#!/usr/bin/env python

"""
An Jython dropbox for importing HCS image datasets produced by the scripts that generate platonic screening data.

The folder loaded to the dropbox folder should have the same name as the plate that the data will be attached to.
"""

import os
from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1 import SimpleImageDataConfig, ImageMetadata, Location, Channel, ChannelColor, ChannelColorComponent
from ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations import ImageTransformationBuffer
from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import Geometry


class ImageDataSetFlexible(SimpleImageDataConfig):
  """
  Extracts tile number, channel code and well code for a given relative path to an image.
  Will be called for each file found in the incoming directory which has the allowed image extension.
    
  Example file name: bDZ01-1A_wD17_s3_z123_t321_cGFP
  Returns:
    ImageMetadata
  """
  def extractImageMetadata(self, imagePath):
    image_tokens = ImageMetadata()

    basename = os.path.splitext(imagePath)[0]
    #
    token_dict = {}
    for token in basename.split("_"):
      token_dict[token[:1]] = token[1:]

    image_tokens.well = token_dict["w"]
    fieldText = token_dict["s"]
    try:
      image_tokens.tileNumber = int(fieldText)
    except ValueError:
      raise Exception("Cannot parse field number from '" + fieldText + "' in '" + basename + "' file name.")

    image_tokens.channelCode = token_dict["c"]
    return image_tokens

  """
  Overrides the default implementation which returns (1, maxTileNumber) geometry.
  
  Calculates the width and height of the matrix of tiles (a.k.a. fields or sides) in the well.
  
  Parameter imageMetadataList: a list of metadata for each encountered image
  Parameter maxTileNumber: the biggest tile number among all encountered images
  Returns:
    Geometry
  """
  def getTileGeometry(self, imageTokens, maxTileNumber):
    return Geometry.createFromRowColDimensions(maxTileNumber / 3, 3);
  
  """
  Overrides the default implementation which does the same thing (to demonstrate how this can be done). 
  
  For a given tile number and tiles geometry returns (x,y) which describes where the tile is
  located on the well.
  
  Parameter tileNumber: number of the tile
  Parameter tileGeometry: the geometry of the well matrix
  Returns:
     Location
  """
  def getTileCoordinates(self, tileNumber, tileGeometry):
    columns = tileGeometry.getWidth()
    row = ((tileNumber - 1) / columns) + 1
    col = ((tileNumber - 1) % columns) + 1
    return Location(row, col)

  def getChannelColor(self, channelCode):
    # codes should be in upper case
    dict = { "GFP" : ChannelColor.GREEN, "DAPI" : ChannelColor.BLUE, "CY3" : ChannelColor.RED_BLUE, "CY5" : ChannelColor.RED }
    if channelCode in dict:
      return dict[channelCode]
    else:
      return None

def getAvailableChannelTransformations():
  """
  Create a collection of transformations that are applicable to the image
  """
  transforms = ImageTransformationBuffer()
  transforms.appendImageMagicConvert("-radial-blur 30", "Radial Blur")
#  transforms.appendImageMagicConvert("-motion-blur 0x12+45", "Motion Blur")
  return transforms.getTransformations()

def process(transaction):
  incoming = transaction.getIncoming()
  if incoming.isDirectory(): 
    imageDataset = ImageDataSetFlexible()
    imageDataset.setRawImageDatasetType()
    imageDataset.setPlate("PLATONIC", incoming.getName())

    transforms = getAvailableChannelTransformations()
    for resolution in ['128x128']:
      representation = imageDataset.addGeneratedImageRepresentationWithResolution(resolution)
      for channel in ["DAPI", "GFP", "Cy5"]:
        representation.setTransformation(channel, transforms[0].getCode())

    # Add transforms to the channels
    channels = [ Channel(code, code) for code in ["DAPI", "GFP", "Cy5"]]
    for channel in channels:
      channel.setAvailableTransformations(transforms)

    dataSet = transaction.createNewImageDataSet(imageDataset, incoming)
    transaction.moveFile(incoming.getPath(), dataSet)