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 | hpfem/hermes-examples | 2d-advanced/maxwell/resonator-time-domain-II-rk/definitions.h | .h | 2,813 | 97 | #include "hermes2d.h"
/* Namespaces used */
using namespace Hermes;
using namespace Hermes::Hermes2D;
using namespace Hermes::Hermes2D::Views;
using namespace Hermes::Hermes2D::RefinementSelectors;
/* Initial condition for E */
class CustomInitialConditionWave : public ExactSolutionVector < double >
{
public:
Cus... | Unknown |
2D | hpfem/hermes-examples | 2d-advanced/maxwell/resonator-time-domain-II-rk/main.cpp | .cpp | 7,037 | 171 | #include "definitions.h"
// This example solves a time-domain resonator problem for the Maxwell's equation.
// It is very similar to resonator-time-domain-I but B is eliminated from the
// equations, thus converting the first-order system into one second -order
// equation in time. The second-order equation in time is... | C++ |
2D | hpfem/hermes-examples | 2d-advanced/maxwell/resonator-time-domain-II-rk/definitions.cpp | .cpp | 4,054 | 124 | #include "definitions.h"
template<typename Real, typename Scalar>
static Scalar int_e_f(int n, double *wt, Func<Real> *u, Func<Real> *v)
{
Scalar result = Scalar(0);
for (int i = 0; i < n; i++)
result += wt[i] * (u->val0[i] * conj(v->val0[i]) + u->val1[i] * conj(v->val1[i]));
return result;
}
template<typen... | C++ |
2D | hpfem/hermes-examples | 2d-advanced/maxwell/microwave-oven/definitions.h | .h | 5,034 | 162 | #include "hermes2d.h"
/* Namespaces used */
using namespace Hermes;
using namespace Hermes::Hermes2D;
using namespace Hermes::Hermes2D::Views;
using namespace Hermes::Hermes2D::RefinementSelectors;
using namespace Hermes::Hermes2D::WeakFormsHcurl;
typedef std::complex<double> complex;
/* Weak forms */
// Jacobian.... | Unknown |
2D | hpfem/hermes-examples | 2d-advanced/maxwell/microwave-oven/plot_graph.py | .py | 628 | 32 | # import libraries
import numpy, pylab
from pylab import *
# plot DOF convergence graph
pylab.title("Error convergence")
pylab.xlabel("Degrees of freedom")
pylab.ylabel("Error [%]")
axis('equal')
data = numpy.loadtxt("conv_dof_est.dat")
x = data[:, 0]
y = data[:, 1]
loglog(x, y, '-s', label="error (est)")
legend()
# ... | Python |
2D | hpfem/hermes-examples | 2d-advanced/maxwell/microwave-oven/main.cpp | .cpp | 8,786 | 232 | #include "definitions.h"
// This example solves adaptively the electric field in a simplified microwave oven.
// The waves are generated using a harmonic surface current on the right-most edge.
// (Such small cavity is present in every microwave oven). There is a circular
// load located in the middle of the main cavi... | C++ |
2D | hpfem/hermes-examples | 2d-advanced/maxwell/microwave-oven/definitions.cpp | .cpp | 6,633 | 199 | #include "definitions.h"
template<typename Real, typename Scalar>
Scalar CustomMatrixForm::matrix_form(int n, double *wt, Func<Scalar> *u_ext[], Func<Real> *u,
Func<Real> *v, GeomVol<Real> *e, Func<Scalar>* *ext) const
{
std::complex<double> ikappa = std::complex<double>(0.0, kappa);
Scalar result1 = Scalar(0);
... | C++ |
2D | hpfem/hermes-examples | 2d-advanced/maxwell/magnetostatics-sensor/definitions.h | .h | 1,186 | 34 | #include "hermes2d.h"
/* Namespaces used */
using namespace Hermes;
using namespace Hermes::Hermes2D;
using namespace Hermes::Hermes2D::Views;
using namespace Hermes::Hermes2D::RefinementSelectors;
using namespace Hermes::Hermes2D::WeakFormsH1;
using namespace Hermes::Hermes2D::WeakFormsMaxwell;
/* Weak forms */
cl... | Unknown |
2D | hpfem/hermes-examples | 2d-advanced/maxwell/magnetostatics-sensor/main.cpp | .cpp | 4,548 | 112 | #include "definitions.h"
// This example shows how to handle stiff nonlinear problems.
//
// PDE: magnetostatics with nonlinear magnetic permeability
// curl[1/mu curl u] = current_density.
