from ij import * from ij import IJ, ImagePlus, ImageListener, VirtualStack, ImageStack from ij.io import DirectoryChooser from ij.gui import ImageCanvas import os from ij.plugin import ContrastEnhancer,StackCombiner,AVI_Reader import random import pickle from java.lang import Exception, Double from java.lang.System import getProperty import sys ### NOTE THIS CODE WAS DESIGNED TO RUN AS A MACRO IN FIJI (IMAGEJ) ### TO USE THIS CODE, FIRST DOWNLOAD AND INSTALL IMAGEJ ### YOU WILL ALSO NEED TO INCLUDE THE "jmatio.jar" IN THE JAR FOLDER ### SINCE FIJI IS CROSS-PLATFORM, THIS "SHOULD" WORK WITH ANY OPERATING ### SYSTEM BUT WE USE IT ON LINUX AND MAC COMPUTERS ### IT MIGHT BE A BIT CONFUSING TO SET THIS SCRIPT UP SO FEEL FREE TO CONTACT ### THE CORRESPONDING AUTHORS FOR HELP. THERE IS A SLIGHTLY EMBARRASSING ### TUTORIAL VIDEO THAT WE CAN FORWARD TO YOU. ### ALSO, I WOULD NOT RECOMMEND BUILDING ON THE SCRIPT, "JYTHON" IS A STUPID ### LANGUAGE AND THE CURRENT POSSIBILITIES WITH POPULAR VR VISUALIZATION ### LIBRARIES WOULD BE WONDERFUL. WE HAVE STARTED TO GO IN THAT DIRECTION. ### IF YOU ARE THINKING THE SAME THING PERHAPS WE SHOULD TALK (benjamin.dunn@ntnu.no) ### VISUALIZATION IS A SURPRISINGLY USEFUL TOOL (THOUGH A BIT OBVIOUS NOW) ##### put jmatio.jar in the jar folder!!!! from com.jmatio.io import MatFileReader, MatFileWriter from com.jmatio.types import MLDouble, MLChar import copy import csv import time from org.apache.commons.math3.linear import Array2DRowRealMatrix, SingularValueDecomposition, LUDecomposition, RealMatrix from org.apache.commons.math3.util import MathArrays from java import io import time import math from jarray import array, zeros from javax.swing import JScrollPane, JPanel, JComboBox, JLabel, JFrame, JTextField, JCheckBox, JButton, JToggleButton, JFileChooser, BorderFactory, JFormattedTextField, JDialog, JSlider, Timer, JOptionPane, MutableComboBoxModel, SpinnerNumberModel, JSpinner, JTextArea, JTable, SwingUtilities, DefaultCellEditor, JTabbedPane from javax.swing.filechooser import FileNameExtensionFilter from javax.swing.table import DefaultTableModel, DefaultTableCellRenderer, TableCellRenderer from javax.swing.event import ChangeListener from java.awt import Color, GridLayout, GridBagLayout, KeyboardFocusManager, Toolkit, GraphicsEnvironment from java.awt.event import ActionListener, ItemListener, ItemEvent, FocusListener, WindowAdapter, KeyListener, KeyEvent from java.text import NumberFormat from org.jfree.chart import ChartFactory, ChartPanel, JFreeChart, ChartFrame from org.jfree.chart.axis import NumberAxis, SymbolAxis, NumberTickUnit from org.jfree.chart.plot import PlotOrientation, XYPlot from org.jfree.chart.renderer.xy import XYLineAndShapeRenderer from org.jfree.data.xy import XYDataset, XYSeries, XYSeriesCollection from org.jfree.ui import ApplicationFrame, RefineryUtilities#, Spacer from org.jfree.data.statistics import HistogramDataset, HistogramType from java.awt.event import MouseAdapter, InputEvent from java.util import BitSet from org.scijava.java3d.utils.geometry import Sphere, Box from org.scijava.java3d.utils.universe import SimpleUniverse from org.scijava.java3d.utils.picking import PickCanvas, PickResult from org.scijava.java3d.utils.behaviors.mouse import MouseRotate, MouseTranslate, MouseZoom from org.scijava.java3d import Canvas3D, BranchGroup, Transform3D, TransformGroup, Shape3D, BoundingSphere, Background, Appearance, ColoringAttributes, Material, DirectionalLight, RenderingAttributes, Switch, LineArray, LineAttributes, IndexedQuadArray, TransparencyAttributes, BoundingBox, View, GraphicsConfigTemplate3D from org.scijava.vecmath import Vector3f, Color3f, Point3d, Vector3d, AxisAngle4d, Matrix3f, Matrix3d import ij.measure.Minimizer import ratemapgenerator from javax.sound.sampled import AudioInputStream, AudioSystem, Clip print (sys.version) # a = Double.NaN # print a # if Double.isNaN(a): # print "a is NaN!" clear = lambda: os.system('cls' if os.name=='nt' else 'clear') class plotthingy(): def updatet(self, t, winsize): mm = t-winsize if(mm < 0): mm = 0 MM = mm+2*winsize else: MM = t+winsize if(MM > len(self.xvals)-1): MM = len(self.xvals)-1 mm = MM-2*winsize if(mm < 0): mm = 0 if(MM-mm < 0.01): MM = mm+0.01 (self.plot.getDomainAxis()).setRange(mm, MM) self.seriesT.clear() self.seriesT.add(t, self.rangemm, False) self.seriesT.add(t, self.rangeMM, True) def updatebitchskippies(self, skippies): self.seriesA.clear() if(len(self.centeredvals)>2): for i in range(0, len(self.xvals), skippies): if(i == len(self.xvals)-1): self.seriesA.add(self.xvals[i], self.centeredvals[i], True) else: self.seriesA.add(self.xvals[i], self.centeredvals[i], False) if(len(self.tracevals)>2): for i in range(0, len(self.xvals), skippies): if(i == len(self.xvals)-1): self.seriesA.add(self.xvals[i], self.tracevals[i], True) else: self.seriesA.add(self.xvals[i], self.tracevals[i], False) def updatebitchcentered(self, xvals, centeredvals, skippies): self.xvals = xvals self.seriesA.clear() self.seriesB.clear() self.tracevals = [] self.centeredvals = centeredvals if(len(centeredvals)<1): print 'WTF: you need trace data for this shit to work!' stop T = len(xvals) meanval = sum(centeredvals)/float(T) #tempval = 0. #for i in range(0, len(xvals), 1): #tt = (centeredvals[i]-meanval) #tempval += tt*tt/float(T) #stdval = math.sqrt(tempval) #for i in range(0, len(xvals), 1): #self.centeredvals[i] = (centeredvals[i] - meanval)/stdval self.seriesB.add(xvals[0], meanval, True) self.seriesB.add(xvals[T-1], meanval, False) for i in range(0, len(xvals), skippies): if(i == len(xvals)-1): self.seriesA.add(xvals[i], self.centeredvals[i], True) else: self.seriesA.add(xvals[i], self.centeredvals[i], False) #self.rangemm = -3.05 #self.rangeMM = 3.05 self.rangemm = min(self.centeredvals) self.rangeMM = max(self.centeredvals) (self.plot.getRangeAxis()).setRange(self.rangemm, self.rangeMM) mm = min(xvals) MM = max(xvals) if(MM-mm < 0.01): MM = mm+0.01 (self.plot.getDomainAxis()).setRange(mm, MM) def updatebitchtrace(self, xvals, tracevals, skippies): self.xvals = xvals self.tracevals = tracevals self.centeredvals = [] self.seriesA.clear() if(len(tracevals)<1): print 'WTF: you need trace data for this shit to work!' stop maxtraces = -100000000000000000. mintraces = 1000000000000000000. maxnfr = -10000000000000000000. minnfr = 100000000000000000000. for i in range(0, len(xvals), 1): if(tracevals[i]maxtraces): maxtraces = tracevals[i] denom = 1. if(abs(maxtraces-mintraces)>0.0000000001): denom = maxtraces-mintraces for i in range(0, len(xvals), 1): self.tracevals[i] = (tracevals[i] - mintraces)/denom for i in range(0, len(xvals), skippies): if(i == len(xvals)-1): self.seriesA.add(xvals[i], self.tracevals[i], True) else: self.seriesA.add(xvals[i], self.tracevals[i], False) self.rangemm = -0.05 self.rangeMM = 1.05 (self.plot.getRangeAxis()).setRange(-0.05, 1.05) mm = min(xvals) MM = max(xvals) if(MM-mm < 0.01): MM = mm+0.01 (self.plot.getDomainAxis()).setRange(mm, MM) def __init__(self, cc=Color.blue): self.xvals = [] self.seriesA = XYSeries("A") for i in range(2): x = 10.*i/1.-5. y = 0. self.seriesA.add(x, y) self.tracevals = [] self.centeredvals = [] self.seriesT = XYSeries("Time") self.seriesT.add(2, 0, False) self.seriesT.add(2, 1, True) a2 = XYSeriesCollection() a2.addSeries(self.seriesA) a2.addSeries(self.seriesT) if(cc==Color.red): self.seriesB = XYSeries("B") for i in range(2): x = 10.*i/1.-5. y = 0. self.seriesB.add(x, y) a2.addSeries(self.seriesB) self.chart = ChartFactory.createScatterPlot('', '', '', a2, PlotOrientation.VERTICAL, False, False, False) self.plot = self.chart.getXYPlot() renderer = XYLineAndShapeRenderer() renderer.setSeriesLinesVisible(0, True) renderer.setSeriesShapesVisible(0, False) renderer.setSeriesPaint(0, cc) if(cc==Color.red): renderer.setSeriesLinesVisible(2, True) renderer.setSeriesShapesVisible(2, False) renderer.setSeriesPaint(2, Color.black) self.plot.setRenderer(renderer) self.plot.setDomainCrosshairVisible(False) self.plot.setRangeCrosshairVisible(False) self.plot.setDomainGridlinesVisible(False) self.plot.setRangeGridlinesVisible(False) self.plot.setDomainMinorGridlinesVisible(False) self.plot.setRangeMinorGridlinesVisible(False) self.plot.setDomainPannable(False) self.plot.setRangePannable(False) self.plot.setDomainZeroBaselineVisible(True) self.plot.setRangeZeroBaselineVisible(False) self.plot.setBackgroundPaint(Color.white) self.plot.getRangeAxis().setVisible(False) self.plot.getDomainAxis().setVisible(False) self.panel = ChartPanel(self.chart) class plotrenderer(DefaultTableCellRenderer) : def __init__(self): DefaultTableCellRenderer.__init__(self) self.emptypanel = JPanel() # EMPTY PANEL self.winsize = 5000 self.timeguy = [] self.allplots = [] self.alltypies = [] self.N = 0 self.currentskippy = 5 def updatewindowsize(self, winsize, skippies): self.winsize = int(round(winsize)) if(abs(skippies-self.currentskippy)>0.1): self.currentskippy = int(round(skippies + 0.)) for i in range(len(self.allplots)): self.allplots[i].updatebitchskippies(self.currentskippy) def addone(self, xvals, plottingvalues, typie): self.timeguy = xvals self.alltypies.append(typie) if(typie == 'centered'): newone = plotthingy(Color.red) newone.updatebitchcentered(xvals, plottingvalues, self.currentskippy) else: newone = plotthingy() newone.updatebitchtrace(xvals, plottingvalues, self.currentskippy) self.allplots.append(newone) self.N = len(self.allplots) def getTableCellRendererComponent(self, table, value, isSelected, hasFocus, rowIndex, vColIndex): if(value == None or value<0): return self.emptypanel indN = table.convertRowIndexToModel(rowIndex) self.allplots[indN].updatet(value, self.winsize) return self.allplots[indN].panel class labelcellrenderer(DefaultTableCellRenderer): def __init__(self): self.scrollpane = JScrollPane() self.labelcell = JTextArea() self.labelcell.setLineWrap(True) self.labelcell.setWrapStyleWord(True) self.scrollpane.getViewport().add(self.labelcell) def getTableCellRendererComponent(self, table, value, isSelected, hasFocus, row, column): if(isSelected): self.scrollpane.setForeground(table.getSelectionForeground()) self.scrollpane.setBackground(table.getSelectionBackground()) self.labelcell.setForeground(table.getSelectionForeground()) self.labelcell.setBackground(table.getSelectionBackground()) else: self.scrollpane.setForeground(table.getForeground()) self.scrollpane.setBackground(table.getBackground()) self.labelcell.setForeground(table.getForeground()) self.labelcell.setBackground(table.getBackground()) self.labelcell.setText(String(value)) self.setSize(table.getColumnModel().getColumn(column).getWidth(), self.labelcell.getPreferredSize().height) if(table.getRowHeight(row) < self.labelcell.getPreferredSize().height): table.setRowHeight(row, self.labelcell.getPreferredSize().height) return self.labelcell class labelcelleditor(DefaultCellEditor): def __init__(self): self.labelcell = JTextArea() self.labelcell.setLineWrap(True) self.labelcell.setWrapStyleWord(True) self.scrollpane = JScrollPane() self.scrollpane.getViewport().add(self.labelcell) DefaultCellEditor.__init__(self, JCheckBox()) def getTableCellEditorComponent(self, table, value, isSelected, row, col): self.labelcell.setText(String(value)) return(self.scrollpane) def getCellEditorValue(self): return self.labelcell.getText() class analysistablemodel(DefaultTableModel): def setupdatefunction(self, updatefunction): self.updatefunction = updatefunction def causeanupdate(self): self.updatefunction.updatet(-1) def __init__(self): self.currentt = 0 self.updatefunction = None self.windowsize = 10 self.data = [] self.plottingvalues = [] self.columnNames = ['#', ' ', 'Label', 'Value', 'Plot'] self.columnClasses = [Integer, Boolean, JTextArea, Float, ChartPanel] DefaultTableModel.__init__(self, self.data, self.columnNames) def addathing(self, label, plottingvals): i = len(self.data) self.data.append( [Integer(i+1), Boolean(1), label, Float(0.), 1] ) self.plottingvalues.append(plottingvals) self.setDataVector(self.data, self.columnNames) def updatet(self, tvid=-100): if(tvid<0): t = self.currentt else: t = tvid if(t == self.currentt): return self.currentt = t for i in range(len(self.data)): if(Boolean(self.getValueAt(i, 1)) == Boolean(1)): self.setValueAt((self.plottingvalues[i])[t], i, 3) self.data[i][4] = t self.fireTableCellUpdated(i, 4) def getRowCount(self): return(len(self.data)) def getColumnCount(self): return(len(self.columnNames)) def getValueAt(self, rowI, colI): return(self.data[rowI][colI]) def getColumnName(self, columnIndex): return self.columnNames[columnIndex] def getColumnClass(self, columnIndex): return self.columnClasses[columnIndex] def isCellEditable(self, rowIndex, columnIndex): if(columnIndex == 1 or columnIndex == 2): return(True) return(False) def setValueAt (self, value, rowIndex, columnIndex): if(columnIndex == 1): value = Boolean(value) self.data[rowIndex][columnIndex] = value self.fireTableCellUpdated(rowIndex, columnIndex) if(value == Boolean(1)): self.updatet(-1) else: self.data[rowIndex][4] = -1 self.fireTableCellUpdated(rowIndex, 4) self.data[rowIndex][3] = 0 else: self.data[rowIndex][columnIndex] = value self.fireTableCellUpdated(rowIndex, columnIndex) class analysistable(JPanel): def addanewrowtothetable(self, plotvalues, texty, typie): T = len(plotvalues) self.chartrendererthing.addone(range(T), plotvalues, typie) self.tablemodel.addathing(texty, plotvalues) def loadanalysisdata(self, filename): dafile = open(filename) rawfile = dafile.readlines() reader = csv.reader(dafile) Ta = len(rawfile)-1 dafile.seek(0) Na = -1 for row in reader: Na = len(row) break dafile.seek(0) labels = [] typies = [] analdata = [] for i in range(Na): analdata.append(zeros(Ta, 'd')) print 'Printing the first 10 lines of the analysis csv file (just a visual check)' count = 0 for row in reader: if(count < 10): print row for j in range(Na): if(count == 0): labels.append(row[j]) elif(count == 1): typies.append(row[j]) else: valval = float(row[j]) if(valval < -100000): valval = 0. (analdata[j])[count-2] = valval count += 1 if( count%(25000) == 0 ): print '%2.2f percent done reading in the analysis csv file'%(100*float(count)/float(Ta)) print '%2.2f percent done reading in the analysis csv file'%(100*float(count)/float(Ta)) dafile.close() for i in range(len(labels)): self.addanewrowtothetable(analdata[i], labels[i], typies[i]) return def setupdatefunction(self, updatefunction): self.tablemodel.setupdatefunction(updatefunction) self.updatefunction = updatefunction def __init__(self): self.updatefunction = None self.currentt = 0 self.setLayout(GridBagLayout()) self.setAlignmentX(Component.LEFT_ALIGNMENT) c = GridBagConstraints() c.insets = Insets(2, 2, 2, 2) c.weighty = 0 c.weightx = 0 c.fill = c.BOTH c.weightx = 1 c.weighty = 0.0001 c.gridx = 0 c.gridy = 0 c.gridwidth = 1 c.gridheight = 1 c.weightx = 0.001 self.add(JLabel('Window size (frames) '), c) c.weightx = 0.999 c.gridx = 1 self.jwindowsize = JTextField('5000') self.add(self.jwindowsize, c) c.gridx = 2 c.weightx = 0.001 self.add(JLabel(' Increment (frames) '), c) c.gridx = 3 c.weightx = 0.999 self.jskippies = JTextField('5') self.add(self.jskippies, c) c.gridx = 4 class buttonlistener(ActionListener): def __init__(self, parent): self.papa = parent def