import glob, os

#source='BGal_*.box'
#emxOutfile = open("10013.emx", "w")

source='2013*.box'
emxOutfile = open("10011.emx", "w")

micrographString="""  <micrograph fileName="%s.mrc">
    <pixelSpacing>
      <X unit="A/px">0.99</X>
      <Y unit="A/px">0.99</Y>
      </pixelSpacing>
    <acceleratingVoltage unit="kV">300.0</acceleratingVoltage>
    <cs unit="mm">4.1</cs>
  </micrograph>
"""
particleString="""  <particle fileName="%s_part.mrcs" index="%d">
    <centerCoord>
      <X unit="px">%0.1f</X>
      <Y unit="px">%0.1f</Y>
    </centerCoord>
    <micrograph fileName="%s.mrc"/>
  </particle>
"""
particleName=""
oldParticleName="kk"

counter =-1

emxOutfile.write("""<?xml version='1.0' encoding='utf-8'?>
<EMX version="1.0">'
""")
for boxFile in sorted(glob.glob(source)):
    particleName=os.path.splitext(os.path.basename(boxFile))[0]
    emxOutfile.write(micrographString%(particleName))

for boxFile in sorted(glob.glob(source)):
    particleName=os.path.splitext(os.path.basename(boxFile))[0]
    if particleName != oldParticleName:
       oldParticleName = particleName
       counter=1

    for line in open(boxFile, "r"):
        if len(line) > 4:
            value = line.split("\t")
            x = int(value[0])+float(value[2])/2
            y = 4096 - int(value[1]) - float(value[3])/2
#            y = int(value[1])+float(value[3])/2
            emxOutfile.write(particleString%(particleName,counter,x,y,particleName))
            counter += 1
        else:
            print("skip line %s"%line)


emxOutfile.write("</EMX>")