// The following parameters can be changed:
// Initial polynomial degree.
const int P_INIT = 2;
// Stopping criterion for t... | C++ |
2D | hpfem/hermes-examples | 2d-advanced/maxwell/magnetostatics-sensor/definitions.cpp | .cpp | 2,051 | 45 | #include "definitions.h"
CustomWeakFormMagnetostatics::CustomWeakFormMagnetostatics(std::string material_iron_1, std::string material_iron_2,
CubicSpline* mu_inv_iron, std::string material_air,
std::string material_copper, double mu_vacuum,
double current_density, int order_inc) : WeakForm<double>(1)
{
// Jaco... | C++ |
2D | hpfem/hermes-examples | 2d-advanced/maxwell/magnetostatics-sensor/plot_spline.py | .py | 299 | 18 | # import libraries
import numpy, pylab
from pylab import *
data = numpy.loadtxt("spline.dat")
x = data[:, 0]
y = data[:, 1]
plot(x, y, '-o', label="cubic spline")
data = numpy.loadtxt("spline_der.dat")
x = data[:, 0]
y = data[:, 1]
plot(x, y, '-*', label="derivative")
legend()
# finalize
show()
| Python |
2D | M3RG-IITD/FNO-StressStrain | FNO-StressStrain.ipynb | .ipynb | 1,070,096 | 1,536 | {
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"## @meermehran -- M3RG Lab -- Indian Institute of Technology, Delhi\n",
"## @date : 4July2022\n",
"\n",
"####################################--DESCRIPTION##############################... | Unknown |
2D | M3RG-IITD/FNO-StressStrain | Adam.py | .py | 5,328 | 141 | import math
import torch
from torch import Tensor
from typing import List, Optional
from torch.optim.optimizer import Optimizer
def adam(params: List[Tensor],
grads: List[Tensor],
exp_avgs: List[Tensor],
exp_avg_sqs: List[Tensor],
max_exp_avg_sqs: List[Tensor],
state_steps... | Python |
2D | M3RG-IITD/FNO-StressStrain | utility.py | .py | 11,347 | 339 | ## @meermehran || M3RG Lab || Indian Institute of Technology, Delhi
import torch
import numpy as np
import scipy.io
import h5py
import torch.nn as nn
import operator
from functools import reduce
from functools import partial
import matplotlib as mpl
import matplotlib.pyplot as plt
##### UTILITLY FUNCTIONS #####
d... | Python |
2D | M3RG-IITD/FNO-StressStrain | abaqus/simulation.py | .py | 19,394 | 395 |
# Crack simulation using Stress Intensity Factor
# https://iopscience.iop.org/article/10.1088/2399-1984/ab36f0/pdf (ARTICLE FOR MATERIAL PROPERTY)
from abaqusConstants import *
from caeModules import *
import abaqus
from part import *
from material import *
from section import *
from assembly import *
from step import... | Python |
2D | M3RG-IITD/FNO-StressStrain | benchmarking/UNet.ipynb | .ipynb | 198,781 | 1,871 | {
"cells": [
{
"cell_type": "code",
"execution_count": null,
"id": "e7a4212e-365b-4ab5-9dc6-1ef148e975ea",
"metadata": {},
"outputs": [],
"source": [
"## @meermehran -- M3RG Lab -- Indian Institute of Technology, Delhi\n",
"## @date : 28Sept2022\n",
"\n",
"##########################... | Unknown |
2D | M3RG-IITD/FNO-StressStrain | benchmarking/FNO.ipynb | .ipynb | 205,084 | 2,034 | {
"cells": [
{
"cell_type": "code",
"execution_count": 46,
"id": "6699f0bf-c2e8-4fc4-b19a-7c98ccdfe7ef",
"metadata": {},
"outputs": [],
"source": [
"## @meermehran -- M3RG Lab -- Indian Institute of Technology, Delhi\n",
"## @date : 28Sept2022\n",
"\n",
"############################... | Unknown |
2D | M3RG-IITD/FNO-StressStrain | benchmarking/ResNet.ipynb | .ipynb | 198,774 | 1,972 | {
"cells": [
{
"cell_type": "code",
"execution_count": null,
"id": "21985619-70e2-45de-8d87-b5f1b8995033",
"metadata": {},
"outputs": [],
"source": [
"## @meermehran -- M3RG Lab -- Indian Institute of Technology, Delhi\n",
"## @date : 28Sept2022\n",
"\n",
"##########################... | Unknown |
2D | M3RG-IITD/FNO-StressStrain | benchmarking/utility.py | .py | 3,537 | 139 | ### @meermehran || M3RG Lab || IIT Delhi
import torch
import numpy as np
import scipy.io
import h5py
import torch.nn as nn
import operator
from functools import reduce
from functools import partial
#################################################
#
# Utilities
#
#################################################
dev... | Python |
2D | SMLM-Challenge/Challenge2016 | BaselineLocalization/BaselineLocalizationAbstract.java | .java | 18,905 | 553 | // =========================================================================================
//
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne... | Java |
2D | SMLM-Challenge/Challenge2016 | BaselineLocalization/BaselineLocalization_3D_Biplane.java | .java | 7,137 | 188 | // =========================================================================================
//
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne... | Java |
2D | SMLM-Challenge/Challenge2016 | BaselineLocalization/BaselineLocalization_2D.java | .java | 2,341 | 64 | //=========================================================================================
