# MIT License # Copyright (c) 2017 dcolam from __future__ import with_statement, division import sys, time, os, traceback, random, time, ConfigParser, csv, math, fnmatch, locale from ij import IJ, ImagePlus, WindowManager, CompositeImage from org.sqlite import SQLiteConfig from java.lang import Class, System, Double from java.awt import Color, Font from loci.plugins.util import WindowTools as wt from java.sql import DriverManager, SQLException, Types, Statement from ij.gui import GenericDialog, WaitForUserDialog, Roi, ShapeRoi, Overlay, TextRoi from ij.process import ImageProcessor, AutoThresholder from ij.plugin import ChannelSplitter, ImageCalculator, RGBStackMerge, ZProjector, Duplicator, StackEditor, \ Concatenator, RoiEnlarger, RoiRotator from sc.fiji.analyzeSkeleton import AnalyzeSkeleton_ from ij.plugin import ZProjector as zp from fiji.stacks import Hyperstack_rearranger as hyr from ij.plugin.frame.RoiManager import multiMeasure from ij.plugin.filter import EDM, ParticleAnalyzer, Calibrator, Filler, Analyzer, PlugInFilterRunner from ij.measure import Measurements as ms from loci.plugins import BF from ij.plugin.filter import ThresholdToSelection as tts from ij.measure import ResultsTable, Calibration from ij.io import RoiDecoder import org.scijava.command.Command from org.scijava.util import ColorRGB # Main Dialog manager class Dialoger(object): autoMethods = AutoThresholder.getMethods() allMethods = ["Manual"] allMethods += autoMethods def __init__(self): self.input_path_dir = '' self.output_path_dir = '' self.ext = '' self.delimiter = "_" self.filenames = [] self.groupedFiles = {} self.zStack = False self.test = False self.c1 = Channel() self.c2 = Channel() self.c3 = Channel() self.c4 = Channel() self.output_path_dict = {} self.channels = [self.c1, self.c2, self.c3, self.c4] self.overwriteDB = False self.getOptions() self.loadfilenames() [self.getParticleAnalyzerOptions(i) for i, x in enumerate(self.channels) if self.channels[i].pa] for j in self.channels: if any(j.list_1whichChannel): [self.getParticleAnalyzerOptions(i, "coloc") for i, x in enumerate(j.list_1whichChannel) if not self.channels[i].pa and x] def loadfilenames(self): filenames = [] groupedfiles = {} if self.ext[0] != ".": self.ext = "." + self.ext for root, dirs, files in os.walk(self.input_path_dir): group = os.path.split(root)[1] if not group in groupedfiles: groupedfiles[group] = [] for j in files: if os.path.splitext(os.path.join(root, j))[1] == self.ext: groupedfiles[group].append(os.path.join(root, j)) filenames.append(os.path.join(root, j)) if not filenames: WaitForUserDialog("No files have been found. Please, check for correct file-extension (file-type) or for presence of images in the folder").show() sys.exit("Analysis cancelled!") output_path_dir = os.path.join(self.input_path_dir, "Particle_Analysis") if not os.path.isdir(output_path_dir): os.makedirs(output_path_dir) self.output_path_dir = output_path_dir for k in groupedfiles: g_path = os.path.join(self.output_path_dir, k) if not os.path.isdir(g_path): os.makedirs(g_path) self.output_path_dict[k] = g_path output_table = os.path.join(self.output_path_dir, "Output_Table") if not os.path.isdir(output_table): os.makedirs(output_table) self.output_path_dict["output_table_path"] = output_table self.groupedFiles = dict((k, v) for k, v in groupedfiles.items() if v) self.filenames = filenames def getOptions(self): section = "ChannelOptions" ext = cp.cp.get(section, "ext") delimiter = cp.cp.get(section, "delimiter") zStackBool = cp.cp.getboolean(section, "zStackBool") c1Name = cp.cp.get(section, "c1Name") c1Opt_boolList = eval(cp.cp.get(section, "c1Opt_boolList")) backgroundRadc1 = cp.cp.getfloat(section, "backgroundRadc1") sigmaC1 = cp.cp.getfloat(section, "sigmaC1") c2Name = cp.cp.get(section, "c2Name") c2Opt_boolList = eval(cp.cp.get(section, "c2Opt_boolList")) backgroundRadc2 = cp.cp.getfloat(section, "backgroundRadc2") sigmaC2 = cp.cp.getfloat(section, "sigmaC2") c3Name = cp.cp.get(section, "c3Name") c3Opt_boolList = eval(cp.cp.get(section, "c3Opt_boolList")) backgroundRadc3 = cp.cp.getfloat(section, "backgroundRadc3") sigmaC3 = cp.cp.getfloat(section, "sigmaC3") c4Name = cp.cp.get(section, "c4Name") c4Opt_boolList = eval(cp.cp.get(section, "c4Opt_boolList")) backgroundRadc4 = cp.cp.getfloat(section, "backgroundRadc4") sigmaC4 = cp.cp.getfloat(section, "sigmaC4") testBool = cp.cp.getboolean(section, "testBool") if not headless: gd = GenericDialog("Options") gd.addMessage("Input Folder: %s" % expath) gd.addCheckboxGroup(1, 2, ["Z-project?", "Overwrite old database if it already exists?"], [zStackBool, True]) gd.addStringField("File extension", ext, 10) gd.addStringField("Title separator", delimiter, 10) gd.addMessage( "__________________________________________________________________________________________________________________________________________________") gd.addMessage("Set details for Channel 1") gd.addStringField("Channel 1", c1Name, 8) gd.addCheckboxGroup(1, 4, ["Background Substraction", "Adjust Brightness/Contrast automatically?", "Adjust Brightness/Contrast manually?", "Particle Analysis"], c1Opt_boolList) gd.addNumericField("Background radius:", backgroundRadc1, 0) gd.addNumericField("Gaussian Blur (0 if not, otherwise state the radius)", sigmaC1, 2) gd.addMessage( "__________________________________________________________________________________________________________________________________________________") gd.addMessage("Set details for Channel 2") gd.addStringField("Channel 2", c2Name, 8) gd.addCheckboxGroup(1, 4, ["Background Substraction", "Adjust Brightness/Contrast automatically?", "Adjust Brightness/Contrast manually?", "Particle Analysis"], c2Opt_boolList) gd.addNumericField("Background radius:", backgroundRadc2, 0) gd.addNumericField("Gaussian Blur (0 if not, otherwise state the radius)", sigmaC2, 2) gd.addMessage( "__________________________________________________________________________________________________________________________________________________") gd.addMessage("Set details for Channel 3") gd.addStringField("Channel 3", c3Name, 8) gd.addCheckboxGroup(1, 4, ["Background Substraction", "Adjust Brightness/Contrast automatically?", "Adjust Brightness/Contrast manually?", "Particle Analysis"], c3Opt_boolList) gd.addNumericField("Background radius:", backgroundRadc3, 0) gd.addNumericField("Gaussian Blur (0 if not, otherwise state the radius)", sigmaC3, 2) gd.addMessage( "__________________________________________________________________________________________________________________________________________________") gd.addMessage("Set details for Channel 4") gd.addStringField("Channel 4", c4Name, 8) gd.addCheckboxGroup(1, 4, ["Background Substraction", "Adjust Brightness/Contrast automatically?", "Adjust Brightness/Contrast manually?", "Particle Analysis"], c4Opt_boolList) gd.addNumericField("Background radius:", 50, 0) gd.addNumericField("Gaussian Blur (0 if not, otherwise state the radius)", sigmaC4, 2) gd.addMessage("_________________________________________________________________________________") gd.addCheckbox("Test parameters on random pictures?", testBool) wt.addScrollBars(gd) gd.showDialog() if gd.wasCanceled(): print "User canceled dialog!" sys.exit("Analysis was cancelled") if isinstance(expath, str): input_path_dir = expath else: input_path_dir = expath.getAbsolutePath() zStack = zStackBool = gd.getNextBoolean() ext = gd.getNextString() delimiter = gd.getNextString() self.overwriteDB = gd.getNextBoolean() info_channels = [] for i in range(0, 4): channelName = gd.getNextString() background = gd.getNextBoolean() brightness_auto = gd.getNextBoolean() brightness_man = gd.getNextBoolean() pa = gd.getNextBoolean() radius = gd.getNextNumber() gaussian = gd.getNextNumber() if brightness_auto: brightness_man = False if i == 0: c1Name = channelName c1Opt_boolList = [background, brightness_auto, brightness_man, pa] backgroundRadc1 = radius sigmaC1 = gaussian if i == 1: c2Name = channelName c2Opt_boolList = [background, brightness_auto, brightness_man, pa] backgroundRadc2 = radius sigmaC2 = gaussian if i == 2: c3Name = channelName c3Opt_boolList = [background, brightness_auto, brightness_man, pa] backgroundRadc3 = radius sigmaC3 = gaussian if i == 3: c4Name = channelName c4Opt_boolList = [background, brightness_auto, brightness_man, pa] backgroundRadc4 = radius sigmaC4 = gaussian info_channels.append([channelName, background, radius, brightness_auto, brightness_man, pa, gaussian]) self.channels[i].setInfo(channel_name=channelName, background_substraction=background, background_radius=radius, brightness_auto=brightness_auto, brightness_man=brightness_man, pa=pa, gaussian_blur=gaussian) self.test = testBool = gd.getNextBoolean() l = ["expath", "ext", "delimiter", "zStackBool", "c1Name", "c1Opt_boolList", "backgroundRadc1", "sigmaC1", "c2Name", "c2Opt_boolList", "backgroundRadc2", "sigmaC2", "c3Name", "c3Opt_boolList", "backgroundRadc3", "sigmaC3", "c4Name", "c4Opt_boolList","backgroundRadc4", "sigmaC4", "testBool"] n = [expath, ext, delimiter, zStackBool, c1Name, c1Opt_boolList, backgroundRadc1, sigmaC1, c2Name,c2Opt_boolList, backgroundRadc2, sigmaC2, c3Name, c3Opt_boolList,backgroundRadc3, sigmaC3, c4Name, c4Opt_boolList, backgroundRadc4, sigmaC4, testBool] cp.update(section, dict((na, str(n[i])) for i, na in enumerate(l))) self.input_path_dir = input_path_dir self.zStack = zStack self.ext = ext self.delimiter = delimiter else: self.input_path_dir = expath2 self.zStack = zStackBool self.ext = ext self.overwriteDB = True self.delimiter = delimiter cnames = [c1Name, c2Name, c3Name, c3Name] backgrounds = [backgroundRadc1, backgroundRadc2, backgroundRadc3, backgroundRadc4] radiuss = [sigmaC1, sigmaC2, sigmaC3, sigmaC4] info_channels = [] for i in range(0, 4): channelName = cnames[i] radius = backgrounds[i] if i == 0: background = c1Opt_boolList[0] brightness_auto = c1Opt_boolList[1] brightness_man = c1Opt_boolList[2] pa = c1Opt_boolList[3] c1Name = channelName backgroundRadc1 = radius gaussian = sigmaC1 if i == 1: background = c2Opt_boolList[0] brightness_auto = c2Opt_boolList[1] brightness_man = c2Opt_boolList[2] pa = c2Opt_boolList[3] c2Name = channelName backgroundRadc2 = radius gaussian = sigmaC2 if i == 2: background = c3Opt_boolList[0] brightness_auto = c3Opt_boolList[1] brightness_man = c3Opt_boolList[2] pa = c3Opt_boolList[3] c3Name = channelName backgroundRadc3 = radius gaussian = sigmaC3 if i == 3: background = c4Opt_boolList[0] brightness_auto = c4Opt_boolList[1] brightness_man = c4Opt_boolList[2] pa = c4Opt_boolList[3] c4Name = channelName backgroundRadc4 = radius gaussian = sigmaC4 info_channels.append([channelName, background, radius, brightness_auto, brightness_man, pa, gaussian]) self.channels[i].setInfo(channel_name=channelName, background_substraction=background, background_radius=radius, brightness_auto=brightness_auto, brightness_man=brightness_man, pa=pa, gaussian_blur=gaussian) self.test = False def getParticleAnalyzerOptions(self, channel_number, coloc=''): section = "ParticleAnalysisOptions%s" % channel_number paInOutBool_list = eval(cp.cp.get(section, "paInOutBool_list")) paColocBool_list = eval(cp.cp.get(section, "paColocBool_list")) paEnlarge = cp.cp.getfloat(section, "paEnlarge") paSizeA1 = cp.cp.getfloat(section, "paSizeA1") paSizeB1 = cp.cp.getfloat(section, "paSizeB1") paSizeA2 = cp.cp.getfloat(section, "paSizeA2") paSizeB2 = cp.cp.getfloat(section, "paSizeB2") paCirc1 = cp.cp.getfloat(section, "paCirc1") paCirc2 = cp.cp.getfloat(section, "paCirc2") paMethod = cp.cp.get(section, "paMethod") addMeth1 = cp.cp.get(section, "addMeth1") watershed1 = cp.cp.getboolean(section, "watershed1") addMeth2 = cp.cp.get(section, "addMeth2") watershed2 = cp.cp.getboolean(section, "watershed2") if not headless: if coloc == "coloc": gd = GenericDialog("Options for Channel %s colocalized Particle Analysis" % (channel_number + 1)) else: gd = GenericDialog("Options for Channel %s Particle Analysis" % (channel_number + 1)) gd.addMessage("Set details for Channel %s" % (channel_number + 1)) gd.addMessage("___________________________________________________________________________________") if not coloc == "coloc": gd.addMessage("Colocalisation Options") gd.addCheckboxGroup(1, 2, ["Inside mask?", "Or outside?"], paInOutBool_list) gd.addCheckboxGroup(1, 4, ["C1", "C2", "C3", "C4"], paColocBool_list) gd.addNumericField("Enlarge mask in [um]? (For shrinkage put negative numbers)", paEnlarge, 2) gd.addMessage("___________________________________________________________________________________") gd.addMessage("Particle Analysis Options") if channel_number == 0: gd.addNumericField("Lower Particle Size:", paSizeA1, 3) gd.addNumericField("Higher Particle Size:", paSizeB1, 3) else: gd.addNumericField("Lower Particle Size:", paSizeA2, 3) gd.addNumericField("Higher Particle Size:", paSizeB2, 3) gd.addNumericField("Circularity bottom:", paCirc1, 1) gd.addNumericField("Circularity top:", paCirc2, 1) gd.addChoice("Binary Threshold Method", self.allMethods, paMethod) if channel_number == 0: gd.addStringField("Do you want to test additional thresholds? (Separate only by space)", addMeth1, 8) gd.addCheckbox("Watershed?", watershed1) else: gd.addStringField("Do you want to test additional thresholds? (Separate only by space)", addMeth2, 8) gd.addCheckbox("Watershed?", watershed2) gd.showDialog() if gd.wasCanceled(): print "User canceled dialog!" sys.exit("Analysis was cancelled") if not coloc == "coloc": pa_inside = gd.getNextBoolean() pa_outside = gd.getNextBoolean() paInOutBool_list = [pa_inside, pa_outside] bool_c1 = gd.getNextBoolean() bool_c2 = gd.getNextBoolean() bool_c3 = gd.getNextBoolean() bool_c4 = gd.getNextBoolean() pa_enlarge_mask = paEnlarge = gd.getNextNumber() list_1whichChannel = paColocBool_list = [bool_c1, bool_c2, bool_c3, bool_c4] if channel_number == 0: lowerSize = paSizeA1 = gd.getNextNumber() higherSize = paSizeB1 = gd.getNextNumber() else: lowerSize = paSizeA2 = gd.getNextNumber() higherSize = paSizeB2 = gd.getNextNumber() circ1 = paCirc1 = gd.getNextNumber() circ2 = paCirc2 = gd.getNextNumber() pa_threshold_c1 = paMethod = gd.getNextChoice() if channel_number == 0: pa_addthreshold_c1 = addMeth1 = gd.getNextString() watershed = watershed1 = gd.getNextBoolean() else: pa_addthreshold_c1 = addMeth2 = gd.getNextString() watershed = watershed2 = gd.getNextBoolean() pa_thresholds_c1 = [pa_threshold_c1] if pa_addthreshold_c1: pa_addthreshold_c1 = pa_addthreshold_c1.split(" ") for i in pa_addthreshold_c1: if i in self.allMethods: pa_thresholds_c1.append(i) else: print i + " is not a Threshold!" if not coloc == "coloc": self.channels[channel_number].setInfo(lowerSize=lowerSize, higherSize=higherSize, circ1=circ1, circ2=circ2, method=pa_thresholds_c1, list_1whichChannel=list_1whichChannel, watershed=watershed, pa_inside=pa_inside, pa_outside=pa_outside, pa_enlarge_mask=pa_enlarge_mask) if channel_number == 0: l = ["paInOutBool_list", "paEnlarge", "paColocBool_list", "paSizeA1", "paSizeB1", "paCirc1", "paCirc2","paMethod", "addMeth1", "watershed1"] n = [paInOutBool_list, paEnlarge, paColocBool_list, paSizeA1, paSizeB1, paCirc1, paCirc2, paMethod, addMeth1, watershed1] else: l = ["paInOutBool_list", "paEnlarge", "paColocBool_list", "paSizeA2", "paSizeB2", "paCirc1","paCirc2","paMethod", "addMeth2", "watershed2"] n = [paInOutBool_list, paEnlarge, paColocBool_list, paSizeA2, paSizeB2, paCirc1, paCirc2, paMethod, addMeth2, watershed2] else: self.channels[channel_number].setInfo(lowerSize=lowerSize, higherSize=higherSize, circ1=circ1,circ2=circ2, method=pa_thresholds_c1, watershed=watershed) if channel_number == 0: l = ["paSizeA1", "paSizeB1", "paCirc1", "paCirc2", "paMethod", "addMeth1", "watershed1"] n = [paSizeA1, paSizeB1, paCirc1, paCirc2, paMethod, addMeth1, watershed1] else: l = ["paSizeA2", "paSizeB2", "paCirc1", "paCirc2", "paMethod", "addMeth2", "watershed2"] n = [paSizeA2, paSizeB2, paCirc1, paCirc2, paMethod, addMeth2, watershed2] cp.update(section, dict((na, str(n[i])) for i, na in enumerate(l))) else: if not coloc == "coloc": paInOutBool_list = paInOutBool_list pa_enlarge_mask = paEnlarge list_1whichChannel = paColocBool_list if channel_number == 0: lowerSize = paSizeA1 higherSize = paSizeB1 else: lowerSize = paSizeA2 higherSize = paSizeB2 circ1 = paCirc1 circ2 = paCirc2 pa_threshold_c1 = paMethod if channel_number == 0: pa_addthreshold_c1 = addMeth1 watershed = watershed1 else: pa_addthreshold_c1 = addMeth2 watershed = watershed2 pa_thresholds_c1 = [pa_threshold_c1] if pa_addthreshold_c1: pa_addthreshold_c1 = pa_addthreshold_c1.split(" ") for i in pa_addthreshold_c1: if i in self.allMethods: pa_thresholds_c1.append(i) else: print i + " is not a Threshold!" if not coloc == "coloc": self.channels[channel_number].setInfo(lowerSize=lowerSize, higherSize=higherSize, circ1=circ1, circ2=circ2, method=pa_thresholds_c1, list_1whichChannel=list_1whichChannel, watershed=watershed, pa_inside=paInOutBool_list[0], pa_outside=paInOutBool_list[1], pa_enlarge_mask=pa_enlarge_mask) else: self.channels[channel_number].setInfo(lowerSize=lowerSize, higherSize=higherSize, circ1=circ1, circ2=circ2, method=pa_thresholds_c1, watershed=watershed) # At the beginning of the Script, this object sets up the SelectionManager and the Dialoger and gathers all parameters class testParameters(object): def __init__(self): self.d = "" self.s = "" self.another = False self.newparams = False self.start = False def dialog(self): self.another = False self.newparams = False self.start = False gd = GenericDialog("Test parameter mode - Select just one option") gd.addCheckbox("Test another image?", False) gd.addCheckbox("Try new parameters?", False) gd.addCheckbox("Start Experiment", True) gd.showDialog() if gd.wasCanceled(): print "User canceled dialog!" sys.exit("Analysis was cancelled") self.another = gd.getNextBoolean() self.newparams = gd.getNextBoolean() self.start = gd.getNextBoolean() def startScript(self): self.d = Dialoger() self.s = SelectionManager() cp.writeIni() cp.readIni() if self.d.test: filepath = random.choice(self.d.filenames) print "*****************************************************" print "Testing Parameters on image: %s \n" % os.path.split(filepath)[1] l = Image(filepath, self.d, self.s, True) self.stitch(filepath) self.dialog() while self.another: IJ.run("Close All") filepath = random.choice(self.d.filenames) print "*****************************************************" print "Testing Parameters on image: %s \n" % os.path.split(filepath)[1] l = Image(filepath, self.d, self.s, True) self.stitch(filepath) self.dialog() if self.newparams: self.startScript() if self.start: IJ.run("Close All") return self.d, self.s else: return self.d, self.s def stitch(self, filepath): imp = BF.openImagePlus(filepath)[0] if WindowManager.getImageCount() > 1: titles = WindowManager.getImageTitles() count = WindowManager.getImageCount() ids = [WindowManager.getNthImageID(i) for i in range(1, count + 1)] imps = [WindowManager.getImage(i) for i in ids] stack = Concatenator().concatenate(imps, False) stack.show() stack.setT(1) for i, t in enumerate(titles): stack.setT(i + 1) IJ.run("Set Label...", "label=]%s" % t) imp.show() WaitForUserDialog("Inspect results compared to original image and then proceed").show() stack.close() imp.close() else: WaitForUserDialog("Inspect results compared to original image and then proceed").show() IJ.getImage().close() return