keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/SampleFactory_2016.java | .java | 200 | 14 | package smlms.sample;
public class SampleFactory_2016 {
public SampleFactory_2016() {
new SampleFactoryDialog();
}
public static void main(String args[]) {
new SampleFactoryDialog();
}
}
| Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/Beads_Generator.java | .java | 3,263 | 120 | package smlms.sample;
import ij.IJ;
import java.util.ArrayList;
import smlms.file.PositionFile;
import smlms.tools.Point3D;
import smlms.tools.PsRandom;
import additionaluserinterface.WalkBar;
public class Beads_Generator {
private int nx = 6400; // 320 * 20 = 6400nm
private int ny = 6400; // 320 * 20 = 640... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/Description.java | .java | 6,919 | 222 | package smlms.file;
import ij.IJ;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import smlms.tools.Tools;
public class Description {
private HashMap<Integer, Fields> fields = new HashMap<Inte... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/FluorophoreComponent.java | .java | 6,254 | 196 | package smlms.file;
import ij.IJ;
import imageware.ImageWare;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.BorderFactory;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import ... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/Fluorophores_Explorer.java | .java | 1,134 | 45 | package smlms.file;
import ij.IJ;
import ij.gui.GUI;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.swing.JButton;
import javax.swing.JDialog;
import javax.swing.JFrame;
import additionaluserinterface.GridPanel;
import additionaluserinterface.Settings;
public class Fluorophor... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/Fields.java | .java | 1,203 | 56 | package smlms.file;
import java.util.HashMap;
import java.util.Iterator;
public enum Fields {
ID ("id"),
X ("x"), // in nm
Y ("y"), // in nm
Z ("z"), // in nm
FRAME ("frame"),
PHOTONS ("photons"),
CHANNEL ("channel"),
FRAMEON ("frameon"), // number of frame ON
TOTAL ("total"),
BACK... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/TableStatistics.java | .java | 3,263 | 134 | package smlms.file;
import ij.IJ;
import java.awt.Dimension;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import javax.swing.JFrame;
import javax.swing.JScrollPane;
import javax.swing.JTable;
import javax.swing.table.DefaultTab... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/Fluorophores.java | .java | 6,447 | 244 | package smlms.file;
import ij.IJ;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import javax.swing.JLabel;
public class Fluorophores extends Ar... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/LinearTransformAxis.java | .java | 568 | 37 | package smlms.file;
import java.util.ArrayList;
public class LinearTransformAxis {
public double a = 1.0;
public double b = 0.0;
public LinearTransformAxis() {
}
public LinearTransformAxis(double b) {
this.b = b;
}
public LinearTransformAxis(double a, double b) {
this.a = a;
this.b = b;
}
public... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/Fluorophore.java | .java | 5,217 | 182 | // =========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG),
// http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique F�d�rale de Lausanne (EPFL), Lausanne,
// Switzerland
//
... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/Description_Builder.java | .java | 4,863 | 173 | package smlms.file;
import ij.IJ;
import ij.gui.GUI;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileReader;
import... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/PositionFile.java | .java | 1,405 | 58 | package smlms.file;
import ij.IJ;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import smlms.tools.Point3D;
import additionaluserinterface.WalkBar;
public class PositionFile {
private String path;
private String filename;
p... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/file/Statistics.java | .java | 871 | 44 | package smlms.file;
public class Statistics {
public String name;
public int count;
public double min;
public double max;
public double mean;
public double stdev;
public double histo[];
public double domain[];
public double evolution[] = new double[1];
private int nbins = 100;
private boolean init = fals... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/SequenceFactory_Batch_2016.java | .java | 7,840 | 222 | package smlms.simulation;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.gui.GenericDialog;
import ij.io.FileSaver;
import ij.io.Opener;
import imageware.Builder;
import imageware.ImageWare;
import java.io.File;
import java.util.ArrayList;
import smlms.file.Description;
import smlms.file.Fluoroph... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/SequenceFactory.java | .java | 16,194 | 475 | package smlms.simulation;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.gui.Overlay;
import ij.gui.Roi;
import ij.gui.TextRoi;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.process.FloatProcessor;
import imageware.ImageWare;
import java.io.BufferedWriter;
import java.io.File;
import java... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/SequenceReporting.java | .java | 18,608 | 418 | package smlms.simulation;
import ij.IJ;
import ij.ImagePlus;
import ij.io.FileSaver;
import ij.io.Opener;
import imageware.ImageWare;
import java.io.File;
import java.util.ArrayList;
