def Dialog(imp): dpi = 300 # a4 width in inches defaultWidth = 11.69 defaultHeight = defaultWidth / ratio defaultAspectRatio = 1.41 if imp: gd = GenericDialogPlus("Cover Maker") gd.addMessage("Input Options") gd.addFileField("Select image database", "", 20) gd.addMessage("Cover Maker Options") gd.addNumericField("tile width", 12, 0) gd.addNumericField("tile height", 9, 0) gd.showDialog() if gd.wasCanceled(): print "User canceled dialog!" return databasepath = gd.getNextString() tilewidth = gd.getNextNumber() tileheight = gd.getNextNumber() return databasepath, imp.getWidth(), imp.getHeight(), int( tilewidth), int(tileheight) else: IJ.showMessage("You should have at least one image open.")
def Dialog(imp): dpi = 300 # a4 width in inches defaultWidth = 11.69 defaultHeight = defaultWidth/ratio defaultAspectRatio = 1.41 if imp: gd = GenericDialogPlus("Cover Maker") gd.addMessage("Input Options") gd.addFileField("Select image database", "", 20) gd.addMessage("Cover Maker Options") gd.addNumericField("tile width", 12, 0) gd.addNumericField("tile height", 9, 0) gd.showDialog() if gd.wasCanceled(): print "User canceled dialog!" return databasepath = gd.getNextString() tilewidth = gd.getNextNumber() tileheight = gd.getNextNumber() print 'path:', databasepath return databasepath, imp.getWidth(), imp.getHeight(), int(tilewidth), int(tileheight) else: IJ.showMessage( "You should have at least one image open." )
def get_user_params(event): """ Allows user to select file and user parameters Parameters ---------- event : Event Waits for get_user_params_JB JButton to be pressed Returns ------- dict Dict containing filename, number of Gaussians to fit, % of dataset to import, whether to specify grey value limits, minimum grey value and maximum grey value to consider (optional) """ # Open user dialog gui = GenericDialogPlus("Define user parameters") gui.addFileField("Image filename", "Select image file") gui.addNumericField("Number of Gaussians to fit: ", 2, 0) gui.addNumericField("Percentage of dataset to import: ", 15, 0) gui.addCheckbox("Specify grey value limits?", False) gui.addNumericField("Min grey value (optional): ", 0, 0) gui.addNumericField("Max grey value (optional): ", 255, 0) gui.showDialog() # Extract user parameters if gui.wasOKed(): user_params = {} # empty dict user_params['img_fname'] = str(gui.getNextString()) user_params['n_gaussians'] = int(gui.getNextNumber()) user_params['pct_stack_import'] = float(gui.getNextNumber()) user_params['specify_gv'] = gui.getNextBoolean() user_params['min_gv'] = float(gui.getNextNumber()) user_params['max_gv'] = float(gui.getNextNumber()) # Create results directory results_dir = os.path.splitext(user_params['img_fname'])[0] + "_results" if os.path.isdir(results_dir) == False: os.mkdir(results_dir) print("Results directory: {}".format(results_dir)) # Write user parameters to text file user_params_fname = os.path.join(results_dir, "Users_Params.csv") with open(user_params_fname, "wb") as f: w = csv.DictWriter(f, user_params.keys()) w.writeheader() w.writerow(user_params) # Write directory to look for user params to text file in main/ temp_user_dir = os.path.join(os.path.dirname(__file__), "temp_user_dir.txt") if os.path.isfile(temp_user_dir) == True: os.remove(temp_user_dir) # delete temp_user_dir.txt if present f = open(temp_user_dir, "w") f.write(user_params_fname) f.close() return user_params
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)
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)