actionPerformed(self, event): self.papa.chartrendererthing.updatewindowsize(float(self.papa.jwindowsize.getText()), float(self.papa.jskippies.getText())) self.papa.tablemodel.updatet(-1) updatesize = JButton('Update') updatesize.addActionListener(buttonlistener(self)) self.add(updatesize, c) self.tablemodel = analysistablemodel() self.table = JTable(self.tablemodel) self.table.setRowHeight(50) self.table.setFillsViewportHeight(True); self.chartrendererthing = plotrenderer() self.chartrendererthing.updatewindowsize(float(self.jwindowsize.getText()), float(self.jskippies.getText())) self.table.setDefaultRenderer(ChartPanel, self.chartrendererthing) self.table.setDefaultRenderer(JTextArea, labelcellrenderer()) self.table.setDefaultEditor(JTextArea, labelcelleditor()) ((self.table.getColumnModel()).getColumn(0)).setPreferredWidth(40) ((self.table.getColumnModel()).getColumn(1)).setPreferredWidth(40) ((self.table.getColumnModel()).getColumn(2)).setPreferredWidth(100) ((self.table.getColumnModel()).getColumn(3)).setPreferredWidth(80) ((self.table.getColumnModel()).getColumn(4)).setPreferredWidth(875) self.table.setAutoCreateRowSorter(True) self.table.getRowSorter().setSortable(4, False) c.gridy = 1 c.gridx = 0 c.gridwidth = 5 c.weighty = 1. self.add(JScrollPane(self.table), c) class superfunfilter(JDialog): def __init__(self, parentguy): self.parentguy = parentguy self.setLocationRelativeTo(None) self.setTitle("Fun filter") firingratepanel = JPanel() firingratepanel.setLayout(GridBagLayout()) cpan = GridBagConstraints() cpan.insets = Insets(3, 3, 3, 3) cpan.fill = GridBagConstraints.HORIZONTAL cpan.gridx = 0 cpan.gridy = 0 cpan.gridwidth = 1 firingratepanel.add(JLabel('Time bin width (ms)'), cpan) cpan.gridx = 3 self.timebin = JTextField('20 ') firingratepanel.add(self.timebin, cpan) cpan.gridx = 0 cpan.gridy = 1 firingratepanel.add(JLabel('Smoothing window size (ms)'), cpan) cpan.gridx = 3 self.frtimewindow = JTextField('200 ') firingratepanel.add(self.frtimewindow, cpan) cpan.gridwidth=4 cpan.gridy = 2 cpan.gridx = 0 frhist = JButton('Firing rate histograms') class frhistlistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.displayfiringratehistogram(float(self.parentguy.timebin.getText()), float(self.parentguy.frtimewindow.getText())) frhist.addActionListener(frhistlistener(self)) firingratepanel.add(frhist, cpan) cpan.gridy = 3 firingratepanel.add(JLabel(''), cpan) cpan.gridwidth = 1 cpan.gridy = 6 cpan.gridx = 0 firingratepanel.add(JLabel('Minimum firing rate (Hz)'), cpan) cpan.gridx = 3 self.minfiringrate = JTextField('60') firingratepanel.add(self.minfiringrate, cpan) cpan.gridy = 8 cpan.gridx = 0 firingratepanel.add(JLabel('Minimum time min rate sustained (ms)'), cpan) cpan.gridx = 3 self.frtimesustained = JTextField('40') firingratepanel.add(self.frtimesustained, cpan) cpan.gridy = 9 cpan.gridx = 0 firingratepanel.add(JLabel('Added slowdown time around event (ms)'), cpan) cpan.gridx = 3 self.addslowdowntime = JTextField('200') firingratepanel.add(self.addslowdowntime, cpan) extfileguy = JPanel() self.moviefilename = JLabel("Movie file (csv)") extfileguy.add(self.moviefilename) self.moviefilepath = '' class moviefilenamelistener(ActionListener): def __init__(self, jguy): self.jguy = jguy def actionPerformed(self, event): fc = JFileChooser(self.jguy.parentguy.data.currentdirectory) fc.setFileFilter(FileNameExtensionFilter("Movie file", ["csv"])) fc.setDialogTitle('Movie file with segments of cool') ret = fc.showOpenDialog(None) if(ret == 0): self.jguy.moviefilepath = fc.selectedFile.getAbsolutePath() self.jguy.moviefilename.setText('%s'%(fc.selectedFile.getName())) moviefilenamebut = JButton('...') moviefilenamebut.addActionListener(moviefilenamelistener(self)) extfileguy.add(moviefilenamebut) self.tabbedpane = JTabbedPane() self.tabbedpane.addTab('External file', extfileguy) self.tabbedpane.addTab('Cells', firingratepanel) self.tabbedpane.setEnabledAt(1, False) self.setLayout(GridBagLayout()) self.cguy = GridBagConstraints() self.cguy.insets = Insets(3, 3, 3, 3) self.cguy.fill = GridBagConstraints.HORIZONTAL self.cguy.gridy = 0 self.cguy.gridx = 0 self.cguy.gridwidth=4 self.add(self.tabbedpane, self.cguy) self.cguy.gridx = 0 self.cguy.gridy = 10 self.cguy.gridwidth=1 self.add(JLabel('In rate speed up'), self.cguy) self.cguy.gridx = 3 self.inratespeedup = JTextField('0.1') self.add(self.inratespeedup, self.cguy) self.cguy.gridy = 12 self.cguy.gridx = 0 self.add(JLabel('Out rate speed up'), self.cguy) self.cguy.gridx = 3 self.outratespeedup = JTextField('100') self.add(self.outratespeedup, self.cguy) self.cguy.gridy = 14 self.cguy.gridx = 0 self.cguy.gridwidth=4 class fastforwardlistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): whichtab = self.parentguy.tabbedpane.getSelectedIndex() if(whichtab==0): self.parentguy.parentguy.funwithfiringratefilterfromfile(self.parentguy.moviefilepath, float(self.parentguy.inratespeedup.getText()), float(self.parentguy.outratespeedup.getText())) else: self.parentguy.parentguy.funwithfiringratefilter(float(self.parentguy.timebin.getText()), float(self.parentguy.frtimewindow.getText()), float(self.parentguy.minfiringrate.getText()), float(self.parentguy.frtimesustained.getText()), float(self.parentguy.addslowdowntime.getText()), float(self.parentguy.inratespeedup.getText()), float(self.parentguy.outratespeedup.getText())) return fastforwardbut = JButton('Fast forward to highlights') fastforwardbut.addActionListener(fastforwardlistener(self)) self.add(fastforwardbut, self.cguy) self.pack() self.repaint() class supertemplateadjuster(JDialog): def __init__(self, parentguy): self.parentguy = parentguy self.setLocationRelativeTo(None) self.setTitle("Template adjustment land") self.setLayout(GridBagLayout()) self.cguy = GridBagConstraints() self.cguy.insets = Insets(3, 3, 3, 3) self.cguy.fill = GridBagConstraints.HORIZONTAL self.cguy.gridx = 0 self.cguy.gridy = 0 self.cguy.gridwidth = 1 self.add(JLabel('x offset'), self.cguy) self.cguy.gridx = 3 self.xoffset = JTextField('0 ') self.add(self.xoffset, self.cguy) self.cguy.gridx = 0 self.cguy.gridy = 1 self.cguy.gridwidth = 1 self.add(JLabel('y offset'), self.cguy) self.cguy.gridx = 3 self.yoffset = JTextField('0 ') self.add(self.yoffset, self.cguy) self.cguy.gridx = 0 self.cguy.gridy = 2 self.cguy.gridwidth = 1 self.add(JLabel('z offset'), self.cguy) self.cguy.gridx = 3 #self.zoffset = JTextField('0 ') self.zoffset = JSpinner() self.zoffset.setModel(SpinnerNumberModel(0.,-1.,1.,0.01)) #mySpinner.setEditor(new JSpinner.NumberEditor(mySpinner,"##.#")); #JFormattedTextField txt = ((JSpinner.NumberEditor) mySpinner.getEditor()).getTextField(); #((NumberFormatter) txt.getFormatter()).setAllowsInvalid(false); self.add(self.zoffset, self.cguy) self.pack() self.repaint() class pickguy(MouseAdapter): def __init__(self, pickcanvas, parentguy): self.pickcanvas = pickcanvas self.parentguy = parentguy def mouseClicked(self, e): self.pickcanvas.setShapeLocation(e) res = self.pickcanvas.pickClosest() if(res == None): return ems = e.getModifiers() if(ems == InputEvent.BUTTON1_MASK): self.parentguy.setdapointwithdacolorandstuff(res.getNode(PickResult.SHAPE3D), 1) if(ems == InputEvent.BUTTON3_MASK): self.parentguy.setdapointwithdacolorandstuff(res.getNode(PickResult.SHAPE3D), -1) class crazydatafileio(JPanel): def getstartandstoptimestamps(self, withit): centerpanel = JPanel() centerpanel.setLayout(GridLayout(8,2)) centerpanel.add(JLabel("TRACKING start time stamp ")) Astart = JTextField(15) centerpanel.add(Astart) if(self.starttrackingtimestamp>-0.0001): Astart.setText('%d'%(int(round(1000000.*self.starttrackingtimestamp)))) centerpanel.add(JLabel("TRACKING end time stamp ")) Astop = JTextField(15) if(self.stoptrackingtimestamp>-0.0001): Astop.setText('%d'%(int(round(1000000.*self.stoptrackingtimestamp)))) centerpanel.add(Astop) centerpanel.add(JLabel("SESSION start time stamp ")) Bstart = JTextField(15) centerpanel.add(Bstart) if(self.startsessiontimestamp>-0.0001): Bstart.setText('%d'%(int(round(1000000.*self.startsessiontimestamp)))) centerpanel.add(JLabel("SESSION end time stamp ")) Bstop = JTextField(15) centerpanel.add(Bstop) if(self.stopsessiontimestamp>-0.0001): Bstop.setText('%d'%(int(round(1000000.*self.stopsessiontimestamp)))) centerpanel.add(JLabel("VT1 start time stamp ")) Cstart = JTextField(15) centerpanel.add(Cstart) if(self.startratcamtimestamp>-0.0001): Cstart.setText('%d'%(int(round(1000000.*self.startratcamtimestamp)))) centerpanel.add(JLabel("VT1 end time stamp " )) Cstop = JTextField(15) centerpanel.add(Cstop) if(self.stopratcamtimestamp>-0.0001): Cstop.setText('%d'%(int(round(1000000.*self.stopratcamtimestamp)))) if(withit==True): centerpanel.add(JLabel("Capture frame rate " )) FRATE = JTextField(15) centerpanel.add(FRATE) if(self.framerate>-0.0001): FRATE.setText('%d'%(int(round(self.framerate)))) centerpanel.add(JLabel("Rat cam frame rate " )) CAMFRATE = JTextField(15) centerpanel.add(CAMFRATE) CAMFRATE.setText('%d'%(int(round(self.ratcamframerate)))) centerpanel.validate() centerpanel.setVisible(True) sel = JOptionPane.showConfirmDialog(None, centerpanel, 'Enter Mr Time Stamps', JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE) if(sel == JOptionPane.OK_OPTION): if(len(Astart.getText())>0): self.starttrackingtimestamp = float(Astart.getText())/1000000. #convert to seconds if(len(Bstop.getText())>0): self.stoptrackingtimestamp = float(Astop.getText())/1000000. #convert to seconds if(len(Bstart.getText())>0): self.startsessiontimestamp = float(Bstart.getText())/1000000. #convert to seconds if(len(Bstop.getText())>0): self.stopsessiontimestamp = float(Bstop.getText())/1000000. #convert to seconds if(len(Cstart.getText())>0): self.startratcamtimestamp = float(Cstart.getText())/1000000. if(len(Cstop.getText())>0): self.stopratcamtimestamp = float(Cstop.getText())/1000000. if(withit==True): if(len(FRATE.getText())>0): self.framerate = float(FRATE.getText()) if(len(CAMFRATE.getText())>0): self.ratcamframerate = float(CAMFRATE.getText()) def getpointsfromcsvfile(self, csvfile): dafile = open(csvfile) rawfile = dafile.readlines() T = len(rawfile) - 6 reader = csv.reader(dafile) dafile.seek(0) count = 0 whatyguy = zeros(T, 'i') negguy = zeros(T, 'd') for i in range(T): whatyguy[i] = -10000 negguy[i] = -10000 emptyguy = [] for i in range(3): emptyguy.append(copy.deepcopy(negguy)) emptyguy.append(whatyguy) ## neuron label number emptyguy.append(negguy) ## 'distance' measure (set as -1 if set by user) #dapoints.append(copy.deepcopy(emptyguy)) whiches = 0 axisguys = 0 dapoints = [] daframerate = 0. firstframe = -1. firsttime = -1. conversionfactor = 1. print 'Printing the first 10 lines of the csv file and then the first 30 rows in the subsequent data structure (just a visual check)' for row in reader: if(count < 10): print row if(len(row)<1): count += 1 continue if(count == 0): whiches = zeros(len(row), 'i') for i in range(len(whiches)): if('Length Unit' in row[i] and 'Centimeters' in row[i+1]): print 'Note, converting from centimeters to meters for arbitrary reasons' conversionfactor = 0.01 daframerate = (float(row[7])) elif(count == 2): whiches = zeros(len(row), 'i') for i in range(len(whiches)): if('Marker' in row[i]): whiches[i] = 10 else: whiches[i] = -100 elif(count == 3): ids = [] for i in range(len(row)): if(len(row[i])>0): which = -1 for j in range(len(ids)): if(row[i] in ids[j]): which = j break if(which<0): which = len(ids) ids.append(row[i]) if(whiches[i]>-1): whiches[i] = which+0 elif(count == 5): for i in range(len(row)): if("Positi" not in row[i]): whiches[i] = -100 elif(count == 6): axisguys = zeros(len(row), 'i') for i in range(len(row)): if("X" in row[i] and whiches[i]>-1): axisguys[i] = 1 elif("Y" in row[i] and whiches[i]>-1): axisguys[i] = 2 elif("Z" in row[i] and whiches[i]>-1): axisguys[i] = 0 else: axisguys[i] = -100 elif(count > 7): #if(count == 8): #firstframe = float(row[0]) #firsttime = float(row[1]) #if(count == 9): #self.framerate = (float(row[0])-firstframe) / (float(row[1])-firsttime) dingo = [] for i in range(len(row)): if(whiches[i]>-1 and axisguys[i]>-1 and axisguys[i]<3): if(len(row[i])<1): continue whichguy = -1 for j in range(len(dingo)): if(whiches[i] == dingo[j]): whichguy = j if(whichguy<0): whichguy = len(dingo) dingo.append(whiches[i]) if(whichguy > len(dapoints)-1): dapoints.append(copy.deepcopy(emptyguy)) if(whichguy > len(dapoints)-1): print 'wtf, this shit is broken' stop ((dapoints[whichguy])[axisguys[i]])[count-6] = conversionfactor * float(row[i]) count += 1 if( count%(5000) == 0 ): if(count == 5000): for i in range(30): outy = "%04d"%i for j in range(len(dapoints)): for k in range(3): outy += ' %1.3f'%( ((dapoints[j])[k])[i] ) if(j20): break print 'Getting rid of time here (because it does not matter)' print 'and reducing the points to only those that appear stationary in at least one fourth of the template recording' trypoints = [] for n in range(N): for t in range(T): found = False for ii in range(len(trypoints)): dd = 0. for d in range(3): dd += ( ((templepoints[n])[d])[t] - (trypoints[ii])[d] )**2 dd = math.sqrt(dd) print dd if ( dd<0.01 ): if(found == True): print 'Crap: found two points!!' stop (trypoints[ii])[3] += 1 found = True print 'value of dd when true', dd print ii, trypoints[ii] print ((templepoints[n])[0])[t], ((templepoints[n])[1])[t], ((templepoints[n])[2])[t] print '' if(found == False): trypoints.append( [ ((templepoints[n])[0])[t], ((templepoints[n])[1])[t], ((templepoints[n])[2])[t], 1 ] ) self.templatepoints = [] for n in range(len(trypoints)): if((trypoints[n])[3] > 0.25*float(T)): if( (trypoints[n])[0] > -1000. and (trypoints[n])[1] > -1000. and (trypoints[n])[2] > -1000.): (trypoints[n])[3] = 1 self.templatepoints.append( copy.deepcopy(trypoints[n]) ) def exportalldata(self, datafile): def addaguytoexport(output, aguy, aguyname): aguyXYZ = zeros(3*len(aguy), 'd') for i in range(len(aguy)): if(aguy[i] == None): aguyXYZ[i*3] = -1000000000000000000000000000000000 aguyXYZ[i*3+1] = -1000000000000000000000000000000000 aguyXYZ[i*3+2] = -1000000000000000000000000000000000 else: if(i<4): print i, aguyname, (aguy[i]).x, (aguy[i]).y, (aguy[i]).z aguyXYZ[i*3] = (aguy[i]).x aguyXYZ[i*3+1] = (aguy[i]).y aguyXYZ[i*3+2] = (aguy[i]).z output.append(MLDouble(aguyname, aguyXYZ, 1)) print 'Length = ', len(aguyXYZ) return output output = [] output = addaguytoexport(output, self.headorigin, 'headorigin') output = addaguytoexport(output, self.headX, 'headX') output = addaguytoexport(output, self.headY, 'headY') output = addaguytoexport(output, self.headZ, 'headZ') output.append(MLDouble('framerate', [self.framerate], 1)) n = len(self.points) d = len(self.points[0]) t = len((self.points[0])[0]) print 'Number of points', len(self.points), ', number of dimensions', len(self.points[0]), 'length of time', len((self.points[0])[0]) pointsdata = zeros(n*d*t, 'd') iii = 0 for i in range(n): pp = self.points[i] for j in range(d): dd = pp[j] for k in range(t): pointsdata[iii] = dd[k] iii = iii+1 output.append(MLDouble('pointdata', pointsdata, 1)) output.append(MLDouble('pointdatadimensions', [n, d, t], 1)) output.append(MLDouble('bbtransXY', [self.boundingboxtransX, self.boundingboxtransY], 1)) output.append(MLDouble('bbscaleXY', [self.boundingboxscaleX, self.boundingboxscaleY], 1)) output.append(MLDouble('bbrot', [self.boundingboxrotation], 1)) output.append(MLDouble('trackingTS', [self.starttrackingtimestamp, self.stoptrackingtimestamp], 