def accept(self, dir, name):

reg = re.compile('\.tif$')

regMax = re.compile('\max.tif$')

m = reg.search(name)

m2 = regMax.search(name)

if m and not m2:

return 1

else:

def accept(self, dir, name):

reg = re.compile('\.lsm$')

regMax = re.compile('\max.lsm$')

m = reg.search(name)

m2 = regMax.search(name)

if m and not m2:

return 1

else:

msgStr = ''

for i in (range(indent)):

msgStr += ' '

print ' ',

print text #to command line

if not os.path.isfile(fullFilePath):

bPrintLog('\nERROR: runOneFile() did not find file: ' + fullFilePath + '\n',0)

return 0

elif not fullFilePath.endswith('tif'):

msg = fullFilePath +" is not a deconvoluted tif file"

bPrintLog(msg,2)

else:

bPrintLog(time.strftime("%H:%M:%S") + ' starting runOneFile()for overwrite: ' + fullFilePath, 1)

#open and overwrite the deconvoluted file as 16 bit

imp = Opener().openImage(fullFilePath) #deconvoluted file

if imp.getBitDepth() == 32:

imp.show()

msgStr = "Converting 32 to 16-bit..."

bPrintLog(msgStr,3)

IJ.run("16-bit")

msgStr = "Overwriting 32-bit with 16-bit File in" + fullFilePath

bPrintLog(msgStr,3)

IJ.run(imp,"Save","") #save as replace without asking

if not os.path.isdir(sourceFolder):

bPrintLog('\nERROR: runOneFolder() did not find folder: ' + sourceFolder + '\n',0)

return 0

tifNames = [file.name for file in File(sourceFolder).listFiles(Filter())]

numTifs = len(tifNames)

bPrintLog('source deconvolution Folder: ' + sourceFolder,1)

bPrintLog('Number of deconvoluted tifs: ' + str(numTifs),1)

count = 1

for tifName in tifNames:

msgStr = '--->>> Opening ' + str(count) + ' of ' + str(numTifs)

bPrintLog(msgStr, 0)

if tifName.endswith('tif'):

fileFullPath = os.path.join(sourceFolder,tifName)

convert32to16(fileFullPath)

else:

msg = "Not a deconvoluted tif file: " +tifName

count += 1

mouseID = os.path.basename(mouseFolder[:-1]) #remove '/'

bPrintLog('Mouse Folder is: ' + mouseFolder,1)

bPrintLog('Mouse ID is: ' + mouseID,1)

targetFolder = mouseFolder + mouseID + '_raw' #files moved to raw with python code

if os.path.isdir(targetFolder):

runOneFolder(targetFolder)

else:

if not os.path.isdir(dayFolder):

bPrintLog('\nERROR: runOneDay() did not find folder: ' + dayFolder + '\n',0)

return 0

dirNames = [file for file in os.listdir(dayFolder) if os.path.isdir(os.path.join(dayFolder,file))]

numDirs = len(dirNames)

bPrintLog('dayFolder is:' + dayFolder,0)

bPrintLog('Number of subFolders: ' + str(numDirs),1)

#put option here so we do not have to click for each folder

for dirName in dirNames:

mouseFolder = os.path.join(dayFolder, dirName)+ '/' # did not add '/' to the end

bPrintLog('*********************************',0)

msg = 'Mouse folder is: ' +mouseFolder

bPrintLog(msg, 1)

dateDirs = [file for file in os.listdir(monthDir) if os.path.isdir(os.path.join(monthDir,file))]

numDates = len(dateDirs)

monthInfo = os.path.basename(monthDir)

msg = " Number of dates imaged in month %s is %d" %(monthInfo,numDates)

bPrintLog(msg,0)

ind = 1

for imageDate in dateDirs:

msg = "*Running imaging date %s (%d/%d)" %(imageDate, ind,numDates)

bPrintLog(msg,0)

dateDir = os.path.join(monthDir,imageDate)

overWriteDate(dateDir)

types = ['oneDay','oneMouse','oneFile','oneMonth','OneFolder','mapManager']

gd = GenericDialog('Define Source Options')

#gd.addMessage('Choose the Source type:')

gd.addChoice('Source Type:',types,types[0])

gd.showDialog()

if gd.wasCanceled():

bPrintLog('user cancel the plugin',1)

return 0

else:

srcType = gd.getNextChoiceIndex()

#run one day

if srcType == 0:

dayFolder = DirectoryChooser('Please Choose A Directory Of .tif Files').getDirectory()

if not os.path.isdir(dayFolder):

bPrintLog('\nERROR: runOneDay() did not find folder: ' + dayFolder + '\n',0)

return 0

overWriteDate(dayFolder)

#run one mouse

if srcType == 1:

mouseFolder = DirectoryChooser('Please Choose A Mouse Directory Of .tif Files').getDirectory()

if not mouseFolder:

exit(1)

overWriteMouse(mouseFolder)

#run one file

if srcType == 2:

od = OpenDialog("Choose a convoluted tif file to overwrite", None)

srcDirectory = od.getDirectory()

srcFile = od.getFileName()

if srcFile != None:

fileFullPath = os.path.join(srcDirectory,srcFile)

convert32to16(fileFullPath)

#run one month

if srcType == 3:

monthFolder = DirectoryChooser('Please Choose A MONTH Directory Of .tif Files').getDirectory()

if not os.path.isdir(monthFolder):

bPrintLog('\nERROR: runOneMonth() did not find folder: ' + monthFolder + '\n',0)

return 0

runOneMonth(monthFolder)

#run one Folder

if srcType == 4:

srcFolder = DirectoryChooser('Please Choose A folder Of .tif Files').getDirectory()

if not os.path.isdir(srcFolder):

bPrintLog('\nERROR: runOneFolder() did not find folder: ' + srcFolder + '\n',0)

return 0

runOneFolder(srcFolder)

if srcType == 5: #align centain map's raw folder

mapPath = 'G:/ZY/MapManager3'

#mapNames = raw_input('type maps initials seperated with ,: ').split(',') #raw_input does not work here

#mapNames = tuple(mapNames)

mapNames = "F58,F59" #preset

#get map names

gd = GenericDialog('Choose maps for alignment')

gd.addStringField("maps root path",mapPath,50)

gd.addStringField("maps name initials sep = ','(empty for all)",mapNames,50)

gd.showDialog()

if gd.wasCanceled():

bPrintLog('user cancel the plugin',0)

return 0

mapPath = gd.getNextString()

mapNames = tuple(gd.getNextString().split(','))

mapFolders = [f for f in os.listdir(mapPath) if f.startswith(mapNames) and os.path.isdir(os.path.join(mapPath,f))]

if len(mapFolders) == 0:

bPrintLog('\nERROR: no map folder found',0)

return 0

bPrintLog('Map Folder number: ' + str(len(mapFolders)),0)

#put option here so we do not have to click for each folder

sourceFolders= [mapPath + '/' + mapFolder + '/raw/raw_userRaw' for mapFolder in mapFolders]

for srcFolder in sourceFolders: