os
from os import path, mkdir
import csv

#below from 
#https://stackoverflow.com/questions/736043/checking-if-a-string-can-be-converted-to-float-in-python
def isfloat(value):
  try:
    float(value)
    return True
  except ValueError:
    return False

def doPlot():
	lineseparator = "\n"
	cellseparator = ","
	plotColor=[]
	plotColor = ("black", "red", "blue", "#32a852", "#7132a8", "#9C2005", "#754F04", "magenta", "darkGray", "gray", "lightGray", "green", "#9C6905", "cyan", "orange", "pink", "yellow");
	#Call below is a feature of Fiji/IJ2
	#See https://imagej.net/scripting/parameters
	k = len(listOfPaths)
	#for i in range(0, k):
		#print(listOfPaths[i])

	## Ask if a single X and multiple Y columns or paired columns
	gd = GenericDialog("Data Structure")
	dataStructure = ["Single X column", "Paired X and Y columns"]
	gd.addRadioButtonGroup("Data structure:", ["Single X column", "Paired X and Y columns"], 1,2,"Paired X and Y columns")
	gd.showDialog()	
	if gd.wasOKed():
		pairedChoice = gd.getNextRadioButton()
	else: 
		return None

	#if pairedChoice == "Single X column":
		#IJ.showMessage("Not implented yet!")
		#return None	

	for i in range(0, k):
		#read in data from CSV file
		#copies the whole file to an array of lines
		#have to type cast pathnames to Python str
		text_file = open(str(listOfPaths[i]), "r")
		#Use a Java method instead (need JVM 7+)
		file = File(str(listOfPaths[i]))
		#get file name using getName()
		filename = file.getName()
		
		#read whole file to a string
		data = text_file.read()
		#close file
		text_file.close()		
		#separate into lines of text
		lines=data.split(lineseparator)
		numRows = len(lines)	
		# recreates the columns headers
		labels=lines[0].split(cellseparator)
		#get total columns
		numCol = len(labels)
		
		if pairedChoice == "Paired X and Y columns":
			# If paired columns		
			#set up plot using ImageJ plot function
			myPlot=Plot(filename, "X", "Y")
			myPlot.setLineWidth(2)
			#IJ.open(str(listOfPaths[i]))	
			legendString = labels[0] + " v. " + labels[1]
			for m in range(0, numCol/2):
				x1=[]
				y1=[]
				#Iterate over each row in the csv using reader object
				#assume header row; skip this, since we already did this above
				for j in range(1,numRows):
					row=lines[j].split(cellseparator)
					#print("Row:")
					#print(row)
					#print(len(row))
					#added this because some CSV files have a trailing carriage return...
					if (len(row) > 1):				
					#need to add code to check for empty cells, since ImageJ
					#produces CSV files in which there can be unequal numbers of rows with empty cells
					#Jython interpreter crashes when trying to convert to float if cell is blank
					#ImageJ plot functions are savvy about blank cells, but this code isn't!
						if ((isfloat(row[2*m])) and (isfloat(row[2*m+1]))):
							x1.append(float(row[2*m]))
							y1.append(float(row[2*m+1]))
				myPlot.setColor(plotColor[m])
				myPlot.add("Line",x1,y1)
				if (m > 0):
					legendString = legendString + "\t" + labels[2*(m)] + " v. " + labels[2*m+1]
		
			#Removes gridlines; delete if you like these...
			myPlot.setFormatFlags(0x330f)
			myPlot.show()
			myPlot.setColor("black")
			myPlot.setLegend(legendString,Plot.AUTO_POSITION)
			myPlot.setLimitsToFit(True)

		else:
			# If single X column and multiple Y columns
			#set up plot using ImageJ plot function
			myPlot=Plot(filename, "X", "Y")
			myPlot.setLineWidth(2)
			#IJ.open(str(listOfPaths[i]))	
			legendString = ""
			for m in range(1, numCol):
				x1=[]
				y1=[]
				#Iterate over each row in the csv using reader object
				#assume header row; skip this, since we already did this above
				for j in range(1,numRows):
					row=lines[j].split(cellseparator)
					#print("Row:")
					#print(row)
					#print(len(row))
					#added this because some CSV files have a trailing carriage return...
					if (len(row) > 1):				
					#need to add code to check for empty cells, since ImageJ
					#produces CSV files in which there can be unequal numbers of rows with empty cells
					#Jython interpreter crashes when trying to convert to float if cell is blank
					#ImageJ plot functions are savvy about blank cells, but this code isn't!
						if ((isfloat(row[0])) and (isfloat(row[m]))):
							x1.append(float(row[0]))
							y1.append(float(row[m]))
				myPlot.setColor(plotColor[m])
				myPlot.add("Line",x1,y1)
				if (m == 1):
					legendString = labels[m]
				else:
					legendString = legendString + "\t" + labels[m]
		
			#Removes gridlines; delete if you like these...
			myPlot.setFormatFlags(0x330f)
			myPlot.show()
			myPlot.setColor("black")
			myPlot.setLegend(legendString,Plot.AUTO_POSITION)
			myPlot.setLimitsToFit(True)

#main
#@ File[] listOfPaths (label="select files", style="files")
doPlot()