# The list of files. #imFileNames = ["test_file.nrrd", "test_file2.nrrd", "test_file3.nrrd"] # The list of roi files (Needs to have same number of entries as .im files above). #roiFileNames = ["test_file.rois.zip", "test_file2.rois.zip", "test_file3.rois.zip"] # List of statistics. # Others: "mean", "stddev", "median", "N/D", # "min", "max", "sum", "mode", "area", # "group", "roix", "roiy", # "roiwidth", "roiheight" stats = ["group", "area", "mean", "stddev", "N/D"] #//////////////////////////// # Initialize stuff. #//////////////////////////// ui = UI() ui.show() #//////////////////////////// # Loop over files. #//////////////////////////// for i in range(len(imFileNames)): imFile = File(imFileNames[i]) roiFile = File(roiFileNames[i]) #IJ.log("Opening: "+imFileNames[i]) ui.openFile(imFile) #IJ.log("Opening: "+roiFileNames[i]) ui.openFile(roiFile) #////////////////////////////
imFileName = ["test_file.nrrd", "test_file2.nrrd", "test_file3.nrrd"] # The list of roi files (Needs to have same number of entries as .im files above). roiFileName = ["test_file.rois.zip", "test_file2.rois.zip", "test_file3.rois.zip"] # List of statistics. # Others: "mean", "stddev", "median", "N/D", # "min", "max", "sum", "mode", "area", # "group (table only)", "roix", "roiy", # "roiwidth", "roiheight" stats = ["mean", "stddev"] #//////////////////////////// # Initialize stuff. #//////////////////////////// ui = UI() ui.show() #//////////////////////////// # Loop over files. #//////////////////////////// for i in range(len(imFileName)): #where is this going? #print "Opening: " #+ imFileName[i] + ", " roiFileName[i] imFile = File(imDirName, imFileName[i]) roiFile = File(imDirName, roiFileName[i]) IJ.log("Opening: "+imFileName[i]) ui.openFile(imFile) IJ.log("Opening: "+roiFileName[i]) ui.openFile(roiFile)
import com.nrims.data as nrimsData import com.nrims.UI as nrimsUI import java.io.File as File import java.lang as lang import java.util.ArrayList as ArrayList import java.lang.Integer as Integer import sys from java.lang.System import getProperty sys.path.append(getProperty("fiji.dir") + "/plugins/Scripts/Plugins/OpenMIMS Scripts/") import os import jarray IJ.log("Starting auto Turbo reg") ui = nrimsUI.getInstance() if ui == None: IJ.log("No instance of OpenMims window") else: openSum = ui.getOpenSumImages() if len(openSum) != 0: #copy sum and source image #setting sum image to first one for testing's sake sumImage = openSum[0] target = sumImage.duplicate() source = IJ.getImage().duplicate() #scale image targetProcessor = target.getProcessor()
import java.io.File as File import java.lang as lang import java.util.ArrayList as ArrayList import java.lang.Integer as Integer import sys from java.lang.System import getProperty sys.path.append(getProperty("fiji.dir") + "/plugins/Scripts/Plugins/OpenMIMS Scripts/") import os import jarray #//////////////////////////// # Get existing instance of OpenMims #//////////////////////////// IJ.log("Starting auto Turbo reg") ui = nrimsUI.getInstance() if ui == None: IJ.log("No instance of OpenMims window") else: openSum = ui.getOpenSumImages() if len(openSum) != 0: #//////////////////////////// # copy sum and source image # source = image we want to modify through turboreg # target = image that we are fitting source to # note: setting sum image to first one for testing's sake, ideally we'll find another solution #//////////////////////////// sumImage = openSum[0] target = sumImage.duplicate() source = IJ.getImage().duplicate()
from org.jfree.data.xy import DefaultXYDataset from java.awt import Color, Rectangle print "\nStarting 'QSA-ScatterPlot'." print "Grab images." #imgA = WindowManager.getImage("25.90:test_file") #imgB = WindowManager.getImage("26.93/25.90:test_file") imgA = WindowManager.getImage("12.12:test_file") imgB = WindowManager.getImage("13.01/12.12:test_file") ui = UI.getInstance() rois = ui.getRoiManager().getAllROIs() print "Create empty dataset" dataset = DefaultXYDataset() print "Create ScatterPlot" chart = ChartFactory.createScatterPlot( "Scatter Plot", imgA.getTitle(), imgB.getTitle(), dataset, PlotOrientation.VERTICAL, True, False, False); # random test data # #print "Add series to dataset"