What our teachers don't tell us in school is that we will spend most of our scientific or engineering career in front of computers, trying to beat them into submission. My formal training in computational science is nil, which I suspect is true of 90 percent of the scientists and engineers in the world. In this book, I attempt to bring together in one place the very basic facts that every technical person should know about computers. The computers of today still require you to know quite a bit about them in order to use them effectively for technical data analysis. Scientists and engineers who are computer novices should read this book cover to cover (that is, in my modest opinion). Experienced computer users should use this book as a reference. There are nuggets of useful information in this book waiting to be discovered by even the most computer-literate of you. Changes in the Second Edition Numerous corrections and clarifications were made throughout the text. Thanks to all of you who sent in your comments on the first edition. In addition, the index and glossary have been greatly improved.
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"If your experiments generate a large amount of data and you want to know what scientific data formats are available to assist in the storage and visualisation of the data, then this book is for you." Australian & New Zealand Physicist
"The books real strength lies in the breadth and detail of the material covered and the simple explanations provided." - Endeavour
I introduction.- Five Researchers and Their Data.- Judy ReSyrch―Fan Simulation.- Michael Astroe―FITS Data.- Dr. Tim Boans―MRI Scans.- Jeanne Beeker―Solubility Experiments.- Wolfram Herth―Ground Water Information.- Important Questions to Answer.- How Are the Numbers Stored?.- How Is the Data Organized?.- What Is the Dimensionality of the Data.- Is the Data on a Grid?.- What Is the Best Way to Analyze the Data?.- II Numbers in Computers.- 1. An Overview of Numbers in Computers.- Turning Data into Numbers.- Storing Numbers on Computers.- Binary Numbers and ASCII Text Numbers.- Evaluating Number Formats.- 2. Byte Numbers.- Bits and Bytes.- Unsigned Bytes.- Signed Bytes.- Twos-Complement vs. Ones-Complement.- Hexadecimal Representation.- Octal Numbers.- Kilobytes and Megabytes.- Byte Numbers: Advantages and Pitfalls.- Computational Resources.- Range of Values.- Numerical Precision.- Calculations with Bytes.- Portability.- Summary.- 3. Integers and Fixed-Point Numbers.- Short Integers and Long Integers.- Fixed-Point Numbers.- Range of Values.- Numerical Precision.- Calculations.- Truncation Error.- Calculations: The Right Way.- Byte Order.- Integers and Fixed-Point: Advantages and Pitfalls.- Computational Resources.- Range of Values.- Numerical Precision.- Calculations with Integers.- Portability.- Summary.- 4. Floating-Point Numbers.- Single-Precision Floating-Point.- Binary Fractional Numbers.- Decoding a Floating-Point Number.- Normalized Numbers.- VAX Floating-Point.- Single-Precision Range of Values.- Numerical Precision of Single-Precision Floats.- Problems with Floating-Point Calculations.- The Mystery of the Vanishing Significant Digits.- The Case of Almost-Equal Numbers.- The Trouble with Floating-Point Comparisons.- A Bevy of Roundoff Errors.- The Riddle of the Stairstep Graph.- Special Floating-Point Values.- Zero.- NaN.- INF.- Denormalized Numbers.- Additional Floating-Point Formats.- Double-Precision Floating-Point Numbers.- Complex Numbers.- Extended Formats.- Floating-Point: Advantages and Pitfalls.- Computational Resources.- FPUs.- MIPS and MFLOPS.- Range of Values.- Numerical Precision.- Calculations with Floating-Point Numbers.- Portability.- Summary.- 5. ASCII Text Numbers.- ASCII Characters.- Control Characters.- Foreign Languages.- ASCII Text Strings.- ASCII Numbers.- Exponential Notation ASCII Numbers.- Separating Numbers―ASCII Delimiters.- Space, Tab, and Comma as Delimiters.- Storing a Position but Not a Number.