Rowland NMR Toolkit (RNMRTK) Overview
|
|
- Allan Shields
- 6 years ago
- Views:
Transcription
1 Rowland NMR Toolkit (RNMRTK) Overview Originally developed as a platform for developing new NMR data processing methods Now widely used as a general processing platform Provides Rich set of apodization (window) functions DFT processing General processing tools (phasing, reversing, truncating, etc.) Robust, efficient Linear Prediction (LP) extrapolation MaxEnt reconstruction (deconvolution, uniform or nonuniform sampling) universal data reader exports to nmrpipe, XEASY, Felix Generates synthetic data, noise (testing/error analysis) Based on a program VNMR developed by Jeff Hoch in the late 1970 s Redesigned in 1985 and then in the early 1990s Free for Academic use and included in NMRbox l 1 -norm real (LONER) has recently been added
2 RNMRTK Suite of Programs section Manages the shared memory sections rnmrtk The main processing program in the Toolkit Loading, apodization, DFT, phasing, saving, etc. flip Forward linear prediction msa / msa2d / msa3d Maximum entropy reconstruction in one, two, and three dimensions inject Add synthetic peaks to time domain data select / zsample Expands or compresses NUS data seepln / contour graphical display for 1D and 2D data Many others
3 RNMRTK Shared memory With a suite of programs for performing tasks How do you get data output from one command to the next command without needing to write out intermediate files? Pipes (nmrpipe strategy) Shared memory (RNMRTK strategy) A shared memory section is a chunk of persistent memory where NMR data can be stored and used by different programs. section RNMRTK program to manage (create / delete) shared memory sections section -c The size of the shared memory section is the product of the arguments multiplied by 4 (32 bit data) plus 512 extra bytes for a header. Shared memory sections must be large enough to store all the data including processing section -d Deletes the shared memory section
4 RNMRTK Shared memory The maximum size of shared memory sections is defined by kernel values shmmax and shmall. NMRbox takes care of these advanced settings. Example: cd UCHC-2017/large-HNCO procpar.prl 25 The data set size is 512 x 128 x 128 complex points (1024 x 256 x 256 actual size) section -c Shared memory section is just large enough to hold time domain data However, it is not large enough to handle any zero-fills rnmrtk loadvnmr./fid rnmrtk seepar section -c rnmrtk rnmrtk%> seepar Deletes the shared memory section and replaces it. Existing data is deleted! rnmrtk%> loadvnmr./fid rnmrtk%> FFT rnmrtk%> DIM t3 rnmrtk%> FFT rnmrtk%> seepar rnmrtk%> exit section -d Shared memory sections will stay persistent until deleted or a reboot
5 rnmrtk Command for performing many of the traditional processing techniques Can be run: one command at a time in interactive mode scripted Row (column) oriented. Many commands need to have the dimension set RNMRTK rnmrtk
6 RNMRTK Issuing commands Arguments are entered as different classes: floats (defined as a number with a decimal) setpar SF integers (defined as a number without a decimal) zerofill 2048 string (defined as a character string without a period) sinebell square 70.0 filename (defined as a character string with a decimal point) loadvnmr./fid load hsqc.sec The order of arguments entered is important, but only within a given class of argument sstdc COS sstdc COS 20 rnmrtk is case insensitive (except for filenames) DIM command sets the dimension which is necessary for many commands rnmrtk << EOF LOAD test.sec LOAD command does not need dimension set DIM t1 FFT FFT command must have dimension set EOF
7 RNMRTK Issuing commands From the command line: bash% rnmrtk loadvnmr./fid bash% rnmrtk setpar SF bash% * DIM command not persistent In interactive mode bash% rnmrtk rnmrtk% loadvnmr./fid rnmrtk% DIM t2 rnmrtk% FFT rnmrtk% exit bash% As a script bash% processing_script.com bash% Typical script #! bin/bash section c rnmrtk << EOF loadvnmr./fid setpar PPM dim t2 zerofill 1024 fft 0.5 phase realpart EOF rnmrtk << EOF dim t1 zerofill 128 fft 0.5 realpart save test.sec EOF Here doc Cannot have spaces at the beginning of lines
8 Varian rnmrtk loadvnmr./fid RNMRTK Load data Bruker Need to create a parameter file called ser.par Example: Dom T1 T2 T3 N 64 C 140 C 512 C sw sf ppm Quad Order of dimensions in memory (after loading) STATES STATES STATES Format Little-endian Int Layout t2:280 t1:128 t3:1024 Layout defines order of dimensions in input file Note spacing between value and C # of padding bytes at beginning of fid # of padding bytes at end of fid # of header bytes Endian is defined by the computer architecture NOTE: spectrum-translator being developed to handled data conversions so little need to manually create load script anymore