1)) output.append(MLDouble('sessionTS', [self.startsessiontimestamp, self.stopsessiontimestamp], 1)) output.append(MLDouble('ratcamTS', [self.startratcamtimestamp, self.stopratcamtimestamp], 1)) if(len(self.allcellnames)>0): for i in range(len(self.allcells)): output.append(MLChar('cellname_%05d'%i, self.allcellnames[i])) output.append(MLDouble('cell_%05d'%i, self.allcells[i], 1)) print datafile MatFileWriter(datafile, output) return def savetrackeddata(self, trackingdatafile): superOorientsARRAY = [] superXorientsARRAY = [] superYorientsARRAY = [] superZorientsARRAY = [] for i in range(len(self.headorigin)): if(self.headorigin[i] == None): superOorientsARRAY.append([0,0,0]) superXorientsARRAY.append([0,0,0]) superYorientsARRAY.append([0,0,0]) superZorientsARRAY.append([0,0,0]) else: superOorientsARRAY.append([(self.headorigin[i]).x, (self.headorigin[i]).y, (self.headorigin[i]).z]) superXorientsARRAY.append([(self.headX[i]).x, (self.headX[i]).y, (self.headX[i]).z]) superYorientsARRAY.append([(self.headY[i]).x, (self.headY[i]).y, (self.headY[i]).z]) superZorientsARRAY.append([(self.headZ[i]).x, (self.headZ[i]).y, (self.headZ[i]).z]) mat = {'points':self.points, 'pointlabels':self.pointlabels} mat['headoriginarray'] = superOorientsARRAY mat['headXarray'] = superXorientsARRAY mat['headYarray'] = superYorientsARRAY mat['headZarray'] = superZorientsARRAY mat['starttrackingtimestamp'] = self.starttrackingtimestamp mat['stoptrackingtimestamp'] = self.stoptrackingtimestamp mat['startsessiontimestamp'] = self.startsessiontimestamp mat['stopsessiontimestamp'] = self.stopsessiontimestamp mat['startratcamtimestamp'] = self.startratcamtimestamp mat['stopratcamtimestamp'] = self.stopratcamtimestamp mat['boundingboxrotation'] = self.boundingboxrotation mat['boundingboxtransX'] = self.boundingboxtransX mat['boundingboxtransY'] = self.boundingboxtransY mat['boundingboxscaleX'] = self.boundingboxscaleX mat['boundingboxscaleY'] = self.boundingboxscaleY mat['framerate'] = self.framerate if(".pkl" in trackingdatafile): pickle_file = open(trackingdatafile,'wb') pickle.dump(mat, pickle_file) pickle_file.close() return def initializefrompklfile(self, trackingdatafile): pickle_file = open(trackingdatafile,'rb') mat = pickle.load(pickle_file) if('pointlabels' in mat): self.pointlabels = mat['pointlabels'] for i in range(len(self.pointlabels.keys())): self.jbigguy.mysuperpointlabeler.addmearow(self.pointlabels.keys()[i]) for i in range(len(self.pointlabels.keys())): for j in range(len(self.jbigguy.mysuperpointlabeler.combolist)): if(self.jbigguy.mysuperpointlabeler.combolist[j].namy == self.pointlabels.keys()[i]): self.jbigguy.mysuperpointlabeler.combolist[j].setSelectedIndex( (self.jbigguy.cnames.keys()).index( (self.pointlabels[ self.pointlabels.keys()[i] ])[0] ) ) for j in range(len(self.jbigguy.mysuperpointlabeler.pointtypecombolist)): if(self.jbigguy.mysuperpointlabeler.pointtypecombolist[j].namy == self.pointlabels.keys()[i]): self.jbigguy.mysuperpointlabeler.pointtypecombolist[j].setSelectedIndex( (self.jbigguy.pointtypes).index( (self.pointlabels[ self.pointlabels.keys()[i] ])[1] ) ) pickle_file.close() self.analysisprogression = 0 #(at least) if('framerate' in mat): self.framerate = float(mat['framerate']) #print 'Frame rate is ', self.framerate if("points" not in mat): print 'File (%s) is screwed, it should have the variable points in it'%trackingdatafile return(-1) self.points = mat['points'] self.plen = len( (self.points[0])[0] ) if("starttrackingtimestamp" in mat): self.starttrackingtimestamp = mat['starttrackingtimestamp'] self.stoptrackingtimestamp = mat['stoptrackingtimestamp'] if("startsessiontimestamp" in mat): self.startsessiontimestamp = mat['startsessiontimestamp'] self.stopsessiontimestamp = mat['stopsessiontimestamp'] if('startratcamtimestamp' in mat): self.startratcamtimestamp = mat['startratcamtimestamp'] self.stopratcamtimestamp = mat['stopratcamtimestamp'] if('boundingboxrotation' in mat): self.boundingboxrotation = mat['boundingboxrotation'] self.boundingboxtransX = mat['boundingboxtransX'] self.boundingboxtransY = mat['boundingboxtransY'] self.boundingboxscaleX = mat['boundingboxscaleX'] self.boundingboxscaleY = mat['boundingboxscaleY'] self.jbigguy.adjustdisplaybox() if('headoriginarray' in mat): self.analysisprogression = 1 superOorientsARRAY = mat['headoriginarray'] superXorientsARRAY = mat['headXarray'] superYorientsARRAY = mat['headYarray'] superZorientsARRAY = mat['headZarray'] self.headorigin = [] self.headX = [] self.headY = [] self.headZ = [] for i in range(len(superXorientsARRAY)): if(math.fabs((superXorientsARRAY[i])[0]) + math.fabs((superXorientsARRAY[i])[1]) + math.fabs((superXorientsARRAY[i])[2]) < 0.01): self.headorigin.append(None) self.headX.append(None) self.headY.append(None) self.headZ.append(None) else: self.headorigin.append(Vector3d( (superOorientsARRAY[i])[0], (superOorientsARRAY[i])[1], (superOorientsARRAY[i])[2] )) self.headX.append(Vector3d( (superXorientsARRAY[i])[0], (superXorientsARRAY[i])[1], (superXorientsARRAY[i])[2] )) self.headY.append(Vector3d( (superYorientsARRAY[i])[0], (superYorientsARRAY[i])[1], (superYorientsARRAY[i])[2] )) self.headZ.append(Vector3d( (superZorientsARRAY[i])[0], (superZorientsARRAY[i])[1], (superZorientsARRAY[i])[2] )) def initializefrommatfile(self, trackingdatafile): matfilereader = MatFileReader(trackingdatafile) bbtransXY = (matfilereader.getMLArray('bbtransXY')).getArray() bbscaleXY = (matfilereader.getMLArray('bbscaleXY')).getArray() bbrot = (matfilereader.getMLArray('bbrot')).getArray() print 'trans',bbtransXY print 'scale',bbscaleXY print 'rotation',bbrot self.boundingboxtransX = (bbtransXY[0])[0] self.boundingboxtransY = (bbtransXY[0])[1] self.boundingboxscaleX = (bbscaleXY[0])[0] self.boundingboxscaleY = (bbscaleXY[0])[1] self.boundingboxrotation = (bbrot[0])[0] print 'trans', self.boundingboxtransX, self.boundingboxtransY print 'scale', self.boundingboxscaleX, self.boundingboxscaleY print 'rotation', self.boundingboxrotation self.jbigguy.adjustdisplaybox() trackingTS = (matfilereader.getMLArray('trackingTS')).getArray() sessionTS = (matfilereader.getMLArray('sessionTS')).getArray() ratcamTS = (matfilereader.getMLArray('ratcamTS')) if(ratcamTS != None): ratcamTS = ratcamTS.getArray() self.startratcamtimestamp = (ratcamTS[0])[0] self.stopratcamtimestamp = (ratcamTS[0])[1] print 'ratcam ts', ratcamTS print 'tracking ts', trackingTS print 'session ts', sessionTS print len(trackingTS), 'is two?' self.starttrackingtimestamp = (trackingTS[0])[0] self.stoptrackingtimestamp = (trackingTS[0])[1] self.startsessiontimestamp = (sessionTS[0])[0] self.stopsessiontimestamp = (sessionTS[0])[1] print 'tracking ts', self.starttrackingtimestamp, self.stoptrackingtimestamp print 'tracking ts minus', self.starttrackingtimestamp-math.floor(self.starttrackingtimestamp), self.stoptrackingtimestamp-math.floor(self.stoptrackingtimestamp) print 'session ts', self.startsessiontimestamp, self.stopsessiontimestamp pdd = (matfilereader.getMLArray('pointdatadimensions')).getArray() pointsdata = (matfilereader.getMLArray('pointdata')).getArray() n = int(round( (pdd[0])[0] )) d = int(round( (pdd[0])[1] )) T = int(round( (pdd[0])[2] )) print 'making point array of size', n, d, T whatyguy = zeros(T, 'i') negguy = zeros(T, 'd') for i in range(T): whatyguy[i] = -10000 negguy[i] = -10000 emptyguy = [] for i in range(3): emptyguy.append(copy.deepcopy(negguy)) emptyguy.append(whatyguy) ## neuron label number emptyguy.append(copy.deepcopy(negguy)) ## 'distance' measure (set as -1 if set by user) self.points = [] for i in range(n): self.points.append(copy.deepcopy(emptyguy)) print len(self.points[0]), 'should be the same as', d iii = 0 numkinds = 0 for i in range(n): for j in range(d): for k in range(T): if(j==3): ## this is where it crapped out ((self.points[i])[j])[k] = int(round( (pointsdata[0])[iii] )) if(((self.points[i])[j])[k] > numkinds): numkinds = ((self.points[i])[j])[k] else: ((self.points[i])[j])[k] = (pointsdata[0])[iii] iii = iii+1 self.plen = T def addaguyfromimport(aguy): valguy = [] aguyXYZ = matfilereader.getMLArray(aguy) if(aguyXYZ == None): return None aguyXYZ = (aguyXYZ.getArray())[0] for i in range(T): if(aguyXYZ[i*3] < -1000000): valguy.append(None) else: valguy.append(Vector3d( [ aguyXYZ[i*3], aguyXYZ[i*3+1], aguyXYZ[i*3+2] ] )) return valguy self.headorigin = addaguyfromimport('headorigin') self.headX = addaguyfromimport('headX') self.headY = addaguyfromimport('headY') self.headZ = addaguyfromimport('headZ') self.framerate = (((matfilereader.getMLArray('framerate')).getArray())[0])[0] self.analysisprogression = 0 if(self.headorigin != None): self.analysisprogression = 1 for i in range(numkinds+1): self.jbigguy.mysuperpointlabeler.addmearow(i) #for i in range(len(self.pointlabels.keys())): #for j in range(len(self.jbigguy.mysuperpointlabeler.combolist)): #if(self.jbigguy.mysuperpointlabeler.combolist[j].namy == self.pointlabels.keys()[i]): #self.jbigguy.mysuperpointlabeler.combolist[j].setSelectedIndex( (self.jbigguy.cnames.keys()).index( (self.pointlabels[ self.pointlabels.keys()[i] ])[0] ) ) #for j in range(len(self.jbigguy.mysuperpointlabeler.pointtypecombolist)): #if(self.jbigguy.mysuperpointlabeler.pointtypecombolist[j].namy == self.pointlabels.keys()[i]): #self.jbigguy.mysuperpointlabeler.pointtypecombolist[j].setSelectedIndex( (self.jbigguy.pointtypes).index( (self.pointlabels[ self.pointlabels.keys()[i] ])[1] ) ) return def gettrackeddatafromfile(self, trackingdatafile): base, ext = os.path.splitext(trackingdatafile) self.framerate = 120. ### DEFAULT VALUE COULD BE WRONG!!! if('csv' in ext): self.analysisprogression = 0 self.initializefromcsvfile(trackingdatafile) self.plen = len( (self.points[0])[0] ) if('pkl' in ext): self.initializefrompklfile(trackingdatafile) if('mat' in ext): self.initializefrommatfile(trackingdatafile) def getcelldatafromfile(self, filenames): self.allcells = [] self.allcellnames = [] earliesttimepoint = 1000000000000000000000000000000000000000 latesttimepoint = -100000000000000000000000000000000000000 for i in range(len(filenames)): matfilereader = MatFileReader(filenames[i]) cellts = (matfilereader.getMLArray('cellTS')).getArray() values = zeros(len(cellts), 'd') for j in range(len(cellts)): values[j] = (cellts[j])[0] if(values[j] > latesttimepoint): latesttimepoint = values[j] if(values[j] < earliesttimepoint): earliesttimepoint = values[j] name = '%d cell'%i for temp in range(len(filenames[i])-4, 0, -1): if( (filenames[i])[temp] == 'T' ): name = (filenames[i])[temp:(len(filenames[i])-4)] break self.allcellnames.append(name) self.allcells.append(values) matfilereader = 0 self.getstartandstoptimestamps(True) #print 'Earliest time point in matlab files is:', earliesttimepoint #print 'Latest time point in matlab files is:', latesttimepoint self.jbigguy.addspikestostuff(self.allcells, self.allcellnames) def addthingies(self): tempty = JPanel() self.jcheckorigpoints = JCheckBox() class jcheckerorigpoints(ItemListener): def __init__(self, parentguy): self.parentguy = parentguy def itemStateChanged(self, e): self.parentguy.jbigguy.settimepoint() self.jcheckorigpoints.addItemListener(jcheckerorigpoints(self)) tempty.add(self.jcheckorigpoints) tempty.add(JLabel('Show points')) self.revalidate() self.setVisible(True) self.jcheckorigpoints.setSelected(True) labelpointsbut = JButton('Tracking') class labelpointlistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.jbigguy.mysuperpointlabeler.setVisible(True) labelpointsbut.addActionListener(labelpointlistener(self)) tempty.add(labelpointsbut) tempty.validate() c = GridBagConstraints() c.anchor = GridBagConstraints.WEST c.insets = Insets(3, 3, 3, 3) c.fill = GridBagConstraints.HORIZONTAL c.gridy = 0 c.gridx = 3 c.gridwidth=2 self.add(tempty, c) def __init__(self, jbigguy): self.plen = -1 self.headorigin = None self.jbigguy = jbigguy self.analysisprogression = -1 self.starttrackingtimestamp = -1. self.stoptrackingtimestamp = -1. self.startsessiontimestamp = -1. self.stopsessiontimestamp = -1. self.startratcamtimestamp = -1. self.stopratcamtimestamp = -1. self.boundingboxrotation = 0. self.boundingboxtransX = 0. self.boundingboxtransY = 0. self.boundingboxscaleX = 1. self.boundingboxscaleY = 1. self.currentdirectory = '' preferencefile = '%s/Lib/trackedpointprefs.txt'%(getProperty('python.home')) if(os.path.exists(preferencefile)): preffile = open(preferencefile,'r') for line in preffile: if(len(line)>0): vals = line.split() if(len(vals)==2): if(vals[0] == 'LAST_DIRECTORY'): self.currentdirectory = vals[1] preffile.close() self.ratcamframerate = 25. self.allcells = [] self.allcellnames = [] self.setLayout(GridBagLayout()) self.pointlabels = {} self.headorigin = [] self.headX = [] self.headY = [] self.headZ = [] c = GridBagConstraints() c.anchor = GridBagConstraints.WEST c.insets = Insets(3, 3, 3, 3) c.gridx = 0 c.gridy = 0 c.fill = GridBagConstraints.HORIZONTAL class opentrackingdatalistener(ActionListener): def __init__(self, jguy): self.jguy = jguy self.fc = JFileChooser(self.jguy.currentdirectory) self.fc.setFileFilter(FileNameExtensionFilter("*.pkl, *.mat or *.csv file", ["mat","pkl","csv"])) def actionPerformed(self, event): ret = self.fc.showOpenDialog(None) if(ret == 0): self.jguy.jbut1.setEnabled(False) self.jguy.spikingloadbutton.setEnabled(True) self.jguy.ratcamloadbutton.setEnabled(True) self.jguy.analysisdatabutton.setEnabled(True) self.jguy.currentdirectory = self.fc.getCurrentDirectory() preferencefile = '%s/Lib/trackedpointprefs.txt'%(getProperty('python.home')) preffile = open(preferencefile,'w') preffile.write('LAST_DIRECTORY %s'%self.jguy.currentdirectory) preffile.close() self.jguy.jtrackingdata.setText( self.fc.selectedFile.getName() ) self.jguy.gettrackeddatafromfile(self.fc.selectedFile.getAbsolutePath()) if(self.jguy.plen > 0): self.jguy.jbigguy.setsuperpoints() self.jguy.jexportdata.setVisible(True) self.jguy.repaint() self.jguy.jbigguy.jcomboskippies.setEnabled(True) self.jguy.jbigguy.jcombospeedups.setEnabled(True) self.jguy.jbigguy.jbutfun.setEnabled(True) self.jguy.jbigguy.jcomboskippies.setSelectedIndex(0) self.jguy.jbigguy.jcombospeedups.setSelectedIndex(3) SwingUtilities.windowForComponent(self.jguy).revalidate() SwingUtilities.windowForComponent(self.jguy).pack() self.jtrackingdata = JLabel('Tracking data (pkl, mat or csv file)') self.jtrackingdata.setPreferredSize(Dimension(500,20)) self.add(self.jtrackingdata,c) self.jbut1 = JButton('Load') #jbut1.setPreferredSize(Dimension(20,20)) self.jbut1.addActionListener(opentrackingdatalistener(self)) c.gridx=1 self.add(self.jbut1,c) class savestepbuttonlistener(ActionListener): def __init__(self, jguy): self.jguy = jguy def actionPerformed(self, event): fc = JFileChooser(self.jguy.currentdirectory) fc.setFileFilter(FileNameExtensionFilter("Pickled (*.pkl)", ["pkl"])) ret = fc.showSaveDialog(None) if(ret == 0): self.jguy.jtrackingdata.setText( fc.selectedFile.getName() ) self.jguy.jtrackingdata.setPreferredSize(Dimension(500,20)) self.jguy.savetrackeddata(fc.selectedFile.getAbsolutePath()) SwingUtilities.windowForComponent(self.jguy).revalidate() SwingUtilities.windowForComponent(self.jguy).pack() ## save the data!! jbut3 = JButton('Save') #jbut3.setPreferredSize(Dimension(60,20)) jbut3.addActionListener(savestepbuttonlistener(self)) c.gridx=2 self.add(jbut3, c) c.gridy=1 c.gridx=0 self.jspikingdata = JLabel('Spiking data (mat files)') self.jspikingdata.setPreferredSize(Dimension(500,20)) self.add(self.jspikingdata,c) self.spikingloadbutton = JButton('Load') #jbut2.setPreferredSize(Dimension(20,20)) class openneuraldatalistener(ActionListener): def __init__(self, jguy): self.jguy = jguy def actionPerformed(self, event): fc = JFileChooser(self.jguy.currentdirectory) fc.setMultiSelectionEnabled(True) fc.setFileFilter(FileNameExtensionFilter("matlab files (*.mat)", ["mat"])) ret = fc.showOpenDialog(None) if(ret == 0): names = [] justname = '' for i in range(len(fc.selectedFiles)): names.append( (fc.selectedFiles[i]).getAbsolutePath() ) if(len(names)==1): self.jguy.jspikingdata.setText(names[0]) else: self.jguy.jspikingdata.setText('%s and friends'%(names[0])) self.jguy.jspikingdata.setPreferredSize(Dimension(500,20)) self.jguy.getcelldatafromfile(names) self.jguy.spikingloadbutton.setEnabled(False) self.jguy.jbutratemaps.setVisible(True) self.jguy.jexportdata.setVisible(True) self.jguy.repaint() SwingUtilities.windowForComponent(self.jguy).revalidate() SwingUtilities.windowForComponent(self.jguy).pack() self.spikingloadbutton.addActionListener(openneuraldatalistener(self)) self.spikingloadbutton.setEnabled(False) c.gridx=1 self.add(self.spikingloadbutton,c) self.ratemapguy = ratemapgenerator.ratemapthingy() class makeratemaplistener(ActionListener): def __init__(self, jguy): self.jguy = jguy def actionPerformed(self, event): self.jguy.ratemapguy.gogogo( self.jguy ) self.jbutratemaps = JButton('Rate maps') self.jbutratemaps.addActionListener(makeratemaplistener(self)) c.gridx=3 self.add(self.jbutratemaps,c) self.jbutratemaps.setVisible(False) class exportforratemaplistener(ActionListener): def __init__(self, jguy): self.jguy = jguy def actionPerformed(self, event): fc = JFileChooser(self.jguy.currentdirectory) fc.setFileFilter(FileNameExtensionFilter("Matlab file (*.mat)", ["mat"])) ret = fc.showSaveDialog(None) if(ret == 0): self.jguy.exportalldata(fc.selectedFile.getAbsolutePath()) self.jexportdata = JButton('Export all') self.jexportdata.addActionListener(exportforratemaplistener(self)) c.gridx=4 self.add(self.jexportdata,c) self.jexportdata.setVisible(False) c.gridy=2 c.gridx=0 self.avifile = JLabel('Rat cam video file (avi file)') self.avifile.setPreferredSize(Dimension(500,20)) self.add(self.avifile,c) self.ratcamloadbutton = JButton('Open') class openavibuttonlistener(ActionListener): def __init__(self, jguy): self.jguy = jguy def actionPerformed(self, event): fc = JFileChooser(self.jguy.currentdirectory) fc.setFileFilter(FileNameExtensionFilter("Rat cam video", ["avi"])) ret = fc.showOpenDialog(None) if(ret == 0): self.jguy.ratcamloadbutton.setEnabled(False) self.jguy.avifile.setText(fc.selectedFile.getName()) self.jguy.actualavifile = fc.selectedFile.getAbsolutePath() self.jguy.avifile.setPreferredSize(Dimension(500,20)) self.jguy.getstartandstoptimestamps(True) self.jguy.jbigguy.synchwithratcam() self.jguy.repaint() SwingUtilities.windowForComponent(self.jguy).revalidate() SwingUtilities.windowForComponent(self.jguy).pack() self.ratcamloadbutton.addActionListener(openavibuttonlistener(self)) self.ratcamloadbutton.setEnabled(False) c.gridx=1 self.add(self.ratcamloadbutton,c) c.gridy=3 c.gridx=0 self.templatefile = JLabel('Template file (csv file)') self.templatefile.setPreferredSize(Dimension(500,20)) self.add(self.templatefile, c) self.templatefilebutton = JButton('Load') class templatefilebuttonlistener(ActionListener): def __init__(self, jguy): self.jguy = jguy def actionPerformed(self, event): fc = JFileChooser(self.jguy.currentdirectory) fc.setFileFilter(FileNameExtensionFilter("Template file", ["csv"])) ret = fc.showOpenDialog(None) if(ret == 0): self.jguy.adjusttemplatefilebutton.setEnabled(True) self.jguy.templatefile.setText(fc.selectedFile.getName()) self.jguy.templatefile.setPreferredSize(Dimension(500,20)) self.jguy.addtemplatefromcsvfile(fc.selectedFile.getAbsolutePath()) #self.jguy.jbigguy.setsuperpoints() self.jguy.jbigguy.settemplatepoints() self.jguy.repaint() self.templatefilebutton.addActionListener(templatefilebuttonlistener(self)) self.templatefilebutton.setEnabled(True) c.gridx=1 self.add(self.templatefilebutton,c) self.templateadjuster = supertemplateadjuster(self) self.templateadjuster.setVisible(False) class adjusttemplatefilebuttonlistener(ActionListener): def __init__(self, jguy): self.jguy = jguy def actionPerformed(self, event): self.jguy.templateadjuster.setVisible(True) self.adjusttemplatefilebutton = JButton('Adjust it') self.adjusttemplatefilebutton.addActionListener(adjusttemplatefilebuttonlistener(self)) self.adjusttemplatefilebutton.setEnabled(False) c.gridx=2 self.add(self.adjusttemplatefilebutton,c) c.gridy=4 c.gridx=0 self.analysisdata = JLabel('Analysis files (csv)') self.analysisdata.setPreferredSize(Dimension(500,20)) self.add(self.analysisdata, c) self.analysisdatabutton = JButton('Add one') class analysisdatabuttonlistener(ActionListener): def __init__(self, jguy): self.jguy = jguy def actionPerformed(self, event): fc = JFileChooser(self.jguy.currentdirectory) fc.setFileFilter(FileNameExtensionFilter("Template file", ["csv"])) fc.setDialogTitle('Analysis data (assumed length of traces)') ret = fc.showOpenDialog(None) if(ret == 0): self.jguy.analysisdata.setText('%s added'%(fc.selectedFile.getName())) self.jguy.jbigguy.datatable.loadanalysisdata(fc.selectedFile.getAbsolutePath()) self.jguy.repaint() self.jguy.jbigguy.analysisstuffthingy.setVisible(True) self.analysisdatabutton.addActionListener(analysisdatabuttonlistener(self)) self.analysisdatabutton.setEnabled(False) c.gridx=1 self.add(self.analysisdatabutton,c) self.revalidate() self.setVisible(True) class superpointlabeler(JDialog): def addmearow(self, namy): class combocellguylistener(ItemListener): def __init__(self, parentguy): self.parentguy = parentguy def itemStateChanged(self, e): self.parentguy.parentguy.settimepoint() class JComboWithName(JComboBox): def setnamy(self, namy): self.namy = namy self.cguy.gridy = self.cguy.gridy+1 self.cguy.gridwidth=1 self.cguy.gridx=0 jpp = JPanel() jpp.add(JLabel('%s'%namy)) jcb = JCheckBox() self.jcheckboxpoints.append(jcb) class jcheckboxpointslistener(ItemListener): def __init__(self, parentguy): self.parentguy = parentguy #self.namy = namy def itemStateChanged(self, e): #if(e.getSource().isSelected()): self.parentguy.parentguy.settimepoint() jcb.addItemListener(jcheckboxpointslistener(self)) jcb.setSelected(True) jpp.add(jcb) self.add(jpp, self.cguy) pointypecombo = JComboWithName(self.parentguy.pointtypes) pointypecombo.setnamy(namy) def checkitnow(indy): for i in range(len(self.pointtypecombolist)): if((self.pointtypecombolist[i]).getSelectedIndex()==indy): return False return True firstgoodone = len(self.parentguy.pointtypes)-1 for i in range(len(self.parentguy.pointtypes)): if(checkitnow(i) == True): firstgoodone = i break pointypecombo.setSelectedIndex(firstgoodone) self.pointtypecombolist.append(pointypecombo) gowithindex = 0 self.cguy.gridx = 1 self.add(pointypecombo, self.cguy) newcombo = JComboWithName(self.parentguy.cnames.keys()) newcombo.setnamy(namy) someind = int(math.floor(random.random()*(len(self.parentguy.cnames.keys())-1))) newcombo.setSelectedIndex( someind ) self.combolist.append(newcombo) newcombo.addItemListener(combocellguylistener(self)) self.cguy.gridx = 2 self.cguy.gridwidth = 2 self.add(newcombo, self.cguy) class assignbuttonslistener(ActionListener): def __init__(self, parentguy, namy): self.parentguy = parentguy self.namy = namy def actionPerformed(self, event): if(event.getSource().isSelected()): self.parentguy.parentguy.currentpointassigner = self.namy for i in range(len(self.parentguy.togglebuttons)): if(self.parentguy.togglebuttons[i] == event.getSource()): continue else: self.parentguy.togglebuttons[i].setSelected(False) else: self.parentguy.parentguy.currentpointassigner = -10 newbutton = JToggleButton('Assign points') self.cguy.gridx = 4 newbutton.addActionListener(assignbuttonslistener(self, namy)) self.add(newbutton, self.cguy) self.togglebuttons.append(newbutton) class findnextthinglistener(ActionListener): def __init__(self, parentguy, namy): self.parentguy = parentguy self.namy = namy def actionPerformed(self, event): self.parentguy.parentguy.gotonextwithnonamy(self.namy) findnextguy = JButton('Go to next empty') self.cguy.gridx = 6 self.cguy.gridwidth = 1 findnextguy.addActionListener(findnextthinglistener(self, namy)) self.add(findnextguy, self.cguy) #self.cguy.gridx = 5 #self.add(JLabel(' '), self.cguy) #removeass = JButton('Remove assignments') #self.cguy.gridx = 6 #self.add(removeass, self.cguy) self.pack() self.repaint() def __init__(self, parentguy): self.parentguy = parentguy self.combolist = [] self.pointtypecombolist = [] self.togglebuttons = [] self.jcheckboxpoints = [] self.setLocationRelativeTo(None) self.setTitle("Tracking interface") self.setLayout(GridBagLayout()) self.cguy = GridBagConstraints() self.cguy.insets = Insets(3, 3, 3, 3) self.cguy.gridx = 0 self.cguy.gridy = 0 self.cguy.gridwidth=2 self.cguy.fill = GridBagConstraints.HORIZONTAL fitboxtopath = JButton('Fit display floor to points') class fitboxlistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.fitdisplayboxtopath() return fitboxtopath.addActionListener(fitboxlistener(self)) self.add(fitboxtopath, self.cguy) self.cguy.gridy = 1 trytofillin = JButton('Fill in after hand labeled') class trytofillinlistener(ActionListener): def __init__(self, parentguy, whichthing): self.parentguy = parentguy self.whichthing = whichthing def actionPerformed(self, event): if(self.whichthing==1): self.parentguy.parentguy.fillinpoints(self.whichthing, 0.01*float(self.parentguy.fillintol1.getText())) else: self.parentguy.parentguy.fillinpoints(self.whichthing, 0.01*float(self.parentguy.fillintol0.getText())) return trytofillin.addActionListener(trytofillinlistener(self, 1)) self.add(trytofillin, self.cguy) self.cguy.gridx = 2 self.cguy.gridwidth = 1 self.add(JLabel('Tolerance (cm)'), self.cguy) self.cguy.gridx = 3 self.fillintol1 = JTextField('1') self.add(self.fillintol1, self.cguy) # Go to specific frame self.cguy.gridy = 2 goToFrame = JButton('Go to frame') class goToFramelistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.gotospecificframe(int(self.parentguy.frameNumber.getText())) return goToFrame.addActionListener(goToFramelistener(self)) self.cguy.gridx = 0 self.cguy.gridwidth = 2 self.add(goToFrame, self.cguy) self.cguy.gridx = 2 self.cguy.gridwidth = 1 self.add(JLabel('Frame Number'), self.cguy) self.cguy.gridx = 3 self.frameNumber = JTextField('0') self.add(self.frameNumber, self.cguy) self.cguy.gridy = 3 superheadcheckbutton = JButton('Assign within tolerance (slow)') class superheadchecklistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.superheadfindaverage() val = 0.01*float(self.parentguy.rmsdistval.getText()) self.parentguy.parentguy.superheadfillin(val) superheadcheckbutton.addActionListener(superheadchecklistener(self)) self.cguy.gridx = 0 self.cguy.gridwidth = 2 self.add(superheadcheckbutton, self.cguy) self.cguy.gridx = 2 self.cguy.gridwidth = 1 self.add(JLabel('Tolerance (cm)'), self.cguy) self.cguy.gridx = 3 self.rmsdistval = JTextField('0.05') self.add(self.rmsdistval, self.cguy) superautobutton = JButton('Automate the rest') class superautobuttonlistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.superheadfindaverage() val = 0.01*float(self.parentguy.rmsdistval.getText()) self.parentguy.parentguy.superheadfillin(val, 1) self.parentguy.parentguy.fillinpoints(0, 0.01*float(self.parentguy.fillintol0.getText())) self.parentguy.parentguy.getheadorigin() val = float(self.parentguy.transcsysval.getText()) self.parentguy.parentguy.transformcsystomin(val, 1) self.parentguy.parentguy.optimizefororientationstuff(float(self.parentguy.minspeedfortranf.getText()), int(round(float(self.parentguy.numbinstocalculatedom.getText()))), 1) self.parentguy.parentguy.settimepoint() superautobutton.addActionListener(superautobuttonlistener(self)) self.cguy.gridx = 6 self.add(superautobutton, self.cguy) self.cguy.gridy = 4 self.cguy.gridx = 0 self.cguy.gridwidth=2 trytofillin2 = JButton('Fill in from any (slow)') trytofillin2.addActionListener(trytofillinlistener(self, 0)) self.add(trytofillin2, self.cguy) self.cguy.gridx = 2 self.cguy.gridwidth = 1 self.add(JLabel('Tolerance (cm)'), self.cguy) self.cguy.gridx = 3 self.fillintol0 = JTextField('1') self.add(self.fillintol0, self.cguy) self.cguy.gridy = 5 #self.cguy.gridx = 0 #self.jcheckcsysthingy = JCheckBox() #class jcheckcsysthingylistener(ItemListener): #def __init__(self, parentguy): #self.parentguy = parentguy #def itemStateChanged(self, e): #self.parentguy.parentguy.settimepoint() #self.jcheckcsysthingy.addItemListener(jcheckcsysthingylistener(self)) #self.add(self.jcheckcsysthingy, self.cguy) self.cguy.gridx = 0 self.cguy.gridwidth = 2 headoriginbut = JButton('Head csys maker') class gettheheadthinglistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.getheadorigin() self.parentguy.parentguy.settimepoint() headoriginbut.addActionListener(gettheheadthinglistener(self)) self.add(headoriginbut, self.cguy) self.cguy.gridy = 6 self.cguy.gridx = 0 self.cguy.gridwidth = 2 transformcsystominbut = JButton('Transform to min shakes') class transformcsystominlistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): val = float(self.parentguy.transcsysval.getText()) self.parentguy.parentguy.transformcsystomin(val) transformcsystominbut.addActionListener(transformcsystominlistener(self)) self.add(transformcsystominbut, self.cguy) self.cguy.gridx = 2 self.cguy.gridwidth = 1 self.add(JLabel('Num bins'), self.cguy) self.cguy.gridx = 3 self.transcsysval = JTextField('20') self.transcsysval.setColumns(4) self.add(self.transcsysval, self.cguy) self.cguy.gridy = 7 self.cguy.gridx = 0 self.cguy.gridwidth = 2 transformcsystomatch = JButton('Transform to match DOM') self.add(transformcsystomatch, self.cguy) self.cguy.gridx=2 self.cguy.gridwidth=1 self.add(JLabel('Min speed (cm/s)'), self.cguy) self.cguy.gridx=3 self.minspeedfortranf = JTextField('10.') self.minspeedfortranf.setColumns(4) self.add(self.minspeedfortranf, self.cguy) self.cguy.gridx=4 self.add(JLabel('Num bins'), self.cguy) self.cguy.gridx=5 self.numbinstocalculatedom = JTextField('50') self.numbinstocalculatedom.setColumns(4) self.add(self.numbinstocalculatedom, self.cguy) class transformcsystomatchlistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.optimizefororientationstuff(float(self.parentguy.minspeedfortranf.getText()), int(round(float(self.parentguy.numbinstocalculatedom.getText())))) transformcsystomatch.addActionListener(transformcsystomatchlistener(self)) self.cguy.gridy = 8 # Check duplicate labelled markers checkDuplicateLabels = JButton('Check duplicates') class checkDuplicatesListener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.checkduplicatelabels() return checkDuplicateLabels.addActionListener(checkDuplicatesListener(self)) self.cguy.gridx = 0 self.cguy.gridwidth = 2 self.add(checkDuplicateLabels, self.cguy) # Remove label duplicate labelled markers removeDuplicateLabels = JButton('Remove duplicates') class removeDuplicatesListener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.removeduplicatelabels() return removeDuplicateLabels.addActionListener(removeDuplicatesListener(self)) self.cguy.gridx = 2 self.cguy.gridwidth = 2 self.add(removeDuplicateLabels, self.cguy) # find unlabelled markers findUnlabelled = JButton('Go to next unlabelled') class findUnlabelledListener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.findunlabelled() return findUnlabelled.addActionListener(findUnlabelledListener(self)) self.cguy.gridx = 4 self.cguy.gridwidth = 2 self.add(findUnlabelled, self.cguy) addalabelpoint = JButton('Add a labeled point') self.cguy.gridx = 0 self.cguy.gridy = 9 self.cguy.gridwidth = 4 self.add(addalabelpoint, self.cguy) class addalabelpointlistener(ActionListener): def __init__(self, lilparentguy): self.lilparentguy = lilparentguy def actionPerformed(self, event): self.lilparentguy.addmearow(len(self.lilparentguy.combolist)) addalabelpoint.addActionListener(addalabelpointlistener(self)) statusbutton = JButton('Status') class statusbuttonlistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.parentguy.statusoflabeling() return statusbutton.addActionListener(statusbuttonlistener(self)) self.cguy.gridx = 4 self.cguy.gridwidth=2 self.add(statusbutton, self.cguy) self.pack() #self.setVisible(True) class trackeddatastruct(JPanel): def gotospecificframe(self, frameNum): self.jslider.setValue(frameNum) return def statusoflabeling(self): # clear(); n = len(self.data.points) print n countlabeled = 0 counttotal = 0 counthead = 0 countheadfinished = 0 whichheads = [] whichheads.append(0) whichheads.append(1) whichheads.append(2) whichheads.append(3) startlackingcsys = 0 startlackingcsysoflongest = 0 longesttripwithouthead = 0 thresholdfordisplay = 5 print 'Displaying all stretches of missed head that are longer than %d time points'%thresholdfordisplay for t in range(self.data.plen): if(self.data.headorigin != None and len(self.data.headorigin)>10): if(self.data.headorigin[t] != None): countheadfinished += 1 if(t>1): if(self.data.headorigin[t-1] == None): dt = t-startlackingcsys if(dt>thresholdfordisplay): print 'Empty stretch of %d time points, starting at %d'%(dt, startlackingcsys) if(dt>longesttripwithouthead): longesttripwithouthead = dt startlackingcsysoflongest = startlackingcsys else: if(t>1): if(self.data.headorigin[t-1] != None): startlackingcsys = t for i in range(n-1): if( ((self.data.points[i])[3])[t] > -1 ): countlabeled += 1 if( ((self.data.points[i])[3])[t] in whichheads ): ### FIX THIS SO IT GETS IT CORRECT!!! counthead += 1 # else: # print 'unlabled point %d in timeframe %d'%(i,t) if( ((self.data.points[i])[0])[t] > -1000 ): counttotal += 1 perlab = 100. * float(countlabeled)/float(counttotal) perhead = 100. * float(counthead)/float(self.data.plen*4) perheadfinished = 100. * float(countheadfinished)/float(self.data.plen) if(perlab > 90 or perhead > 90): if(self.data.headorigin!=None and len(self.data.headorigin)>10): JOptionPane.showMessageDialog(None, 'Congratulations! You have %2.2f percent overall labeled,\n%2.2f percent of the head points labeled\nand %2.2f percent of the head positions determined\nwith longest stretch being %d time steps, starting at %d'%(perlab, perhead,perheadfinished,longesttripwithouthead, startlackingcsysoflongest)) else: JOptionPane.showMessageDialog(None, 'Congratulations! You have %2.2f percent overall labeled \nand %2.2f percent of the head points labeled'%(perlab, perhead)) else: if(self.data.headorigin!=None and len(self.data.headorigin)>10): JOptionPane.showMessageDialog(None, 'Unfortunately, You have just %2.2f percent overall labeled,\n%2.2f percent of the head points labeled\nand %2.2f percent of the head positions determined\nwith longest stretch being %d time steps, starting at %d'%(perlab, perhead,perheadfinished,longesttripwithouthead, startlackingcsysoflongest)) else: JOptionPane.showMessageDialog(None, 'Unfortunately, You have %2.2f percent overall labeled \nand %2.2f percent of the head points labeled'%(perlab, perhead)) # Check for the duplicate markers def checkduplicatelabels(self): # clear(); n = len(self.data.points) for t in range(self.data.plen): # check duplicate labels ls = [((self.data.points[f])[3])[t] for f in range(n)] # print ls dups = set() seen = set() if len(ls) != len(set(ls)): for f in range(n): lbl = ((self.data.points[f])[3])[t] if lbl not in seen: seen.add(lbl) else: dups.add(lbl) # ((self.data.points[f])[3])[t] = -10000 duplicates = list(sorted(dups)) # if len(duplicates)>0: # print duplicates,t for elem in duplicates: for f in range(n): if ((self.data.points[f])[3])[t] == elem: if (elem!=-10000): print elem,t # Remove the labelling of duplicate markers def removeduplicatelabels(self): n = len(self.data.points) for t in range(self.data.plen): # check duplicate labels ls = [((self.data.points[f])[3])[t] for f in range(n)] # print ls dups = set() seen = set() if len(ls) != len(set(ls)): for f in range(n): lbl = ((self.data.points[f])[3])[t] if lbl not in seen: seen.add(lbl) else: dups.add(lbl) # ((self.data.points[f])[3])[t] = -10000 duplicates = list(sorted(dups)) for elem in duplicates: for f in range(n): if ((self.data.points[f])[3])[t] == elem: ((self.data.points[f])[3])[t] = -10000 # find unlabelled markers def findunlabelled(self): # checking unlabelled markers n = len(self.data.points) startt = self.jslider.getValue() print startt for t in range(startt+1, self.data.plen, 1): where = [] for i in range(n-1): if( ((self.data.points[i])[3])[t] == -10000 ): where.append(i) self.jslider.setValue(t) if where[0]!=n-2: print 'unlabelled:', where return return def gotonextwithnonamy(self, namy): ttt = self.jslider.getValue() n = len(self.data.points) for t in range(ttt+1, self.data.plen, 1): foundit = False for i in range(n-1): if( ((self.data.points[i])[3])[t] == -1 ): foundit = True print t self.jslider.setValue(t) break if(foundit == False): return return def getsidesforsuperhead(self, tt): n = len(self.data.points) sides = zeros(n*n, 'd') for i in range(n): for j in range(i): for xx in range(3): sides[i*n+j] += ( ((self.data.points[i])[xx])[tt] - ((self.data.points[j])[xx])[tt] )**2 sides[j*n+i] = sides[i*n+j] return(sides) def superheadfillin(self, thresh, debug=0): print 'Filling in guys within tolerance', thresh n = len(self.data.points) allcombos = [] for i in range(n): for j in range(n): if(i==j): continue for k in range(n): if(i==k or j==k): continue for m in range(n): if(i==m or j==m or m==k): continue allcombos.append([i,j,k,m]) headnames = [] headnames.append(0) headnames.append(1) headnames.append(2) headnames.append(3) mindists = zeros(self.data.plen, 'd') howmanyofeach = zeros(len(allcombos), 'i') H0 = zeros(self.data.plen, 'i') H1 = zeros(self.data.plen, 'i') H2 = zeros(self.data.plen, 'i') H3 = zeros(self.data.plen, 'i') told = self.jslider.getValue() n = len(self.data.points) if(len(headnames)<4): print 'cant find head because not enough points are identified' return for t in range(self.data.plen): allsides = self.getsidesforsuperhead(t) mindists[t] = 100000000000. found = 0 counter = -1 tvals = zeros(6, 'd') whichcanskip = zeros(len(allcombos), 'i') for ii in range(n): if(((self.data.points[ii])[4])[t] < -100): continue else: disname = ((self.data.points[ii])[3])[t] isaheadguy = False for i in range(len(headnames)): if(headnames[i] == disname): isaheadguy = True if(isaheadguy == True): for jj in range(len(allcombos)): keepme = False for kk in range(4): if(disname == headnames[kk] and (allcombos[jj])[kk] == ii): keepme = True if(keepme == False): whichcanskip[jj] = 1 else: for jj in range(len(allcombos)): keepme = True for kk in range(4): if((allcombos[jj])[kk] == ii): keepme = False if(keepme == False): whichcanskip[jj] = 1 print t, jj, 'skipped because point in place is something else' dists = zeros(len(allcombos), 'd') numfound = 0 for xx in range(len(allcombos)): if(whichcanskip[xx] == 1): dists[xx] = 100000000000000000 continue counter = 0 dodo = zeros(6,'d') for ii in range(1,4,1): for jj in range(ii): counter += 1 sidevalue = allsides[ ((allcombos[xx])[ii]) * n + (allcombos[xx])[jj] ] dodo[counter-1] = sidevalue dists[xx] += (sidevalue - self.avevals[counter-1])**2 dists[xx] = math.sqrt(dists[xx]/6.) if(dists[xx] < mindists[t]): mindists[t] = dists[xx] H0[t] = (allcombos[xx])[0] H1[t] = (allcombos[xx])[1] H2[t] = (allcombos[xx])[2] H3[t] = (allcombos[xx])[3] if(dists[xx] < thresh): numfound += 1 howmanyofeach[numfound] += 1 if((t%100)==0 or t==self.data.plen-1): self.jslider.setValue(t) if(debug==0): if(t==5000): strout = 'Out of the first 5000,\n' for i in range(len(howmanyofeach)): if(howmanyofeach[i] > 0): strout = '%s%d that passed the threshold %d times\n'%(strout, howmanyofeach[i], i) strout = '%sWould you like to continue and have it do the labeling?'%strout if(JOptionPane.showConfirmDialog(None,strout ,"Question",JOptionPane.YES_NO_OPTION) != JOptionPane.YES_OPTION): return if(len(headnames)<4): print 'cant find head because not enough points are identified' return for t in range(self.data.plen): if(mindists[t] < thresh): if(((self.data.points[H0[t]])[4])[t] != -1): ((self.data.points[H0[t]])[3])[t] = headnames[0] ((self.data.points[H0[t]])[4])[t] = mindists[t] if(((self.data.points[H1[t]])[4])[t] != -1): ((self.data.points[H1[t]])[3])[t] = headnames[1] ((self.data.points[H1[t]])[4])[t] = mindists[t] if(((self.data.points[H2[t]])[4])[t] != -1): ((self.data.points[H2[t]])[3])[t] = headnames[2] ((self.data.points[H2[t]])[4])[t] = mindists[t] if(((self.data.points[H3[t]])[4])[t] != -1): ((self.data.points[H3[t]])[3])[t] = headnames[3] ((self.data.points[H3[t]])[4])[t] = mindists[t] if((t%100)==0 or t==self.data.plen-1): self.jslider.setValue(t) self.jslider.setValue(told) def superheadfindaverage(self): headnames = [] headnames.append(0) headnames.append(1) headnames.append(2) headnames.append(3) ### GET AVERAGE VALUES FROM THE FIRST 4 POINTS n = len(self.data.points) allvalues = [] tinds = [] for i in range(6): allvalues.append([]) for t in range(self.data.plen): allsides = self.getsidesforsuperhead(t) found = 0 counter = 0 tvals = zeros(6, 'd') for ii in range(1,4,1): ind0 = -10 for yy in range(n): if(headnames[ii] == ((self.data.points[yy])[3])[t]): ind0 = yy for jj in range(ii): counter += 1 ind1 = -10 for xx in range(n): if(headnames[jj] == ((self.data.points[xx])[3])[t]): ind1 = xx if(ind0>-1 and ind1>-1): found += 1 tvals[counter-1] = allsides[ind0*n+ind1] if(found == 6): tinds.append(t) for i in range(6): (allvalues[i]).append(tvals[i]) self.avevals = zeros(6,'d') if(len(allvalues[0])>0): for i in range(6): self.avevals[i] = sum(allvalues[i])/float(len(allvalues[i])) print 'average values', self.avevals dists = zeros(len(allvalues[0]), 'd') mindist = 100000000. self.closestpointtoaveragepoints = None for i in range(len(allvalues[0])): for j in range(6): dists[i] += ((allvalues[j])[i] - self.avevals[j])**2 dists[i] = math.sqrt(dists[i]) if(dists[i] < mindist): pnts = [] for xxx in range(4): pnt = [] for poop in range(n): if(headnames[xxx] == ((self.data.points[poop])[3])[i]): for yyy in range(3): pnt.append( ((self.data.points[poop])[yyy])[i] + 0. ) pnts.append(pnt) if(len(pnts)==4): mindist = dists[i] self.closestpointtoaveragepoints = pnts mv = sum(dists)/float(len(dists)) stddist = 0 for i in range(len(allvalues[0])): stddist += (dists[i] - mv)**2 stddist = math.sqrt(stddist/float(len(allvalues[0]))) print 'max rms distance of values', max(dists) print 'min rms distance of values', min(dists) print 'mean rms distance of values', mv print 'std rms distance of values', stddist print 'closest point to the average (used for getting head coordinates)' print self.closestpointtoaveragepoints badindices = [] for i in range(len(allvalues[0])): if(abs(dists[i]-mv)>4*stddist): badindices.append(tinds[i]) print 'indices of those more than 4*std from the mean (if any):', badindices def adjustdisplaybox(self): #### WOULDN'T IT MAKE MORE SENSE TO DO THIS IN ALL DEGREES A FREEDOM (ALL THREE ANGLES) t0 = Transform3D() t0.rotZ(self.data.boundingboxrotation) t1 = Transform3D() t1.setTranslation(Vector3f( self.data.boundingboxtransX, self.data.boundingboxtransY, -0.1)) t2 = Transform3D() t2.setScale( Vector3d(self.data.boundingboxscaleX, self.data.boundingboxscaleY, 1.) ) ## note default box has side of '1' tt = Transform3D() tt.mul(t0,t1) tt.mul(t2) self.boxtgroup.setTransform(tt) def fitdisplayboxtopath(self): TT = len((self.data.points[0])[0]) npts = len(self.data.points) def getextremesofpoints(checkang): minxxx = 100000000000. maxxxx = -100000000000. minyyy = 100000000000. maxyyy = -100000000000. cosguy = math.cos(checkang) singuy = math.sin(checkang) for i in range(npts): thingies = ((self.data.points[i])[3]) xpts = ((self.data.points[i])[0]) ypts = ((self.data.points[i])[1]) for t in range(TT): if(thingies[t]>-1): tempX = (xpts[t])*cosguy - (ypts[t])*singuy tempY = (ypts[t])*cosguy + (xpts[t])*singuy if(tempX > maxxxx): maxxxx = tempX if(tempX < minxxx): minxxx = tempX if(tempY > maxyyy): maxyyy = tempY if(tempY < minyyy): minyyy = tempY return([maxxxx, minxxx, maxyyy, minyyy]) def getarea(pp, dummy): vs = getextremesofpoints(pp[0]) return( (vs[0]-vs[1])*(vs[2]-vs[3]) ) #return area of rectangle mmm = ij.measure.Minimizer() mmm.setFunction(getarea, 1) mmm.setMaxError(0.00001) mmm.setMaxRestarts(50) mmm.minimize([random.random()*0.1-0.05], [0.1]) winval = getarea(mmm.getParams(), 1.) zeroval = getarea([0.], 0.) pp = mmm.getParams() vs = getextremesofpoints(pp[0]) print 'Optimal rotation:', -pp[0], 'box extremes', vs self.data.boundingboxrotation = -pp[0] self.data.boundingboxtransX = (vs[0]+vs[1])/2. self.data.boundingboxtransY = (vs[2]+vs[3])/2. self.data.boundingboxscaleX = vs[0]-vs[1] self.data.boundingboxscaleY = vs[3]-vs[2] self.adjustdisplaybox() def fillinpoints(self, whichkind, thresh): ## GET THRESHOLD FROM GUI thresh2 = thresh**2 TT = len((self.data.points[0])[0]) npts = len(self.data.points) told = self.jslider.getValue() for t in range(TT): for i in range(npts): if( (whichkind==0 and ((self.data.points[i])[3])[t] > -1) or ( whichkind == 1 and abs(((self.data.points[i])[4])[t] + 1) < 0.001 ) ): ppp = [ ((self.data.points[i])[0])[t], ((self.data.points[i])[1])[t], ((self.data.points[i])[2])[t] ] if(t+1 -1 ): if( ((self.data.points[minind])[3])[ttt] != ((self.data.points[i])[3])[t]): print 'Conflicting guy at time', ttt break ((self.data.points[minind])[3])[ttt] = ((self.data.points[i])[3])[t] + 0 ((self.data.points[minind])[4])[ttt] = math.sqrt(mindist) + 0. ppp = [ ((self.data.points[minind])[0])[ttt], ((self.data.points[minind])[1])[ttt], ((self.data.points[minind])[2])[ttt] ] else: break ppp = [ ((self.data.points[i])[0])[t], ((self.data.points[i])[1])[t], ((self.data.points[i])[2])[t] ] if(t>0): for ttt in range(t-1, -1, -1): minind = -100 mindist = 1000000. for j in range(npts): dist = (ppp[0] - ((self.data.points[j])[0])[ttt])**2 + (ppp[1] - ((self.data.points[j])[1])[ttt])**2 + (ppp[2] - ((self.data.points[j])[2])[ttt])**2 if(dist < mindist): mindist = dist minind = j if( mindist < thresh2 ): if( ((self.data.points[minind])[3])[ttt] > -1 ): if( ((self.data.points[minind])[3])[ttt] != ((self.data.points[i])[3])[t]): print 'Conflicting guy at time', ttt break ((self.data.points[minind])[3])[ttt] = ((self.data.points[i])[3])[t] + 0 ((self.data.points[minind])[4])[ttt] = math.sqrt(mindist) + 0. ppp = [ ((self.data.points[minind])[0])[ttt], ((self.data.points[minind])[1])[ttt], ((self.data.points[minind])[2])[ttt] ] else: break if( t%100 == 0 ): self.jslider.setValue(t) self.jslider.setValue(told) def synchwithratcam(self): fnamepoop = self.data.actualavifile if(os.path.isfile(fnamepoop)): centerpanel = JPanel() centerpanel.setLayout(GridLayout(2,2)) centerpanel.add(JLabel("Convert to gray ")) convtogray = JCheckBox("") convtogray.setSelected(True) centerpanel.add(convtogray) centerpanel.add(JLabel("Load virtually ")) loadvirtually = JCheckBox("") loadvirtually.setSelected(True) centerpanel.add(loadvirtually) centerpanel.validate() centerpanel.setVisible(True) sel = JOptionPane.showConfirmDialog(None, centerpanel, 'Ratcam infomation', JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE) im0 = AVI_Reader().makeStack(fnamepoop, 1, 0, loadvirtually.isSelected(), convtogray.isSelected(), False) self.implus = ImagePlus('%s'%(fnamepoop),im0) self.implus.show() class ML(ImageListener): def setparentguy(self, parentguy): self.parentguy = parentguy def imageUpdated(self, eventimage): if(self.parentguy.avoidrecursionwithtimepoints == 0 or self.parentguy.avoidrecursionwithtimepoints == 1): return self.parentguy.avoidrecursionwithtimepoints = 1 jj = eventimage.currentSlice self.parentguy.impluscurrentslice = jj timeinother = int(self.parentguy.data.framerate* (self.parentguy.data.startratcamtimestamp + float(jj)/self.parentguy.data.ratcamframerate - self.parentguy.data.starttrackingtimestamp) ) if(timeinother<0): timeinother = 0 if(timeinother>self.parentguy.data.plen-1): timeinother = self.parentguy.data.plen-1 self.parentguy.jslider.setValue(int(timeinother)) self.parentguy.avoidrecursionwithtimepoints = 2 ml = ML() ml.setparentguy(self) self.implus.addImageListener(ml) print 'estimated number of seconds from rat cam', float(self.implus.getNSlices())/self.data.ratcamframerate print 'estimated number of seconds from tracking', float(self.data.plen)/self.data.framerate print 'estimated from ttl start and stop', self.data.stoptrackingtimestamp - self.data.starttrackingtimestamp print 'estimated from session start and stop', float(self.data.stopsessiontimestamp-self.data.startsessiontimestamp)/1000. print 'estimated from vt1 start and stop', float(self.data.stopratcamtimestamp-self.data.startratcamtimestamp)/1000. #print 'original number of frames', numoforiginalframes print 'number of frames in gui', self.implus.getNSlices() def settimepoint(self, t=-100,told=-100): if(self.avoidrecursionwithtimepoints == 0): return if(self.avoidrecursionwithtimepoints == 2): self.avoidrecursionwithtimepoints = 0 if(t<0): if(self.jslider == None): self.avoidrecursionwithtimepoints = 2 return t = self.jslider.getValue() if(t>self.data.plen-1): self.avoidrecursionwithtimepoints = 2 return ####MOOOGOOO/datatable self.datatable.tablemodel.updatet(t) if(self.implus != None and self.avoidrecursionwithtimepoints == 0): timeinother = int( self.data.ratcamframerate * ((float(t)/self.data.framerate) + self.data.starttrackingtimestamp - self.data.startratcamtimestamp) ) if(timeinother != self.impluscurrentslice): if(timeinother>-1 and timeinother5): ### CHECK THINGY!! if(self.data.headorigin[t] != None): self.coordsysSwitch.setWhichChild(Switch.CHILD_ALL) mm = Matrix3d() mm.setColumn(0, self.data.headX[t]) mm.setColumn(1, self.data.headY[t]) mm.setColumn(2, self.data.headZ[t]) tt = Transform3D(mm, self.data.headorigin[t], 1.) self.wickedheadTG.setTransform(tt) else: self.coordsysSwitch.setWhichChild(Switch.CHILD_NONE) else: self.coordsysSwitch.setWhichChild(Switch.CHILD_NONE) self.data.pointlabels = {} for i in range(len(self.mysuperpointlabeler.combolist)): self.data.pointlabels[self.mysuperpointlabeler.combolist[i].namy] = [ (self.cnames.keys())[ self.mysuperpointlabeler.combolist[i].getSelectedIndex() ], self.pointtypes[ self.mysuperpointlabeler.pointtypecombolist[i].getSelectedIndex() ] ] chkchkpointboxes = {} for i in range(len(self.mysuperpointlabeler.combolist)): chkchkpointboxes[self.mysuperpointlabeler.combolist[i].namy] = (self.mysuperpointlabeler.jcheckboxpoints[i]).isSelected() #if(self.data.analysisprogression > 4): if(self.jcombonames!=None): ind = self.jcombonames.getSelectedIndex() self.spikesSwitches[ind].setWhichChild(Switch.CHILD_MASK) self.fadedspikesSwitches[ind].setWhichChild(Switch.CHILD_MASK) bs = BitSet(len(self.allcells[ind])) bs2 = BitSet(len(self.allcells[ind])) sesstime = float(t)/self.data.framerate + self.data.starttrackingtimestamp - self.data.startsessiontimestamp for i in range(len(self.allcells[ind])): if( (self.allcells[ind])[i] <= sesstime and (self.allcells[ind])[i] > sesstime-10.): bs.set(i) if( (self.allcells[ind])[i] < sesstime-10.): bs2.set(i) if(told>-0.1): oldsesstime = float(told)/self.data.framerate + self.data.starttrackingtimestamp - self.data.startsessiontimestamp #if(math.fabs((self.allcells[ind])[i] - sesstime)<= 1./self.data.framerate): if((self.allcells[ind])[i]>oldsesstime and (self.allcells[ind])[i]<=sesstime): self.AudioClip.stop() self.AudioClip.setFramePosition(0) self.AudioClip.start() self.spikesSwitches[ind].setChildMask(bs) self.fadedspikesSwitches[ind].setChildMask(bs2) tt = float(t)/(self.data.framerate) mm = math.floor(tt/60.) #self.currtime.setText('%02d minutes and %02.1f seconds, rotz = %f'%(mm, (tt-mm*60.), zzzzzz)) self.currtime.setText('%02d minutes, %02.1f seconds, frame number %d '%(mm, (tt-mm*60.), t)) if(self.data.analysisprogression > -1): bs = BitSet(len(self.pointsTGarray)) if(self.data.jcheckorigpoints.isSelected()==False): # and self.jchecknonheadpoints.isSelected()==False): self.pointsSwitch.setWhichChild(Switch.CHILD_NONE) #for i in range(len(self.pointsTGarray)): #bs.set(i) else: self.pointsSwitch.setWhichChild(Switch.CHILD_MASK) for i in range(len(self.pointsTGarray)): xx = ((self.data.points[i])[0])[t] if( xx < -1000 ): continue pp = ((self.data.points[i])[3])[t] if(pp > -1): if(chkchkpointboxes[pp]==False): continue bs.set(i) yy = ((self.data.points[i])[1])[t] zz = ((self.data.points[i])[2])[t] tt = Transform3D() tt.setTranslation( Vector3f(xx, yy, zz) ) (self.pointsTGarray[i]).setTransform(tt) ap = Appearance() ca = ColoringAttributes() if(((self.data.points[i])[3])[t] > -1): ccind = (self.data.pointlabels[pp])[0] cc = self.cnames[ccind] ca.setColor(cc[0]/255., cc[1]/255., cc[2]/255.) else: ca.setColor(Color3f(0.1,0.1,0.1)) ap.setColoringAttributes(ca) (self.pointsSParray[i]).setAppearance(ap) self.pointsSwitch.setChildMask(bs) self.avoidrecursionwithtimepoints = 2 def getdirofmov(self): self.dirofmov = [] dtguy = self.data.framerate #### PARAMETER!! for t in range(self.data.plen): if(t(self.data.plen-dtguy-1)): self.dirofmov.append(None) elif(math.fabs(self.dists[t-dtguy])>0.0001 or math.fabs(self.dists[t+dtguy])>0.0001 or math.fabs(self.dists[t])>0.0001): #### PARAMETER!!!! self.dirofmov.append(None) elif( (math.fabs((self.ddxx[0])[t]) + math.fabs((self.ddxx[1])[t]) + math.fabs((self.ddxx[2])[t]) < 0.01) ): self.dirofmov.append(None) else: xxdir = (self.adjpts[0])[t+dtguy] - (self.adjpts[0])[t-dtguy] yydir = (self.adjpts[1])[t+dtguy] - (self.adjpts[1])[t-dtguy] zzdir = (self.adjpts[2])[t+dtguy] - (self.adjpts[2])[t-dtguy] lenvec = math.sqrt(xxdir*xxdir + yydir*yydir + zzdir*zzdir) if(lenvec<=0.1): #### PARAMETER!!!! self.dirofmov.append(None) else: self.dirofmov.append(Vector3d(xxdir/lenvec, yydir/lenvec, zzdir/lenvec)) def optimizefororientationstuff(self, minspeed, ddtt, debug=0): superXorients = [] superYorients = [] superZorients = [] dirofmov = [] avespeeds = [] for t in range(ddtt, self.data.plen-ddtt, 1): if(self.data.headorigin[t] == None or self.data.headorigin[t-ddtt] == None or self.data.headorigin[t+ddtt] == None): continue xxdir = (self.data.headorigin[t+ddtt]).x - (self.data.headorigin[t-ddtt]).x yydir = (self.data.headorigin[t+ddtt]).y - (self.data.headorigin[t-ddtt]).y zzdir = (self.data.headorigin[t+ddtt]).z - (self.data.headorigin[t-ddtt]).z lenvec = math.sqrt(xxdir*xxdir + yydir*yydir + zzdir*zzdir) avespeed = 100.*lenvec*(self.data.framerate)/(2.*ddtt) # in cm/s if(avespeed > minspeed): ### only keep time points when he is really moving avespeeds.append(avespeed) dirofmov.append(Vector3d(xxdir/lenvec, yydir/lenvec, zzdir/lenvec)) superXorients.append( self.data.headX[t] ) #Vector3d( (self.data.headX[t]).x, (self.data.headX[t]).y, (self.data.headX[t]).z ) ) superYorients.append( self.data.headY[t] )# Vector3d( (self.data.headY[t]).x, (self.data.headY[t]).y, (self.data.headY[t]).z ) ) superZorients.append( self.data.headZ[t] )# Vector3d( (self.data.headZ[t]).x, (self.data.headZ[t]).y, (self.data.headZ[t]).z ) ) def rotatetheguys(xxx, yyy, zzz, ppp): #rotate about the 'x' rotate = Matrix3d() rotate.set(AxisAngle4d(xxx, ppp[0])) rotate.transform(yyy, yyy) rotate.transform(zzz, zzz) #rotate about the 'y' rotate = Matrix3d() rotate.set(AxisAngle4d(yyy, ppp[1])) rotate.transform(xxx, xxx) rotate.transform(zzz, zzz) #rotate about the 'z' rotate = Matrix3d() rotate.set(AxisAngle4d(zzz, ppp[2])) rotate.transform(yyy, yyy) rotate.transform(xxx, xxx) return(xxx, yyy, zzz) uupp = Vector3d(0., 0., 1.) def costfunctionforrotations(ppp, dummy): totalcost = 0. superXorientsOPT = copy.deepcopy(superXorients) superYorientsOPT = copy.deepcopy(superYorients) superZorientsOPT = copy.deepcopy(superZorients) rat = 0.9 ang1err = 0. ang2err = 0. for i in range(len(dirofmov)): superXorientsOPT[i], superYorientsOPT[i], superZorientsOPT[i] = rotatetheguys(superXorientsOPT[i], superYorientsOPT[i], superZorientsOPT[i], ppp) ang1 = (dirofmov[i]).angle(superXorientsOPT[i]) ang2 = uupp.angle(superZorientsOPT[i]) ang1err += math.fabs(ang1) ang2err += math.fabs(ang2) totalcost += (rat)*ang1*ang1 + (1.-rat)*ang2*ang2 if(False): print rat, ppp[0], ppp[1], ppp[2], totalcost/float(len(dirofmov)), ang1err/float(len(dirofmov)), ang2err/float(len(dirofmov)) return totalcost/float(len(dirofmov)) mmm = ij.measure.Minimizer() mmm.setFunction(costfunctionforrotations, 3) mmm.setMaxError(0.001) mmm.setMaxRestarts(5) mmm.minimize([random.random()*2.*math.pi, random.random()*2.*math.pi, random.random()*2.*math.pi], [1.,1.,1.]) ppp = mmm.getParams() winval = costfunctionforrotations(ppp, -1.) zeroval = costfunctionforrotations([0.,0.,0.], -1.) ## rotate them strout = 'Rotations = %f, %f, %f\n'%(ppp[0], ppp[1], ppp[2]) strout = '%svalue at winner = %f\n'%(strout,winval) strout = '%svalue at zero = %f\n'%(strout, zeroval) if(debug==0): strout = '%sWould you like to use these?'%(strout) if(JOptionPane.showConfirmDialog(None,strout ,"Question",JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION): for t in range(self.data.plen): if(self.data.headorigin[t] == None): continue self.data.headX[t], self.data.headY[t], self.data.headZ[t] = rotatetheguys(self.data.headX[t], self.data.headY[t], self.data.headZ[t], ppp) self.settimepoint() else: print strout for t in range(self.data.plen): if(self.data.headorigin[t] == None): continue self.data.headX[t], self.data.headY[t], self.data.headZ[t] = rotatetheguys(self.data.headX[t], self.data.headY[t], self.data.headZ[t], ppp) self.settimepoint() def transformcsystomin(self, ddtt, debug=0): if(len(self.data.headorigin) < 5): print 'You need to get head coordinate thing going before you can transform them (of course)' return ddtt = int(ddtt) ooo = Array2DRowRealMatrix(self.data.plen,3) dddxxx = Array2DRowRealMatrix(self.data.plen,3) dddyyy = Array2DRowRealMatrix(self.data.plen,3) dddzzz = Array2DRowRealMatrix(self.data.plen,3) zzz = zeros(3, 'd') indo = [] indp = [] indm = [] for t in range(self.data.plen): chk = False if(t>ddtt-1 and t-1): n=3 AA = Array2DRowRealMatrix(n,3) onefs = [] for i in range(4): if(skipone == i): continue AA.setRow(len(onefs), pnt[i]) onefs.append(1./float(n)) onefourths = Array2DRowRealMatrix(1,n) onefourths.setRow(0, onefs) muA = onefourths.multiply(AA) cAs = Array2DRowRealMatrix(n,3) for i in range(n): cAs.setRow(i, ((AA.getRowMatrix(i)).subtract(muA)).getRow(0)) #Asvd = SingularValueDecomposition(cAs) #AS = Asvd.getSingularValues() #AV = Asvd.getV() axisguys = Array2DRowRealMatrix(4,3) #axisguys.setRow(0,muA.getRow(0)) #for i in range(3): #axisguys.setRow(i+1, (muA.add(AV.getRowMatrix(i))).getRow(0)) for i in range(4): axisguys.setRow(i,muA.getRow(0)) for i in range(3): # Add [1,0,0] to x-dir, etc.... axisguys.addToEntry(i+1, i, 1.) return cAs, muA, axisguys def rigidtransform(self, cAs, muA, axisguys, B): n = B.getRowDimension() onefs = [] for i in range(n): onefs.append(1./float(n)) onefourths = Array2DRowRealMatrix(1,n) onefourths.setRow(0, onefs) muB = onefourths.multiply(B) cBs = Array2DRowRealMatrix(n,3) for i in range(n): cBs.setRow(i, ((B.getRowMatrix(i)).subtract(muB)).getRow(0)) H = (cAs.transpose()).multiply(cBs) Bsvd = SingularValueDecomposition(H) Ut = Bsvd.getUT() V = Bsvd.getV() R = V.multiply(Ut) if((LUDecomposition(R)).getDeterminant() < 0): vc = V.getColumn(2) for i in range(len(vc)): vc[i] = -1.*vc[i] V.setColumn(2, vc) R = V.multiply(Ut) temp = R.multiply( muA.transpose() ) tt = (muB.transpose()).subtract(temp) RRtAX = (R.multiply(axisguys.transpose())) orig = Vector3d( ((RRtAX.getColumnMatrix(0)).add(tt)).getColumn(0) ) headX = Vector3d( ((RRtAX.getColumnMatrix(1)).add(tt)).getColumn(0) ) headX.sub(orig) headY = Vector3d( ((RRtAX.getColumnMatrix(2)).add(tt)).getColumn(0) ) headY.sub(orig) headZ = Vector3d( ((RRtAX.getColumnMatrix(3)).add(tt)).getColumn(0) ) headZ.sub(orig) return orig, headX, headY, headZ def getheadorigin(self): headnames = [] headnames.append(0) headnames.append(1) headnames.append(2) headnames.append(3) self.superheadfindaverage() ### AS AN ALTERNATIVE APPROACH ### THIS WILL BE CLEANER IF POINTS ARE ARTIFICIALLY ADDED TO THE DATA TO COMPLETE THE ### RIGID BODY. THEY DO NOT HAVE TO BE DISPLAYED BUT THIS THING OF APPLYING THE COORDINATE ### SYSTEM BY CONSIDERING THEM DIFFERENTLY IS CONFUSING. I DONT SEE ANYTHING ### WRONG WITH THE WAY IT IS CURRENTLY (THOUGH MAYBE THE ACTUALLY POSITION OF THE HEAD MIGHT GET ### DISPLACED SLIGHTLY SINCE THE CENTER OF THE POINTS (IN FIRST PART) WOULD BE DIFFERENT IF IT IS ### FOR 3 POINTS OR 4. EITHER WAY, THOSE POINTS ARE NOT ACTUALLY USE TO CALULATE ANYTHING CURRENTLY ### IT IS THE ANGLES THAT ARE USED AND THE NECK POINT BUT MAYBE THE DIFFERENCE BETWEEN THE NECK POINT ### AND THE HEAD ORIGIN COULD BE IMPROVED, ASSUMING THIS IS LESS OPTIMAL. cAs, muA, axisguys = self.getfirstpartforcoordsys(self.closestpointtoaveragepoints) cAs0, muA0, axisguys0 = self.getfirstpartforcoordsys(self.closestpointtoaveragepoints, 0) cAs1, muA1, axisguys1 = self.getfirstpartforcoordsys(self.closestpointtoaveragepoints, 1) cAs2, muA2, axisguys2 = self.getfirstpartforcoordsys(self.closestpointtoaveragepoints, 2) cAs3, muA3, axisguys3 = self.getfirstpartforcoordsys(self.closestpointtoaveragepoints, 3) print 'axis guys' print axisguys self.data.headorigin = [] self.data.headX = [] self.data.headY = [] self.data.headZ = [] n = len(self.data.points) ### note, the 'axisguys' are the axis as they relate to the original points ### so we are rotating and translating them from a reference frame of when they have ### all four points to the other (so no need to have axisguys1, etc.) for i in range(self.data.plen): def getletter(ZZZ): pnt = [-100000000,0,0] for poop in range(n): if(headnames[ZZZ] == ((self.data.points[poop])[3])[i]): for yyy in range(3): pnt[yyy] = ((self.data.points[poop])[yyy])[i] + 0. return(pnt) AA = getletter(0) BB = getletter(1) CC = getletter(2) DD = getletter(3) if(AA[0]>-10000 