//
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne... | Java |
2D | SMLM-Challenge/Challenge2016 | BaselineLocalization/BaselineLocalization_3D_Astigmatism.java | .java | 3,388 | 85 | //=========================================================================================
//
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne... | Java |
2D | SMLM-Challenge/Challenge2016 | BaselineLocalization/BaselineLocalizationOperators.java | .java | 10,923 | 334 | //=========================================================================================
//
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne... | Java |
2D | SMLM-Challenge/Challenge2016 | BaselineLocalization/BaselineLocalization_3D_DoubleHelix.java | .java | 7,292 | 203 | //=========================================================================================
//
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne... | Java |
2D | SMLM-Challenge/Challenge2016 | BaselineLocalization/BaselineLocalizationParticle.java | .java | 2,963 | 98 | //=========================================================================================
//
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/psf_generation/generate_psf_lut4.m | .m | 13,029 | 470 | function imPsfAvg= generate_psf_lut4(fname,pixSzIn, pixSzOut, nMol,frz0,saveName,varargin)
%averages and interpolates PSF in XY
% assumes we dont have to interpolate in Z
nargin= numel(varargin);
MAXSHIFT = 300;%Max PSF shift (nm) when recentring anything larger generates an error
ctrdWindowSzNm = 1500;
boxSzNm =5000;... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Simulator/psf_generation/imreadstack.m | .m | 633 | 36 | function imstack = imreadstack( path1)
% imstack = imreadstack( path1)
%
% Description:
% Automatically load all the images in a stack as a
% 3D matrix
%
% Inputs:
% path
%
% Outputs:
% imstack
%
% History:
% 130208 - First alpha complete (SH)
% 180208 - Function headers and help standardised (SH)
%
% Author:... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Simulator/psf_generation/psfGeneration160517.m | .m | 1,059 | 35 | %---------------
%astig PSF
fname = 'experimental-PSFs/AS-ZStack-6Beads-3um-10nmStep-AstigCylLens-5xAverage.tif';
saveName = 'interpolated-PSFs/astig-PSF-JBS-10nm-voxel.tif';
frz0 = 156;
pixSzIn = 160;
pixSzOut = [10];
nMol = 4;
generate_psf_lut4(fname,pixSzIn, pixSzOut, nMol,frz0,saveName);
%---------------
%DH PSF
f... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Simulator/photophysics/brightness_palmSubframe.m | .m | 3,230 | 124 | function [photons]=brightness_palmSubframe(Ion,Ton,Tdark,Tbl,frames)
% INPUTS
% Ion: mean photon emission during on state
% frames: # of frames
% Rates defined here:
% %
%for 4 state system:
%
% UNIFORM 1/Tbl
% OFF ------> ON ------> BLEACH
% |/\
% | |
% 1/Ton | | 1/Tdark
% ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Simulator/photophysics/testSimCore2_160518.m | .m | 3,705 | 136 | % Test simulation - PALM like photokinetics
% tomas.lukes@epfl.ch
nfluo = 1000;
Ion = 5000;
frames = 200;
%FP-like param
Ton = 3;
Tdark = 2.5;
Tbl=1.5;
% giving mean on time per blink 1 frame
% Note "mean on time per blink" calculation below is an overestimate for small on-times due to quantization error
%% Generate... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Simulator/photophysics/activation_4states.m | .m | 13,728 | 383 | function rateEffectiveActivations = activation_4states(Ton, Tdark, Tbleaching, nframes, framerate, fov, pixelsize, dye, power_laser, path)
% ACTIVATION_4STATES - Activate a list of fluorophores with a 4-states model
%
% Description
%
% UNIFORM 1/Tbl
% OFF ------> ON ------> BLEACH
% | /\
% ... | MATLAB |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/Test_EMCCD.java | .java | 3,908 | 116 |
import org.apache.commons.math3.distribution.GammaDistribution;
import org.apache.commons.math3.distribution.PoissonDistribution;
import smlms.tools.PsRandom;
public class Test_EMCCD {
private PsRandom psrand = new PsRandom(1234);
public static void main(String[] arg) {
new Test_EMCCD();
}
public Test_EMCC... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/model/Bessel.java | .java | 3,740 | 97 | //=====================================================================================
// Project: PSF Generator
//
// Organization: Biomedical Imaging Group (BIG)
// Ecole Polytechnique Federale de Lausanne (EPFL)
// Lausanne, Switzerland
//
// Information: http://bigwww.epfl.ch/deconvolution/
//
// Reference:
// Al... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/model/GibsonLanniParameters.java | .java | 2,776 | 104 | package bpalm.model;
import ij.IJ;
import java.io.Serializable;
/**
* This class manages all parameters of the Gibson-Lanni model.
*
* @author Hagai Kirshner, Biomedical Imaging Group, Ecole Polytechnique Federale de Lausanne (EPFL)
*/
public class GibsonLanniParameters implements Serializable {
/** Working ... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/model/KirchhoffDiffractionSimpson.java | .java | 5,321 | 175 | package bpalm.model;
/**
* Kirchhoff Diffraction integral formula for the Gibson and Lanni PSF model
*
* @author Hagai Kirshner, Biomedical Imaging Group, Ecole Polytechnique Federale de Lausanne (EPFL)
*/
public class KirchhoffDiffractionSimpson{
// Gibson & Lanni parameters of the acquisition
private Gibso... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/simulator/BiplaneAlgorithm.java | .java | 4,507 | 145 | package bpalm.simulator;
import ij.IJ;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import smlms.simulation.PSFModule;
import bpalm.model.KirchhoffDiffractionSimpson;
/**
* This class manages all aspects of the algorithm for generating the data.
*
* @author Hagai Kirshner... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/simulator/PoissonRandomNumber.java | .java | 733 | 34 | package bpalm.simulator;
import java.util.Random;
public class PoissonRandomNumber extends Random {
public PoissonRandomNumber() {
super();
}
public double nextPoisson(double lambda) {
if (lambda==0) return 0.0;
else if (lambda<100) {
// Knuth algorithm
double L = Math.exp(-lambda);
int k = 0... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/simulator/SliceOfPSF.java | .java | 3,121 | 81 | package bpalm.simulator;
import ij.IJ;
import bpalm.model.KirchhoffDiffractionSimpson;
// This class generates a slice of single source according to the the Gibson-Lanni PSF model.
// @author Hagai Kirshner, Biomedical Imaging Group, Ecole Polytechnique Federale de Lausanne (EPFL)
/**
*
* @author Hagai Kirshner, B... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/simulator/BPALMParameters.java | .java | 1,879 | 73 | package bpalm.simulator;
import bpalm.model.GibsonLanniParameters;
/**
* This class manages all parameters of the acquisition, output and sample tabs of the BiplaneDataGenerator plugin.
*
* @author Hagai Kirshner, Biomedical Imaging Group, Ecole Polytechnique Federale de Lausanne (EPFL)
* @author Thomas Pengo, La... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/simulator/Particle.java | .java | 406 | 27 | package bpalm.simulator;
public class Particle {
public double x,y,z,t;
public Particle() {
x=0; y=0; z=0; t=0;
}
public Particle(Particle p) {
x=p.x;
y=p.y;
z=p.z;
t=p.t;
}
public Particle scale(double fX, double fY, double fZ) {
x=x*fX; y=y*fY; z=z*fZ;
return this;
}
public Particle of... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/simulator/common/generators/Function.java | .java | 167 | 8 | package bpalm.simulator.common.generators;
public interface Function {
public double getX(double t);
public double getY(double t);
public double getZ(double t);
}
| Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/simulator/common/generators/UniformParticleGenerator.java | .java | 446 | 22 | package bpalm.simulator.common.generators;
import bpalm.simulator.Particle;
public class UniformParticleGenerator extends ParticleGenerator {
public UniformParticleGenerator() {}
@Override
public Particle nextParticle() {
Particle p = new Particle(template);
p.x = randomGenerator.nextDouble();
p.y = r... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/simulator/common/generators/FunctionParticleGenerator.java | .java | 628 | 31 | package bpalm.simulator.common.generators;
import bpalm.simulator.Particle;
public class FunctionParticleGenerator extends ParticleGenerator {
Function theFunction;
public FunctionParticleGenerator() {
this(new SpiralFunction());
}
public FunctionParticleGenerator(Function theFunction) {
this.theFunction ... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/simulator/common/generators/ParticleGenerator.java | .java | 1,480 | 56 | package bpalm.simulator.common.generators;
import java.util.Random;
import bpalm.simulator.Particle;
/**
* A particle generator, as the name indicates, generates a particle according to a particular
* pattern. The particle is generated each time a "nextParticle" is called.
