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Merge.py
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Merge.py
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#! /usr/bin/python
# system libs
import sys
import platform
import os
import re
import shutil
# External libs
from xml.etree.ElementTree import parse
from time import localtime, strftime
import PySide
from PySide.QtCore import *
from PySide.QtGui import *
import InformationStructure
class Merge():
#init main window
def __init__(self, mergefile, parent=None):
print("-Create Merge object")
self.Structure = InformationStructure.InformationStructure(mergefile.objectName())
def AddFiles(self, iFile1, iFile2):
print("-Add Files and structures")
# structure 1
self.Structure1 = InformationStructure.InformationStructure(iFile1.objectName())
# structure 2
self.Structure2 = InformationStructure.InformationStructure(iFile2.objectName())
def UpdateStructures(self):
print("-Update structures")
if (self.Structure1.GetAttribute("Extension") == ".meg") and\
(self.Structure2.GetAttribute("Extension") == ".meg"):
print ".meg files"
file1 = open(self.Structure1.GetAttribute("FullName"), "r")
igot1 = file1.readlines()
file2 = open(self.Structure2.GetAttribute("FullName"), "r")
igot2 = file2.readlines()
readingData = 0
for i in range(len(igot1)):
if (igot1[i].find("</ImageSessionData>") > -1):
print ("finish reading data")
break
if (readingData == 1):
self.Structure1.AddInformation(igot1[i])
self.Structure2.AddInformation(igot2[i])
if (igot1[i].find("<ImageSessionData>") > -1):
readingData = 1
elif (self.Structure1.GetAttribute("Extension") == ".megx") and\
(self.Structure2.GetAttribute("Extension") == ".megx"):
print ".megx files"
else:
print("types doesn't match or are not .meg or .megx")
def CompareStructures(self):
print("-Compare structures")
attributes = self.Structure1.GetAttributes()
for name in attributes:
if (attributes != "DimensionTM"):
self.CompareParameter(name)
else:
self.AddParameters(name)
def CompareParameter(self, parameter):
message = "-Compare " + parameter
print(message)
if( (self.Structure1.GetAttribute(parameter)) == self.Structure2.GetAttribute(parameter)):
line = parameter + " " + str(self.Structure1.GetAttribute(parameter))
self.Structure.AddInformation(line)
print(line)
else:
text = parameter + " not matching:\n " + \
str(self.Structure1.GetAttribute(parameter)) + " or " + \
str(self.Structure2.GetAttribute(parameter))
(test,ok) = QInputDialog.getText(None, "Parameter", text)
if ok:
modify_line = parameter + " " + test
print modify_line
self.Structure.AddInformation(modify_line)
else:
print ("ERROR")
return
def AddParameters(self, parameter):
message = "-Add " + parameter
print(message)
timeRange = eval(self.Structure1.GetAttribute(parameter)) + eval(self.Structure2.GetAttribute(parameter))
line = parameter + " " + str(timeRange)
self.Structure.AddInformation(line)
print(line)
def Merge(self):
print("Start Merging")
# create/open the file
f = open(self.Structure.GetAttribute("FullName"), 'w+')
# write first line
f.write("MegaCapture\n")
# write image session data in the .meg(x) file
f.write("<ImageSessionData>\n")
attributes = self.Structure1.GetAttributes()
for name in attributes:
attribute = name + " " + str(self.Structure.GetAttribute(name)) + "\n"
f.write(attribute)
f.write("</ImageSessionData>\n")
# images information
# T: 0 to end
# time: current time
time = strftime("%Y-%m-%d %H:%M:%S", localtime() )
time_value = "DateTime " + time + "\n"
# stagex: 1000
stagex_value = "StageX 1000\n"
# stagey: -1000
stagey_value = "StageY -1000\n"
# pinhole: 44.216
pinhole_value = "Pinhole 44.216\n"
# file type
filetype_value = self.Structure.GetAttribute("FileType")
# get number of z slices
z_slices = self.Structure.GetAttribute("DimensionZS")