import smlms.tools.Tools;
import smlms.tools.Zip;
public class SequenceReporting {
private SequenceFactoryDialog dialog;
public ... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/SequenceFactory_2016.java | .java | 212 | 14 | package smlms.simulation;
public class SequenceFactory_2016 {
public SequenceFactory_2016() {
new SequenceFactoryDialog();
}
public static void main(String args[]) {
new SequenceFactoryDialog();
}
}
| Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/ProjectionModule.java | .java | 3,016 | 97 | package smlms.simulation;
import ij.IJ;
import ij.ImagePlus;
import ij.io.FileSaver;
import ij.process.FloatProcessor;
import ij.process.ImageConverter;
import java.io.File;
public class ProjectionModule {
private FloatProcessor maxPR; // Working resolution
private FloatProcessor maxCR; // Camera resolution
pri... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/DownsamplingModule.java | .java | 532 | 23 | package smlms.simulation;
public class DownsamplingModule {
public float[][] run(float[][] image, int downsampling) {
int mx = image.length;
int my = image[0].length;
int nx = mx / downsampling;
int ny = my / downsampling;
float[][] camera = new float[nx][ny];
for(int x=0; x<nx; x++)
for(int y=0; y<ny;... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/Generate_Beads.java | .java | 2,321 | 72 | package smlms.simulation;
import ij.IJ;
import smlms.file.Description;
import smlms.file.Fluorophores;
public class Generate_Beads {
public static String path = "/Users/sage/Desktop/beads/beads6/";
public static String pathPSF = "/Users/sage/Desktop/beads/psf/";
public static String filename = path + "activations... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/NoiseModule.java | .java | 7,383 | 250 | package smlms.simulation;
import ij.IJ;
import imageware.Builder;
import imageware.ImageWare;
import java.io.PrintStream;
import org.apache.commons.math3.distribution.GammaDistribution;
import org.apache.commons.math3.distribution.PoissonDistribution;
import smlms.tools.ArrayOperations;
import smlms.tools.Chrono;
im... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/AutofluorescenceModule.java | .java | 6,558 | 228 | package smlms.simulation;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.process.FloatProcessor;
import imageware.Builder;
import imageware.ImageWare;
import java.util.Vector;
import org.apache.commons.math3.distribution.PoissonDistribution;
import smlms.file.Fluorophores;
import smlms.tools.Arr... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/ReportHTML.java | .java | 2,542 | 80 | package smlms.simulation;
import ij.IJ;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintStream;
public class ReportHTML extends PrintStream {
public ReportHTML(Strin... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/SequenceFactoryDialog.java | .java | 40,587 | 985 | package smlms.simulation;
import ij.IJ;
import ij.gui.GUI;
import imageware.ImageWare;
import java.awt.Color;
import java.awt.Frame;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowEvent;
import java.awt.event.WindowListener;
import java.io.File;
import java.util.A... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/AutofluorescenceSource.java | .java | 2,289 | 74 | package smlms.simulation;
import imageware.ImageWare;
import smlms.tools.PsRandom;
public class AutofluorescenceSource {
private double xo;
private double yo;
private double scale;
private double size;
private double xdiffusion[] = new double[10];
private double ydiffusion[] = new double[10];
private PsRandom... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/Viewport.java | .java | 4,452 | 193 | package smlms.simulation;
import ij.IJ;
import java.io.PrintStream;
import smlms.file.Fluorophore;
import smlms.tools.Point3D;
import smlms.tools.Tools;
public class Viewport {
private double fovx; // nano
private double fovy; // nano
private double thickness; // nano
private double pixelsize; // nano
priv... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/CameraModule.java | .java | 3,099 | 103 | package smlms.simulation;
import ij.ImagePlus;
import ij.io.FileSaver;
import imageware.Builder;
import imageware.ImageWare;
import smlms.tools.Tools;
public class CameraModule {
public static String[] names = new String[] {"TIFF 8-bits", "TIFF 16-bits", "TIFF 32-bits", "JPEG"};
public static String[] quantization... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/Zip_Sequences.java | .java | 1,563 | 53 | package smlms.simulation;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.io.FileSaver;
import ij.io.Opener;
import java.io.File;
import smlms.plugins.Merge_Sequence_Frames;
import smlms.tools.Zip;
public class Zip_Sequences {
public static String path = "/Users/dsage/Desktop/beads/beads6/";
p... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/PSFModule.java | .java | 19,151 | 584 | package smlms.simulation;
import ij.IJ;
import ij.ImagePlus;
import ij.WindowManager;
import ij.io.FileSaver;
import ij.io.Opener;
import ij.process.ImageProcessor;
import imageware.Builder;
import imageware.ImageWare;
import java.io.File;
import smlms.file.Fluorophore;
import smlms.file.Fluorophores;
import smlms.s... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/gl/Bessel.java | .java | 2,709 | 76 | package smlms.simulation.gl;
//import ij.IJ;
/*
* This class evaluates the Bessel function J0(x).