def get_parameters(p): gd = GenericDialogPlus("Please enter parameters") for k in p['expose_to_gui']['value']: if p[k]['type'] == 'boolean': gd.addCheckbox(k, p[k]['value']) elif p[k]['type'] == 'folder': gd.addDirectoryField(k, p[k]['value'], 100) elif p[k]['type'] == 'file': gd.addFileField(k, p[k]['value'], 100) elif p[k]['type'] == 'string': if p[k]['choices']: gd.addChoice(k, p[k]['choices'], p[k]['value']) else: gd.addStringField(k, p[k]['value']) elif p[k]['type'] == 'int': if p[k]['choices']: gd.addChoice(k, p[k]['choices'], p[k]['value']) else: gd.addNumericField(k, p[k]['value'], 0) elif p[k]['type'] == 'float': gd.addNumericField(k, p[k]['value'], 2) gd.showDialog() if gd.wasCanceled(): return for k in p['expose_to_gui']['value']: if p[k]['type'] == 'boolean': p[k]['value'] = gd.getNextBoolean() elif p[k]['type'] == 'folder' or p[k]['type'] == 'file': p[k]['value'] = gd.getNextString() elif p[k]['type'] == 'string': if p[k]['choices']: p[k]['value'] = gd.getNextChoice() else: p[k]['value'] = gd.getNextString() elif p[k]['type'] == 'int': if p[k]['choices']: p[k]['value'] = int(gd.getNextChoice()) else: p[k]['value'] = int(gd.getNextNumber()) elif p[k]['type'] == 'float': p[k]['value'] = gd.getNextNumber() return p
def SaveDialog(imp): dpi = 300 # a4 width in inches defaultWidth = 11.69 defaultHeight = defaultWidth / ratio defaultAspectRatio = 1.41 if imp: gd = GenericDialogPlus("Cover Maker") gd.addMessage("Saving options") gd.addNumericField("resolution (dpi)", dpi, 0) gd.addNumericField("width (pixels)", defaultWidth * dpi, 0) gd.addNumericField("height (pixels)", defaultHeight * dpi, 0) gd.addNumericField("width (inches)", defaultWidth, 2) gd.addNumericField("height (inches)", defaultHeight, 2) gd.addFileField("Select Originals database", "", 20) fields = gd.getNumericFields() resField = fields.get(0) widthPixels = fields.get(1) heightPixels = fields.get(2) widthInches = fields.get(3) heightInches = fields.get(4) # resolution and size listener textListener = ResolutionListener(resField, widthPixels, heightPixels, widthInches, heightInches) resField.addTextListener(textListener) widthInches.addTextListener(textListener) heightInches.addTextListener(textListener) gd.showDialog() if gd.wasCanceled(): print "User canceled dialog!" return newres = gd.getNextNumber() newwidth = gd.getNextNumber() newheight = gd.getNextNumber() originalspath = gd.getNextString() return int(newwidth), int(newheight), newres, originalspath else: IJ.showMessage("You should have at least one image open.")
def SaveDialog(imp): dpi = 300 # a4 width in inches defaultWidth = 11.69 defaultHeight = defaultWidth/ratio defaultAspectRatio = 1.41 if imp: gd = GenericDialogPlus("Cover Maker") gd.addMessage("Saving options") gd.addNumericField("resolution (dpi)", dpi, 0) gd.addNumericField("width (pixels)", defaultWidth*dpi, 0) gd.addNumericField("height (pixels)", defaultHeight*dpi, 0) gd.addNumericField("width (inches)", defaultWidth, 2) gd.addNumericField("height (inches)", defaultHeight, 2) gd.addFileField("Select Originals database", "", 20) fields = gd.getNumericFields() resField = fields.get(0) widthPixels = fields.get(1) heightPixels = fields.get(2) widthInches = fields.get(3) heightInches = fields.get(4) # resolution and size listener textListener = ResolutionListener(resField, widthPixels, heightPixels, widthInches, heightInches) resField.addTextListener(textListener) widthInches.addTextListener(textListener) heightInches.addTextListener(textListener) gd.showDialog() if gd.wasCanceled(): print "User canceled dialog!" return newres = gd.getNextNumber() newwidth = gd.getNextNumber() newheight = gd.getNextNumber() originalspath = gd.getNextString() return int(newwidth), int(newheight), newres, originalspath else: IJ.showMessage( "You should have at least one image open." )
def getSettings(self): gd = GenericDialogPlus("Settings") gd.addNumericField("Distance in pixel", 600, 0) gd.addNumericField("Distance in cm", 2.54, 2) gd.addNumericField("Min. size (cm^2)", 0.5, 2) gd.addDirectoryField("Directory", IJ.getDirectory("home")) gd.addStringField("File extension", "*.jpg", 8) gd.showDialog() if gd.wasCanceled(): sys.exit() else: distPixel = gd.getNextNumber() distCm = gd.getNextNumber() minSize = gd.getNextNumber() * (distPixel / distCm) ** 2 imageDir = gd.getNextString() ext = gd.getNextString() return (distPixel, distCm, minSize, imageDir, ext)
