import glob, os
import pyworkflow.em.packages.relion as relion
import pyworkflow.em.metadata as md
import datetime
initTime = datetime.datetime.now()

fnStar='particles_data.star'
#fnStar='shiny_200.star'
emxOutfile = open("10025.emx", "w")

micrographString="""  <micrograph fileName="%s">
    <pixelSpacing>
      <X unit="A/px">%4.2f</X>
      <Y unit="A/px">%4.2f</Y>
      </pixelSpacing>
    <acceleratingVoltage unit="kV">%4.1f</acceleratingVoltage>
    <cs unit="mm">%2.1f</cs>
  </micrograph>
"""
particleString="""  <particle fileName="%s" index="%d">
    <centerCoord>
      <X unit="px">%0.1f</X>
      <Y unit="px">%0.1f</Y>
    </centerCoord>
    <micrograph fileName="%s.mrc"/>
  </particle>
"""

emxOutfile.write("""<?xml version='1.0' encoding='utf-8'?>
<EMX version="1.0">'
""")
oldMic="kk"


#read relion star file
mdStar = md.MetaData(fnStar)
for imgRow in md.iterRows(mdStar):
    micName  = imgRow.getValue(md.RLN_MICROGRAPH_NAME)
    if oldMic == micName:
        pass
    else:
        oldMic = micName
        voltage  = imgRow.getValue(md.RLN_CTF_VOLTAGE)
        cs       = imgRow.getValue(md.RLN_CTF_CS)
        cameraPixelSize = imgRow.getValue(md.RLN_CTF_DETECTOR_PIXEL_SIZE)
        magnification = imgRow.getValue(md.RLN_CTF_MAGNIFICATION)
        sampling = cameraPixelSize * 10000 / magnification
        emxOutfile.write(micrographString%(micName,sampling,sampling,voltage,cs))
oldMic="kk"
index = 1
mdStar = md.MetaData(fnStar)
for imgRow in md.iterRows(mdStar):
    partNameAux  = imgRow.getValue(md.RLN_IMAGE_NAME)
    partName  = partNameAux[7:] 
    index = int(partNameAux[0:6])
    micName  = imgRow.getValue(md.RLN_MICROGRAPH_NAME)
    x  = imgRow.getValue(md.RLN_IMAGE_COORD_X)
    y  = imgRow.getValue(md.RLN_IMAGE_COORD_Y)
    #if oldMic == micName:
    #    index += 1
    #else:
    #    oldMic = micName
    #    index=1
    emxOutfile.write(particleString%(partName,index,x,y,micName))


emxOutfile.write("</EMX>")
b = datetime.datetime.now()
print("Time (h,m,s)",b-initTime)