- Fixed Format Delimited Files.- Delimited Files―Summary.- ASCII Line Separators.- Additional Binary vs. ASCII Text Issues.- Binary vs. ASCII Text File Transfers.- Character Encoded Binary.- Binary Coded Decimal.- NFS Mounts.- ASCII Text: Advantages and Pitfalls.- Computational Resources.- Range of Values.- Numerical Precision.- Calculations with ASCII Text.- Portability.- Summary.- III The Data Universe.- 6. A Map of the Data Universe.- Data Values, Locations, and Descriptions.- Defining Data Location.- Independent Variables and Dependent Variables.- U.S. Weather Example.- The Dimensionality of Data.- Adding a Dimension.- Organizing Data Storage.- Column Data.- 2D Matrix Data.- 3D Matrix Data.- Polygonal Data.- Summary.- 7. Column Data.- Column Datafiles on Disk.- Text String Columns.- Visualizing Column Data.- Linegraphs and Bar Charts.- Scatter Plots and Parametric Plots.- Parametric Plots vs. Linegraphs.- 3D Scatter Plots.- Beyond Three Dimensions.- An Observation on Good Graphs.- Summary.- 8. 2D Matrix Data.- 2D Matrix Datafiles on Disk.- An Example of a 2D Matrix Datafile.- ASCII Text and Binary 2D Matrix Datafiles.- Row-Major vs. Column-Major Order.- Images as 2D Matrix Datafiles.- Advantages of 2D Matrix Datafiles.- 2D Matrix Grids.- Uniform Grids and No Grids.- Non-Uniform Grids.- Warped Grids.- Sparse Grids.- The Dimensionality of 2D Matrix Data.- 2D Matrix Files as Column Files.- Column Files as 2D Matrix Files.- Visualizing 2D Matrix Data.- Color Raster Imaging.- Surface Plots.- Contour Plots.- Vector Plots.- Summary.- 9. 3D Matrix (Volumetric) Data.- 3D Matrix Datafiles on Disk.- ASCII Text and Binary 3D Matrix Datafiles.- 3D Matrix Grids.- The Dimensionality of 3D Matrix Data.- 3D Matrix File from a Series of 2D Matrix Files.- Series of 2D Matrix Files from a 3D Matrix File.- Visualizing 3D Matrix Data.- Slicing and Dicing.- Isosurfaces.- Volumetric Visualization.- Vector Fields and Streamlines.- Summary.- 10. Polygonal Data.- Unstructured Grids vs. Structured Grids.- Structured Grids.- Unstructured Grids.- Node-Based Data vs. Cell-Based Data.- Polygonal Data on Disk.- A Cube Example.- Binary vs. ASCII Text.- From Surfaces to Solids.- Visualizing Polygonal Data.- Polygonal to 3D Matrix.- Photorealistic Rendering.- Summary.- 11. Conversions and Adding Dimensions.- Column Data to 2D Matrix Data.- Step 1: Gridding Scatter Data.- A 3 by 3 Grid Example.- A 4 by 4 Grid Example.- Selecting Destination Grid Size.- Reducing Bin Averaging.- Reducing Missing Values.- Missing Data Rags.- Step 2: Filling Missing Data.- Nearest Neighbor Fill.- Linear Interpolation.- Linear Interpolation Along Rows.- Linear Interpolate Along Columns and Rows.- Smooth Fill.- Weighted Fill.- Weighted Factor Functions.- Cutoff Radius.- Secondary Passes.- Comparing Weighted Fill and Smooth Fill.- Weighted Fill: Pros and Cons.- Kriging.- Variances.- Creating the Variance Matrix.- Minimizing the Variance Matrix.- Co-Linear Points.- Subdividing the Region.- A Small Kriging Example.- A Larger Kriging Example.- Kriging Summary.- Other Conversions.- Column Data to 3D Matrix Data.- Polygonal Data to Matrix Data.- Matrix Data to Column Data.- 2D Matrix to 3D Matrix.- 3D Matrix to 2D Matrix.- Adding Dimensions.- 1D Data to 2D Data: An Example.- Summary.- IV Data Formats.- 12. Data Formats Overview.- Scientific Data and Graphics File Formats―Introduction.- The Importance of Standards.- Scientific Data Formats―The First Revolution.- Scientific Data Formats vs. Graphics Formats.- Graphics Formats.- Home Growing a Bitmap File Format.- The SILI Format.- Data Compression.- Home Growing a Vector File Format.- Binary vs. ASCII Text Encoded Vector Graphics Files.- Bitmap Graphics Formats vs. Vector Graphics Formats.- Scientific Data Formats.- Annotations.- Data Organization.- Levels of Abstraction.- Data Models.- Organizational Concepts.- Sequential Organization.- Rat File Organization.- Hierarchical Organization.- Relational Organization.- Object-Oriented Organization.