and BB[0]>-10000 and CC[0]>-10000 and DD[0]>-10000): coords = Array2DRowRealMatrix(4,3) coords.setRow(0,AA) coords.setRow(1,BB) coords.setRow(2,CC) coords.setRow(3,DD) orig, headX, headY, headZ = self.rigidtransform(cAs, muA, axisguys, coords) elif(AA[0]<-10000 and BB[0]>-10000 and CC[0]>-10000 and DD[0]>-10000): coords = Array2DRowRealMatrix(3,3) coords.setRow(0,BB) coords.setRow(1,CC) coords.setRow(2,DD) orig, headX, headY, headZ = self.rigidtransform(cAs0, muA0, axisguys, coords) elif(AA[0]>-10000 and BB[0]<-10000 and CC[0]>-10000 and DD[0]>-10000): coords = Array2DRowRealMatrix(3,3) coords.setRow(0,AA) coords.setRow(1,CC) coords.setRow(2,DD) orig, headX, headY, headZ = self.rigidtransform(cAs1, muA1, axisguys, coords) elif(AA[0]>-10000 and BB[0]>-10000 and CC[0]<-10000 and DD[0]>-10000): coords = Array2DRowRealMatrix(3,3) coords.setRow(0,AA) coords.setRow(1,BB) coords.setRow(2,DD) orig, headX, headY, headZ = self.rigidtransform(cAs2, muA2, axisguys, coords) elif(AA[0]>-10000 and BB[0]>-10000 and CC[0]>-10000 and DD[0]<-10000): coords = Array2DRowRealMatrix(3,3) coords.setRow(0,AA) coords.setRow(1,BB) coords.setRow(2,CC) orig, headX, headY, headZ = self.rigidtransform(cAs3, muA3, axisguys, coords) else: self.data.headorigin.append(None) self.data.headX.append(None) self.data.headY.append(None) self.data.headZ.append(None) continue self.data.headorigin.append(orig) self.data.headX.append(headX) self.data.headY.append(headY) self.data.headZ.append(headZ) if(i<100): print 'ABCD(0)', AA[0], BB[0], CC[0], DD[0] print 'AA', AA print 'headx', headX print 'heady', headY print 'headz', headZ def addspikestostuff(self, allcells, allcellnames): self.funfilter.tabbedpane.setEnabledAt(1, True) self.spikesSwitches = [] self.fadedspikesSwitches = [] ap = Appearance() mat = Material() mat.setEmissiveColor( Color3f(1,0.35,0.35) ) mat.setDiffuseColor( Color3f(1,0.1,0.1) ) mat.setSpecularColor( Color3f(1,0.1,0.7) ) mat.setShininess(100.) #[0,128] ap.setMaterial(mat) ap2 = Appearance() ap2.setMaterial(mat) #trans = TransparencyAttributes(TransparencyAttributes.FASTEST, 0.7) #ap2.setTransparencyAttributes(trans) ddddd = self.data.startsessiontimestamp - self.data.starttrackingtimestamp newcells = [] for i in range(len(allcells)): acellarray = [] sw = Switch() sw.setCapability(Switch.ALLOW_SWITCH_WRITE) sw.setCapability(Switch.ALLOW_SWITCH_READ) sw.setCapability(Switch.ALLOW_CHILDREN_WRITE); sw.setCapability(Switch.ALLOW_CHILDREN_EXTEND); tt = Transform3D() sw2 = Switch() sw2.setCapability(Switch.ALLOW_SWITCH_WRITE) sw2.setCapability(Switch.ALLOW_SWITCH_READ) sw2.setCapability(Switch.ALLOW_CHILDREN_WRITE); sw2.setCapability(Switch.ALLOW_CHILDREN_EXTEND); tt2 = Transform3D() #print 'datime', (allcells[i])[0], (allcells[i])[len(allcells[i])-1], allcellnames[i] for j in range(len(allcells[i])): jjj = int(math.floor(((allcells[i])[j] + ddddd)*(self.data.framerate))) #### 120 because that is the hertz of the recording thing if(jjj > self.data.plen-1): jjj = self.data.plen-1 print 'Cell', i, 'spike', j, 'happened after tracking ended, it will not be used' continue if(jjj < 0): jjj = 0 print 'Cell', i, 'spike', j, 'happened before tracking started, it will not be used' continue ##sesstime = float(t)/120.+self.data.starttrackingtimestamp - self.data.startsessiontimestamp closest = -1 closestval = 10000000000000. for k in range(jjj-24, jjj+25, 1): if(k<0 or k>self.data.plen-1): continue if(self.data.headorigin[k] == None): continue if(math.fabs(k-jjj)len(cellstuff)-1): endi = len(cellstuff)-1 firingrates[ii] = 1000. * float(sum( cellstuff[starti:endi] )) / (float(endi-starti) * binsize) return(firingrates) def funfiltertimerstuff(self, inratespeedup, outratespeedup, slowdowntimesintrackingtime): class onesettimerperformer(ActionListener): def __init__(self, parentguy, inratespeedup, outratespeed, slowdowntimesintrackingtime): self.parentguy = parentguy self.inrate = inratespeedup self.outrate = outratespeedup self.slowdowntimesintrackingtime = slowdowntimesintrackingtime self.startervalue = self.parentguy.jslider.getValue() self.currenttime = self.startervalue self.totaltime = 0. def actionPerformed(self, a): if(self.parentguy.funfilter.isVisible() == False): self.parentguy.onesettimer.stop() oldcv = int(round(self.currenttime)) incv = int(round(self.currenttime+ self.inrate)) if( self.slowdowntimesintrackingtime[oldcv] == 1 or self.slowdowntimesintrackingtime[incv] == 1): cv = incv self.currenttime += self.inrate self.totaltime += self.inrate else: self.currenttime += self.outrate self.totaltime += self.outrate cv = int(round(self.currenttime)) if(cv >= self.parentguy.data.plen-1): self.parentguy.jslider.setValue(0) self.currenttime = 0. else: self.parentguy.jslider.setValue(cv) if(self.totaltime>self.parentguy.data.plen): self.parentguy.jslider.setValue(self.startervalue) self.parentguy.onesettimer.stop() if(self.onesettimer == None): self.onesettimer = Timer(1, onesettimerperformer(self, inratespeedup, outratespeedup, slowdowntimesintrackingtime)) else: acs = self.onesettimer.getActionListeners() for ac in acs: self.onesettimer.removeActionListener(ac) ac = 0. self.onesettimer.addActionListener( onesettimerperformer(self, inratespeedup, outratespeedup, slowdowntimesintrackingtime) ) self.onesettimer.start() def funwithfiringratefilterfromfile(self, moviefilename, inratespeedup, outratespeedup): if(self.onesettimer != None): if(self.onesettimer.isRunning() == True): self.onesettimer.stop() return slowdowntimesintrackingtime = zeros(self.data.plen, 'i') dafile = open(moviefilename) reader = csv.reader(dafile) dafile.seek(0) slowdownsegments = [] for row in reader: if(len(row)==2): ii = int(round(float(row[0]))) jj = int(round(float(row[1]))) if(jjself.data.plen-1 or jj>self.data.plen-1): print 'WTF? %s has a line with entries'%moviefilenam, row continue if(jj == self.data.plen-2): jj = self.data.plen-1 for i in range(ii, jj+1, 1): slowdowntimesintrackingtime[i] = 1 else: print 'Skipped row, due to unrecognized formatting:', row self.funfiltertimerstuff(inratespeedup, outratespeedup, slowdowntimesintrackingtime) def funwithfiringratefilter(self, binsize, winsize, minfr, tsustained, addedslowdowntime, inratespeedup, outratespeedup): if(self.onesettimer != None): if(self.onesettimer.isRunning() == True): self.onesettimer.stop() return if(binsize>winsize): print 'Bin size is larger than window size, that does not make sense' return if(binsize>tsustained): print 'Bin size is larger than the time sustained, that does not make sense' return firingrates = self.calculatefiringrates(binsize, winsize) sustainedwindowsize = int(round( (tsustained/binsize) / 2. )) addedslowdowntime = int(round( (addedslowdowntime) )) ### SHOULD THIS BE SCALED?? slowdowntimes = zeros(len(firingrates), 'i') for i in range(sustainedwindowsize, len(firingrates)-sustainedwindowsize): mininwindow = min(firingrates[(i-sustainedwindowsize):(i+sustainedwindowsize)]) if(mininwindow > minfr): #print i, 'Min firing rate', minfr, 'data min', mininwindow for j in range(i-sustainedwindowsize-addedslowdowntime, i+sustainedwindowsize+addedslowdowntime, 1): if(j<0 or j>len(slowdowntimes)-1): continue slowdowntimes[j] = 1 if(max(slowdowntimes)<1): print 'No events found, try again' return slowdowntimesintrackingtime = zeros(self.data.plen, 'i') for i in range(len(slowdowntimesintrackingtime)): sesstime = 1000. * (float(i)/float(self.data.framerate) + self.data.starttrackingtimestamp - self.data.startsessiontimestamp) ind = int(math.floor( sesstime / binsize)) if(ind<0 or ind>len(slowdowntimes)-1): print 'frame number', i, 'at tracking time', 1000.*(float(i)/float(self.data.framerate) + self.data.starttrackingtimestamp), print ', which minus the start session time gives you this', 1000. * (float(i)/float(self.data.framerate) + self.data.starttrackingtimestamp - self.data.startsessiontimestamp), print 'which is outside the bounds of the estimated firing rates with length =', len(slowdowntimes), 'and index =', ind print 'please check the that all the time stamps are correct!!' print 'estimated length (s) of the tracking data from the original csv data', float(self.data.plen)/float(self.data.framerate) print 'estimated length (s) of the tracking data from the time stamps', (self.data.stoptrackingtimestamp - self.data.starttrackingtimestamp) print 'frame rate', self.data.framerate, 'number of frames', self.data.plen print 'for now we just skip this point but there should be a mistake somewhere' continue if(slowdowntimes[ind]>0): slowdowntimesintrackingtime[i] = 1 #print i, firingrates[ind] self.funfiltertimerstuff(inratespeedup, outratespeedup, slowdowntimesintrackingtime) def displayfiringratehistogram(self, binsize, winsize): if(binsize>winsize): print 'Bin size is larger than window size, that does not make sense' return firingrates = self.calculatefiringrates(binsize, winsize) dataset = HistogramDataset() dataset.setType(HistogramType.FREQUENCY) dataset.addSeries("Hist",firingrates,30) chart = ChartFactory.createHistogram('', 'Firing rate (Hz)', '', dataset, PlotOrientation.VERTICAL, False, False, False) #chartpanpan = JPanel() chartpan = ChartPanel(chart) #chartpanpan.add(chartpan) #chartpanpan.validate() #chartpanpan.setVisible(True) frame = JFrame('Firing rate histogram for cell %s, bin size %0.2f, smoothing size %0.2f'%(self.data.allcellnames[self.jcombonames.getSelectedIndex()], binsize, winsize)) frame.add(chartpan) frame.setLocation(500,300) #frame.setResizable(False) frame.pack() frame.setVisible(True) def settemplatepoints(self): self.templatepointsSwitch.removeAllChildren() self.templatepointsTGarray = [] self.templatepointsSParray = [] for ii in range(len(self.data.templatepoints)): p = self.data.templatepoints[ii] tt = Transform3D() tt.setTranslation(Vector3f(p[0], p[1], p[2])) ap = Appearance() ca = ColoringAttributes() ca.setColor(178./255., 34./255., 34./255.) # firebrick ap.setColoringAttributes(ca) cc = Sphere(0.005, Sphere.ENABLE_APPEARANCE_MODIFY, ap) tg = TransformGroup(tt) tg.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE) tg.addChild(cc) bgstupid = BranchGroup() bgstupid.addChild(tg) bgstupid.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE) self.templatepointsSwitch.addChild(bgstupid) self.templatepointsTGarray.append(tg) self.templatepointsSParray.append(cc) self.templatepointsSwitch.setWhichChild(Switch.CHILD_ALL) def setsuperpoints(self): self.pointsSwitch.removeAllChildren() self.pointsTGarray = [] self.pointsSParray = [] for ii in range(len(self.data.points)): tt = Transform3D() tt.setTranslation(Vector3f(0.,0., 0.)) ap = Appearance() mat = Material() mat.setEmissiveColor( Color3f(0.1,0.65,0.35) ) mat.setDiffuseColor( Color3f(0.1,0.6,0.1) ) mat.setSpecularColor( Color3f(0.1,0.1,0.7) ) mat.setShininess(50.) #[0,128] ap.setMaterial(mat) cc = Sphere(0.015, Sphere.ENABLE_APPEARANCE_MODIFY, ap) tg = TransformGroup(tt) tg.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE) tg.addChild(cc) bgstupid = BranchGroup() bgstupid.addChild(tg) bgstupid.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE) ## THIS MIGHT DO WHAT I THINK IT DOES :) self.pointsSwitch.addChild(bgstupid) self.pointsTGarray.append(tg) self.pointsSParray.append(cc) #self.pointsSwitch.addChild(self.pointsbranchgroup) self.jslider = JSlider(JSlider.HORIZONTAL, 0, self.data.plen, 1) c = GridBagConstraints() c.insets = Insets(3, 3, 3, 3) c.gridx = 0 c.gridy = 0 c.fill = GridBagConstraints.HORIZONTAL c.gridx = 1 c.gridy = 1 c.gridwidth=8 self.add(self.jslider, c) class sliderchanger(ChangeListener): def __init__(self, parentguy): self.parentguy = parentguy self.oldvalue = 0 def stateChanged(self, e): currval = e.getSource().getValue() if((currval-self.oldvalue) < 50. and (currval-self.oldvalue)>0.): self.parentguy.settimepoint(currval, self.oldvalue) else: self.parentguy.settimepoint(currval) self.oldvalue = currval self.jslider.addChangeListener(sliderchanger(self)) self.jslider.setPreferredSize(Dimension(500,40)) class timerperformer(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy self.skippies = 1 def actionPerformed(self, a): cv = self.parentguy.jslider.getValue() if(cv == self.parentguy.data.plen-1): self.parentguy.jslider.setValue(0) else: self.parentguy.jslider.setValue(cv+self.skippies) self.timeractionperformer = timerperformer(self) self.timer = Timer(2, self.timeractionperformer) startstopbut = JButton(':P') #startstopbut.setPreferredSize(Dimension(40, 20)); class startstoplistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): if(self.parentguy.timer.isRunning()): self.parentguy.timer.stop() else: self.parentguy.timer.start() startstopbut.addActionListener(startstoplistener(self)) c.gridx=0 c.gridwidth=1 self.add(startstopbut, c) self.data.addthingies() self.revalidate() self.repaint() self.settimepoint() SwingUtilities.windowForComponent(self).revalidate() SwingUtilities.windowForComponent(self).pack() def setdapointwithdacolorandstuff(self, frompicker, addorremove): if(self.currentpointassigner < 0): return t = self.jslider.getValue() #print t, len( ((self.data.points[0])[3]) ) for i in range(len(self.pointsSParray)): if(frompicker != (self.pointsSParray[i]).getShape()): continue if(addorremove>0): ((self.data.points[i])[3])[t] = self.currentpointassigner ((self.data.points[i])[4])[t] = -1 else: ((self.data.points[i])[3])[t] = -10 ((self.data.points[i])[4])[t] = -10000000 self.settimepoint(t) def __init__(self): self.avoidrecursionwithtimepoints = 2 self.implus = None self.impluscurrentslice = 1 soundName = '%s/Lib/spike.wav'%(getProperty('python.home')) self.AudioClip = AudioSystem.getClip() self.AudioSystemGuy = AudioSystem.getAudioInputStream(io.File(soundName).getAbsoluteFile()) self.AudioClip.open(self.AudioSystemGuy) self.avevals = None self.jslider = None self.timer = None self.onesettimer = None self.numberofnamedpoints = 0 self.currentpointassigner = -10 self.jcombonames = None #self.setBorder(BorderFactory.createLineBorder(Color.black)) self.pointtypes = ['first head', 'second head', 'third head', 'fourth head', 'neck', 'middle', 'ass', 'garbage', 'user defined (1)', 'user defined (2)', 'user defined (3)', 'user defined (4)', 'user defined (5)', 'user defined (6)', 'user defined (7)', 'user defined (8)', 'user defined (9)', 'user defined (10)' ] self.cnames = {'fire brick': (178, 34, 34), 'cadet blue': (95, 158, 160), 'indigo': (75, 0, 130), 'sea green': (46, 139, 87), 'medium violet red': (199, 21, 133), 'old lace': (253, 245, 230), 'yellow': (255, 255, 0), 'slate gray': (112, 128, 144), 'medium spring green': (0, 250, 154), 'medium slate blue': (123, 104, 238), 'light yellow': (255, 255, 224), 'pale turquoise': (175, 238, 238), 'navajo white': (255, 222, 173), 'orange red': (255, 69, 0), 'misty rose': (255, 228, 225), 'black': (0, 0, 0), 'dark sea green': (143, 188, 143), 'crimson': (220, 20, 60), 'brown': (165, 42, 42), 'turquoise': (64, 224, 208), 'yellow green': (154, 205, 50), 'pale goldenrod': (238, 232, 170), 'light slate gray': (119, 136, 153), 'dark olive green': (85, 107, 47), 'cyan': (0, 255, 255), 'green yellow': (173, 255, 47), 'silver': (192, 192, 192), 'gray': (128, 128, 128), 'dark violet': (148, 0, 211), 'teal': (0, 128, 128), 'dark gray': (169, 169, 169), 'dark orange': (255, 140, 0), 'peach puff': (255, 218, 185), 'deep pink': (255, 20, 147), 'steel blue': (70, 130, 180), 'forest green': (34, 139, 34), 