9 cd UCHC-2017/large-HNCO more rnmrtk.com RNMRTK DFT Notes: SETPAR can be used to define parameters not set properly during conversion SEFIX1 is used to swap data that has been collected with sensitivity enhancement and not pre-shuffled during conversion./rnmrtk.com
10 Maximum Entropy Reconstruction (MaxEnt) MaxEnt can be performed in one dimension (msa), two dimension (msa2d) and three dimensions (msa4d) The acquisition dimension is often processed with a DFT and not with MaxEnt There are two modes for processing with MaxEnt Constant aim Must define def and aim Constant lambda Must define def and lambda When all the dimensions are NOT processed with MaxEnt, such as when the acquisition dimension is processed with a DFT, you MUST use Constant Lambda mode 2D Data sets Option 1: Process F2 with DFT, and F1 with msa (lambda mode) Option 2: Process F2-F1 planes with msa2d (aim mode) 3D Data sets Option 1: Process F3 with DFT and F1-F2 planes with msa2d (lambda mode) Option 2: Process F3-F2-F1 cube with msa3d (aim mode) 4D Data sets Option 1: Process F4 with DFT and F1-F2-F3 cubes with msa3d (lambda mode)
11 How to choose aim? AIM should be set to a value close to the RMS of the noise. Values too high will cause weak features of the spectrum to be lost Values too low will cause even minute details of the noise to be included (will try to force an exact match to the noise) Clear non-linearities are observed in peak intensities and are dependent on the value of aim unapodized DFT
12 Large values of def lead to reconstructions resembling the DFT Small values of def suppress noise but distort relative peak intensities Like aim, setting def to values near the RMS is generally the most appropriate DEF is less sensitive that AIM and can be altered by orders of magnitude How to choose def?
13 DEF & AIM High DEF, Low AIM Very low DEF, Low AIM Low DEF and Low AIM
14 LAMBDA During a MaxEnt reconstruction in constant aim mode there is a value called lambda that will be written to standard out. When processing data where the acquisition dimension has been processed with the FT you first need to determine values of def and aim based on the spectromter and spectra and then run MaxEnt in constant aim mode, record the converged lambda, and re-run in constant lambda mode. This is critical as in constant aim mode each plane will be scaled by a different amount and thus cause distortions in the peaks. Constant lambda holds the scaling constant.
15 RNMRTK msa2d 2 MODES Maximum Entropy Reconstruction in 2 dimensions Reads parameters from a file and dimensions are specified on invocation line Ex: msa2d t1 t2 msa2d.param Constant Aim parameter file DEBUG 1 NLOOPS 400 DEF 0.1 AIM 2.5 SCALEFIRST 0.5 SCHED./sample_schedule NUSE NOUT PHASE LW JVALUE Max loops, convergence may be quicker NUS Uniform Data will be extrapolated Constant LAMBDA parameter file DEBUG 1 NLOOPS 400 DEF 0.1 LAMBDA 1.0 SCALEFIRST 0.5 SCHED./sample_schedule NUSE NOUT PHASE LW JVALUE For 3D NUS datasets the acquisition dimension is typically processed with conventional FT and then the indirect dimensions are processed with msa2d
16 Let s try a MaxEnt Reconstruction cd UCHC-2017/large-HNCO more msa2d_param wc -l schedule3.scd There are 400 / 16,384 FIDs collected (2.4%)./msa2d.com schedule3.scd test nmrdraw -in test_nudft_proj.ft2 nmrdraw -in test_nudft.ft3 nmrdraw -in test_msa2d_proj.ft2 nmrdraw -in test_msa2d.ft3 You can compare the results to the DFT using 100% of the FIDs nmrdraw -in ft-f1_proj.ft2 nmrdraw -in ft-f2_proj.ft2 nmrdraw -in ft_f3f1.ft3
17 RNMRTK msa2d Monitoring convergence Very important! Ensure that the value of test is less than 0.1 unless fewer than NLOOPS required Without deconvolution convergence typically occurs is around 40 iterations if proper def, aim, lambda values were use. High numbers of loops suggest msa2d is modeling noise With deconvolution the number of loops may be significantly higher. How to check values for Test and the maximum number of loops more msa2d.txt tail msa2d.txt grep Test msa2d.txt Only look at lines that start with Test grep Loop msa2d.txt sort -n -k2
Goals of tutorial. Introduce NMRbox platform
Introduce NMRbox platform Goals of tutorial Showcase NMRbox with NUS tools A dozen different NUS processing tools installed and configured more coming. Demonstrate potential of NMRbox Now that the platform
More informationGoals of tutorial. Showcase NMRbox with NUS tools A dozen different NUS processing tools installed and configured more coming.
