def processFile(filename, inDir, outDir, dichroics, mergeList): if mergeList is None: merge = False else: merge = True filenameExExt = os.path.splitext(filename)[0] filepath = inDir + filename # parse metadata reader = ImageReader() omeMeta = MetadataTools.createOMEXMLMetadata() reader.setMetadataStore(omeMeta) reader.setId(filepath) numChannels = reader.getSizeC() numSlices = reader.getSizeZ() numFrames = reader.getSizeT() seriesCount = reader.getSeriesCount() globalMetadata = reader.getGlobalMetadata() seriesMetadata = reader.getSeriesMetadata() objLensName = globalMetadata['- Objective Lens name #1'] areaRotation = float(seriesMetadata['area rotation #1']) acquisitionValueRotation = float(seriesMetadata['acquisitionValue rotation #1']) if 'regionInfo rotation #1' in seriesMetadata: regionInfoRotation = float(seriesMetadata['regionInfo rotation #1']) else: regionInfoRotation = float(0) totalRotation = areaRotation + regionInfoRotation physSizeX = omeMeta.getPixelsPhysicalSizeX(0) physSizeY = omeMeta.getPixelsPhysicalSizeY(0) pxSizeX = physSizeX.value(UNITS.MICROM) pxSizeY = physSizeY.value(UNITS.MICROM) # log metadata IJ.log("\nMETADATA") #IJ.log("Filename: " + filepath) IJ.log("Number of series: " + str(seriesCount)) IJ.log("Number of channels: " + str(numChannels)) IJ.log("Number of frames: " + str(numFrames)) IJ.log("Number of slices: " + str(numSlices)) IJ.log("Objective lens: " + objLensName) IJ.log("FOV rotation: " + str(areaRotation)) IJ.log("ROI rotation: " + str(regionInfoRotation)) IJ.log("Total rotation: " + str(totalRotation)) IJ.log("Pixel size:") IJ.log("\t\tX = " + str(physSizeX.value()) + " " + physSizeX.unit().getSymbol()) IJ.log("\t\tY = " + str(physSizeY.value()) + " " + physSizeY.unit().getSymbol()) if merge: tifDir = outDir + "." + str(datetime.now()).replace(" ", "").replace(":", "") + "/" if not os.path.exists(tifDir): os.makedirs(tifDir) IJ.log("\nCreated temporary folder: " + tifDir + "\n") else: IJ.log("Unable to create temporary folder!\n") else: tifDir = outDir + filenameExExt + "/" if not os.path.exists(tifDir): os.makedirs(tifDir) IJ.log("\nCreated subfolder: " + tifDir + "\n") else: IJ.log("\nSubfolder " + tifDir + " already exists.\n") # correct images tifFilePaths = [] for i in range(numChannels): ip = extractChannel(oirFile=filepath, ch=i) if dichroics[i] == "DM1": IJ.log("Channel " + str(i+1) + " was imaged using DM1, so no correction required.") else: offsets = getOffset(obj=objLensName,dm=dichroicDict[dichroics[i]]) xom = offsets['x'] yom = offsets['y'] if abs(totalRotation) > 0.1: rotOff = rotateOffset(x=xom, y=yom, angle=-totalRotation) xom = rotOff['x'] yom = rotOff['y'] xop = int(round(xom/pxSizeX)) yop = int(round(yom/pxSizeY)) IJ.log("Channel " + str(i+1) + " offsets") IJ.log("\t\tMicrometres") IJ.log("\t\t\t\tx = " + str(xom)) IJ.log("\t\t\t\ty = " + str(yom)) IJ.log("\t\tPixels") IJ.log("\t\t\t\tx = " + str(xop)) IJ.log("\t\t\t\ty = " + str(yop)) IJ.run(ip, "Translate...", "x=" + str(-xop) + " y=" + str(-yop) + " interpolation=None stack") tifFilePath = tifDir + filenameExExt + "_ch_"+str(i+1)+".tif" tifFilePaths.append(tifFilePath) if os.path.exists(tifFilePath): IJ.log("\nOutput file exists: " + tifFilePath) IJ.log("Rerun plugin choosing a different output folder") IJ.log("or delete file and then rerun plugin.") IJ.log("Image processing terminated!