* It uses the polynomial approximations on p. 369-70 of Abramowitz & Stegun.
* The error in J0 is supposed to be less than or equal to 5 x 10^-8.
* The error in J1 is supposed to be less than or equal to 4 x 10^-8, relat... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/gl/PSFParameters.java | .java | 3,686 | 144 | package smlms.simulation.gl;
//import ij.IJ;
public class PSFParameters {
public double affineTransformA[][] = new double[][] {{1, 0}, {0, 1}};
public double affineTransformB[] = new double[] {0, 0};
/* Optical acquisition Parameters (from the user) */
/* ------------------------------------------------ */
... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/gl/PSFValue.java | .java | 4,981 | 164 | package smlms.simulation.gl;
/**
* Calculating values of the Gibson and Lanni PSF model
*
**/
public class PSFValue {
// Gibson & Lanni parameters of the acquisition
public PSFParameters p;
// Gibson and Lanni parameters
public double NA = 1.4;
public double LAMBDA = 500E-9;
public int MAGNIFICATION = 100... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/Cosine.java | .java | 1,218 | 40 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/ZFunction.java | .java | 1,262 | 54 | package smlms.simulation.defocussed2dfunction;
public class ZFunction {
final static public int ZFUNC_EXPO = 0;
final static public int ZFUNC_ANGLE = 1;
final static public int ZFUNC_EXPO2 = 2;
final static public int ZFUNC_CONSTANT = 3;
static public String[] names = new String[] {"Exponential", "Li... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/Lorentz.java | .java | 1,309 | 43 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/Support.java | .java | 818 | 22 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/Rectangle.java | .java | 1,136 | 39 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/DoubleHelix.java | .java | 1,501 | 48 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/Defocussed2DFunction.java | .java | 862 | 21 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/Airy.java | .java | 1,284 | 42 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/Linear.java | .java | 1,140 | 38 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/ElongatedGaussian.java | .java | 1,568 | 52 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/Astigmatism.java | .java | 1,305 | 43 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/simulation/defocussed2dfunction/Gaussian.java | .java | 1,257 | 40 | //=========================================================================================
//
// Project: Localization Microscopy
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
// Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Tools/verifications/check_psf.py | .py | 2,928 | 85 | #!/usr/bin/env python
#
# Check that the PSF in the simulations matches the reference PSF.
#
# Hazen 04/16
#
import numpy
import sys
import tifffile
if (len(sys.argv) != 4):
print "usage: <psf.tiff> <images dir> <activations.csv>"
exit()
#
# This assumes that the z values in the activations file are
# in the... | Python |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/computeSplineBasis3.m | .m | 276 | 12 | function x = computeSplineBasis3(x) %n = 3
x = abs(x);
%ind = (x >= 0 & x < 1);
%x(ind) = 2/3 - x(ind).^2 + x(ind).^3/2;
%ind = (x >= 1 & x < 2);
%x(ind) = (2 - x(ind)).^3/6;
%ind = (x >= 2);
%x(ind) = 0;
x = 1/12*(abs(x - 2).^3 - 4*abs(x - 1).^3 + 3*(x - 2).*x.^2 + 4);
end | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/ktensor.m | .m | 196 | 8 | function GR = ktensor(gr)
if length(gr)==2
GR = kron(gr{1}, gr{2}');
else
GRXY = kron(gr{1}, gr{2}');
GR = arrayfun(@(z) z*GRXY,gr{3},'UniformOutput',false);
GR = cat(3,GR{:});
end | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/prob_dens.m | .m | 675 | 21 | function prob_distr = prob_dens(camera_model,gain,eta,u)
%Probability density of camera model for a single initial photonelectron
if min(u)<0
error('u must be positive');
end
switch camera_model
case 'EMCCD'
%2004 Basden / 2016 Chao, exponential distribbution with param
%1/gain, plot p(u) for ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/main_EMCCD.m | .m | 509 | 22 | %Implementation from
m = 300;
p = 3e2;
c = unique(max(-2e3:2e4 + m*p,0));
n = 1;
gpm = @(c) 1/(factorial(n-1).*m.^n).*c.^(n-1).*exp(-c/m);
%figure(2);
%plot(c,gpm(c));
Gpm = @(c) exp(-p).*(c==0) + sqrt(p./(c.*m)).*exp(-c./m - p).*besseli(1,2*sqrt(c.*p./m));
prob_distr = prob_dens('EMCCD',m, p, c);
figure(3);
plot... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/computeIntegralDer.m | .m | 5,856 | 110 | function integr = computeIntegralDer(coeffxy,pos_mol,NsplPix,delta,cam_siz,der)
%Output: siz
%Integrate spline basis function of degree 2/3 for der/other dimension rsp.