Introduce NMRbox platform Goals of tutorial Showcase NMRbox with NUS tools A dozen different NUS processing tools installed and configured more coming. Demonstrate potential of NMRbox Now that the platform
More informationCONNJUR Workflow Builder: Tutorial. Where to download:
CONNJUR Workflow Builder: Tutorial Part I: Introduction 1.1 About CONNJUR and CONNJUR Workflow Builder (CWB) The CONNJUR Project is to develop an open source integration environment for biomolecular NMR
More informationQuick Start Guide to nmrpipe Processing of 15 N-HSQC data
Quick Start Guide to nmrpipe Processing of 15 N-HSQC data Data conversion: We make the basic assumption here that the data set was recorded on an INOVA-class or later model of NMR instrument running VNMRJ.
More informationIf you have suggestions or requests please ask!
Tutorial Nonuniform Sampling Software nus-tool v0.3 Presenter Adam Schuyler A. Introduction 1. What is nus-tool? The nus-tool software package is a sample schedule utility that provides functions to generate
More informationFrom FID to 2D: Processing HSQC Data Using NMRPipe Macro Methods
The data recorded during a NMR experiment are stored in the form of a digitized free induction decay (FID), which is in the time domain. In order for us to gain information regarding the chemical environment
More informationNUS: non-uniform sampling
FMP, 10.10.2012 2/48 NMR-spectroscopy uses the nuclear spin that can be thought of as a mixture between gyroscope and magnet 3/48 The frequency of the rotation of the spin in a magnetic field is what we
More informationStatut actuel de NUS et APSY
Statut actuel de NUS et APSY Martial PIOTTO Bruker BioSpin, France 30 ème Réunion Utilisateurs 29-30 Novembre 2016 Innovation with Integrity General features of NUS and APSY Techniques that allow to collect
More informationIntroduction to the Graphical User Interface of TREND
Introduction to the Graphical User Interface of TREND Description: Both GUI and command-line versions of TREND are available. The arguments and usages of the GUI panels are briefly introduced below. Detailed
More informationNUS and hmsist Tutorial
NUS and hmsist Tutorial How to setup NUS experiments on Bruker Spectrometer with PGS? (Topspin 3 and above) How to process NUS experiments on Bruker using hmsist How to think about coding NUS pulse sequences
More informationFFT and Spectrum Analyzer
Objective: FFT and Spectrum Analyzer Understand the frequency domain and some of it's uses Understand the Discrete Fourier Transform Preparation: (i) PC and data acquisition system (ii)fft software Background:
More informationProcessing NMR Data With OS X/Linux Freeware
Processing NMR Data With OS X/Linux Freeware Volume : A User s Guide to NMRPipe by Josh Kurutz, Ph.D. Technical Director of the Biochemistry & Molecular Biology NMR Facility University of Chicago Last
More informationRat 2D EPSI Dual Band Variable Flip Angle 13 C Dynamic Spectroscopy
Rat 2D EPSI Dual Band Variable Flip Angle 13 C Dynamic Spectroscopy In this example you will load a dynamic MRS animal data set acquired on a GE 3T scanner. This data was acquired with an EPSI sequence
More informationHIFI NMR : part1 automated backbone assignments using 3D->2D
HIFI NMR : part automated backbone assignments using 3D->2D Marco Tonelli National Magnetic Resonance Facility At Madison NMRFAM Recording multidimensional experiments is time costly In conventional multidimensional
More informationDAGMan workflow. Kumaran Baskaran
DAGMan workflow Kumaran Baskaran NMRbox summer workshop June 26-29,2017 what is a workflow? Laboratory Publication Workflow management Softwares Workflow management Data Softwares Workflow management
More informationBasic 1D Processing. Opening Saved Data. Start the VnmrJ software. Click File > Open.
