3查看导入列表

import sys
from ij import IJ
from ij.io import DirectoryChooser
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/Scripts/plugins/Utilities")
from MakeImportList4TrakEM2 import make_list

dc = DirectoryChooser('Select 3View dataset base directory')
folder = dc.getDirectory()

if folder is None:
	IJ.log('User canceled the folder selection!')
else:
	dir_RegExp = 'Montage_\d{3}'
	list_filename = 'TrakEM2_import.txt'
	filetype = '.dm3'
	how_many = make_list(filetype, folder, dir_RegExp, list_filename)
	IJ.showProgress(1,1) #in case there is an error, the progress bar still disappears
	IJ.showStatus('Completed. Files added to import list: ' + str(how_many))

import sys
from ij import IJ
from ij.io import DirectoryChooser
from ij.gui import GenericDialog
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/Scripts/plugins/Utilities")
from MakeImportList4TrakEM2 import make_list

def getParameters():  
  gd = GenericDialog("Import parameters")
  gd.addStringField("Import list name", "TrakEM2_import.txt")
  gd.addStringField("Directory RegExp", "Montage_\d{3}")
  gd.addStringField("Filetype filter", ".tif")
  gd.showDialog()  
  #  
  if gd.wasCanceled():  
	print "User canceled dialog!"  
	return  
  # Read out the options  
  list_name = gd.getNextString()  
  reg_exp = gd.getNextString()
  ftype = gd.getNextString()
  return list_name, reg_exp, ftype

dc = DirectoryChooser('Select 3View dataset base directory')
folder2 = dc.getDirectory()

if folder2 is None:
	IJ.log('User canceled the folder selection!')
else:
	param = getParameters()  
	if param is not None:  
		list_name, reg_exp, ftype = param
		how_many = make_list(ftype, folder2, reg_exp, list_name)
		IJ.showProgress(1,1) #in case there is an error, the progress bar still disappears
		IJ.showStatus('Completed. Files added to import list: ' + str(how_many))

import os, re, math, sys
from ij import IJ
from ij.gui import GenericDialog
from loci.formats import ImageReader, MetadataTools

def read_meta(filen2):
	rf = ImageReader()
	meta = MetadataTools.createOMEXMLMetadata()
	rf.setMetadataStore(meta)
	rf.setId(filen2)
	# get stage position:
	planeCount = meta.getPlaneCount(0)
	for p in range(planeCount):
		posX = float(str(meta.getPlanePositionX(0, p)))
		posY = float(str(meta.getPlanePositionY(0, p)))
	try:
		posX, posY
	except NameError:
		posX = posY = 0
	return rf, meta, posX, posY

def getOptions(X, Y, Ol, mnts):
	IJ.showStatus('Asking user for input...')
	gd = GenericDialog("Montage configuration")
	gd.addNumericField("Number of tiles in X", X, 0)  # show 0 decimals
	gd.addNumericField("Number of tiles in Y", Y, 0)  # show 0 decimals
	gd.addNumericField("Overlap (%)", Ol, 1)  # show 1 decimal
	gd.showDialog()  
	if gd.wasCanceled():
		IJ.log('User canceled dialog. Text file not created')
		return
	# Read the input into variables
	pos_x = int(gd.getNextNumber())
	pos_y = int(gd.getNextNumber())
	if (pos_x * pos_y) != mnts:
		IJ.log('The configuration you provided (' + str(pos_x) + 'X by ' + str(pos_y) + 'Y) and number of detected directories (' + str(mnts) + ') do not match.\nText file not created.')
		IJ.showMessage('The configuration you provided and number of detected directories do not match.\nText file not created.')
		return
	overlp = gd.getNextNumber()
	return pos_x, pos_y, overlp
  
def make_list(filetype, folder, dir_RegExp, list_filename): 
	IJ.log('--- Begin creating 3View file list for TrakEM2 import ---')
	IJ.showStatus('Starting...')
	x_now = y_now = counter1 = 0
	import_list = ''