def getOptions(): gui = GenericDialogPlus("Options for Moving TIFF files") gui.addMessage("Select the number of imput files to be used per stitched image") gui.addSlider("", 2, 10, 2) gui.addFileField("Select csv file", "") gui.addMessage("Add key values and corresponding genotype, when finished, leave fields empty") gui.addStringField("Key :", prefs.get(None, "key1", "p")) gui.addToSameRow() gui.addStringField("Genotype :", prefs.get(None, "genotype1", "PROM-1_HA")) gui.addStringField("Key :", prefs.get(None, "key2", "p")) gui.addToSameRow() gui.addStringField("Genotype :", prefs.get(None, "genotype2", "PROM-1_HA")) gui.addStringField("Key :", prefs.get(None, "key3", "p")) gui.addToSameRow() gui.addStringField("Genotype :", prefs.get(None, "genotype3", "PROM-1_HA")) gui.addStringField("Key :", prefs.get(None, "key4", "p")) gui.addToSameRow() gui.addStringField("Genotype :", prefs.get(None, "genotype4", "PROM-1_HA")) gui.addStringField("Key :", prefs.get(None, "key5", "p")) gui.addToSameRow() gui.addStringField("Genotype :", prefs.get(None, "genotype5", "PROM-1_HA")) gui.showDialog() if gui.wasOKed(): tiffs_per_image = int(gui.getNextNumber()) csv_file = str(gui.getNextString()) genotypes = {} for i in range(5): key = str(gui.getNextString()) value = str(gui.getNextString()) if key != "": genotypes[key] = value else: return if len(genotypes) > 0: a = list(genotypes.items())[0] prefs.put(None, "key1", a[0]) prefs.put(None, "genotype1", a[1]) if len(genotypes) > 1: a = list(genotypes.items())[1] prefs.put(None, "key2", a[0]) prefs.put(None, "genotype2", a[1]) if len(genotypes) > 2: a = list(genotypes.items())[2] prefs.put(None, "key3", a[0]) prefs.put(None, "genotype3", a[1]) if len(genotypes) > 3: a = list(genotypes.items())[3] prefs.put(None, "key4", a[0]) prefs.put(None, "genotype4", a[1]) if len(genotypes) > 4: a = list(genotypes.items())[4] prefs.put(None, "key5", a[0]) prefs.put(None, "genotype5", a[1]) return tiffs_per_image, csv_file, genotypes
def make_dialog(): parameters = {} gd = GenericDialogPlus("Grid Stitch SDC Data") gd.addMessage( "Warning!\n"\ "In order to display a fused image upon completion of stitching\n"\ "please disable Fiji's ImageJ2 options. When enabled an ImageJ\n"\ "exception will be displayed upon completion. This exception can\n" "be safely ignored.") gd.addMessage( "Information\n"\ "This plugin is a wrapper around the Fiji 'Grid Stitching' plugin.\n"\ "It allows tiles generated in SlideBook to be directly stitched by\n"\ "by first writing out the individual tiles, executing the 'Grid Stitching'\n"\ "plugin and writing the fused image to disk.") gd.addMessage("") gd.addNumericField("grid_size_x", 3, 0) gd.addNumericField("grid_size_y", 3, 0) gd.addCheckbox("Select channel",False) gd.addNumericField("", 0, 0) gd.addCheckbox("Are the Z slices separate files?",False) gd.addDirectoryField("directory", "", 50) gd.showDialog() if (gd.wasCanceled()): return parameters['gridX'] = int(math.ceil(gd.getNextNumber())) parameters['gridY'] = int(math.ceil(gd.getNextNumber())) parameters['select_channel'] = gd.getNextBoolean() parameters['channel'] = None if parameters['select_channel']: parameters['channel'] = int(gd.getNextNumber()) parameters['separate_z'] = gd.getNextBoolean() directory = str(gd.getNextString()) if directory is None: # User canceled the dialog return None else: directory = os.path.abspath(directory) parameters['directory'] = directory + os.path.sep return parameters
