Mathematica Â® in the Laboratory

, by Samuel Dick , Alfred Riddle , Douglas Stein

Note: Supplemental materials are not guaranteed with Rental or Used book purchases.

ISBN: 9780521581370 | 0521581370
Cover: Hardcover
Copyright: 5/28/1997

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MathematicaÂ®in the Laboratory is a hands-on guide which shows how to harness the power and flexibility of Mathematica in the control of data-acquisition equipment and the analysis of experimental data. It explains how to use Mathematica to import, manipulate, visualise and analyse data from existing files. The generation and export of test data are also covered. The control of laboratory equipment is dealt with in detail, including the use of Mathematica's MathLinkÂ® system in instrument control, data processing, and interfacing. Many practical examples are given, which can either be used directly or adapted to suit a particular application. The book sets out clearly how Mathematica can provide a truly unified data-handling environment, and will be invaluable to anyone who collects or analyses experimental data, including astronomers, biologists, chemists, mathematicians, geologists, physicists and engineers. The book is fully compatible with Mathematica 3.0.

Preface

1 Importing data from files

(38)

1.1 File operations in general

(3)

1.1.1 Locating files

(2)

1.2 File types

(1)

1.3 Data structures

(2)

1.4 Simple ASCII files

(16)

1.4.1 Numbers and strings from free-format ASCII files

(3)

1.4.2 String-number conversion

(1)

1.4.3 Files with embedded comments

(3)

1.4.4 Variably named files

(4)

1.4.5 File-content catalogs

(3)

1.4.6 Numbers and strings from fixed-format ASCII files

(2)

1.5 ASCII files created by spreadsheets

(6)

1.6 Mathematica files

(1)

1.7 DXF files

(6)

1.8 Binary files

(3)

1.9 References

(1)

2 Visualizing data

(48)

2.1 The art of visualization

(1)

2.2 Standard graph-plotting functions

(2)

2.3 Augmenting standard Mathematica graphs

(1)

2.4 Data fusion

(5)

2.5 Coping with awkward data

(8)

2.5.1 Axis reversal

(5)

2.5.2 Complex numbers

(1)

2.5.3 Unwrapping cyclic phase data

(2)

2.6 Making your own graphs

(18)

2.6.1 Polar surface plot

(7)

2.6.2 Bar charts and Manhattan plots

(10)

2.7 Acquisition-system problems

(5)

2.7.1 Glitch removal

(2)

2.7.2 Cyclic errors

(2)

2.7.3 Stuck ADC or encoder bits

(1)

2.8 Listening to your data

(8)

2.8.1 Simple waveforms

(2)

2.8.2 Listening to the inaudible: Using modulation

(4)

2.9 References

(1)

3 Data analysis

(55)

3.1 Statistical characteristics

(5)

3.1.1 Preparing data

(1)

3.1.2 Statistics without numbers

(2)

3.2 Comparing theory and data

(8)

3.2.1 Generating theoretical results

(2)

3.2.2 Plotting theory and data

(3)

3.2.3 Plotting theory-data differences

(3)

3.3 Fitting functions to data

100

(41)

3.3.1 Mathematica's built-in fitting functions

100

(7)

3.3.1.1 Linear fitting

101

(3)

3.3.1.2 Nonlinear fitting

104

(4)

3.3.2 Fitting functions to complex data

108

(11)

3.3.2.1 Simple RC filter

109

(3)

3.3.2.2 LC resonator

112

(7)

3.3.3 Spline-based fitting

119

(9)

3.3.4 Filtering data to remove noise

128

(13)

3.3.4.1 Rejecting outliers

128

(5)

3.3.4.2 Smoothing and filtering

133

(8)

3.4 References

141

(1)

4 Generating test data

142

(16)

4.1 Creating perfect data

142

(3)

4.2 Creating random numbers

145

(12)

4.2.1 Adding noise to simulated data

146

(6)

4.2.2 Random numbers from custom distributions

152

(5)

4.3 References

157

(1)

5 Exporting data

158

(11)

5.1 Basic file operations

158

(1)

5.2 Mathematica output to ASCII files

158

(6)

5.2.1 Evaluated and unevaluated expressions

159

(1)

5.2.2 Definitions

159

(1)

5.2.3 Expressions in C/FORTRAN/TeX forms

160

(1)

5.2.4 Formatted numbers

161

(3)

5.3 Mathematica output to binary files

164

(4)

5.3.1 Numbers

165

(2)

5.3.2 Strings

167

(1)

5.4 References

168

(1)

6 Introduction to instrument control and data acquisition

169

(21)

6.1 Anatomy of an instrument data acquisition system

170

(5)

6.1.1 Standards in instrumentation

170

(2)

6.1.2 Designing your software

172

(1)

6.1.3 Layerology

173

(2)

6.1.3.1 Top (application) layer

173

(1)

6.1.3.2 Hardware assessment layer

173

(1)

6.1.3.3 The computing layer

174

(1)

6.2 Coping with your data

175

(13)

6.2.1 Data assessment

176

(1)

6.2.2 Transmission time

176

(1)

6.2.3 Compression

177

(10)

6.2.4 Binary and ASCII forms

187

(1)