%Use integral relation with (sum of shifted) basis func of degree 3/4 rsp.
%For one camera pixel (others are shifted version of this integral)
siz = si... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/computeEta.m | .m | 2,211 | 58 | function eta = computeEta(pos_mol,c,delta,cam_siz)
%siz = sqrt(Ntotpix)*ones(1,2);
%siz = ceil([Nx*step(1)/sqrt(Ntotpix),Ny*step(2)/sqrt(Ntotpix)]);%
%campix_step = step(1:2).*NsplPix;
siz = size(c);
Bz = computeSplineBasis3(pos_mol(3)/delta(3) - (1:siz(3))');% Nz x 1
NsplPix = ceil(siz(1:2)./cam_siz);%# splines b... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/save_parfor.m | .m | 449 | 21 | function save_parfor(name_mat, struct2save)
% save_parfor
%
% Inputs: name_mat: where the .mat will be saved, absolute path is
% recommended.
% varargin: the variables will be saved, don't pass on the names of
% the variables, i.e, strings.
%
% Outputs:
%
%
% EXAM... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/main_hist_z_photon.m | .m | 283 | 8 | ind = diff(activations.xnano([1:end,end]))==0 & diff(activations.ynano([1:end,end]))==0 & diff(activations.znano([1:end,end]))==0;
Nmol = nnz(ind);
ind = ~ind;
tmp = cumsum(ind);
for kk = 1:Nmol
Nphotons(kk) = sum(activations.intensity(kk==tmp));
Nact(kk) = nnz(kk==tmp);
end | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/main_extract_photons_mat.m | .m | 720 | 22 | z_oi = [-15,15];
fold_name = 'res';
modality = 'DH';
tmp = struct2table(dir(fullfile(fold_name,modality,'stack_*')));
Np_set = height(tmp);
%%
z_vec = -750:10:750;
ind_oi = z_vec > z_oi(1) & z_vec < z_oi(2);
fprintf('Number of z-slices per bin : %i\n', nnz(ind_oi));
CRLB = table(ones(Np_set,1),ones(Np_set,1),ones(N... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/computeCubicSplineCoefs.m | .m | 2,203 | 69 | function coefs=computeCubicSplineCoefs(im)
%-------------------------------------------------
% function coefs=computeCubicSplineCoefs(im)
%
% Decompose the image im on a B-spline basis
%
% Exemple (in 2D):
% im=double(imread('cell.tif'));
% coefs=computeCubicSplineCoefs(im);
% sz=size(im);
% [C,R]=mesh... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/probCamera.m | .m | 1,820 | 47 | function pkz = probCamera(z,nu,sig,umin,umax,gain,cam_model,eta,mode,reltol,abstol,Npoints) %,step_int
%reltol = 1e-8;
%abstol = 1e-11;
%z = vpa(z);
switch cam_model
case 'EMCCD'
switch mode
case 0 %simplified expr.
%integrate over u from umin to umax
pkz = integ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/noise_coef_fct_vec.m | .m | 672 | 27 | function coeff = noise_coef_fct_vec(z, umin, umax, eta, sig, nu, gain, cam_model, reltol, abstol,Npoints)
%fprintf('doing vectorial way...');
%arrayfun is slower than a loop (+0.05 sec/element)
%tic
%coeff = arrayfun(@(x) noise_coef_fct(x, umin, umax, eta, sig, nu, gain, cam_model, reltol, abstol),z);
%toc
%tic
coef... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/main_test_bounds.m | .m | 4,873 | 134 | %U: 75, Z: 50 for nu = 0.000213528237267334
maxsigU = 100;%25:25:200;
maxsigZ = 100;%[25:25:200];%[10,25,50,75,100,125,150,175];
minSigU = 100;
minSigZ = 100;
minNu = 1e-5;
maxNu = 250;
Ninterval = 16;
Npoints = 5e3;
parpool(min(feature('NumCores'),Ninterval));
camera_model = 'EMCCD';%'none';%
%nphoton = 5e8;
QE = 0.9... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/main_cramer_rao.m | .m | 3,710 | 133 | %Cramer-Rao bounds
clear
dir_name = '~/Documents/SMLM/analysis/psf/';%'~/Downloads/PSF GL 200x200x151.tif';%
modality = 'AS';
Nz = 151;
[PSF,summedPSF,Nx,Ny] = load_PSF(dir_name,modality,Nz);
%% Fit cubic spline from 3D psf
%[Nx,Ny,Nz] = size(PSF);
d = [3*ones(1,3),0,0,0];%degree of Bsplines
dx = 10;%nm
dy = 10;%nm
dz... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/computeSplineBasis2.m | .m | 64 | 5 | function y = computeSplineBasis2(x)
y = max(1 - abs(x),0);
end | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/noise_coef_fct.m | .m | 2,558 | 62 | function coeff = noise_coef_fct(z, umin, umax, eta, sig, nu, gain,cam_model,reltol,abstol,Npoints)
%NOISE_COEF_FCT
%syms u;
integr_type = 2;
if true %max(-(umin:umax).*((umin:umax) + 2*eta - 2*z)/(2*sig^2) - (umin:umax)/gain) > 70
% No simplification
pkz = probCamera(z,nu,sig,umin,umax,gain,cam_model,eta,... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/computedEta.m | .m | 3,192 | 73 | function deta = computedEta(N, c, Ntotpix, delta, pos_mol,mu,cam_siz)
%Output : Ncampix x ndims(c)
%Ncampix: total number of camera pixel
deta = zeros(Ntotpix,ndims(c));
[Nx,Ny,Nz] = size(c);% V := prod(size(c))
%cam_siz = sqrt(Ntotpix)*ones(1,2);
NsplPix = ceil([Nx,Ny]./cam_siz);%# splines basis fct per camera pixel... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/computeCramerRao.m | .m | 3,941 | 110 | function [I,cam_coef,nu,deta,par] = computeCramerRao(c,delta,cam_pix,pos_mol,varargin)
%c: spline coefficients of PSF fitting
%step: step between knot
%cam_pix: camera pixel size in the object plane
%pos: molecule position (0,0) at the top left
par = inputParser;
addParameter(par,'QE',0.9,@isnumeric);
addParameter(par... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/load_PSF.m | .m | 1,605 | 57 | function [PSF,summed,Nx,Ny] = load_PSF(dir_name, modality,Nz)
switch modality
case {'2D','AS','DH'}
fname = fullfile(dir_name, sprintf('%s-Exp.tif', modality));
case 'BP'
fname{1} = fullfile(dir_name, sprintf('%s+250.tif', modality));
fname{2} = fullfile(dir_name, sprintf('%s-250.tif', ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/evaluateCubicSpline.m | .m | 5,357 | 148 | function y=evaluateCubicSpline(coefs,x)
%-------------------------------------------------
% function y=evaluateCubicSpline(coefs,x)
%
% See the functions below for a description of the parameters
%
% Exemple (in 2D):
% im=double(imread('cell.tif'));
% coefs=computeCubicSplineCoefs(im);
% sz=size(im);
% ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/main_auto_run.m | .m | 3,867 | 140 | %Cramer-Rao bounds
clear
modality_set = {'BP','AS','DH','2D'};
Nmod = length(modality_set);
dir_name = '~/Documents/SMLM/analysis/psf/';%'~/Downloads/PSF GL 200x200x151.tif';%
Nz = 151;
%%0
for l = 1%:Nmod
modality = modality_set{l};
[PSF,summedPSF,Nx,Ny] = load_PSF(dir_name,modality,Nz);
%% Fit cubic ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/CramerRao/computeSplineBasis4.m | .m | 259 | 7 | function x = computeSplineBasis4(x)
x = 1/48*((x - 5/2).^4.*(-sign(x - 5/2)) + 5*(x - 3/2).^4.*sign(x - 3/2)...
- 10*(x - 1/2).^4.*sign(x - 1/2) + 10*(x + 1/2).^4.*sign(x + 1/2) ...
- 5*(x + 3/2).^4.*sign(x + 3/2) + (x + 5/2).^4.*sign(x + 5/2));
end | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/wobble_correction/generateWobbleStandalone.m | .m | 25 | 2 | mcc -mv wobble_correct.m
| MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/wobble_correction/wobble_correct.m | .m | 39,024 | 1,267 | function varargout = wobble_correct(varargin)
% WOBBLE_CORRECT MATLAB code for wobble_correct.fig
% WOBBLE_CORRECT, by itself, creates a new WOBBLE_CORRECT or raises the existing
% singleton*.
%
% H = WOBBLE_CORRECT returns the handle to a new WOBBLE_CORRECT or the handle to
% the existing singleton... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Tools/FileConversionUtilities/tiffs_to_tiff.py | .py | 466 | 23 | #!/usr/bin/env python
#
# Convert a mess of tiff files into a single multi-page tiff file.
#
# Hazen 04/16
#
import glob
import sys
import tifffile
if (len(sys.argv) != 3):
print("usage: <tiff file> <tiff dir>")
exit()
tiff_files = sorted(glob.glob(sys.argv[2] + "*.tif"))
with tifffile.TiffWriter(sys.argv[1... | Python |
2D | SMLM-Challenge/Challenge2016 | Tools/pupil_functions/zernike.c | .c | 3,009 | 152 | /*
* C library for calculating Zernike polynomials.