*
* This default implementation gene... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/bpalm/simulator/common/generators/SpiralFunction.java | .java | 453 | 17 | package bpalm.simulator.common.generators;
public class SpiralFunction implements Function {
double turns;
public SpiralFunction() {
this(1);
}
public SpiralFunction(double turns) {
this.turns = turns;
}
@Override public double getX(double t) { return (t*Math.sin(t*2*Math.PI*turns)/2+.5); }
@Override ... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/AssessmentTable.java | .java | 4,553 | 147 | package smlms.assessment;
import ij.IJ;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionAdapter;
import java.util.ArrayList;
import java.util.HashMap;
import javax.swing.JFrame;
import javax.swing.JScrollPane;
import java... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/FluorophorePair.java | .java | 1,378 | 43 | //=========================================================================================
//
// Project: Single-Molecule Localization Microscopy
// Benchmarking of Localization Microscopy Software for Super-resolution Imaging
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/Localization_Assessment_Batch.java | .java | 1,830 | 62 | package smlms.assessment;
import ij.IJ;
import java.io.File;
import java.util.ArrayList;
import javax.swing.JLabel;
import smlms.file.Description;
import smlms.file.Fluorophores;
import additionaluserinterface.WalkBar;
public class Localization_Assessment_Batch {
public static String groundtruth = "/Users/sage/... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/CompareLocalization.java | .java | 8,352 | 270 | //=========================================================================================
//
// Project: Single-Molecule Localization Microscopy
// Benchmarking of Localization Microscopy Software for Super-resolution Imaging
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/Localization_Assessment.java | .java | 1,105 | 32 | package smlms.assessment;
//=========================================================================================
//
// Project:
// Single-Molecule Localization Microscopy Challenge 2016
// http://bigwww.epfl.ch/smlm/
//
// Author:
// Daniel Sage, http://bigwww.epfl.ch/sage/
// Biomedical Imaging Group (BIG)
// E... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/CompareResult.java | .java | 6,547 | 188 | //=========================================================================================
//
// Project: Single-Molecule Localization Microscopy
// Benchmarking of Localization Microscopy Software for Super-resolution Imaging
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/AssessmentDialog.java | .java | 4,551 | 142 | package smlms.assessment;
import ij.IJ;
import ij.gui.GUI;
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.JDialog;
import javax.swing.JFrame;
import javax.swing.JLabel;
import jav... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/hungarian/Matching.java | .java | 1,101 | 31 | //=========================================================================================
//
// Project: Single-Molecule Localization Microscopy
// Benchmarking of Localization Microscopy Software for Super-resolution Imaging
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/hungarian/BellmanFord.java | .java | 2,077 | 68 | //=========================================================================================
//
// Project: Single-Molecule Localization Microscopy
// Benchmarking of Localization Microscopy Software for Super-resolution Imaging
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/hungarian/WeightedEdge.java | .java | 1,319 | 42 | //=========================================================================================
//
// Project: Single-Molecule Localization Microscopy
// Benchmarking of Localization Microscopy Software for Super-resolution Imaging
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/assessment/hungarian/MaximumWeightedMatching.java | .java | 4,889 | 184 | //=========================================================================================
//
// Project: Single-Molecule Localization Microscopy
// Benchmarking of Localization Microscopy Software for Super-resolution Imaging
//
// Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/rendering/RenderingDialog.java | .java | 12,047 | 359 | package smlms.rendering;
import ij.CompositeImage;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
import ij.gui.GUI;
import ij.gui.Roi;
import ij.process.ImageProcessor;
import ij.process.LUT;
import imageware.ImageWare;
import java.awt.Color;
import java.awt.Rectangle;
import java.... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/rendering/RenderingTable.java | .java | 5,758 | 210 | package smlms.rendering;
import ij.IJ;
import ij.ImagePlus;
import ij.WindowManager;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionAdapter;
import java.util.ArrayList;