Basic 1D Processing Opening Saved Data Start the VnmrJ software. Click File > Open. This will open a pop-up window. Clicking Home will take you to the data directory within your account. You can create
More informationMestReC Cheat Sheet. by Monika Ivancic, July 1 st 2005
MestReC Cheat Sheet by Monika Ivancic, July 1 st 2005 This Cheat Sheet is to be used at UW-Madison as a quick guide to processing using the MestReC NMR software. You may find more help at the MestReC homepage
More informationShell scripting and system variables. HORT Lecture 5 Instructor: Kranthi Varala
Shell scripting and system variables HORT 59000 Lecture 5 Instructor: Kranthi Varala Text editors Programs built to assist creation and manipulation of text files, typically scripts. nano : easy-to-learn,
More informationSIVIC GUI Overview. SIVIC GUI Layout Overview
SIVIC GUI Overview SIVIC GUI Layout Overview At the top of the SIVIC GUI is a row of buttons called the Toolbar. It is a quick interface for loading datasets, controlling how the mouse manipulates the
More informationLinux Shell Scripting. Linux System Administration COMP2018 Summer 2017
Linux Shell Scripting Linux System Administration COMP2018 Summer 2017 What is Scripting? Commands can be given to a computer by entering them into a command interpreter program, commonly called a shell
More informationIntro to 2D NMR: Homonuclear correlation COSY, lr-cosy, and DQ-COSY experiments
Homework 9 Chem 636, Spring 2014 due at the beginning of lab April 8-10 updated 8 Apr 2014 (cgf) Intro to 2D NMR: Homonuclear correlation COS, lr-cos, and DQ-COS experiments Use Artemis (Av-400) or Callisto
More information${Unix_Tools} exercises and solution notes
${Unix_Tools exercises and solution notes Markus Kuhn Computer Science Tripos Part IB The shell Exercise : Write a shell command line that appends :/usr/xr6/man to the end of the environment variable $MANPATH.
More informationLinux Systems Administration Shell Scripting Basics. Mike Jager Network Startup Resource Center
Linux Systems Administration Shell Scripting Basics Mike Jager Network Startup Resource Center mike.jager@synack.co.nz These materials are licensed under the Creative Commons Attribution-NonCommercial
More informationName: Problem 1: (25 points) Short Answers. a) (5 points) Executing a program
Problem 1: (25 points) Short Answers a) (5 points) Executing a program Name: Following is a list of tasks that must be done to run a program written in C Sort the tasks into the order in which they are
More informationNMRProcFlow Macro-command Reference Guide
NMRProcFlow Macro-command Reference Guide This document is the reference guide of the macro-commands Daniel Jacob UMR 1332 BFP, Metabolomics Facility CGFB Bordeaux, MetaboHUB - 2018 1 NMRProcFlow - Macro-command
More informationNMR Assignments using NMRView I: Introduction to NMRView
NMR Assignments using NMRView I: Introduction to NMRView In your home directory, you should have a subdirectory called nmrview. The contents of that directory should be as shown below (subdirectories are
More informationsottotitolo A.A. 2016/17 Federico Reghenzani, Alessandro Barenghi
Titolo presentazione Piattaforme Software per la Rete sottotitolo BASH Scripting Milano, XX mese 20XX A.A. 2016/17, Alessandro Barenghi Outline 1) Introduction to BASH 2) Helper commands 3) Control Flow
More informationCA Compiler Construction
CA4003 - Compiler Construction David Sinclair When procedure A calls procedure B, we name procedure A the caller and procedure B the callee. A Runtime Environment, also called an Activation Record, is
More informationNMR Assignments using NMRView I: Introduction to NMRView
NMR Assignments using NMRView I: Introduction to NMRView For Mac OS X, you should have a subdirectory nmrview. At UGA this is /Users/bcmb8190/nmrview. The contents should look like this: -in the file hsqc.tcl
More informationFinal Exam CS4LP Time : 1 hour 30 minutes Close books
Final Exam CS4LP Time : 1 hour 30 minutes Close books 1. Briefly explain what is a physical sound and its principal characteristics. Variation of pressure propagating in space. We measure sound in decibel.
More informationBasics. I think that the later is better.
Basics Before we take up shell scripting, let s review some of the basic features and syntax of the shell, specifically the major shells in the sh lineage. Command Editing If you like vi, put your shell
More informationIntegers. N = sum (b i * 2 i ) where b i = 0 or 1. This is called unsigned binary representation. i = 31. i = 0
Integers So far, we've seen how to convert numbers between bases. How do we represent particular kinds of data in a certain (32-bit) architecture? We will consider integers floating point characters What
More informationT 1 Relaxation Measurement: The Inversion-Recovery Experiment (Using IconNMR) Revised
T 1 Relaxation Measurement: The Inversion-Recovery Experiment (Using IconNMR) Revised 4-21-2015 Relaxation times are divided into two types: longitudinal, which concerns change in magnetization along the
More informationPROCESSING 2D SPECTRA USING VNMRJ JB Stothers NMR Facility Materials Science Addition 0216 Department of Chemistry Western University
PROCESSING 2D SPECTRA USING VNMRJ JB Stothers NMR Facility Materials Science Addition 0216 Department of Chemistry Western University 1. INTRODUCTION...1 1.1. About this Worksheet... 1 1.2. A Very Brief
More informationKJM Proton T1 Spectra on the AVI-600 and AVII-600. Version 1.0
KJM 9250 Proton T1 Spectra on the AVI-600 and AVII-600 Version 1.0 Professor Emeritus Alistair Lawrence Wilkins, University of Waikato, New Zealand. February 2018 Proton T1 Spectra on the AVI-600 and AVII-600
More informationBash Script. CIRC Summer School 2015 Baowei Liu
Bash Script CIRC Summer School 2015 Baowei Liu Filename Expansion / Globbing Expanding filenames containing special characters Wild cards *?, not include... Square brackets [set]: - Special characters:!