- Evaluating Data Formats.- Type of Format.- Hardware Issues.- Features.- Availability and Support.- Summary.- 13. Popular Graphics File Formats.- CGM (Computer Graphics Metafile).- Summary.- Overview of Disk Format.- References.- DXF (Data Interchange Format).- Summary.- Overview of Disk Format.- References.- EPS (Encapsulated PostScript).- Summary.- Overview of Disk Format.- References.- GIF (Graphics Interchange Format).- Summary.- Overview of Disk Format.- References.- GKS (Graphical Kernel System).- Summary.- Overview of Subroutine Library.- References.- PHIGS (Programmer Hierarchical Interactive Graphics Sandard).- Summary.- Overview of Subroutine Library.- References.- PICT.- Summary.- Overview of Disk Format.- PICT Bitmaps.- References.- PostScript.- Summary.- Overview of Disk Format.- References.- TIFF (Tag Image File Format).- Summary.- Overview of Disk Format.- TIFF Tagged Pointers.- TIFF Image Strips.- TIFF Example.- References.- 14. Popular Scientific Data Formats.- BUFR (Binary Universal Format for Representation of Data).- GRIB (Gridded Binary Format).- Summary.- Overview of the BUFR Disk Format.- BUFR Data Descriptors.- Scaling of BUFR Data Values.- A BUFR Example.- Overview of the GRIB Disk Format.- GRIB Section 1―Product Definition.- GRIB Section 2―Grid Definition.- GRIB Section 3―Bitmap.- GRIB Section 4―Data.- References.- CDF (Common Data Format).- Summary.- Overview of the CDF Format.- CDF Records and Variables.- CDF Variances.- CDF Virtual Values.- CDF Attributes, Data Types, Encoding, and Datafiles.- CDF Subroutine Library.- CDF Skeleton Files.- References.- DLIS (Digital Log Interchange Standard).- RP66 (Recommended Practice 66).- Summary.- Overview of the DLIS Format.- DLIS Disk Files.- DLIS Logical Records.- DLIS Logical Record Segments.- DLIS Objects.- DLIS Components.- DLIS Summary.- References.- FITS (Flexible Image Transport System).- Summary.- Overview of Disk Format.- FITS Header.- FITS Records.- Optional FITS Keywords.- FITS Bintables.- References.- HDF (Hierarchical Data Format).- Summary.- Overview of the HDF Subroutine Library.- Overview of the HDF Disk Format.- HDF Directory Structure.- HDF Data Descriptors.- HDF Data Descriptor Tags.- HDF Data Descriptor Reference Numbers.- HDF Groups.- HDF Scientific Datasets.- HDF Vdata Records.- HDF Extended Tags.- References.- netCDF (Network Common Data Form).- Summary.- Overview of the netCDF Format.- CDF Dimensions and Dimensionality.- CDL (Network Common Data Form Language.- References.- PDS (Planetary Data System).- Summary.- Overview of the PDS Format.- PDS Database Organization.- PDS Datafile Organization.- References.- Plot3D.- Summary.- Overview of the Plot3D Format.- References.- SEG-Y (SEG Digital Tape Format Y).- SEG-A (SEG Digital Tape Format A).- SEG-B (SEG Digital Tape Format B).- SEG-C (SEG Digital Tape Format C).- SEG-D (SEG Digital Tape Format D).- Summary.- Overview of the SEG Formats.- Overview of the SEG-Y Format.- References.- 15. Additional Formats.- Candis (C-Language for Analysis and Display).- References.- DICOM (Digital Imaging and Communications in Medicine).- ACR-NEMA (Am. Coll. of Radiology―Nat. Elect. Manuf. Assoc.).- References.- Erdas.- Flux.- GF3 (General Format 3).- IGES (Initial Graphics Exchange Specification).- PDES (Product Data Exchange Using STEP).- PBM (Portable Bitmap).- PGM (Portable Gray Map).- PPM (Portable Pixel Map).- PNM (Portable Any Map).- PCX.- PDB.- SBF (SERI Broadband Format).- SDTS (Spatial Data Transfer Standard).- FIPS 173 (Federal Information Processing Standard 173).- References.- SNAP (Simplified Numerical Analysis Postprocessing).- WMF (Microsoft Windows Metafile).- XBM (X Window Bitmap).- XWD (X Window Dump).- V Bringing It All Together.- Bringing It All Together.- Judy ReSyrch―Fan Simulation.- Michael Astroe―FITS Data.- Dr. Tim Boans―MRI Scans.- Jeanne Beeker―Solubility Experiments.- Wolfram Herth―Ground Water Information.- Summary.
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