* Has issues for polynomials where n >= 13?
*
* Hazen 10/14
*
* Compilation instructions:
*
* Linux:
* gcc -fPIC -g -c -Wall zernike.c
* gcc -shared -Wl,-soname,zernike.so.1 -o zernike.so.1.0.1 zernike.o -lc
* ln -s zernike.so.1.0.1 zernike.so
*
* Wind... | C |
2D | SMLM-Challenge/Challenge2016 | Tools/pupil_functions/pupil_math.py | .py | 8,308 | 241 | #!/usr/bin/python
#
# Some math for calculating PSFs from pupil functions.
#
# All units are in microns.
#
# Hazen 03/16
#
import math
import numpy
import scipy
import scipy.fftpack
import tifffile
import zernike_c as zernikeC
class Geometry(object):
## __init__
#
# @param size The number of pixels in t... | Python |
2D | SMLM-Challenge/Challenge2016 | Tools/pupil_functions/zernike_c.py | .py | 1,741 | 65 | #!/usr/bin/python
#
# Simple Python interface to zernike.c
#
# Hazen 10/14
#
import ctypes
import numpy
from numpy.ctypeslib import ndpointer
import os
import sys
directory = os.path.dirname(__file__)
if (directory == ""):
directory = "./"
else:
directory += "/"
if(sys.platform == "win32"):
zernike = cty... | Python |
2D | SMLM-Challenge/Challenge2016 | Assessment/RealDataAssessment/NPC_plotter.m | .m | 4,545 | 133 | function NPC_plotter(fname,savename);
%savename = fname(1:end-4);
data =importdata(fname);
fr = data(:,1);
x= data(:,2);
y= data(:,3);
z= data(:,4);
phot= data(:,5);
%whole image
rangez=[-500,500]
rangex = [0,20000];
rangey = [0,20000]
pixSz=20;
satVal3d=0.005
satVal2d=0.005
blurSigma=3;
box = [rangex(1),rangey... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/RealDataAssessment/renderStormData.m | .m | 5,683 | 229 | function [srIm,yIm,xIm,density] = renderStormData(X,Y,varargin)
%TODO saturate Xpercent before gamma correction
%TODO use a faster gaussian filter
% box = [xstart ystart xwidth yheight]
%Author: S Holden
pixSize=20;
sigma=10;
gammaVal = 1;
satVal =0.0;
zlim = [-600 600];
nz =10;
satVal=0;
isBox = false;
box=[];
is3D ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/RealDataAssessment/plotZcrossSection.m | .m | 1,431 | 47 | function [srIm_XZ X1] = plotZcrossSection(x,y,z,xyPos,lineWidth,rangez, pixSz,satVal,blurSigma,useAngleFormat)
if ~exist('useAngleFormat','var')
useAngleFormat=false;
end
if ~useAngleFormat
Dx = (xyPos(2,1)-xyPos(1,1));
Dy = (xyPos(2,2)-xyPos(1,2));
X0 = [xyPos(1,1),xyPos(1,2)]
lineLength = sqrt(D... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/RealDataAssessment/stormCmap.m | .m | 424 | 15 | %---------------------
function [cmap stormHue linearHue]=stormCmap(ncolor);
linearHue = linspace(0,1,ncolor);
cmap=colormap(jet(ncolor));
cmaphsv=rgb2hsv(cmap);
stormHue= cmaphsv(:,1);
stormHue=unique(stormHue,'stable');
nVal = numel(stormHue);
stormHue = [interp1(1:nVal,stormHue,linspace(1,nVal,ncolor))]';
sat = one... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/RealDataAssessment/lmCompDriftCor.m | .m | 679 | 35 | function savename = lmCompDriftCor(fname )
data =importdata(fname);
fr = data(:,1);
x= data(:,2);
y= data(:,3);
z= data(:,4);
if size(data,2)>4
phot= data(:,5);
end
drift=driftcorrection3D_so(x,y,z,fr,[]);%4th arg is the parameters arg
%have to supply p even if its just empty (standard)
figname = [fname(1:end-4),... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/RealDataAssessment/tubulin_plotter.m | .m | 5,905 | 178 | function tubulin_plotter(fname,savename)
data =importdata(fname);
fr = data(:,1);
x= data(:,2);
y= data(:,3);
z= data(:,4);
phot= data(:,5);
%whole image
rangez=[-750,500]
rangex = [0,40000];
rangey = [0,40000]
pixSz=30;
satVal3d=0.005
satVal2d=0.005
blurSigma=3;
box = [rangex(1),rangey(1),rangex(2)-rangex(1),ran... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/RealDataAssessment/driftCorrectAll.m | .m | 1,316 | 39 | %run this on a directory containing the real data csv files
% Or copy to said directory
%modify this list to match the files you want to analyse
%Need to add to the matlab path:
% 'Challenge2016\Assessment\RealDataAssessment'
% 'Challenge2016\Assessment\Matlab\driftCorrection'
fnameTubulinList = {...
