from ij import IJ, ImagePlus, ImageStack from ij.io import FileSaver from ij.process import ImageConverter, StackConverter from mpicbg.ij.integral import Scale import os import sys from os import path, walk from loci.formats import ImageReader from loci.formats import ImageWriter from fiji.util.gui import GenericDialogPlus from java.awt.event import TextListener import zipfile import zlib def ScaleImageToSize(ip, width, height): """Scale image to a specific size using Stephans scaler""" smaller = ip.scale( width, height ) return smaller def SaveToZip(zf, ip, baseDir, counter): fs = FileSaver(ip) fs.setJpegQuality(75) fs.saveAsJpeg(baseDir + "/tmp.jpeg") zipName = str(counter) + ".jpeg" zf.write(baseDir + "/tmp.jpeg", arcname=zipName) os.remove(baseDir + "/tmp.jpeg") def DirList(baseDir): r = ImageReader() imgStats = {} for root, dirs, files in os.walk(str(baseDir)): for f1 in files: if f1.endswith(".jpg") or f1.endswith(".jpe") or f1.endswith(".jpeg"): id = root + "/" + f1 r.setId(id) if r is None: print "Couldn\'t open image from file:", id continue w = r.getSizeX() h = r.getSizeY() imgStats[str(w) + "_" + str(h)] = imgStats.get(str(w) + "_" + str(h), 0)+1 IJ.log("Found image: " + str(id)) #counter += 1 r.close() #print summary summary = '' for k, v in imgStats.iteritems(): dim = k.split("_") ratio = float(dim[0])/float(dim[1]) IJ.log("Found " + str(v) + " images of dimension " + str(dim[0]) + "x" + str(dim[1]) + " apect ratio " + str(round(ratio, 2))) summary = summary + "\nFound " + str(v) + " images of dimension " + str(dim[0]) + "x" + str(dim[1]) + " apect ratio " + str(round(ratio, 2)) return summary def PrepareDatabase(minw, maxw, baseDir, aspectRatio, majorWidth, majorHeight): outputpath = baseDir + "/" + str(majorWidth) + "_" + str(majorHeight) + "_orig.tif" #initialize stacks and labels stackScaled = [] stackOrig = ImageStack(majorWidth, majorHeight) imageNames = [] for i in range(minw, maxw+1): stackScaled.append(ImageStack(i, int(round(i/aspectRatio, 0)))) imageNames.append('') counter = 0 # initialize zip file for originals zf = zipfile.ZipFile(baseDir + "/originals.zip", mode='w', compression=zipfile.ZIP_DEFLATED, allowZip64=1) zf.writestr('from_string.txt', 'hello') zf.close() zf = zipfile.ZipFile(baseDir + "/originals.zip", mode='a', compression=zipfile.ZIP_DEFLATED, allowZip64=1) for root, dirs, files in os.walk(str(baseDir)): for f1 in files: if f1.endswith(".jpg") or f1.endswith(".jpe") or f1.endswith(".jpeg"): id = root + "/" + f1 IJ.redirectErrorMessages() IJ.redirectErrorMessages(1) imp = IJ.openImage(id) if imp is None: print "Couldn\'t open image from file:", id continue # skip non RGBimages if imp.getProcessor().getNChannels() != 3: print "Converting non RGB image:", id if imp.getStackSize() > 1: StackConverter(imp).convertToRGB() else: ImageConverter(imp).convertToRGB() #skip images with different aspect ratio width = imp.getWidth() height = imp.getHeight() ratio = round(float(width)/float(height), 2) # this makes the ratio filering approximate, minor variations in image dimensions will be ignored if ratio != aspectRatio: IJ.log("Skipping image of size: " + str(width) + "," + str(height)) continue # now scale the image within a given range scale = Scale(imp.getProcessor()) IJ.log("Scaling image " + str(counter) + " " + str(id)) for i in range(minw, maxw+1): stackScaled[i-minw].addSlice(None, ScaleImageToSize(scale, i, int(round(i/aspectRatio, 0)))) imageNames[i-minw] += str(id) + ";" # save the originals to a temp directory scaledOrig = ImagePlus(None, ScaleImageToSize(scale, majorWidth, majorHeight)) SaveToZip(zf, scaledOrig, baseDir, counter) counter += 1 zf.close() # save the stacks for i in range(minw, maxw+1): impScaled = ImagePlus(str(minw) + "_" + str(int(round(i/aspectRatio, 0))), stackScaled[i-minw]) impScaled.show() #print imageNames impScaled.setProperty('Info', imageNames[i-minw][:-1]) fs = FileSaver(impScaled) filepath = baseDir + "/" + str(i) + "_" + str(int(round(i/aspectRatio, 0))) + ".tif" IJ.log("Saving output stack" + str(filepath)) fs.saveAsTiffStack(filepath) #IJ.save(impScaled, filepath); IJ.log("Done") def DialogAnalyze(): dpi = 300 defaultAspectRatio = 1.41 gd = GenericDialogPlus("Cover Maker") gd.addMessage("Prepare Image database") gd.addDirectoryField("Select base directory containing images", "", 20) gd.showDialog() if gd.wasCanceled(): print "User canceled dialog!" return imageBaseDir = gd.getNextString() return imageBaseDir class RatioToDim(TextListener): def __init__(self, aspRatio, minw, maxw, minh, maxh): self.aspRatio = aspRatio self.minw = minw self.maxw = maxw self.minh = minh self.maxh = maxh def textValueChanged(self, e): source = e.getSource() if source == self.aspRatio: #print "bla " + str(self.minw.getText)# + " " + str(float(source.getText())) self.minh.setText(str(int(round(float(self.minw.getText())/float(source.getText()))))) self.maxh.setText(str(int(round(float(self.maxw.getText())/float(source.getText()))))) elif source == self.minw: self.minh.setText(str(int(round(float(source.getText())/float(self.aspRatio.getText()), 0)))) elif source == self.maxw: self.maxh.setText(str(int(round(float(source.getText())/float(self.aspRatio.getText()), 0)))) def DialogGenerate(imageBaseDir, summary): dpi = 300 defaultAspectRatio = 1.33 defaultTileWidth = 15 defaultOriginalWidth = 150 defaultOriginalHeight = 113 defaultTileHeight = round(defaultTileWidth/defaultAspectRatio) gd = GenericDialogPlus("Cover Maker") gd.addMessage("Prepare Image database") gd.addDirectoryField("Select base directory containing images", imageBaseDir, 20) gd.addMessage(summary) gd.addNumericField("Aspect ratio", defaultAspectRatio, 2) gd.addNumericField("Original width", defaultOriginalWidth, 0) gd.addNumericField("Original height", defaultOriginalHeight, 0) gd.addNumericField("minimal tile width", defaultTileWidth, 0) gd.addNumericField("maximal tile width", defaultTileWidth, 0) gd.addNumericField("minimal tile height", defaultTileHeight, 0) gd.addNumericField("maximal tile height", defaultTileHeight, 0) fields = gd.getNumericFields() aspRatio = fields.get(0) minw = fields.get(3) maxw = fields.get(4) minh = fields.get(5) maxh = fields.get(6) # resolution and size listener textListener = RatioToDim(aspRatio, minw, maxw, minh, maxh) aspRatio.addTextListener(textListener) minw.addTextListener(textListener) maxw.addTextListener(textListener) gd.showDialog() if gd.wasCanceled(): print "User canceled dialog!" return imageBaseDir = gd.getNextString() aspectRatio = gd.getNextNumber() majorWidth = gd.getNextNumber() majorHeight = gd.getNextNumber() mintilewidth = gd.getNextNumber() maxtilewidth = gd.getNextNumber() return int(mintilewidth), int(maxtilewidth), imageBaseDir, float(aspectRatio), int(majorWidth), int(majorHeight) imageBaseDir = '' summary = '' #imageBaseDir = DialogAnalyze() #summary = DirList(imageBaseDir) (minw, maxw, imageBaseDir, aspectRatio, majorWidth, majorHeight) = DialogGenerate(imageBaseDir, summary) PrepareDatabase(minw, maxw, imageBaseDir, aspectRatio, majorWidth, majorHeight)