import java.uti... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/rendering/Rendering_2016.java | .java | 188 | 14 | package smlms.rendering;
public class Rendering_2016 {
public Rendering_2016() {
new RenderingDialog();
}
public static void main(String args[]) {
new RenderingDialog();
}
}
| Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/rendering/RenderingParameters.java | .java | 765 | 39 | package smlms.rendering;
import ij.ImagePlus;
public class RenderingParameters {
public String name;
public ImagePlus imp;
public double pixelsize;
public double fwhm;
public String method;
public double min[]; // x, y, z, frame, photons
public double max[]; // x, y, z, frame, photons
public RenderingP... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/rendering/Rendering.java | .java | 8,041 | 264 | package smlms.rendering;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.process.ColorProcessor;
import imageware.ImageWare;
import java.util.ArrayList;
import smlms.file.Fluorophore;
import smlms.tools.Point3D;
import smlms.tools.Volume;
import additionaluserinterface.WalkBar;
public class Rende... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/Chart.java | .java | 7,122 | 223 | package smlms.tools;
import ij.IJ;
import ij.ImagePlus;
import ij.io.FileSaver;
import ij.process.ColorProcessor;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics2D;
import java.awt.Rectangle;
import java.awt.Stroke;
import java.awt.geom.Rectangle2D;
import java.... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/NormalizedVariable.java | .java | 4,845 | 147 | package smlms.tools;
import java.util.ArrayList;
public class NormalizedVariable {
public ArrayList<double[]> linears = new ArrayList<double[]>();
public ArrayList<double[]> cosines = new ArrayList<double[]>();
public ArrayList<double[]> sigmoids = new ArrayList<double[]>();
public double constant = 0.0;
p... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/Progress.java | .java | 724 | 29 | package smlms.tools;
import ij.IJ;
public class Progress {
private double chrono;
public Progress() {
chrono = System.nanoTime();
}
public void print(String message) {
double c = (System.nanoTime() - chrono);
if (c < 1e3)
IJ.log(String.format("%3.1f ns // ", c) + message);
else if (c < 1e6)
IJ.... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/Drawing.java | .java | 3,544 | 122 | package smlms.tools;
import ij.ImagePlus;
import ij.gui.ImageCanvas;
import ij.gui.ImageWindow;
import ij.process.ByteProcessor;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Graphics;
import java.awt.Graphics2D;
import java.awt.Image;
import java... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/TableDouble.java | .java | 4,084 | 152 | package smlms.tools;
import ij.IJ;
import ij.ImagePlus;
import ij.WindowManager;
import java.awt.Color;
import java.awt.Component;
import java.awt.Dimension;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import javax.swing.JFrame;
import javax.swing.JScro... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/Verbose.java | .java | 1,307 | 45 | //=========================================================================================
//
// 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
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/PsRandom.java | .java | 39,459 | 972 | /* Program PsRandom
*
* Class for obtaining a single decimal or binary pseudorandom number
* or a sequence of decimal or binary pseudorandom numbers
* Supplements the Java random class with the generation of
* of lorentzian, poissonian, logistic, student's t, pareto,
* exponential, gumbel, weibull, frechet, ... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/Volume.java | .java | 1,784 | 83 | package smlms.tools;
import imageware.Builder;
import imageware.ImageWare;
import smlms.file.Fluorophore;
public class Volume {
public double x1;
public double x2;
public double y1;
public double y2;
public double z1;
public double z2;
public Volume(double x1, double x2, double y1, double y2, double z1, dou... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/Zip.java | .java | 1,935 | 73 | package smlms.tools;
import ij.IJ;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
public class Zip {
static public void zipFolder(String dir, String zipFileName) {
File dirObj = new File(dir);
tr... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/Vector3D.java | .java | 212 | 13 | package smlms.tools;
public class Vector3D {
public Point3D origin;
public Point3D extremity;
public Vector3D(Point3D origin, Point3D extremity) {
this.origin = origin;
this.extremity = extremity;
}
}
| Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/Chrono.java | .java | 2,279 | 85 | //=========================================================================================
//
// 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
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/Point3D.java | .java | 2,119 | 86 | //=========================================================================================