\n") return FileSaver(ip).saveAsTiff(tifFilePath) if merge: max_list = [] for i in range(len(mergeList)): if mergeList[i] != None: mergeList[i] = readSingleChannelImg(tifFilePaths[mergeList[i]]) channel = mergeList[i]#https://python.hotexamples.com/examples/ij.plugin/RGBStackMerge/mergeChannels/python-rgbstackmerge-mergechannels-method-examples.html projector = ZProjector(channel) projector.setMethod(ZProjector.MAX_METHOD) projector.doProjection() max_list.append(projector.getProjection()) merged = RGBStackMerge.mergeChannels(mergeList, False) merged_max = RGBStackMerge.mergeChannels(max_list, False) mergedChannelFilepath = outDir + filenameExExt + ".tif" maxMergedChannelFilepath = outDir + filenameExExt + "_max.tif" if os.path.exists(mergedChannelFilepath): IJ.log("\nOutput file exists: " + mergedChannelFilepath) IJ.log("Rerun plugin choosing a different output folder") IJ.log("or delete file and then rerun plugin.") IJ.log("Image processing terminated!\n") FileSaver(merged).saveAsTiff(mergedChannelFilepath) FileSaver(merged_max).saveAsTiff(maxMergedChannelFilepath) for tf in tifFilePaths: os.remove(tf) os.rmdir(tifDir) IJ.log("\nFinished processing file:\n" + filepath + "\n") if merge: IJ.log("Image file with channels aligned:\n" + outDir + filenameExExt + ".tif\n") else: IJ.log("Aligned images (one tiff file for each channel) can be found in:\n" + tifDir + "\n")
def processFile(): # start logging IJ.log("\n______________________________\n\n\t\tOlympus DM correction\n\t\tVersion " + pluginVersion +"\n______________________________\n") # ask user for file ofd = OpenDialog("Choose a file", None) filename = ofd.getFileName() if filename is None: IJ.log("User canceled the dialog!\nImage processing canceled!\n") return directory = ofd.getDirectory() filepath = directory + filename IJ.log("File path: " + filepath) if not filename.endswith(".oir"): IJ.log("Not an Olympus (.oir) file.\nNo image to process.\n") return filenameExExt = os.path.splitext(filename)[0] # parse metadata reader = ImageReader() omeMeta = MetadataTools.createOMEXMLMetadata() reader.setMetadataStore(omeMeta) reader.setId(filepath) numChannels = reader.getSizeC() numSlices = reader.getSizeZ() numFrames = reader.getSizeT() seriesCount = reader.getSeriesCount() globalMetadata = reader.getGlobalMetadata() seriesMetadata = reader.getSeriesMetadata() objLensName = globalMetadata['- Objective Lens name #1'] areaRotation = float(seriesMetadata['area rotation #1']) acquisitionValueRotation = float(seriesMetadata['acquisitionValue rotation #1']) if 'regionInfo rotation #1' in seriesMetadata: regionInfoRotation = float(seriesMetadata['regionInfo rotation #1']) else: regionInfoRotation = float(0) totalRotation = areaRotation + regionInfoRotation physSizeX = omeMeta.getPixelsPhysicalSizeX(0) physSizeY = omeMeta.getPixelsPhysicalSizeY(0) pxSizeX = physSizeX.value(UNITS.MICROM) pxSizeY = physSizeY.value(UNITS.MICROM) # log metadata IJ.log("\nMETADATA") #IJ.log("Filename: " + filepath) IJ.log("Number of series: " + str(seriesCount)) IJ.log("Number of channels: " + str(numChannels)) IJ.log("Number of frames: " + str(numFrames)) IJ.log("Number of slices: " + str(numSlices)) IJ.log("Objective lens: " + objLensName) IJ.log("FOV rotation: " + str(areaRotation)) IJ.log("ROI rotation: " + str(regionInfoRotation)) IJ.log("Total rotation: " + str(totalRotation)) IJ.log("Pixel size:") IJ.log("\t\tX = " + str(physSizeX.value()) + " " + physSizeX.unit().getSymbol()) IJ.log("\t\tY = " + str(physSizeY.value()) + " " + physSizeY.unit().getSymbol()) # ask user to identify dichroic mirror used for each channel gdDM = GenericDialog("Dichroic mirrors") DMs = ["DM1", "DM2", "DM3", "DM4", "DM5"] for i in range(numChannels): gdDM.addChoice("Channel " + str(i+1), DMs, DMs[0]) gdDM.addCheckbox("Merge channels", False) gdDM.showDialog() if gdDM.wasCanceled(): IJ.log("User canceled the dialog!\nImage processing canceled!