#screen = IJ.getScreenSize()

#screenWidth = screen.width

#screenHeight = screen.height

#impSize = imp.getWindow().getSize()

od = OpenDialog("Choose image file", None)

file_path = od.getDirectory() #dir=File.getParent(od)

file_name = od.getFileName() #name=FIle.getName(od)

if not file_name:

printLog("--Cancelled by user.",0)

else:

imp =Opener().openImage(file_path, file_name)

imp.show()

imp.getWindow().setLocation(0,0)

file_name = imp.getTitle()

file_path = IJ.getDirectory('image')

printLog("filepath is "+file_path,1)

[SI_version,nFrame,zStepSize,nStacks]=zyGetProperty(imp,"SI_version,nFrame,zStepSize,nStacks") #need correct nSlices? do not delete any

nSlices = imp.getNSlices()/nFrame #otherwise, calculate by fiji function

msgStr = "The image has "+str(nFrame)+" frames from "+str(nStacks)+" stacks, was collected by ScanImage version "+str(SI_version)

printLog(msgStr,0)

if nFrame == 1:

printLog("User need to import a file with multi-frames",0)

else:

#duplicate one for resorting

IJ.run(imp,"Duplicate...", "title=resortStack duplicate range=1-%d" %imp.getNSlices()) #bad fiji set this getNSlice() as all slice

resort_stack=IJ.getImage()

resort_stack.getWindow().setLocation(0,0)

IJ.run(resort_stack, "Label...", "format=0 starting=1 interval=1 x=5 y=20 font=18");

#number pickup for every numRep

IJ.selectWindow(file_name)

#(width, height, nChannels, nSlices, nFrames) = imp.getDimensions(), bad fiji alway get wrong

numRep = int(nFrame)

m = int(nSlices) #real slice number when correcting the nFrames

sPick = []

printLog("-Current tif file:"+file_name,1)

printLog("-nSlice="+str(m)+", nFrame="+str(numRep),2)

printLog("-start picking the best repeat.",1)

for i in range(0,m):

j = i*numRep+1 #Z-step number

#make montage to check all repeats at the same time for pickup

IJ.run(imp,"Make Montage...", "columns="+str(numRep/nStacks)+" rows="+str(nStacks)+" scale=1 first="+str(j)+" last="+str(j+numRep-1)+" increment=1 border=1 font=12 label")

m1_imp = IJ.getImage()

IJ.run(m1_imp,"8-bit", "")

m1_imp.getWindow().setLocation(530,0)

IJ.run(m1_imp,"Set... ", "zoom=92 x=0 y=0")

m1_title=m1_imp.getTitle()

#merge the previous one if i>0

if i==0:

prePick = 1 #use first slice as mask

IJ.run(resort_stack,"Duplicate...", "title=Max_z duplicate range=1-1" )

zMax=IJ.getImage()

zMax_win = zMax.getWindow().setLocation(0,580)

else:

prePick = sPick[i-1] #use previous selected slice as mask

#duplicate numRep times of previous, concatenate, make montage, for merging channel as red with m1_imp

m2_imp = mkMask(imp,prePick,numRep,nStacks)

#merge the mask, and make new m1_imp as a 2-slice stack: Green (original) with merged

m1_imp = zyMergeView(m1_imp,m2_imp)

#pickup the best slice with slice number

pickN = pickNum(numRep,nStacks)

if not pickN:

break

else:

pickN = pickN+j-1

#do the moveSlice on resort_stack: move to the initial of pick: j

resort_stack = moveSlice(resort_stack,pickN,j)

#preview Z projection in a copy of resort_stack

zMax.close() #clear previous Z projection

zMax = preview_Z(resort_stack,numRep,i+1) #show the new preview based on new pick

#store the lucky slice number for making the substack in the future

sPick.append(int(pickN))

#mmp = IJ.getImage()

m1_imp.close()

if len(sPick) == m:

#means you have pick all slices required, but not cancel during process (break all out)

IJ.selectWindow(file_name)

outList =",".join(str(e) for e in sPick) #better to make a str: outList="slices=1,2,3"

printLog("-Slices picked by user:"+outList,1)

#print outlist

IJ.run(imp,"Make Substack...", "slices=%s" %(outList)) #all need to be str

sr_imp = IJ.getImage()

sr_imp.setTitle('P_'+file_name)