'3D-DAOSTOR... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/RealDataAssessment/real3dAnalysis.m | .m | 1,886 | 54 | %run this on a directory containing the real data csv files
% Or copy to said directory
%modify this list to match the files you want to analyse
%Need to add to path:
% 'lm-challenge2016\Challenge2016\Assessment\Matlab\3dPlotTools'
% 'lm-challenge2016\Challenge2016\Assessment\Matlab\driftCorrection\driftcorrection3... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/RealDataAssessment/plot3DSTORMcolorbar.m | .m | 2,619 | 88 | function h = plot3DSTORMcolorbar(dims, orientation,zLim,nTick,varargin)
% PLOT_COLORBAR plot a standalone colorbar for inclusion in a publication
% H = PLOT_COLORBAR(DIMS, ORIENTATION TITLE_STRING) Plot a colorbar for
% inclusion in a publication. DIMS sets the length and width of the
% colorbar (in v... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/rnd_loc.m | .m | 431 | 21 | function loc = rnd_loc(ave_dens,nframes,fov)
%RND_LOC Random Localization
% ave_dens : Number of fluorophores per frame on average
% nframes : number of frame
% fov : Field Of View
Nmol_tot = ave_dens*nframes;
if iscolumn(fov)
fov = fov';
end
maxInt = 1e4;
loc = repmat([fov, maxInt], Nmol_tot, 1).*rand(Nmo... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/importFullPairings.m | .m | 3,220 | 86 | function pairingsMT1 = importFullPairings(filename, startRow, endRow)
%IMPORTFILE Import numeric data from a text file as a matrix.
% PAIRINGSMT1 = IMPORTFILE(FILENAME) Reads data from text file FILENAME
% for the default selection.
%
% PAIRINGSMT1 = IMPORTFILE(FILENAME, STARTROW, ENDROW) Reads data from
% rows... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/main_3dcolor_winners.m | .m | 7,136 | 173 | %Script for winners visualisations
%2D LD 3D-DAOSTORM
%2D HD SMfit
%AS LD CSpline
%AS HD SMolPhot
%BP LD MIATool
%BP HD ThunderSTORM
%DH LD CSpline
%DH HD CSpline
clear
winners = table(cell(10,1),cell(10,1),cell(10,1),'VariableNames',{'modality','density','software'});
winners.modality{1} = 'AS';winners.density{1} = '... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/gauss_render_intensity.m | .m | 2,836 | 100 | function im = gauss_render_intensity(data, sig, pix_size, im_size,doCorr)
% data : list of particles Nparticles x 2-3 => (x,y)+z (opt) (nm)
% sig : sigma (nm) for each dimension
% pix_size
% im_size, size of obtained image
% varargin{1} : do the Z correction or not
doNorm = 1;
D = size(data,2);
if isscalar(sig)
si... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/main_set_param_plot.m | .m | 2,145 | 68 | %% Load pairings file resulting from assessment program
clear pos
path = '~/Dropbox/smlm/figures/';
software = 'SMAP';%'STORMChaser';%
modality = 'BP';
dataset = 'MT1.N1.LD';
wobble = true;
photonT = true;
%File must be in the path
fname = dir(fullfile('assessment_results',software,...
sprintf('pairings____%s____%s... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/saveResults.m | .m | 10,448 | 214 | function saveResults(results, results_mol, results_graph, res_folder)
%SAVERESULTS Save all the results
%Save results in final file
fname = ['results____',...
results{1}.participant,'.csv'];
fileID = fopen(strcat(res_folder,filesep,...
results{1}.participant,filesep,fname),'w');
formatSpec = strcat('%s,%s,%s,%... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/importLocations.m | .m | 2,519 | 67 | function [VarName27,VarName28,VarName29,VarName30,VarName31] = importLocations(filename, startRow, endRow)
%IMPORTFILE Import numeric data from a text file as column vectors.