	try:
		f = open(folder + list_filename, 'w') # Save the text file for importing in same root folder, auto overwrite
	except IOError:
		IJ.log('Error: can\'t create file in selected directory')
		return
	else:
		IJ.showStatus('Reading directories...')
		subdirs = sorted(os.walk(folder).next()[1]) # create list with the contents of the directory, selecting only 1st level directories and sorting them ascending. Sorting is fundamental for correctly reading of stage position values and for correct positioning os the tiles in each montage
		subdirs[:] = [sd for sd in subdirs if re.match(dir_RegExp, sd, flags=0)] # filter the dirs that match the RegExp. For 3View the name is 'Montage_xxx'. This allows for some flexibility: users can have other folders together with the stack folders such as TrakEM2 minimaps folder
		montage_size = len(subdirs) # count how many dirs were selected - to calculate configuration of montage and progress reporting
		if montage_size == 0:
			IJ.log('Error: No directories found matching RegExp pattern \'' + dir_RegExp + '\' in ' + folder)
			return
		try:
			scnd_dir = subdirs[1] # check if there is more than one folder, setting at the same time the variable for the second (folder in the list) index position - [1]
		except IndexError:
			# since there is only one folder, move on with settings to create a file list for just one position. The whole else: part below will be skipped
			IJ.log('Only one directory detected. Creating file list for single position z-stack')
			x_coord = y_coord = 1
			x_now = y_now = x_img_size = y_img_size = overlap = 0
		else:
			IJ.log(str(montage_size) + ' matching directories found in ' + folder)
			# get values for calc of montage configuration and overlap
			files_2nd_dir = os.listdir(os.path.join(folder,scnd_dir))
			files_2nd_dir[:] = [fn1 for fn1 in files_2nd_dir if os.path.isfile(os.path.join(folder,scnd_dir,fn1))and fn1.endswith(filetype)] 
			IJ.showStatus('Reading stage coordinates 1/3...')
			try: # stop if no files are found in the 2nd folder:
				r1, meta1, pos2_Xstage, pos2_Ystage = read_meta(os.path.join(folder, scnd_dir, files_2nd_dir[0])) # pick a file from the second folder to read metadata
				r1.close()
			except IndexError:
				IJ.log('Error: the 2nd directory in the list does not contain any files of type ' + filetype)
				return
			last_dir = subdirs[-1] # pick one file from the last folder to read metadata
			files_lastdir = os.listdir(os.path.join(folder,last_dir))
			files_lastdir[:] = [fn2 for fn2 in files_lastdir if os.path.isfile(os.path.join(folder,last_dir,fn2))and fn2.endswith(filetype)]
			IJ.showStatus('Reading stage coordinates 2/3...')
			try:
				r2, meta2, posLast_Xstage, posLast_Ystage = read_meta(os.path.join(folder, last_dir, files_lastdir[0]))
				r2.close()
			except IndexError:
				IJ.log('Error: the last directory in the list does not contain any files of type ' + filetype)
				return
		for d, dirs in enumerate(subdirs):
			filenames = sorted(os.listdir(os.path.join(folder,dirs))) # the sorting is just to try and hide the darker, overlap areas of the image to be in front when displaying the montage in TrakEM2. This is probably not necessary if some contrast homogenization is performed after importing
			filenames[:] = [fn3 for fn3 in filenames if os.path.isfile(os.path.join(folder,dirs,fn3))and fn3.endswith(filetype)] # make sure there are no dirs ending in desired filetype (one never knows~) and filter for the filetype
			filenames_size = len(filenames) # for progress bar only
			for p, filen in enumerate(filenames):
				try: # check if metadata was read already and extract metadata info from the 1st file on the list - if it was not, get this info by executing the except clause. This makes the metadata routine run only once in the beginning. Being nested inside the else: stm above, metadata is only read if it's not a single position acquisition - in this case it wouldn't be necessary. Also, complete calc of overlap and montage configuration
					overlap
				except NameError:
					IJ.showStatus('Reading stage coordinates 3/3...')
					try:
						r3, meta3, pos1_Xstage, pos1_Ystage = read_meta(os.path.join(folder, dirs, filen))
					except IndexError:
						IJ.log('Error: the first directory in the list does not contain any files of type ' + filetype)
						r3.close()
						return
					IJ.showStatus('Reading more metadata...')
					x_img_size = r3.getSizeX()
					y_img_size = r3.getSizeY()
					r3.close()
					pSizeX = float(str(meta3.getPixelsPhysicalSizeX(0))) # getPixelsPhysicalSizeX(0) it's an object, and needs both str and float before it can be used in calculations
					pSizeY = float(str(meta3.getPixelsPhysicalSizeY(0)))
					IJ.log('Read image size ' + str(x_img_size) + ' X ' + str(y_img_size))
					IJ.log('Read pixel dimensions ' + str(round(pSizeX * 1000, 1)) + ' X ' + str(round(pSizeY * 1000, 1)) + ' nm')
					# next 2 are needed to calculate overlap:
					deltaX1 = pos2_Xstage - pos1_Xstage
					deltaY1 = pos2_Ystage - pos1_Ystage #only for single column montage
					# if deltaX1=0 then something went wrong with the metadata reading and the user has to manually input the coordinate values. note that for the case of a single folder deltaX1 would theoretically also be =0 (but this code doesn't even allow for that, since it requires at least 2 folders for the calculation)