# get number of channels
nb_channels = "2"
# get number of time points
nb_time_points = self.Structure.GetAttribute("DimensionTM")
# basename
# has to be 00 or gofigure crashes
name_common = self.Structure.GetAttribute("ShortName") +\
"-PL00" + \
"-CO00" + \
"-RO00" + \
"-ZT00" + \
"-YT00" + \
"-XT00"
name = "Filename " + name_common
print ("- Writing .meg file")
# write .meg file
for i in range(eval(nb_time_points)):
for j in range(eval(nb_channels)):
for k in range(eval(z_slices)):
f.write("<Image>\n")
# complete name
name_value = name +\
"-TM" + str(i) +\
"-ch" + str(j) +\
"-zs" + str(k) +\
"." + filetype_value + "\n"
# add other fields
f.write(name_value)
f.write(time_value)
f.write(stagex_value)
f.write(stagey_value)
f.write(pinhole_value)
f.write("</Image>\n")
#----------------------------------------------------------------
print ("- Copying files from 1st directory to new directory")
#----------------------------------------------------------------
#----------------------------------------------------------------
# get all files to be merged and remove .meg file
first_directory = os.listdir( self.Structure1.GetAttribute("DirName") )
# get position of the "-"
position = [0]
for m in re.finditer('-', first_directory[0]):
position.append( m.start() )
# move first folder
for file_name in first_directory:
(shortname, extension) = os.path.splitext(file_name)
if extension != ".meg":
# old abs path
old_abs_path = self.Structure1.GetAttribute("DirName") + "/" + file_name
# new path
# gather informations which vary between images
old_time = file_name[position[7]+1+2:position[8]]
old_channel = file_name[position[8]+1+2:position[9]]
old_z = file_name[position[9]+1+2: len(file_name)- len(filetype_value) -1]
while len(old_channel) < 2:
old_channel = "0" + old_channel
while len(old_time) < 4:
old_time = "0" + old_time
while len(old_z) < 4:
old_z = "0" + old_z
# create new name with new structure + gathered informations
name_value = name_common +\
"-TM" + old_time +\
"-ch" + old_channel +\
"-zs" + old_z +\
"." + filetype_value
new_abs_path = self.Structure.GetAttribute("DirName") + "/" + name_value
print old_abs_path
print new_abs_path
shutil.copy(old_abs_path, new_abs_path)
#----------------------------------------------------------------
print ("- Copying files from 2st directory to new directory")
#----------------------------------------------------------------
#----------------------------------------------------------------
# get all files to be merged and remove .meg file
first_directory2 = os.listdir( self.Structure2.GetAttribute("DirName") )
first_time = self.Structure1.GetAttribute("DimensionTM")
# get position of the "-"
position2 = [0]
for m2 in re.finditer('-', first_directory2[0]):
position2.append( m2.start() )
# move first folder
for file_name2 in first_directory2:
(shortname2, extension2) = os.path.splitext(file_name2)
if extension2 != ".meg":
# old abs path
old_abs_path2 = self.Structure2.GetAttribute("DirName") + "/" + file_name2
# new path
# gather informations which vary between images
old_time2 = str( int(file_name2[position2[7]+1+2:position2[8]]) + int(first_time) )
old_channel2 = file_name2[position2[8]+1+2:position2[9]]
old_z2 = file_name2[position2[9]+1+2: len(file_name2)- len(filetype_value) -1]
while len(old_channel2) < 2:
old_channel2 = "0" + old_channel2
while len(old_time2) < 4:
old_time2 = "0" + old_time2
while len(old_z2) < 4:
old_z2 = "0" + old_z2
# create new name with new structure + gathered informations
name_value2 = name_common +\
"-TM" + old_time2 +\
"-ch" + old_channel2 +\
"-zs" + old_z2 +\
"." + filetype_value
new_abs_path2 = self.Structure.GetAttribute("DirName") + "/" + name_value2
print old_abs_path2
print new_abs_path2
shutil.copy(old_abs_path2, new_abs_path2)
print "- Merge Completed"