//
// 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
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/tools/ArrayOperations.java | .java | 7,818 | 284 | //=========================================================================================
//
// 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/tools/Tools.java | .java | 4,146 | 158 | //=========================================================================================
//
// 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
//
// Cond... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/plugins/Test_JComboBox.java | .java | 561 | 26 | package smlms.plugins;
import java.awt.Font;
import javax.swing.JComboBox;
import javax.swing.JFrame;
public class Test_JComboBox {
public static void main(String args[]) {
new Test_JComboBox();
}
public Test_JComboBox() {
JFrame frame = new JFrame("Test");
JComboBox cmb = new JComboBox(new String[] {"x ... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/plugins/Format_PSF.java | .java | 6,911 | 251 | package smlms.plugins;
import ij.IJ;
import ij.ImagePlus;
import ij.WindowManager;
import ij.gui.GenericDialog;
import ij.gui.OvalRoi;
import ij.gui.Plot;
import ij.process.ImageConverter;
import ij.process.ImageProcessor;
import imageware.Builder;
import imageware.ImageWare;
public class Format_PSF {
public Format... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/plugins/Test_JFreeChart.java | .java | 423 | 25 | package smlms.plugins;
import smlms.tools.Chart;
public class Test_JFreeChart {
public static void main(String args[]) {
new Test_JFreeChart();
}
public Test_JFreeChart() {
int N = 1000;
double x[] = new double[N];
double y[] = new double[N];
for(int i=0; i<N; i++) {
x[i] = Math.random();
y[i... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/plugins/Generate_Beads.java | .java | 2,106 | 70 | package smlms.plugins;
import java.io.File;
import java.util.ArrayList;
import smlms.file.Fluorophore;
import smlms.file.Fluorophores;
import smlms.simulation.CameraModule;
import smlms.simulation.PSFModule;
import smlms.simulation.SequenceFactory;
import smlms.simulation.Viewport;
import smlms.tools.Point3D;
public... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/plugins/Test_RandomVariable.java | .java | 773 | 31 | package smlms.plugins;
import ij.gui.Plot;
import smlms.tools.NormalizedVariable;
public class Test_RandomVariable {
public static void main(String args[]) {
double xmin = -100;
double xmax = 900;
int n = (int)(xmax - xmin);
double x[] = new double[n];
for(int i=0; i<n; i++)
x[i] = xmin + i;
Normali... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/plugins/AffineTransform_PSF.java | .java | 916 | 18 | package smlms.plugins;
import ij.IJ;
public class AffineTransform_PSF {
public AffineTransform_PSF() {
IJ.selectWindow("BP-000.tif");
IJ.run("TransformJ Scale", "x-factor=1.0 y-factor=1.0 z-factor=1.0 interpolation=[cubic B-spline]");
IJ.run("TransformJ Rotate", "z-angle=3 y-angle=0.0 x-angle=0.0 interpolatio... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/plugins/Normalized_PSF.java | .java | 1,800 | 72 | package smlms.plugins;
import ij.IJ;
import ij.ImagePlus;
import ij.WindowManager;
import ij.io.FileSaver;
import imageware.Builder;
import imageware.ImageWare;
public class Normalized_PSF {
public static void main(String args[]) {
new Normalized_PSF();
}
public Normalized_PSF() {
//String filename = "/Use... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/plugins/Test_Random_1.java | .java | 1,294 | 56 | package smlms.plugins;
import smlms.tools.PsRandom;
public class Test_Random_1 {
public static void main(String args[]) {
double mx = 125;
double my = 125;
double mz = 11;
double chrono = System.nanoTime();
for(int i=0; i<1000; i++) {
PsRandom rand = new PsRandom();
double p = rand.nextDouble()*mx*m... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/plugins/Merge_Sequence_Frames.java | .java | 1,977 | 57 | package smlms.plugins;
import ij.IJ;
import ij.ImagePlus;
import ij.io.FileSaver;
import ij.io.Opener;
import imageware.Builder;
import imageware.ImageWare;
import java.io.File;
import smlms.tools.Zip;
public class Merge_Sequence_Frames {
public static String dataset = "MT2.N2";
public static void main(String... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/plugins/Normalize_PSF_Batch.java | .java | 2,611 | 106 | package smlms.plugins;
import ij.IJ;
import ij.ImagePlus;
import ij.io.FileSaver;
import ij.io.Opener;
import imageware.Builder;
import imageware.ImageWare;
import java.io.File;
public class Normalize_PSF_Batch {
public static String path = "/Users/sage/Desktop/activation/psf/";
public static void main(String ... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/Tube.java | .java | 5,042 | 188 | package smlms.sample;
import ij.IJ;
import java.util.ArrayList;
import smlms.tools.NormalizedVariable;
import smlms.tools.Point3D;
public class Tube extends Item {
//private CurveSpline axis;