More informationBASH SHELL SCRIPT 1- Introduction to Shell
BASH SHELL SCRIPT 1- Introduction to Shell What is shell Installation of shell Shell features Bash Keywords Built-in Commands Linux Commands Specialized Navigation and History Commands Shell Aliases Bash
More informationCS 307: UNIX PROGRAMMING ENVIRONMENT KATAS FOR EXAM 2
CS 307: UNIX PROGRAMMING ENVIRONMENT KATAS FOR EXAM 2 Prof. Michael J. Reale Fall 2014 COMMAND KATA 7: VARIABLES Command Kata 7: Preparation First, go to ~/cs307 cd ~/cs307 Make directory dkata7 and go
More informationJNTUWORLD. 4. Prove that the average value of laplacian of the equation 2 h = ((r2 σ 2 )/σ 4 ))exp( r 2 /2σ 2 ) is zero. [16]
Code No: 07A70401 R07 Set No. 2 1. (a) What are the basic properties of frequency domain with respect to the image processing. (b) Define the terms: i. Impulse function of strength a ii. Impulse function
More information2 Dimensional NMR User s Brief Guide
2D NMR Handout 7/17/18 Weiguo Hu 2 Dimensional NMR User s Brief Guide (This handout presumes your thorough familiarity with the 1D handout commands and their use!) Options There are a vast number of 2D
More informationCSE 15L Winter Midterm :) Review
CSE 15L Winter 2015 Midterm :) Review Makefiles Makefiles - The Overview Questions you should be able to answer What is the point of a Makefile Why don t we just compile it again? Why don t we just use
More informationUsing bash. Administrative Shell Scripting COMP2101 Fall 2017
Using bash Administrative Shell Scripting COMP2101 Fall 2017 Bash Background Bash was written to replace the Bourne shell The Bourne shell (sh) was not a good candidate for rewrite, so bash was a completely
More informationProcessing data with Bruker TopSpin
Processing data with Bruker TopSpin This exercise has three parts: a 1D 1 H spectrum to baseline correct, integrate, peak-pick, and plot; a 2D spectrum to plot with a 1 H spectrum as a projection; and
More informationAbbie M. Diak, PhD Loyola University Medical Center Dept. of Radiation Oncology
Abbie M. Diak, PhD Loyola University Medical Center Dept. of Radiation Oncology Outline High Spectral and Spatial Resolution MR Imaging (HiSS) What it is How to do it Ways to use it HiSS for Radiation
More informationJava Oriented Object Programming II Files II - Binary I/O Lesson 3
Java Oriented Object Programming II Files II - Binary I/O Lesson 3 The objectives in this lesson are: Convert Binary to Hexadecimals (vice versa) Understand Binary Code Use Hex Editors Explain how Streams
More informationAnisotropy-preserving 5D interpolation by hybrid Fourier transform
Anisotropy-preserving 5D interpolation by hybrid Fourier transform Juefu Wang and Shaowu Wang, CGG Summary We present an anisotropy-preserving interpolation method based on a hybrid 5D Fourier transform,
More informationExamination in Image Processing
Umeå University, TFE Ulrik Söderström 203-03-27 Examination in Image Processing Time for examination: 4.00 20.00 Please try to extend the answers as much as possible. Do not answer in a single sentence.