					#(or close to zero - most likely in a case of 'multiple ROI' acquisition (there would be stage movement) instead of 'montage') but that situation was already covered above and at that step the overlap var was initiated; in that situation this whole except NameError: is skipped and no deltaX1 calc is ever performed
					if deltaX1 == 0:
						IJ.log('Warning: Could not read stage position from files. Asking for user input')
						options1 = getOptions(0, 0, 0, montage_size)
						if options1 is None:
							overlap = 0 # to prevent "UnboundLocalError: local variable 'overlap' referenced before assignment". Rrom http://docs.python.org/2/reference/simple_stmts.html : "When return passes control out of a try statement with a finally clause, that finally clause is executed before really leaving the function."
							return
						x_coord, y_coord, ovlap1 = options1
						overlap = 1 - (ovlap1 / 100)
						IJ.log('User provided montage configuration ' + str(x_coord) + 'X by ' + str(y_coord) + 'Y and ' + str(ovlap1) + '% overlap')
					# if deltaX1 > 0 means the second position(dir) is in the X axis(to the right instead of down); otherwise the next folder is in the Y axis and therefore a single column montage# this is because the stage is at an angle (45  without scan rotation) with the montage axis This check is not robust enough to accomodate a 0 deg stage (it may not work with images acquired without a significant axis angle in relation to the images, ie, not with 3View)# also: assumes the coordinate system is always the same in relation to the images; if there are invertions, then this check needs to be reworked
					elif deltaX1 > 0:
						IJ.showStatus('Calculating parameters...')
						overlap = round(math.hypot(deltaX1, deltaY1) / float(x_img_size) * pSizeX, 1) # assumes overlap and pixel size to be the same in x and y
						IJ.log('Calculated overlap: ' + str((1 - round(overlap, 1)) * 100) + '%')
						# calc max stage movement distance measured between 1st and last montage 'positions'
						deltaX2 = posLast_Xstage-pos1_Xstage
						deltaY2 = posLast_Ystage-pos1_Ystage
						# then to 'convert' the stage distance into 'real' montage span distances some more trig needs to be applied because the 45 deg rotation of the axis relative to the image acquisition (FoV)
						bigger_angle = math.atan(deltaY2 / deltaX2) # arc tangent in radians
						smaller_angle = bigger_angle - math.radians(45)
						# hypotenuse of the rectangle formed between the 1st and the last stage position
						montage_hyp = math.hypot(deltaX2, deltaY2)
						# it's a rectangle, the hypotenuse angle will vary. Calcs for x length is 'adjacent side', so cos(x) and calcs for y is 'opposite side', so sin(x)
						montage_Xlenght = round(math.cos(smaller_angle) * montage_hyp, 3)
						montage_Yheight = round(math.sin(smaller_angle) * montage_hyp, 3)
						# and finally calculate the number of tiles in the x and y axis, assuming stage movement is reasonably accurate
						x_coord = int(round(montage_Xlenght / (x_img_size * overlap), 0)) + 1
						y_coord = int(round(montage_Yheight / (y_img_size * overlap), 0)) + 1
						IJ.log('Montage configuration calculated to be ' + str(x_coord) + 'X by ' + str(y_coord) + 'Y')
						if (x_coord * y_coord) != montage_size:
							# create dialog to get user input because the calculated configuration doesn't match the number of folders
							IJ.log('Warning: Calculated montage configuration and total number of folders found do not match')
							options2 = getOptions(x_coord, y_coord, overlap, montage_size)
							if options2 is None:
								overlap = 0 # to prevent UnboundLocalError: local variable 'overlap' referenced before assignment
								return
							x_coord, y_coord, ovlap2 = options2
							overlap = 1 - (ovlap2 / 100)
							IJ.log('User provided montage configuration ' + str(x_coord) + 'X by ' + str(y_coord) + 'Y and ' + str(ovlap2) + '% overlap')
					else:
						# The alternative is a single column montage and for that case the calculations are more simple
						IJ.showStatus('Calculating parameters...')
						overlap = round(math.hypot(deltaX1, deltaY1) / (y_img_size * pSizeY), 1)
						IJ.log('Calculated overlap: ' + str((1 - overlap) * 100) + '%')
						x_coord = 1
						y_coord = montage_size
						IJ.log('Montage configuration should be ' + str(x_coord) + 'X by ' + str(y_coord) + 'Y')
				finally:
					IJ.showStatus('Adding files to import list...')
					reg_expr4_zval = '.+(\\d{4})\\' + filetype + '$' # RegExp to get the z position (number) from the filename
					find_zval = re.match(reg_expr4_zval, filen, flags=0) # get the last 4 digits from the filename
					z_now = int(find_zval.group(1)) # should be the z order/position of the file in the stack. int() removes leading zeros
					# append the file info to the list ASCII 13=Enter ; 92=\ ; 9=TAB
					import_list = os.path.join(dirs, filen) + chr(9) + str(int(x_now*x_img_size*overlap)) + chr(9) + str(int(y_now*y_img_size*overlap)) + chr(9) + str(z_now) + chr(13) + import_list
					counter1 += 1
					progress = int(((((p + 1)/ float(filenames_size)) + d) * 100))
					IJ.showProgress(progress, montage_size * 100)
			x_now += 1 # gone through the contents of one folder; before moving to the next, move the montage position counters
			if (x_now == x_coord): # if all x positions in a row are recorded, reset x and move to next row (y position)
				y_now += 1
				x_now = 0
		f.write(import_list.strip())
		f.close()
		IJ.log(str(counter1) + ' entries were written to the file ' + f.name)
		return counter1