public CurveSegment axis;
public ArrayList<Point3D> nodes;
public NormalizedVariable radius;
public NormalizedVariable... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/Tolerance.java | .java | 79 | 6 | package smlms.sample;
public enum Tolerance {
TENTH, HUNDREDTH, THOUSANDTH
}
| Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/Item.java | .java | 370 | 23 | package smlms.sample;
import smlms.tools.Point3D;
public abstract class Item {
private String name = "";
public Item(String name) {
this.name = name;
}
public String getName() {
return name;
}
public abstract String getInfo();
public abstract String save();
public abstract boolean contains(Point3D p... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/Sample.java | .java | 2,987 | 121 | package smlms.sample;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.PrintStream;
import java.util.ArrayList;
import smlms.tools.Point3D;
import smlms.tools.Progress;
public class Sample extends ArrayList<Item> {
public String name;
p... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/CurveSpline.java | .java | 12,659 | 435 | //=========================================================================================
//
// 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/sample/Microtubules_Generator_2016.java | .java | 10,889 | 312 | package smlms.sample;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.ImageCanvas;
import ij.gui.ImageWindow;
import ij.gui.StackWindow;
import imageware.Builder;
import imageware.ImageWare;
import java.awt.Color;
import java.awt.Graphics;
import java.util.ArrayList;
import smlms.tools.NormalizedVariable;
import sm... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/SampleFactory.java | .java | 16,681 | 532 | package smlms.sample;
import static java.lang.Math.PI;
import static java.lang.Math.abs;
import static java.lang.Math.sqrt;
import ij.IJ;
import imageware.Builder;
import imageware.ImageWare;
import java.util.ArrayList;
import java.util.Random;
import smlms.tools.NormalizedVariable;
import smlms.tools.Point3D;
impor... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/SampleFactoryDialog.java | .java | 13,320 | 381 | package smlms.sample;
import ij.IJ;
import ij.gui.GUI;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.File;
import java.util.ArrayList;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swi... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/Reticulum2T_Generator_2016.java | .java | 9,200 | 320 | package smlms.sample;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.ImageCanvas;
import ij.gui.ImageWindow;
import ij.gui.StackWindow;
import ij.io.FileSaver;
import imageware.Builder;
import imageware.ImageWare;
import java.awt.Color;
import java.awt.Graphics;
import java.util.ArrayList;
import smlms.tools.Norma... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/Node.java | .java | 327 | 18 | package smlms.sample;
public class Node {
public double x;
public double y;
public double z;
public double radius;
public double thickness;
public Node(double x, double y, double z, double radius, double thickness) {
this.x = x;
this.y = y;
this.z = z;
this.radius = radius;
this.thickness = thickness... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/Microtubules3T_Generator_2016.java | .java | 9,567 | 332 | package smlms.sample;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.ImageCanvas;
import ij.gui.ImageWindow;
import ij.gui.StackWindow;
import ij.io.FileSaver;
import imageware.Builder;
import imageware.ImageWare;
import java.awt.Color;
import java.awt.Graphics;
import java.util.ArrayList;
import smlms.tools.Norma... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/Reticulum_Generator_2016.java | .java | 12,617 | 368 | package smlms.sample;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.ImageCanvas;
import ij.gui.ImageWindow;
import ij.gui.StackWindow;
import ij.process.FloatProcessor;
import java.awt.Color;
import java.awt.Graphics;
import java.util.ArrayList;
import smlms.tools.NormalizedVariable;
import smlms.tools.Point3D;
i... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/CurveSegment.java | .java | 5,504 | 188 | package smlms.sample;
//=========================================================================================
//
//Project: Localization Microscopy
//
//Author : Daniel Sage, Biomedical Imaging Group (BIG), http://bigwww.epfl.ch/sage/
//
//Organization: Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Sw... | Java |
2D | SMLM-Challenge/Challenge2016 | Simulator/Simulator-Java/src/smlms/sample/Microtubules_Generator_Training.java | .java | 10,240 | 286 | package smlms.sample;
import ij.IJ;
import ij.ImagePlus;
import ij.gui.ImageCanvas;
import ij.gui.ImageWindow;
import ij.gui.StackWindow;
import ij.process.FloatProcessor;
import imageware.ImageWare;
import java.awt.Color;
import java.awt.Graphics;
import java.util.ArrayList;
import smlms.tools.NormalizedVariable;
i... | Java |
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