More informationCSImage Tutorial v August 2000
CSImage Tutorial v 1.0 8 August 2000 To use CSImage you need to have Java2 installed. Development was done using JDK 1.2.2 from Sun Microsystems. The program has been run on Digital Unix (Compaq Tru64
More informationSub-Topic 1: Quoting. Topic 2: More Shell Skills. Sub-Topic 2: Shell Variables. Referring to Shell Variables: More
Topic 2: More Shell Skills Plan: about 3 lectures on this topic Sub-topics: 1 quoting 2 shell variables 3 sub-shells 4 simple shell scripts (no ifs or loops yet) 5 bash initialization files 6 I/O redirection
More informationLECTURE 0: Introduction and Background
1 LECTURE 0: Introduction and Background September 10, 2012 1 Computational science The role of computational science has become increasingly significant during the last few decades. It has become the
More informationRelease Notes Spinsight Version 4.1
Release Notes Spinsight Version 4.1 Spinsight 4.1 can be installed over any previous version of Spinsight. It is not necessary that you have 3.5.2 before installing 4.1. Details of new software features
More informationChapter 9. Shell and Kernel
Chapter 9 Linux Shell 1 Shell and Kernel Shell and desktop enviroment provide user interface 2 1 Shell Shell is a Unix term for the interactive user interface with an operating system A shell usually implies
More informationTable of contents. Our goal. Notes. Notes. Notes. Summer June 29, Our goal is to see how we can use Unix as a tool for developing programs
Summer 2010 Department of Computer Science and Engineering York University Toronto June 29, 2010 1 / 36 Table of contents 1 2 3 4 2 / 36 Our goal Our goal is to see how we can use Unix as a tool for developing
More informationMuon Data Analysis Workshop: An Introduction to the Practicalities
Muon Data Analysis Workshop: An Introduction to the Practicalities Francis Pratt (ISIS) ISIS Muon Training Course March 2012 Outline A. Acquiring the data B. Location and format of the data C. Data analysis
More informationModule 9 AUDIO CODING. Version 2 ECE IIT, Kharagpur
Module 9 AUDIO CODING Lesson 29 Transform and Filter banks Instructional Objectives At the end of this lesson, the students should be able to: 1. Define the three layers of MPEG-1 audio coding. 2. Define
More informationImage Compression With Haar Discrete Wavelet Transform
Image Compression With Haar Discrete Wavelet Transform Cory Cox ME 535: Computational Techniques in Mech. Eng. Figure 1 : An example of the 2D discrete wavelet transform that is used in JPEG2000. Source:
More informationPROSA. Version 3.4. User s Manual
PROSA Version 3.4 User s Manual Peter Güntert Institut für Molekularbiologie und Biophysik Eidgenössische Technische Hochschule CH-8093 Zürich Switzerland December 1994 1 2 1994 Institut für Molekularbiologie
More informationImage Transformation Techniques Dr. Rajeev Srivastava Dept. of Computer Engineering, ITBHU, Varanasi
Image Transformation Techniques Dr. Rajeev Srivastava Dept. of Computer Engineering, ITBHU, Varanasi 1. Introduction The choice of a particular transform in a given application depends on the amount of
More informationProcessing With Topspin
Processing With Topspin Duncan Howe October 31, 2016 Department Of Chemistry University Of Cambridge 1 Introduction Topspin is a pretty vast piece of software and can do many, many things... There s not
More informationIBM Case Manager Mobile Version SDK for ios Developers' Guide IBM SC
IBM Case Manager Mobile Version 1.0.0.5 SDK for ios Developers' Guide IBM SC27-4582-04 This edition applies to version 1.0.0.5 of IBM Case Manager Mobile (product number 5725-W63) and to all subsequent
More information2015 The MathWorks, Inc. 1
2015 The MathWorks, Inc. 1 C/C++ 사용자를위한 MATLAB 활용 : 알고리즘개발및검증 이웅재부장 2015 The MathWorks, Inc. 2 Signal Processing Algorithm Design with C/C++ Specification Algorithm Development C/C++ Testing & Debugging
More informationComputer Vision. Fourier Transform. 20 January Copyright by NHL Hogeschool and Van de Loosdrecht Machine Vision BV All rights reserved
Van de Loosdrecht Machine Vision Computer Vision Fourier Transform 20 January 2017 Copyright 2001 2017 by NHL Hogeschool and Van de Loosdrecht Machine Vision BV All rights reserved j.van.de.loosdrecht@nhl.nl,
More informationCS2100 Computer Organisation Tutorial #10: Pipelining Answers to Selected Questions
CS2100 Computer Organisation Tutorial #10: Pipelining Answers to Selected Questions Tutorial Questions 2. [AY2014/5 Semester 2 Exam] Refer to the following MIPS program: # register $s0 contains a 32-bit
More informationCHAPTER 4 REVERSIBLE IMAGE WATERMARKING USING BIT PLANE CODING AND LIFTING WAVELET TRANSFORM
74 CHAPTER 4 REVERSIBLE IMAGE WATERMARKING USING BIT PLANE CODING AND LIFTING WAVELET TRANSFORM Many data embedding methods use procedures that in which the original image is distorted by quite a small
More informationAssignment 3: Edge Detection
Assignment 3: Edge Detection - EE Affiliate I. INTRODUCTION This assignment looks at different techniques of detecting edges in an image. Edge detection is a fundamental tool in computer vision to analyse
More informationMulti-frame blind deconvolution: Compact and multi-channel versions. Douglas A. Hope and Stuart M. Jefferies
Multi-frame blind deconvolution: Compact and multi-channel versions Douglas A. Hope and Stuart M. Jefferies Institute for Astronomy, University of Hawaii, 34 Ohia Ku Street, Pualani, HI 96768, USA ABSTRACT
More informationUseful Unix Commands Cheat Sheet
Useful Unix Commands Cheat Sheet The Chinese University of Hong Kong SIGSC Training (Fall 2016) FILE AND DIRECTORY pwd Return path to current directory. ls List directories and files here. ls dir List
More informationSIVIC Scripting Tutorial
SIVIC Scripting Tutorial HMTRC Workshop - March 23-24, 2017 Department of Radiology and Biomedical Imaging, UCSF Supported by NIBIB P41EB013598 Goal: The purpose of this tutorial is to introduce you to
More informationInstruction Sets: Characteristics and Functions
Instruction Sets: Characteristics and Functions Chapter 10 Lesson 15 Slide 1/22 Machine instruction set Computer designer: The machine instruction set provides the functional requirements for the CPU.