def get_parameters(p): gd = GenericDialogPlus("Please enter parameters") for k in p['expose_to_gui']['value']: if p[k]['type'] == 'folder': gd.addDirectoryField(k, p[k]['value'], 100) if p[k]['type'] == 'file': gd.addFileField(k, p[k]['value'], 100) elif p[k]['type'] == 'string': if p[k]['choices']: gd.addChoice(k, p[k]['choices'], p[k]['value']) else: gd.addStringField(k, p[k]['value'], 50) elif p[k]['type'] == 'int': if p[k]['choices']: gd.addChoice(k, p[k]['choices'], p[k]['value']) else: gd.addNumericField(k, p[k]['value'], 0) elif p[k]['type'] == 'float': gd.addNumericField(k, p[k]['value'], 2) gd.showDialog() if gd.wasCanceled(): return(0) for k in p['expose_to_gui']['value']: if p[k]['type'] == 'folder' or p[k]['type'] == 'file': p[k]['value'] = gd.getNextString() elif p[k]['type'] == 'string': if p[k]['choices']: p[k]['value'] = gd.getNextChoice() else: p[k]['value'] = gd.getNextString() elif p[k]['type'] == 'int': if p[k]['choices']: p[k]['value'] = int(gd.getNextChoice()) else: p[k]['value'] = int(gd.getNextNumber()) elif p[k]['type'] == 'float': p[k]['value'] = gd.getNextNumber() return(p)
gd.addNumericField("Columns per well", colNo, 0) gd.addNumericField("Nuclear minimum size (pixels)", nucMinSize, 0) gd.addNumericField("Cardiomyocyte minimum size (pixels)", cmMinSize, 0) gd.showDialog() folderPath = gd.getNextString() + "/" formatString = gd.getNextString() groupBy = re.findall(r"\w+", gd.getNextString()) nucChannel = gd.getNextString() cmChannel = gd.getNextString() stitched = gd.getNextBoolean() nucMethod = gd.getNextChoice() analyzeNucStack = gd.getNextBoolean() brightfield = gd.getNextBoolean() cmMethod = gd.getNextChoice() analyzeCmStack = gd.getNextBoolean() rowNo = int(gd.getNextNumber()) colNo = int(gd.getNextNumber()) nucMinSize = int(gd.getNextNumber()) cmMinSize = int(gd.getNextNumber()) allFileNames = os.listdir(folderPath) jsonStoreDict = {"folderPath": folderPath, "formatString":formatString, "groupBy": ','.join(groupBy), "nucChannel": nucChannel, "cmChannel": cmChannel, "stitched": stitched, "nucMethod": nucMethod, "analyzeNucStack": analyzeNucStack, "brightfield": brightfield, "cmMethod": cmMethod, "analyzeCmStack": analyzeCmStack,
from ij import IJ, ImagePlus from ij.plugin import ImageCalculator from ij.process import ImageProcessor from ij.process import FloatProcessor from fiji.util.gui import GenericDialogPlus #Input parameters gd = GenericDialogPlus("Input Parameters") gd.addDirectoryOrFileField("Select composite color image, 32-bit", "") gd.addNumericField("Pixel size", 4, 0) # show 3 decimals gd.addNumericField("Background color", 150, 0) # show 3 decimals gd.showDialog() directory_w = gd.getNextString() px = int(gd.getNextNumber()) bc = int(gd.getNextNumber()) #path to RGB image IJ.open(str(directory_w)) imp = IJ.getImage() IJ.run("8-bit") IJ.run("32-bit") n_slicesa = imp.getStack().getSize() L = [] for i in range(1, n_slicesa + 1): imp.setSlice(i) n = imp.getProcessor().getPixels() n2 = [int(val) for val in n] L.append(n2) imp.changes = False
munger_actions+="-a " if warp: munger_actions+="-w " if reformat: channels='' if ch01: channels+='01' if ch02: channels+='02' if ch03: channels+='03' if channels != '': munger_actions+="-r "+channels+" " verbose=gd.getNextBoolean() corestouse=gd.getNextNumber() outsuffix=gd.getNextString() regparams=gd.getNextChoice() print regparams regparams=gd.getNextString() mungeropts=gd.getNextString() action=gd.getNextChoice() if action == 'Test': mungeropts+=' -t' if verbose: mungeropts+=' -v' mungeropts+=' -T %d' % (int(corestouse)) if not outsuffix == '': mungeropts += ' -d .'+outsuffix cmd='"%s" -b "%s" %s %s %s -s "%s" %s' % (munger,bindir,munger_actions,regparams,mungeropts,refBrain,image)