6.3 Safety in laboratory systems

188

(1)

6.4 References

189

(1)

7 Understanding MathLink

190

(35)

7.1 The pons asinorum: addtwo

192

(3)

7.2 Using :Evaluate: to include Mathematica code

195

(1)

7.3 Puting and geting arguments manually

196

(2)

7.4 Passing lists and arrays

198

(4)

7.5 Passing arbitrary expressions

202

(2)

7.6 Requesting evaluations by the kernel

204

(2)

7.7 Handling and recovery of MathLink errors

206

(2)

7.8 Handling and recovery of other errors

208

(8)

7.9 Troubleshooting and debugging

216

(2)

7.10 Large projects

218

(2)

7.11 Special topics

220

(4)

7.11.1 Unknown result length from your program

220

(2)

7.11.1.1 Loopback links

220

(2)

7.11.2 Making your function abortable

222

(2)

7.12 References

224

(1)

8 Interfacing I: a simple serial link

225

(24)

8.1 The serial port hardware

226

(4)

8.1.1 Electrical connections

226

(2)

8.1.2 Serial port parameters

228

(2)

8.2 Software specification

230

(1)

8.3 The Macintosh software

230

(12)

8.3.1 Creating the rs232.XXX project

231

(1)

8.3.2 The application C code

231

(6)

8.3.3 The MathLink template file

237

(2)

8.3.4 Building the executable program

239

(1)

8.3.5 The Mathematica code

239

(3)

8.4 The PC/Linux software

242

(4)

8.4.1 Port configuration

242

(1)

8.4.2 Port use

243

(3)

8.5 Problems?

246

(2)

8.5.1 Checking the hardware

246

(1)

8.5.2 Debugging the C code

247

(1)

8.5.3 Response times

248

(1)

8.6 References

248

(1)

9 Interfacing II: more advanced links

249

(51)

9.1 Design issues

249

(4)

9.1.1 Layers

249

(1)

9.1.2 Polling versus synchronous function calls

250

(2)

9.1.2.1 Mathematica code

251

(1)

9.1.2.2 Macintosh Toolbox

251

(1)

9.1.2.3 Drivers

251

(1)

9.1.2.4 Summary

251

(1)

9.1.3 Looping

252

(1)

9.1.4 Latency

252

(1)

9.2 Handling bare hardware (no support libraries)

253

(8)

9.2.1 The template file: SerialDataAcquisition.tm

254

(1)

9.2.2 The C code: SerialDataAcquisition.c

255

(5)

9.2.3 Using SerialDataAcquisition

260

(1)

9.3 Handling hardware with vendor libraries

261

(30)

9.3.1 One-shot oscilloscope

262

(6)

9.3.1.1 The template file: OneShotScope.tm

262

(1)

9.3.1.2 The C code: OneShotScope.c

262

(4)

9.3.1.3 Using OneShotScope

266

(1)

9.3.1.4 Moving on

267

(1)

9.3.2 Continuous acquisition (one channel)

268

(8)

9.3.2.1 The template file: Oscilloscope.tm

269

(1)

9.3.2.2 The C code: Oscilloscope.c

270

(4)

9.3.2.3 Using Oscilloscope

274

(2)

9.3.3 Streaming data to disk

276

(7)

9.3.3.1 The template file: StreamToDisk.tm

277

(1)

9.3.3.2 The C code: StreamToDisk.c

277

(5)

9.3.3.3 Using StreamToDisk

282

(1)

9.3.3.4 Moving on

282

(1)

9.3.4 Generating a waveform

283

(7)

9.3.4.1 The template file: Generate-Waveform.tm

283

(1)

9.3.4.2 The C code: GenerateWaveform.c

284

(4)

9.3.4.3 Using GenerateWaveform

288

(1)

9.3.4.4 Moving on

289

(1)

9.3.5 Additional projects

290

(1)

9.3.5.1 Counting LEDs

290

(1)

9.3.5.2 Times Square (block character generator)

290

(1)

9.3.5.3 Home heating controls

290

(1)

9.3.5.4 Elevator controls

291

(1)

9.3.5.5 Dream away

291

(1)

9.4 Utility routines

291

(8)

9.4.1 The template file: MitlMain.tm

291

(2)

9.4.2 The C code: MitlUtil.c

293

(6)

9.5 References

299

(1)

10 Interface hardware design

300

(11)

10.1 Simple buffer circuits

301

(3)

10.1.1 Attenuators

301

(1)

10.1.2 Amplifiers

302

(2)

10.1.2.1 Inverting-summing amplifier

302

(1)

10.1.2.2 Differential amplifier

303

(1)

10.1.2.3 Going on

304

(1)

10.2 Noise control

304

(5)

10.2.1 Noise in general

305

(1)

10.2.2 Reducing true noise

306

(1)

10.2.3 Switch debounce

307

(1)

10.2.4 Level detection

307

(2)

10.3 Signal generator

309

(1)

10.4 References

310

(1)

Appendix

311

(1)

A.1 Defining your own functions: a brief summary

311

(1)

A.2 Pure anonymous functions

312

(5)

Index

317

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Mathematica Â® in the Laboratory

Summary

Table of Contents

Supplemental Materials