'''
# Previous GUI
# @File(label="Image directory", style="directory") inFolder
# @String(label="Image File Extension", required=false, value=".tif") image_extension
# @Boolean(label="Show stack ?", value="True") ShowStack
# @Boolean(label="Save Stack ?", description="Stacks will be saved in a 'HyperStack' folder in the image folder",value = "True") SaveStack

HYPERSTACK GENERATOR
Read all tif images from an experiment inFolder that contains tif images for the different wells, channel, slices and timepoints
The script will automatically reads the field from the filename (using index in the string - FOLLOWING ACQUIFER-IM04 NAMING CONVENTION ex: -A001--...) to generate the well's stack

TO DO : 
- Prevent exception if no well selected
'''
import os, ij
import ij.plugin as plugin
from ij             import IJ
from fiji.util.gui  import GenericDialogPlus
from java.awt.event import ActionListener

class ListenerClass_All(ActionListener): # extends action listener
	'''Class associated to the Select all button''' 
	
	def actionPerformed(this,event):
		'''Called when 'Select All' is clicked'''
		global Win
		
		for checkbox in Win.getCheckboxes()[2:]: 
			checkbox.setState(True) 


class ListenerClass_None(ActionListener): # extends action listener
	'''Class associated to the Select none button''' 
	
	def actionPerformed(this,event):
		'''Called when 'Select None' is clicked'''
		global Win
		
		for checkbox in Win.getCheckboxes()[2:]: 
			checkbox.setState(False) 
		

ListenerAll  = ListenerClass_All()  # create an instance of the EventListener class
ListenerNone = ListenerClass_None() # create an instance of the EventListener class

# Input GUI window  
Win = GenericDialogPlus("Hyperstack generator - Parameters") # Title of the window
Win.enableYesNoCancel('OK','Cancel') # OK, Cancel (chosen) and Cancel button
Win.hideCancelButton()               # keep only one cancel button

Win.addDirectoryField("Image directory","MyPath")
Win.addStringField("Image file extension",".tif")
Win.addCheckbox("Show stack ?",True)
Win.addCheckbox("Save stack ?",True)

# Generate tick box with plate layout to select well
Wells = []
for letter in ['A','B','C','D','E','F','G','H']:
	for column in range(1,13):
		Wells.append(letter+'%(column)03d' %{"column":column}) # force max 3 digits and leading 0

Win.addCheckboxGroup(8,12,Wells,[True]*96)
Win.addButton('Select all' ,ListenerAll) # add our event listener to the button. Button clicked -> event -> call actionPerformed(MyEvent)
Win.addButton('Select none',ListenerNone)
Win.showDialog()

# Recover Path to template
if (Win.wasOKed()): 
	inFolder        = Win.getNextString()
	image_extension = Win.getNextString()
	Bool            = [checkbox.getState() for checkbox in Win.getCheckboxes()]
	ShowStack       = Bool[0]
	SaveStack       = Bool[1]
	BoolWell        = Bool[2:] 
	Selection       = {well:choice for well,choice in zip(Wells,BoolWell)} 
	#print Selection
	#print len(Wells) # OK 96
	

	# Find image files for the given channel
	#inFolder = str(inFolder) # convert filename object to string object
	WellList    = [] # full list of well to know how many iteration for stacking
	TimeList    = []
	ChannelList = []
	SliceList   = []
	MainList    = [] # contains tuple with (Filename, Well, TimePoint, Channel, Z-Slice)

	for fname in os.listdir(inFolder):
		if fname.endswith(image_extension):
			
			Well = fname[1:5]
			
			if Selection[Well]: # selected in the GUI
				try : # int conversion through an error if the argument string is empty 
					Time 	= int(fname[15:18])
					Channel = int(fname[22:23])
					Slice 	= int(fname[27:30]) 
				except :
					raise Exception("Could not get experimental parameters from filename. Check filename pattern (IM04 convention)")
		
				WellList.append(Well)
				TimeList.append(Time)
				ChannelList.append(Channel)
				SliceList.append(Slice)
				MainList.append((fname,Well,Time,Channel,Slice))

			else : # the well was not selected in the GUI
				continue

			
	if len(MainList) < 1:
		raise Exception("No image files found in %s. Check if extension match and if filenames match IM04 naming convention" % inFolder)

	# Sort list to prepare iteration
	WellList = list(set(WellList)) # turn to a set object to have unique item once only 
	WellList.sort() 			   # sort should be after set since set may change order 

	TimeList = list(set(TimeList)) 
	TimeList.sort() 			  

	ChannelList = list(set(ChannelList)) 
	ChannelList.sort()

	SliceList = list(set(SliceList)) 
	SliceList.sort() 

	# Verification
	print 'Well  : ', WellList
	print 'Time  : ', TimeList
	print 'ChannelIdx  : ', ChannelList
	print 'Z-Slice : ' , SliceList


	MainList.sort( key = lambda field:(field[1], field[2], field[4], -field[3]) ) # sort by Well, Time, Z-slice then Channel (- to have C06 ie BF first) since the hyperstack is created following the default "xyczt" order
	'''
	for i in MainList :
		print i
	'''

	# Open first image to get the image size (needed to setup the stack) or find another way to do the stack
	ImagePath = os.path.join(inFolder,MainList[0][0])
	Image     = ij.IJ.openImage(ImagePath)
	Width  = Image.width
	Height = Image.height

	# Initialise HyperStackConverter object
	HyperStacker = plugin.HyperStackConverter() 

	for well in WellList: # Loop over well to do stack and projection
		
		IJ.log('Process well : '+well+'...')
		SubList = [item for item in MainList if item[1]==well] # Sublist containing (fname,Well,Time,Channel,Slice) for one given well ex: only A001 
		#print 'StackSize : ',len(SubList)
		
		Stack = ij.ImageStack(Width,Height) # create stack objet that will contains all images of this well (further turned into an hyperstack)
		
		for item in SubList : # Loop over tuples of SubList, open associated images and append it to the stack
			filename = item[0]
			ImagePath = os.path.join(inFolder,filename)
			Image = ij.IJ.openImage(ImagePath)
			
			Stack.addSlice(filename,Image.getProcessor()) # conversion to ImageProcessor object to append to stack

		Stack = ij.ImagePlus(well,Stack) # reconverting back to an ImagePlus object to be able to show and save it
		#print Stack
		#Stack.show() # Good

		if 	Stack.getNSlices()>1 : 
			# Convert to Hyperstack
			HyperStack = HyperStacker.toHyperStack(Stack,len(ChannelList), len(SliceList), len(TimeList),"xyczt","grayscale") # convert PROPERLY ORDERED Stack to Hyperstack
		
		else: 
			# Keep as single image
			HyperStack = Stack

			
		if ShowStack : 
			HyperStack.show()

		if SaveStack :
			outFolder = os.path.join(inFolder,'HyperStack')
			if not os.path.exists(outFolder): os.makedirs(outFolder) # create folder if it does not exist (for the first image to save basicly)
			
			outPath = os.path.join(outFolder,well+'.tif')
			IJ.save(HyperStack,outPath)
			
	IJ.log('Done')