# Make montage from qm-nnnnn-sampleID-nnkV-map1
#
# Modifications
# Date Who Ver What
# ---------- --- ------ -------------------------------------------------
# 2014-11-07 JRM 0.1.00 Montage maps created with 01-Prep script
# this version tries to use standard directories
# 2014-11-07 JRM 0.1.10 Added a bTestPaths flag to test loading images
# 2014-11-10 JRM 0.1.11 Be sure to set title
# 2014-11-13 JRM 0.1.12 Option to scale
# 2014-11-24 JRM 0.1.13 This adds annotations and scale bars
# 2014-12-03 JRM 0.2.00 This can work w/o display (headless)
# 2014-12-09 JRM 0.2.10 replaced imp.flush() with imp.close() to fix bug
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
import jmFijiGen as jmg
from ij import IJ
from ij.gui import PointRoi
from java.awt import Color
# check that paths are correct by loading ROI image
bTestPaths = False
# scale the image by scaFac
bScale = True
scaFac = 0.5
# For headless (no display) set to True
bHeadless = True
class KaduParser(Parser):
'''
parser for Kadu v. 0.9.2
'''
protocols = {}
accounts = {}
buddies = {}
contacts = {}
chats = {}
codecs.setDefaultEncoding('utf-8')
def __init__(self):
self.protocols['jabber'] = self.protocol = Dictionaries.getInstance(
).getProtocol('XMPP')
self.protocols['gadu'] = self.protocol = Dictionaries.getInstance(
).getProtocol('GG')
# TODO [Aga] fill this
def loadFiles(self, files):
self.dbFile = files[0] + os.sep + 'history' + os.sep + 'history.db'
self.conf = ""
for f in os.listdir(files[0]):
if f.endswith('xml'):
f0 = open(files[0] + os.sep + f, 'r')
self.conf = f0.read()
f0.close()
break
if self.conf == "" and not os.path.exists(self.dbFile):
ex = ValueError()
ex.message = 'Incorrect kadu directory.'
raise ex
def getUserAccounts(self):
'''
accounts = dict of turples: uuid of account = (uid, protocol, contactid)
'''
self.userAccountsLoadProgress = 0
self.element = ET.XML(self.conf)
accountsxml = self.element.find("Accounts")
useraccounts = []
num = len(accountsxml) / 100
for account in accountsxml:
self.contactxml = self.element.find("Contacts")
iden = ""
for contact in self.contactxml:
if contact.find("Id").text == account.find("Id").text:
iden = contact.attrib["uuid"]
break
acc = UserAccount(0, self.protocols[account.find("Protocol").text],
account.find("Id").text)
self.accounts[account.attrib["uuid"]] = (acc, iden)
useraccounts.append(acc)
self.userAccountsLoadProgress += num
self.userAccountsLoadProgress = 100
return useraccounts
def getContacts(self, userAccounts):
buddiesxml = self.element.find("Buddies")
contactslist = []
for buddy in buddiesxml:
if buddy:
name = buddy.find("Display").text
fname = ""
if buddy.find("FirstName").text != name and buddy.find(
"FirstName").text != None:
fname = buddy.find("FirstName").text
lname = ""
if buddy.find("LastName").text != name and buddy.find(
"LastName").text != None:
lname = buddy.find("LastName").text
c = Contact(0, fname, lname, name)
self.buddies[buddy.attrib["uuid"]] = c
else:
c = Contact(0, "", "", "")
self.buddies[buddy.attrib["uuid"]] = c
contactsxml = self.element.find("Contacts")
for contact in contactsxml:
if self.accounts[contact.find("Account").text][0] in userAccounts:
if contact.find("Buddy").text == None:
c = Contact(0, "", "", contact.find("Id").text)
else:
c = self.buddies[contact.find("Buddy").text]
if not c in contactslist:
contactslist.append(c)
ca = ContactAccount(
0, "",
contact.find("Id").text, "", c, self.accounts[contact.find(
"Account").text][0].getProtocol())
c.addContactAccount(ca)
self.contacts[contact.attrib["uuid"]] = ca
connection = DriverManager.getConnection("jdbc:sqlite:" + self.dbFile)
stmt = connection.createStatement()
chatsxml = self.element.find("Chats")
df = SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss")
for chat in chatsxml:
#print self.accounts[chat.find("Account").text]
if chat.find("Account") != None and self.accounts[chat.find(
"Account").text][0] in userAccounts:
#self.chats[chat.attrib["uuid"]] = (self.accounts[chat.find("Account").text], self.accounts[chat.find("Contact").text])
#chatlist.append((self.accounts[chat.find("Account").text], self.accounts[chat.find("Contact").text]))
rs = stmt.executeQuery(
"SELECT * FROM kadu_messages WHERE chat='" +
chat.attrib["uuid"] + "' ORDER BY send_time")
#conv = Conversation(0, Date(), "", 0, self.contacts[chat.find("Contact").text], self.accounts[chat.find("Account").text][0])
#self.contacts[chat.find("Contact").text].addConversation(conv)
#print self.contacts[chat.find("Contact").text], self.contacts[chat.find("Contact").text].getConversations().size()
#print "Chat ", chat.attrib["uuid"]
msgs = []
#length = 0
#fmsg = ""
#date = None
#enddate = None
while rs.next():
if rs.getString("attributes")[-1] == "0":
recv = 1
else:
recv = 0
msgs.append(
Message(0, None, rs.getString("content"),
df.parse(rs.getString("send_time")), recv))
#conv.addMessage(msg)
#length += 1
self.messagesCount += 1
#if fmsg=="":
# fmsg=rs.getString("content")
#if date == None:
# date = df.parse(rs.getString("send_time"))
#enddate = df.parse(rs.getString("send_time"))
#print "\tROW = ", chat, sender, time, content, out
#conv.setLength(length)
#conv.setTime(date)
#conv.setEndTime(enddate)
#conv.setTitle(fmsg)
#print self.contacts[chat.find("Contact").text]
#print self.accounts[chat.find("Account").text][0]
if len(msgs) > 0:
self.contacts[chat.find("Contact").text].setConversations(
ConversationHelper.messagesToConversations(
msgs, self.contacts[chat.find("Contact").text],
self.accounts[chat.find("Account").text][0]))
self.contactsLoadProgress = 100
return contactslist
"""
make_rgb_from_stack_4.py
make a RGB image from a Weka 4 channel image
Modifications
Date Who Ver What
---------- --- ------ -------------------------------------------------
2019-05-17 JRM 0.1.00 Test function in to generate an RGB image
"""
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
from ij import IJ, WindowManager
def convert_stack_4_to_rgb(imp):
"""
Convert a 4 image stack with a uniform cyan channel 4
to a RGB image.
Parameters
==========
imp ImagePlus
The image to be converted
Returns
=======
# anaBlobParticles.py
#
# A reproducible example of analyzing particles after a watershed transform
# and drawing the features into the original image window. This uses helper
# functions to draw the ROI
#
# Modifications
# Date Who Ver What
# ---------- --- ------ -------------------------------------------------
# 2015-01-03 JRM 0.1.00 Initial test on blob image
from org.python.core import codecs
codecs.setDefaultEncoding("utf-8")
import os
import glob
import time
from math import sqrt
from java.awt import Color
from ij import IJ
from ij import ImagePlus
from ij.gui import Overlay, PointRoi
from ij.measure import ResultsTable, Measurements
from ij.plugin.filter import ParticleAnalyzer
from ij.plugin.frame import RoiManager
import jmFijiGen as jmg
def addRoiToOverlay(imp, roi, labCol=Color.white, linCol=Color.white):