'thistle': (216, 191, 216), 'violet': (238, 130, 238), 'navy': (0, 0, 128), 'orchid': (218, 112, 214), 'blue': (0, 0, 255), 'ghostwhite': (248, 248, 255), 'honeydew': (240, 255, 240), 'purple': (128, 0, 128), 'dark red': (139, 0, 0), 'pale violet red': (219, 112, 147), 'red': (255, 0, 0), 'bisque': (255, 228, 196), 'dim gray': (105, 105, 105), 'wheat': (245, 222, 179), 'corn silk': (255, 248, 220), 'royal blue': (65, 105, 225), 'golden rod': (218, 165, 32), 'gainsboro': (220, 220, 220), 'lemon chiffon': (255, 250, 205), 'light salmon': (255, 160, 122), 'midnight blue': (25, 25, 112), 'alice blue': (240, 248, 255), 'plum': (221, 160, 221), 'rosy brown': (188, 143, 143), 'aqua': (0, 255, 255), 'dark khaki': (189, 183, 107), 'pale green': (152, 251, 152), 'beige': (245, 245, 220), 'azure': (240, 255, 255), 'dark salmon': (233, 150, 122), 'sienna': (160, 82, 45), 'dodger blue': (30, 144, 255), 'sandy brown': (250, 164, 96), 'blue violet': (138, 43, 226), 'lime': (0, 255, 0), 'burlywood': (222, 184, 135), 'seashell': (255, 245, 238), 'light pink': (255, 182, 193), 'fuchsia': (255, 0, 255), 'dark goldenrod': (184, 134, 11), 'dark blue': (0, 0, 139), 'light steel blue': (176, 196, 222), 'peru': (205, 133, 63), 'white': (255, 255, 255), 'medium sea green': (60, 179, 113), 'olive drab': (107, 142, 35), 'ivory': (255, 255, 240), 'indian red': (205, 92, 92), 'cornflower blue': (100, 149, 237), 'chocolate': (210, 105, 30), 'light coral': (240, 128, 128), 'orange': (255, 165, 0), 'olive': (128, 128, 0), 'moccasin': (255, 228, 181), 'medium blue': (0, 0, 205), 'dark slate blue': (72, 61, 139), 'dark orchid': (153, 50, 204), 'light cyan': (224, 255, 255), 'floral white': (255, 250, 240), 'light green': (144, 238, 144), 'dark cyan': (0, 139, 139), 'coral': (255, 127, 80), 'hot pink': (255, 105, 180), 'medium turquoise': (72, 209, 204), 'light goldenrod yellow': (250, 250, 210), 'maroon': (128, 0, 0), 'light sea green': (32, 178, 170), 'spring green': (0, 255, 127), 'light blue': (173, 216, 230), 'lime green': (50, 205, 50), 'saddle brown': (139, 69, 19), 'magenta': (255, 0, 255), 'dark magenta': (139, 0, 139), 'pink': (255, 192, 203), 'lawn green': (124, 252, 0), 'medium aquamarine': (102, 205, 170), 'mint cream': (245, 255, 250), 'dark turquoise': (0, 206, 209), 'snow': (255, 250, 250), 'papaya whip': (255, 239, 213), 'lavender blush': (255, 240, 245), 'medium orchid': (186, 85, 211), 'salmon': (250, 128, 114), 'medium purple': (147, 112, 219), 'antique white': (250, 235, 215), 'deep sky blue': (0, 191, 255), 'dark slate gray': (47, 79, 79), 'tan': (210, 180, 140), 'light gray': (211, 211, 211), 'tomato': (255, 99, 71), 'white smoke': (245, 245, 245), 'light skyblue': (135, 206, 250), 'linen': (250, 240, 230), 'green': (0, 128, 0), 'slate blue': (106, 90, 205), 'powder blue': (176, 224, 230), 'dark green': (0, 100, 0)} self.filename = " " #self.allcells = allcells #self.allcellnames = allcellnames #self.data.plen = len(self.points) #self.makenormalratemaps(8, range(-150,150,10), self.adjpts) #self.getdirofmov() objroot = BranchGroup() objroot.setCapability(BranchGroup.ALLOW_DETACH) objroot.setCapability(BranchGroup.ALLOW_CHILDREN_READ) objroot.setCapability(BranchGroup.ALLOW_CHILDREN_WRITE) white = Color3f(0.9, 0.9, 0.9) bounds = BoundingSphere(Point3d(), 100.0) backg = Background(white) backg.setApplicationBounds(bounds) objroot.addChild(backg) self.maingroup = TransformGroup(Transform3D()) self.maingroup.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE) self.maingroup.setCapability(TransformGroup.ALLOW_TRANSFORM_READ) self.maingroup.setCapability(TransformGroup.ALLOW_CHILDREN_EXTEND) self.maingroup.setCapability(TransformGroup.ALLOW_CHILDREN_WRITE) tt = Transform3D() tt.setTranslation(Vector3f(0.,0., 0.)) self.wickedheadTG = TransformGroup(tt) self.wickedheadTG.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE) self.wickedheadTG.setCapability(TransformGroup.ALLOW_TRANSFORM_READ) self.wickedheadTG.setCapability(TransformGroup.ALLOW_CHILDREN_EXTEND) self.wickedheadTG.setCapability(TransformGroup.ALLOW_CHILDREN_WRITE) self.coordsysSwitch = Switch() self.coordsysSwitch.setCapability(Switch.ALLOW_SWITCH_WRITE) self.coordsysSwitch.setCapability(Switch.ALLOW_SWITCH_READ) self.coordsysSwitch.setCapability(Switch.ALLOW_CHILDREN_WRITE); self.coordsysSwitch.setCapability(Switch.ALLOW_CHILDREN_EXTEND); linebranchgroup = BranchGroup() linebranchgroup.addChild(self.coordsysSwitch) self.maingroup.addChild(linebranchgroup) self.coordsysSwitch.addChild(self.wickedheadTG) iqa = IndexedQuadArray(8, IndexedQuadArray.COORDINATES | IndexedQuadArray.NORMALS, 24) coords = [] scl = 0.08 coords.append( Point3d(1.0*scl, 0.25*scl, 0.375*scl) ) coords.append( Point3d(-0.2*scl, 0.5*scl, 0.5*scl) ) coords.append( Point3d(-0.2*scl, -0.5*scl, 0.5*scl) ) coords.append( Point3d(1.0*scl, -0.25*scl, 0.375*scl) ) coords.append( Point3d(1.0*scl, 0.25*scl, 0.125*scl) ) coords.append( Point3d(-0.2*scl, 0.5*scl, 0) ) coords.append( Point3d(-0.2*scl, -0.5*scl, 0) ) coords.append( Point3d(1.0*scl, -0.25*scl, 0.125*scl) ) coordinds = [ 0, 1, 2, 3, 7, 6, 5, 4, 0, 3, 7, 4, 5, 6, 2, 1, 0, 4, 5, 1, 6, 7, 3, 2 ] iqa.setCoordinates(0, coords) iqa.setCoordinateIndices(0, coordinds) normals = [] normals.append(Vector3f(0.0, 0.0, 1.0)) normals.append(Vector3f(0.0, 0.0, -1.0)) normals.append(Vector3f(1.0, 0.0, 0.0)) normals.append(Vector3f(-1.0, 0.0, 0.0)) normals.append(Vector3f(0.0, 1.0, 0.0) ) normals.append(Vector3f(0.0, -1.0, 0.0)) iqa.setNormals(0, normals) normalIndices = [ 0, 0, 0, 0, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5 ] iqa.setNormalIndices(0, normalIndices) ap = Appearance() mat = Material() mat.setAmbientColor( Color3f(1.0,0.0,0.0) ) mat.setEmissiveColor( Color3f(0.0,0.0,0.0) ) mat.setSpecularColor( Color3f(1.0,1.0,1.0) ) mat.setDiffuseColor( Color3f(1.0,0.0,0.0) ) mat.setShininess(20) #[0,128] ap.setMaterial(mat) #ap.setTransparencyAttributes(TransparencyAttributes(TransparencyAttributes.NONE, 0.)) #self.wickedheadTG.addChild(Shape3D(iqa, ap)) tt = Transform3D() xjump = 0.07 zjump = 0.03 tt.setTranslation(Vector3f(xjump, 0, zjump)) ttgg = TransformGroup(tt) ttgg.addChild(Shape3D(iqa, ap)) self.wickedheadTG.addChild(ttgg) tt = Transform3D() tt.setTranslation(Vector3f(0.1*scl+xjump, -0.3*scl, 0.5*scl+zjump)) ttgg = TransformGroup(tt) ap = Appearance() ca = ColoringAttributes() ca.setColor(Color3f(0.5,0.5,0.1)) ap.setColoringAttributes(ca) ttgg.addChild(Sphere(0.01, ap)) self.wickedheadTG.addChild(ttgg) tt = Transform3D() tt.setTranslation(Vector3f(0.1*scl+xjump, 0.3*scl, 0.5*scl+zjump)) ttgg = TransformGroup(tt) ap = Appearance() ca = ColoringAttributes() ca.setColor(Color3f(0.5,0.5,0.1)) ap.setColoringAttributes(ca) ttgg.addChild(Sphere(0.01, ap)) self.wickedheadTG.addChild(ttgg) tt = Transform3D() tt.setTranslation(Vector3f(1.02*scl+xjump, 0, 0.25*scl+zjump)) ttgg = TransformGroup(tt) ap = Appearance() ca = ColoringAttributes() ca.setColor(Color3f(0.1,0.5,0.1)) ap.setColoringAttributes(ca) ttgg.addChild(Sphere(0.01, ap)) self.wickedheadTG.addChild(ttgg) ap = Appearance() ap.setCapability(Appearance.ALLOW_COLORING_ATTRIBUTES_READ) ap.setCapability(Appearance.ALLOW_COLORING_ATTRIBUTES_WRITE) ca = ColoringAttributes() ca.setCapability(ColoringAttributes.ALLOW_COLOR_READ) ca.setCapability(ColoringAttributes.ALLOW_COLOR_WRITE) ca.setColor(Color3f(0.,1.,0.)) ap.setColoringAttributes(ca) self.wickedheadTG.addChild(Sphere(0.01, ap)) self.pointsTGarray = [] self.pointsSParray = [] self.pointsSwitch = Switch() self.pointsSwitch.setCapability(Switch.ALLOW_SWITCH_WRITE) self.pointsSwitch.setCapability(Switch.ALLOW_SWITCH_READ) self.pointsSwitch.setCapability(Switch.ALLOW_CHILDREN_WRITE); self.pointsSwitch.setCapability(Switch.ALLOW_CHILDREN_EXTEND); pointsbranchgroup = BranchGroup() ### may not be necessary!! pointsbranchgroup.addChild(self.pointsSwitch) pointsbranchgroup.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE) self.maingroup.addChild(pointsbranchgroup) self.pointsSwitch.setWhichChild(Switch.CHILD_MASK) self.templatepointsTGarray = [] self.templatepointsSParray = [] self.templatepointsSwitch = Switch() self.templatepointsSwitch.setCapability(Switch.ALLOW_SWITCH_WRITE) self.templatepointsSwitch.setCapability(Switch.ALLOW_SWITCH_READ) self.templatepointsSwitch.setCapability(Switch.ALLOW_CHILDREN_WRITE); self.templatepointsSwitch.setCapability(Switch.ALLOW_CHILDREN_EXTEND); templatepointsbranchgroup = BranchGroup() ### may not be necessary!! templatepointsbranchgroup.addChild(self.templatepointsSwitch) templatepointsbranchgroup.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE) self.maingroup.addChild(templatepointsbranchgroup) self.templatepointsSwitch.setWhichChild(Switch.CHILD_MASK) tranny1 = Transform3D() tranny1.setTranslation(Vector3f(0.,0., 0.)) self.boxtgroup = TransformGroup(tranny1) self.boxtgroup.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE) self.boxtgroup.setCapability(TransformGroup.ALLOW_TRANSFORM_READ) self.boxtgroup.setCapability(TransformGroup.ALLOW_CHILDREN_EXTEND) self.boxtgroup.setCapability(TransformGroup.ALLOW_CHILDREN_WRITE) tt = Transform3D() tt.setTranslation(Vector3f(0.,0., -0.1)) self.boxtgroup.setTransform(tt) ap = Appearance() mat = Material() mat.setEmissiveColor( Color3f(0.5,0.55,0.55) ) mat.setDiffuseColor( Color3f(0.3,0.3,0.3) ) mat.setSpecularColor( Color3f(0,0,0.7) ) mat.setShininess(50.) #[0,128] ap.setMaterial(mat) #ap.setColoringAttributes( ColoringAttributes (Color3f(0.1, 0.1, 1.0), ColoringAttributes.NICEST) ) ## NOTE NICEST MIGHT BE COOL self.superboxfloor = Box(0.5,0.5, 0.01, ap) self.superboxfloor.setCapability(Box.ENABLE_APPEARANCE_MODIFY); self.boxtgroup.addChild(self.superboxfloor) self.maingroup.addChild(self.boxtgroup) #objroot.addChild(tgroup1) objroot.addChild(self.maingroup) mr = MouseRotate(self.maingroup) mx = MouseZoom(self.maingroup) mt = MouseTranslate(self.maingroup) mr.setSchedulingBounds(bounds) mx.setSchedulingBounds(bounds) mt.setSchedulingBounds(bounds) objroot.addChild(mr) objroot.addChild(mx) objroot.addChild(mt) #lightD = DirectionalLight(Color3f(1,1,1), Vector3f(0,0,-1)) #lightD.setInfluencingBounds(bounds) #objroot.addChild(lightD) objroot.compile() template = GraphicsConfigTemplate3D() template.setDoubleBuffer(GraphicsConfigTemplate3D.REQUIRED) env = GraphicsEnvironment.getLocalGraphicsEnvironment() dev = env.getDefaultScreenDevice() self.canvas3d = Canvas3D(dev.getBestConfiguration(template)) self.canvas3d.setDoubleBufferEnable(True) #canvas3d = Canvas3D(SimpleUniverse.getPreferredConfiguration()) self.canvas3d.setFocusable(True) self.canvas3d.setSize(1000,1000) self.su = SimpleUniverse(self.canvas3d) self.su.addBranchGraph(objroot) (self.su.getViewingPlatform()).setNominalViewingTransform() self.su.getViewer().getView().setFrontClipDistance(0.1) self.su.getViewer().getView().setBackClipDistance(100.) self.su.getViewer().getView().setFrontClipPolicy(View.VIRTUAL_EYE) self.su.getViewer().getView().setBackClipPolicy(View.VIRTUAL_EYE) self.su.getViewer().getView().setDepthBufferFreezeTransparent(True) self.setLayout(GridBagLayout()) c = GridBagConstraints() #c.anchor = GridBagConstraints.WEST c.insets = Insets(3, 3, 3, 3) c.gridx = 0 c.gridy = 0 c.fill = GridBagConstraints.BOTH c.gridwidth=9 self.add(self.canvas3d, c) self.validate() pickcanvas = PickCanvas(self.canvas3d, pointsbranchgroup) pickcanvas.setMode(PickCanvas.BOUNDS) self.canvas3d.addMouseListener(pickguy(pickcanvas, self)) c.gridy=2 c.gridx = 0 c.gridwidth=2 c.fill = GridBagConstraints.NONE c.weightx = 0.9999999 self.currtime = JLabel('Currently no tracking data') self.add(self.currtime, c) self.analysisstuffthingy = JDialog() self.analysisstuffthingy.setPreferredSize(Dimension(1700, 1000)) self.datatable = analysistable() self.analysisstuffthingy.getContentPane().add(self.datatable) self.analysisstuffthingy.pack() self.analysisstuffthingy.setVisible(False) class jcombospeedupslistener(ItemListener): def __init__(self, parentguy): self.parentguy = parentguy self.oldone = 0 def itemStateChanged(self, e): value = int(round(1./float(e.getSource().getSelectedItem()))) self.parentguy.timer.setDelay(value) self.jcombospeedups = JComboBox(['0.001','0.01','0.05','0.1','0.5','1']) self.jcombospeedups.addItemListener(jcombospeedupslistener(self)) c.gridwidth=1 c.anchor = GridBagConstraints.LINE_END c.weightx = 0.0000000000001 c.gridx = 5 self.add(self.jcombospeedups, c) c.gridx = 6 class jcomboskippieslistener(ItemListener): def __init__(self, parentguy): self.parentguy = parentguy self.oldone = 0 def itemStateChanged(self, e): value = int(round(float(e.getSource().getSelectedItem()))) self.parentguy.timeractionperformer.skippies = value self.jcomboskippies = JComboBox(['1','2','5','10','20','50','100','200']) self.jcomboskippies.addItemListener(jcomboskippieslistener(self)) self.add(self.jcomboskippies, c) self.jcomboskippies.setEnabled(False) self.jcombospeedups.setEnabled(False) c.gridx = 7 Abutton = JButton('A') class Abuttonlistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.analysisstuffthingy.setVisible(True) Abutton.addActionListener(Abuttonlistener(self)) self.add(Abutton, c) self.data = crazydatafileio(self) self.openfilerthing = JDialog() self.openfilerthing.getContentPane().add(self.data) self.openfilerthing.pack() self.openfilerthing.setLocationRelativeTo(None) self.openfilerthing.setVisible(False) c.gridx = 8 Fbutton = JButton('F') class Fbuttonlistener(ActionListener): def __init__(self, parentguy): self.parentguy = parentguy def actionPerformed(self, event): self.parentguy.openfilerthing.setVisible(True) Fbutton.addActionListener(Fbuttonlistener(self)) self.add(Fbutton, c) c.gridx = 4 self.funfilter = superfunfilter(self) self.funfilter.setVisible(False) class makefunlistener(ActionListener): def __init__(self, jguy): self.jguy = jguy def actionPerformed(self, event): self.jguy.funfilter.setVisible(True) self.jbutfun = JButton(':)') self.jbutfun.addActionListener(makefunlistener(self)) self.add(self.jbutfun, c) self.jbutfun.setVisible(True) self.jbutfun.setEnabled(False) self.mysuperpointlabeler = superpointlabeler(self) self.settimepoint(1) td = trackeddatastruct() frame = JFrame("Data tracker thing") #frame.getContentPane().add(JScrollPane(td)) frame.getContentPane().add(td) class keyeventguy(KeyEventDispatcher): def dispatchKeyEvent(self, e): if(self.parentguy.timer == None): return if(e.getKeyCode() == KeyEvent.VK_DOWN): if(e.getID() == KeyEvent.KEY_PRESSED): if(self.stepsize==5): self.stepsize = 2 elif(self.stepsize==2): self.stepsize = 1 elif(self.stepsize==10): self.stepsize = 5 elif(self.stepsize==500): self.stepsize = 100 elif(self.stepsize==100): self.stepsize = 10 elif(e.getKeyCode() == KeyEvent.VK_UP): if(e.getID() == KeyEvent.KEY_PRESSED): if(self.stepsize==5): self.stepsize = 10 elif(self.stepsize==1): self.stepsize = 2 elif(self.stepsize==2): self.stepsize = 5 elif(self.stepsize==10): self.stepsize = 100 elif(self.stepsize==100): self.stepsize = 500 elif(e.getKeyCode() == KeyEvent.VK_LEFT): if(e.getID() == KeyEvent.KEY_PRESSED): if(self.parentguy.data.plen>5): val = self.parentguy.jslider.getValue() if(val-self.stepsize>-1): self.parentguy.jslider.setValue(val-self.stepsize) elif(e.getKeyCode() == KeyEvent.VK_RIGHT): if(e.getID() == KeyEvent.KEY_PRESSED): if(self.parentguy.data.plen>5): val = self.parentguy.jslider.getValue() if(val+self.stepsize