\n") return dichroics = [] for i in range(numChannels): dichroics.append(gdDM.getNextChoice()) merge = gdDM.getNextBoolean() IJ.log("\nUser selected dichroic mirrors") for i in range(numChannels): IJ.log("\t\tChannel " + str(i+1) + ": " + dichroics[i]) if merge: channels = [] chDict = {} for i in range(numChannels): chName = "Channel"+str(i+1) channels.append(chName) chDict[chName] = i channels.append("NONE") colourChoices = ["red", "green", "blue", "gray", "cyan", "magenta", "yellow"] gdMerge = GenericDialog("Merge channels") for c in colourChoices: gdMerge.addChoice(c + ":", channels, channels[numChannels]) gdMerge.showDialog() if gdMerge.wasCanceled(): IJ.log("User canceled the dialog!\nImage processing canceled!\n") return IJ.log("\nUser selected channel colours") mergeList = [] for i in range(len(colourChoices)): ch = gdMerge.getNextChoice() if ch == "NONE": mergeList.append(None) else: mergeList.append(chDict[ch]) IJ.log("\t\t" + colourChoices[i] + ": " + ch) # ask user for an output directory dc = DirectoryChooser("Choose folder for output") od = dc.getDirectory() if od is None: IJ.log("User canceled the dialog!\nImage processing canceled!\n") return if merge: tifDir = od + "." + str(datetime.now()).replace(" ", "").replace(":", "") + "/" if not os.path.exists(tifDir): os.makedirs(tifDir) IJ.log("\nCreated temporary folder: " + tifDir + "\n") else: IJ.log("Unable to create temporary folder!\n") else: tifDir = od + filenameExExt + "/" if not os.path.exists(tifDir): os.makedirs(tifDir) IJ.log("\nCreated subfolder: " + tifDir + "\n") else: IJ.log("\nSubfolder " + tifDir + " already exists") # correct images tifFilePaths = [] for i in range(numChannels): ip = extractChannel(oirFile=filepath, ch=i) if dichroics[i] == "DM1": IJ.log("Channel " + str(i+1) + " was imaged using DM1, so no correction required.") else: offsets = getOffset(obj=objLensName,dm=dichroicDict[dichroics[i]]) xom = offsets['x'] yom = offsets['y'] if abs(totalRotation) > 0.1: rotOff = rotateOffset(x=xom, y=yom, angle=-totalRotation) xom = rotOff['x'] yom = rotOff['y'] xop = int(round(xom/pxSizeX)) yop = int(round(yom/pxSizeY)) IJ.log("Channel " + str(i+1) + " offsets") IJ.log("\t\tMicrometres") IJ.log("\t\t\t\tx = " + str(xom)) IJ.log("\t\t\t\ty = " + str(yom)) IJ.log("\t\tPixels") IJ.log("\t\t\t\tx = " + str(xop)) IJ.log("\t\t\t\ty = " + str(yop)) IJ.run(ip, "Translate...", "x=" + str(-xop) + " y=" + str(-yop) + " interpolation=None stack") tifFilePath = tifDir + filenameExExt + "_ch_"+str(i+1)+".tif" tifFilePaths.append(tifFilePath) if os.path.exists(tifFilePath): IJ.log("\nOutput file exists: " + tifFilePath) IJ.log("Rerun plugin choosing a different output folder") IJ.log("or delete file and then rerun plugin.") IJ.log("Image processing terminated!\n") return FileSaver(ip).saveAsTiff(tifFilePath) if merge: for i in range(len(mergeList)): if mergeList[i] != None: mergeList[i] = readSingleChannelImg(tifFilePaths[mergeList[i]]) merged = RGBStackMerge.mergeChannels(mergeList, False) mergedChannelFilepath = od + filenameExExt + ".tif" if os.path.exists(mergedChannelFilepath): IJ.log("\nOutput file exists: " + mergedChannelFilepath) IJ.log("Rerun plugin choosing a different output folder") IJ.log("or delete file and then rerun plugin.") IJ.log("Image processing terminated!\n") FileSaver(merged).saveAsTiff(mergedChannelFilepath) for tf in tifFilePaths: os.remove(tf) os.rmdir(tifDir) IJ.log("\nFinished processing file:\n" + filepath + "\n") if merge: IJ.log("Image file with channels aligned:\n" + od + filenameExExt + ".tif\n") else: IJ.log("Aligned images (one tiff file for each channel) can be found in:\n" + tifDir + "\n")