#imp.changes = 0

#imp.close()

#zMax.close()

#need to do: put a header for sr_imp here

msgStr = "pixel_width=0.102857 pixel_height=0.102857 voxel_depth="+str(zStepSize)

printLog("-Set the property of picked stack "+sr_imp.getTitle()+" to:"+msgStr,1)

IJ.run(sr_imp, "Properties...", msgStr)

pickName = sr_imp.getTitle()

destFolder_SR = os.path.join(file_path, 'Single_rep')

#do multireg alignment

doAlign(sr_imp,destFolder_SR)

zyAddProperty(sr_imp)

saveStack(destFolder_SR,pickName,sr_imp)

destFolder_RS = os.path.join(file_path, 'reSort')

#add Info

zyAddProperty(resort_stack)

saveStack(destFolder_RS,file_name,resort_stack)

else:

m1_imp.close()

resort_stack.changes = 0

imp.changes = 0

imp.close()

zMax.close()

file_name = imp.getTitle()

IJ.selectWindow(file_name)

IJ.setSlice(prePick)

tempFileNames=[]

for pp in range(0,numRep):

tempFileNames.append('temp'+str(pp))

IJ.run(imp,"Duplicate...", "title=" +tempFileNames[pp])

IJ.run("8-bit", "")

cont_imgs = " ".join('image%d=%s' %(c+1,w) for c,w in enumerate(tempFileNames))

IJ.run("Concatenate...", "title=tempStack " +cont_imgs)

tempStack = IJ.getImage()

IJ.run(tempStack,"Make Montage...", "columns="+str(numRep/nStacks)+" rows="+str(nStacks)+" scale=1 first=1 last="+str(numRep)+" increment=1 border=1 font=12")

m2_imp=IJ.getImage()

m2_imp.setTitle("Mask")

tempStack.close()

imp1_title = imp1.getTitle()

IJ.run(imp1, "RGB Color", "")

imp2_title = imp2.getTitle()

IJ.run(imp2, "RGB Color", "")

IJ.run("Merge Channels...", "c1="+imp2_title+" c2="+imp1_title+" keep") #will be RGB

IJ.run("Concatenate...", " title=[PickPan] image1=RGB image2="+imp1_title)

imp1 = IJ.getImage()

imp1.getWindow().setLocation(530,0)

IJ.run(imp1,"Set... ", "zoom=90 x=0 y=0")

imp2.changes = 0

imp2.close()

pickRange=[str(e) for e in range(1,numRep+1)]

#gd = GenericDialog("pick a slice")

gd = NonBlockingGenericDialog("pick a slice") #non-modal dialog will not block selecting others

gd.centerDialog(0) #this could enable the setLocation

gd.setLocation(380,0)

nRow = int(nStacks)

nCol = int(numRep/nStacks)

gd.addRadioButtonGroup("Select sliceNumber",pickRange,nRow,nCol,"1")

gd.showDialog()

if gd.wasCanceled():

printLog("PickNum Was Cancelled by user",0)

return #what should I return? here is no change

else:

pickN = int(gd.getNextRadioButton())

#rename the result and save it to subfolder

if not os.path.isdir(destFolder):

os.makedirs(destFolder)

fullname=os.path.join(destFolder,file_name)

#print (fullname)

fs = FileSaver(imp)

#print 'bSaveStack()', fullPath, 'nslices=', sr_imp.getNSlices()

msgStr = "Dimension:" + str(imp.width) + " X " + str(imp.height) + " X " + str(imp.getNSlices())

printLog("-Save "+file_name+" to "+destFolder,1)

printLog("-"+msgStr,2)

#duplicate another copy without changing original

IJ.run(imp,"Duplicate...", "title=zMaxTemp duplicate range=1-%d" %imp.getNSlices())

zMaxTemp=IJ.getImage()

IJ.run(zMaxTemp,"8-bit", "")

nSlice_real=zMaxTemp.getNSlices()/numRep

#transvert dimension from t along Z to Z along t

IJ.run(zMaxTemp,"Stack to Hyperstack...", "order=xytzc channels=1 slices="+str(nSlice_real)+" frames="+str(numRep)+" display=Color")

IJ.run(zMaxTemp, "Hyperstack to Stack", "")

