import csv

import re

import numpy as np

import SimpleITK as sitk

def extract_coordinates(file):

    csvfile = open(file,'r')

    reader_iter = csv.reader(csvfile,delimiter=',')

    fiducials_coord = list()

    for row in reader_iter:

      #Find row whose first column is a Fiducial MRML node

      match = re.search('vtkMRMLMarkupsFiducialNode.*',row[0])

      if match == None:

        pass

      else:

        if match.end() == len(row[0]):

          #Extract x,y,z and package them in a list

          fiducials_coord.append([row[1],row[2],row[3]])

    #print ("Extracted Fiducial Coordinages "+str(fiducials_coord))

    return fiducials_coord

def extract_indices_annotation(coordinates,image):

    annotation_index = list()

    img = sitk.ReadImage(image)

    cor_arr = np.asarray(coordinates)

    cor_arr = cor_arr.astype(np.float)

    for point in cor_arr:

    #multiple by -1 x and y to convert RAS (Slicer) to LPS (nifti format)

      point[0] = point[0]*-1

      point[1] = point[1]*-1

      annotation_index.append(img.TransformPhysicalPointToIndex(point))

    return annotation_index