More informationCaching and Buffering in HDF5
Caching and Buffering in HDF5 September 9, 2008 SPEEDUP Workshop - HDF5 Tutorial 1 Software stack Life cycle: What happens to data when it is transferred from application buffer to HDF5 file and from HDF5
More informationSteen Moeller Center for Magnetic Resonance research University of Minnesota
Steen Moeller Center for Magnetic Resonance research University of Minnesota moeller@cmrr.umn.edu Lot of material is from a talk by Douglas C. Noll Department of Biomedical Engineering Functional MRI Laboratory
More informationSTP, Unix, SAC tutorial, Ge167 Winter 2014
STP, Unix, SAC tutorial, Ge167 Winter 2014 Asaf Inbal 1 Downloading waveforms In this tutorial we ll learn how to download waveforms using a tool called STP (Seismic Transfer Program) and manipulate them
More informationAccelerated Library Framework for Hybrid-x86
Software Development Kit for Multicore Acceleration Version 3.0 Accelerated Library Framework for Hybrid-x86 Programmer s Guide and API Reference Version 1.0 DRAFT SC33-8406-00 Software Development Kit
More informationMore Scripting Todd Kelley CST8207 Todd Kelley 1
More Scripting Todd Kelley kelleyt@algonquincollege.com CST8207 Todd Kelley 1 Arithmetic Output with printf Input from a file from a command CST8177 Todd Kelley 2 A script can test whether or not standard
More informationEssentials for Scientific Computing: Bash Shell Scripting Day 3
Essentials for Scientific Computing: Bash Shell Scripting Day 3 Ershaad Ahamed TUE-CMS, JNCASR May 2012 1 Introduction In the previous sessions, you have been using basic commands in the shell. The bash
More information5/8/2012. Exploring Utilities Chapter 5
Exploring Utilities Chapter 5 Examining the contents of files. Working with the cut and paste feature. Formatting output with the column utility. Searching for lines containing a target string with grep.
More informationImage Compression for Mobile Devices using Prediction and Direct Coding Approach
Image Compression for Mobile Devices using Prediction and Direct Coding Approach Joshua Rajah Devadason M.E. scholar, CIT Coimbatore, India Mr. T. Ramraj Assistant Professor, CIT Coimbatore, India Abstract
More informationWindshield. Language Reference Manual. Columbia University COMS W4115 Programming Languages and Translators Spring Prof. Stephen A.
Windshield Language Reference Manual Columbia University COMS W4115 Programming Languages and Translators Spring 2007 Prof. Stephen A. Edwards Team members Wei-Yun Ma wm2174 wm2174@columbia.edu Tony Wang
More informationLING 408/508: Computational Techniques for Linguists. Lecture 5
LING 408/508: Computational Techniques for Linguists Lecture 5 Last Time Installing Ubuntu 18.04 LTS on top of VirtualBox Your Homework 2: did everyone succeed? Ubuntu VirtualBox Host OS: MacOS or Windows
More informationDistributed Computations MapReduce. adapted from Jeff Dean s slides
Distributed Computations MapReduce adapted from Jeff Dean s slides What we ve learnt so far Basic distributed systems concepts Consistency (sequential, eventual) Fault tolerance (recoverability, availability)
More informationPackage PepsNMRData. R topics documented: November 1, Type Package Title Datasets for the PepsNMR package Version 1.1.0
Type Package Title Datasets for the PepsNMR package Version 1.1.0 Package PepsNMRData Suggests knitr, markdown, rmarkdown, BiocStyle November 1, 2018 Contact Manon Martin , Bernadette
More informationLimited view X-ray CT for dimensional analysis
Limited view X-ray CT for dimensional analysis G. A. JONES ( GLENN.JONES@IMPERIAL.AC.UK ) P. HUTHWAITE ( P.HUTHWAITE@IMPERIAL.AC.UK ) NON-DESTRUCTIVE EVALUATION GROUP 1 Outline of talk Industrial X-ray
More informationAssignment 3 ITCS-6010/8010: Cloud Computing for Data Analysis
Assignment 3 ITCS-6010/8010: Cloud Computing for Data Analysis Due by 11:59:59pm on Tuesday, March 16, 2010 This assignment is based on a similar assignment developed at the University of Washington. Running
More informationTopic 2: More Shell Skills. Sub-Topic 1: Quoting. Sub-Topic 2: Shell Variables. Difference Between Single & Double Quotes