IJ.run(zMaxTemp, "Z Project...", "start=1 stop="+str(prePickZ)+" projection=[Max Intensity]")

zMax=IJ.getImage()

zMax.getWindow().setLocation(0,580)

zMax.setTitle("Max_Z")

#close input stack without saving

zMaxTemp.changes=0

zMaxTemp.close()

#move a slice order inside a stack from m to n, donot use imp since it is almost global

#make sure this function is not for m<n

m=int(sourceNum)

n=int(destNum)

if m != n:

#metaString = imp.getProperty("Label")

#1.copy the n slice,inset to n+1 (now m become m+1)

imp.setSlice(n)

IJ.run(imp,"Copy","")

IJ.run(imp,"Add Slice","")

IJ.run(imp,"Paste","")

#2. go to m+1 slice, copy and delete

if m>n:

imp.setSlice(m+1)

else:

printLog("ZY expect: m<n",0)

imp.setSlice(m)

IJ.run(imp,"Copy","")

IJ.run(imp,"Delete Slice","")

#3. go to n again, paste here

imp.setSlice(n)

IJ.run(imp,"Paste","")

IJ.run(imp, "Select None", "")

#set metadata back

#imp.setPropery("Label",metaString)

else:

imp.setSlice(n) #when n=m, show the slice to indicate which one has been selected

if not os.path.isdir(destFolder):

os.makedirs(destFolder)

middleSlice = int(imp.getNSlices() // 2) #int() is necc.

imp.setSlice(middleSlice)

filename=imp.getTitle()

transformationFile = destFolder + '\\' + os.path.splitext(filename)[0] + '.txt'

printLog('-MultiStackReg aligning:' + filename +" by Translation",1)

stackRegParams = 'stack_1=[%s] action_1=Align file_1=[%s] stack_2=None action_2=Ignore file_2=[] transformation=[Translation] save' %(imp.getTitle(),transformationFile)

#add user defined field (numSlices, nunFrame, time) in the infor, with \n

infoStr = imp.getProperty('Info')

if 'numSlices' in infoStr or 'zNumSlices' in infoStr:

SI_Info = infoStr.split('\n')[0]

else:

SI_Info = infoStr

nSlices = int(infoStr.split('numberOfZSlices=')[1].split('\r')[0])

nFrame = imp.getNSlices()/nSlices

SI_nFrame = int(SI_Info.split('numberOfFrames=')[1].split('\r')[0])

nStacks = nFrame/SI_nFrame if nFrame > SI_nFrame else 1

newInfo = '\nzNumSlices='+str(nSlices)+'\nzNumFrame='+str(nFrame)+'\nzTotalSlices='+str(imp.getNSlices())+'\nzNumStacks='+str(nStacks)+'\nzModifiedTime='+"'"+time.strftime("%c")+"'\r"

infoStr = SI_Info+newInfo

##(width, height, nChannels, nSlices, nFrames, zStepSize) = zyGetProperty(imp,"fields"), fields sep with ",". =>scanimage file real dimensions

dim = {}

impTitle = imp.getTitle()

infoStr=imp.getProperty("Info")

dim["SI_version"] = infoStr.split('state.software.version=')[1].split('\r')[0]

dim["height"] = infoStr.split('state.acq.linesPerFrame=')[1].split('\r')[0]

dim["width"] = infoStr.split('state.acq.pixelsPerLine=')[1].split('\r')[0]

dim["nChannels"] = infoStr.split('state.acq.numberOfChannelsSave=')[1].split('\r')[0]

dim["nSlices"] = infoStr.split('state.acq.numberOfZSlices=')[1].split('\r')[0]

dim["zStepSize"] = infoStr.split('state.acq.zStepSize=')[1].split('\r')[0]

dim["SI_nFrame"] = infoStr.split('state.acq.numberOfFrames=')[1].split('\r')[0]

dim["nFrame"] = imp.getNSlices()/int(dim['nSlices']) #make need a try or if to get the SI_nFrame

dim["nStacks"] = int(dim["nFrame"])/int(dim["SI_nFrame"]) if int(dim["nFrame"]) > int(dim["SI_nFrame"]) else 1

if "," in fields:

reqFields = fields.split(",")

return [float(dim[field]) for field in reqFields]

else:

msgStr = ''

for i in (range(indent)):

msgStr += ' '

print msgStr,text #to command line