from ij import IJ, ImagePlus from ij.plugin import ImageCalculator from ij.process import ImageProcessor from ij.process import FloatProcessor from fiji.util.gui import GenericDialogPlus import ij.plugin.PlugIn import math #Input parameters gd = GenericDialogPlus("Input Parameters") gd.addNumericField("Wavlength Spacing (nm)", 5, 0) # show 3 decimals gd.addNumericField("Starting Wavelength (nm)", 430, 0) # show 3 decimals gd.addNumericField("Ending Wavelength (nm)", 750, 0) # show 3 decimals gd.showDialog() spacing = int(gd.getNextNumber()) start_wave = int(gd.getNextNumber()) end_wave = int(gd.getNextNumber()) lim = (end_wave - start_wave) / spacing #color matching functions def red(): a0 = 0.2817 a1 = -0.3183 b1 = -0.07613 a2 = 0.1517 b2 = 0.2493 a3 = -0.09975
0.50, 3) gdp.addNumericField("Maximum granule circularity", 1.00, 3) gdp.addNumericField( "Minimum percent overlap between images (0 = no overlap required, 100 = perfect overlap)", 25, 0) gdp.addChoice( "Exclude particles on outside perimeter? Recommended for ATP analysis", yn, "NO") gdp.showDialog() outdir = gdp.getNextString() path_wt = gdp.getNextString() path_dic = gdp.getNextString() path_mut = gdp.getNextString() path_bg = gdp.getNextString() analysistype = gdp.getNextChoice() uThres = gdp.getNextNumber() uGsize = gdp.getNextNumber() uGshape = gdp.getNextNumber() uGshapemax = gdp.getNextNumber() uOverlap = gdp.getNextNumber() uExclude = gdp.getNextChoice() # Files will automatically be output to a new Fiji_Analysis directory. If this directory already exists, files will be overwritten. This checks to make sure the directory does not yet exist. if path.exists(outdir + File.separatorChar + "Fiji_Analysis") and path.isdir(outdir + File.separatorChar + "Fiji_Analysis"): gdchk = GenericDialog("WARNING") gdchk.addMessage( "Analysis folder already exists. Choose a different directory to avoid overwritng your current data" ) gdchk.hideCancelButton()
from ij import IJ, ImagePlus, ImageStack from ij.process import ImageProcessor, FloatProcessor from fiji.util.gui import GenericDialogPlus gd = GenericDialogPlus("Input Parameters") gd.addNumericField("Number of Angles", 10, 0) # show 3 decimals gd.showDialog() ang = 360/int(gd.getNextNumber()) imp = IJ.getImage() n_slices = imp.getStack().getSize() for i in range(1, n_slices+1): imp.setSlice(i) s = ((i*ang)-ang)*-1 IJ.run("Rotate... ", "angle="+str(s) + " grid=1 interpolation=Bilinear slice")
Laurent SV Thomas, Jochen Gehrig bioRxiv 619338; doi: https://doi.org/10.1101/619338""") Win.addHelp( "https://github.com/multi-template-matching/MultiTemplateMatching-Fiji/wiki" ) Win.showDialog() if Win.wasOKed(): template = Win.getNextImage() image = Win.getNextImage() flipv = Win.getNextBoolean() fliph = Win.getNextBoolean() angles = Win.getNextString() method = Win.getNextChoice() n_hit = int(Win.getNextNumber()) score_threshold = Win.getNextNumber() #tolerance = Win.getNextNumber() tolerance = 0 max_overlap = Win.getNextNumber() add_roi = Win.getNextBoolean() show_table = Win.getNextBoolean() # Save for persistence ImageName = image.getTitle() prefs.put("Template", template.getTitle()) prefs.put("Image", ImageName) prefs.put("FlipV", flipv) prefs.put("FlipH", fliph) prefs.put("Angles", angles) prefs.put("Method", method)
munger_actions += "-a " if warp: munger_actions += "-w " if reformat: channels = '' if ch01: channels += '01' if ch02: channels += '02' if ch03: channels += '03' if channels != '': munger_actions += "-r " + channels + " " verbose = gd.getNextBoolean() corestouse = gd.getNextNumber() outsuffix = gd.getNextString() regparams = gd.getNextChoice() print regparams regparams = gd.getNextString() mungeropts = gd.getNextString() action = gd.getNextChoice() if action == 'Test': mungeropts += ' -t' if verbose: mungeropts += ' -v' mungeropts += ' -T %d' % (int(corestouse)) if not outsuffix == '': mungeropts += ' -d .' + outsuffix cmd = '"%s" -b "%s" %s %s %s -s "%s" %s' % (