% [VARNAME27,VARNAME28,VARNAME29,VARNAME30,VARNAME31] =
% IMPORTFILE(FILENAME) Reads data from text file FILENAME for the default
% selecti... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/gauss_render.m | .m | 2,493 | 88 | function im = gauss_render(data, sig, pix_size, im_size,doCorr)
% data : list of particles Nparticles x 2-3 => (x,y)+z (opt) (nm)
% sig : sigma (nm) for each dimension
% pix_size
% im_size, size of obtained image
% varargin{1} : do the Z correction or not
D = size(data,2);
for k=1:D
if k==3 && doCorr
data... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/main_brut_loc_plot.m | .m | 2,393 | 65 | %% Load Brut loc
locup = dir(fullfile(software,'standard',sprintf('%s____%s____%s*',...
dataset,modality,software)));
%header = textscan(fullfile(software,'upload',locup(1).name),'Delimiter',',',0,0);
locup = csvread(fullfile(software,'standard',locup(1).name),1,0);
locup = array2table(locup(:,1:end),'VariableName... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/main_cmp_RMSEz_vs_z.m | .m | 3,724 | 103 | %% LOAD RMSEz vs z from one software for all modalities and plot them
clear data
software = 'SMAP';%'SMAP';%'MIATool';
photonT = true;
dataset = 'MT3.N2.LD';
modalities = {'AS','BP','DHNPC'};
metrics = {'Jaccard','RMSEloc z','RMSEloc xy'};
path = fullfile('assessment_results',software);
fdname = metrics;
for kk = 1... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/savePublic_old.m | .m | 9,792 | 194 | function savePublic_old(results, results_mol, results_graph,res_folder)
%SAVEPUBLIC_OLD save results in public.csv
for k=1:length(results)
strMod{k} = results{k}.modality;
end
strMod = unique(strMod);
fname = 'public.csv';
if isempty(results_graph)
results_graph = fill_results_graph(results);
end
initLen = ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/loc_metrics.m | .m | 6,566 | 210 | function [out,pairings,fig_corr] = loc_metrics(testPos, truePos, radTol, pairings, dim3D, varargin)
%EVALUATION localization assessment with radius tolerance radTol
% INSPIRED BY JAVA CODE OF LOCALIZATION AVAILABLE ON 2016 ISBI CHALLENGE WEBSITE
% Provides usual metrics such as recall, precision, etc.
% Follows Sage's ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/main_PerfvsTolRadius.m | .m | 3,775 | 120 | %% Plot the performance vs radius tolerance curves
clear pos
path = '~/Dropbox/smlm/figures/';
software = 'MIATool-RMS';%'SMAP'
modality = 'AS';
dataset = 'MT1.N1.LD';
wobble = false;
photonT = true;
%File must be in the path
if wobble
fname = dir(fullfile('assessment_results',software,...
sprintf('pairing... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/assessment_frame.m | .m | 12,706 | 299 | function perf_metrics = assessment_frame(param_input)
%ASSESSMENT Performance assessment for SMLM Challenge 2016
% INPUT
% param_input : parameters structure
% OUTPUT
% perf_metrics : structure regrouping the performance assessment results
% and Gaussian rendered of gt and res in addition
% Written by Thanh-an Pham, ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/assessment_main.m | .m | 6,802 | 169 | %% ASSESSMENT PROGRAM (MAIN) NOT THE MOST RECENT (SEE ASSESSMENT_MAIN_AUTOMATIC.M)
% ASSESSMENT SCRIPT written by Thanh-an Pham (EPFL): 12-Jul-2016
% Expect standardized input files in folder 'participant_name/standard'
% converted by participant-specific converter script "convert_(participant_name).m"
%% Parameters
cl... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/main_load_4_fig.m | .m | 5,708 | 149 | %% MAIN FOR FIGURE WHEN MAT FILES AVAILABLE
clear
res_fold = 'assessment_results';
participants = dir(pwd);
ind2rm = false(length(participants),1);
for k=1:length(participants)
ind2rm(k) = ~participants(k).isdir...
|| ~exist(fullfile(participants(k).name,'standard'),'dir');
end
participants(ind2rm) = [];
m... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/savePublic.m | .m | 10,724 | 207 | function savePublic(results, results_mol, results_graph,res_folder)
%SAVEPUBLIC save results in public.csv
for k=1:length(results)
strMod{k} = results{k}.modality;
end
strMod = unique(strMod);
fname = 'public.csv';
if isempty(results_graph)
results_graph = fill_results_graph(results);
end
initLen = length(r... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Assessment/Matlab/depthcolor3D.m | .m | 1,774 | 74 | function [im2D,T1,T2,T3,L] = depthcolor3D(im,colormapType,t,dim,varargin)
%DEPTHCOLOR3D Color code for depth in 3D image im
%im : 3D intensity image (e.g. 3D Gaussian rendered)
%colormapType : string indicating colormap type (e.g. jet, parula)
%t : quantile for max intensity (0 to 1). Change the scaling of color (and
%... | MATLAB |
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