Topic 2: More Shell Skills Sub-Topic 1: Quoting Sub-topics: 1 quoting 2 shell variables 3 sub-shells 4 simple shell scripts (no ifs or loops yet) 5 bash initialization files 6 I/O redirection & pipes 7
More informationبسم اهلل الرمحن الرحيم
بسم اهلل الرمحن الرحيم Fundamentals of Programming C Session # 10 By: Saeed Haratian Fall 2015 Outlines Examples Using the for Statement switch Multiple-Selection Statement do while Repetition Statement
More informationNMR Training VNMRJ 4.2A/VNMRS 400
NMR Training VNMRJ 4.2A/VNMRS 400 The VNMRS/new 400 MHz NMR uses VNMRJ 4.2A. Although VNMRJ is different than VNMRalmost ALL typed commands that you know from VNMR should work. LOGIN: Your username is
More informationCOMPUTER ORGANIZATION & ARCHITECTURE
COMPUTER ORGANIZATION & ARCHITECTURE Instructions Sets Architecture Lesson 5a 1 What are Instruction Sets The complete collection of instructions that are understood by a CPU Can be considered as a functional
More informationALMA Memo 386 ALMA+ACA Simulation Tool J. Pety, F. Gueth, S. Guilloteau IRAM, Institut de Radio Astronomie Millimétrique 300 rue de la Piscine, F-3840
ALMA Memo 386 ALMA+ACA Simulation Tool J. Pety, F. Gueth, S. Guilloteau IRAM, Institut de Radio Astronomie Millimétrique 300 rue de la Piscine, F-38406 Saint Martin d'h eres August 13, 2001 Abstract This
More informationFloating-point to Fixed-point Conversion. Digital Signal Processing Programs (Short Version for FPGA DSP)
Floating-point to Fixed-point Conversion for Efficient i Implementation ti of Digital Signal Processing Programs (Short Version for FPGA DSP) Version 2003. 7. 18 School of Electrical Engineering Seoul
More informationIntroduction to Shell Scripting
Introduction to Shell Scripting Evan Bollig and Geoffrey Womeldorff Presenter Yusong Liu Before we begin... Everyone please visit this page for example scripts and grab a crib sheet from the front http://www.scs.fsu.edu/~bollig/techseries
More informationASPRS LiDAR SPRS Data Exchan LiDAR Data Exchange Format Standard LAS ge Format Standard LAS IIT Kanp IIT Kan ur
ASPRS LiDAR Data Exchange Format Standard LAS IIT Kanpur 1 Definition: Files conforming to the ASPRS LIDAR data exchange format standard are named with a LAS extension. The LAS file is intended to contain
More informationPython Working with files. May 4, 2017
Python Working with files May 4, 2017 So far, everything we have done in Python was using in-memory operations. After closing the Python interpreter or after the script was done, all our input and output
More informationCSC UNIX System, Spring 2015
CSC 352 - UNIX System, Spring 2015 Study guide for the CSC352 midterm exam (20% of grade). Dr. Dale E. Parson, http://faculty.kutztown.edu/parson We will have a midterm on March 19 on material we have
More informationSynthesis Imaging. Claire Chandler, Sanjay Bhatnagar NRAO/Socorro
Synthesis Imaging Claire Chandler, Sanjay Bhatnagar NRAO/Socorro Michelson Summer Workshop Caltech, July 24-28, 2006 Synthesis Imaging 2 Based on the van Cittert-Zernike theorem: The complex visibility
More informationScripting. More Shell Scripts. Adapted from Practical Unix and Programming Hunter College
Scripting More Shell Scripts Adapted from Practical Unix and Programming Hunter College Copyright 2006 2009 Stewart Weiss Back to shell scripts Now that you've learned a few commands and can edit files,
More informationbash Scripting Introduction COMP2101 Winter 2019
bash Scripting Introduction COMP2101 Winter 2019 Command Lists A command list is a list of one or more commands on a single command line in bash Putting more than one command on a line requires placement
More information0. Procedure for Processing of NMR data
0. Procedure for Processing of NMR data 1. Choice if data processing software 2. Installation of the software 3. Obtaining NMR measurement data 4. 1D processing 5. Data output 6. Arrangement of PDF data
More informationCSE 374 Midterm Exam Sample Solution 2/6/12
Question 1. (12 points) Suppose we have the following subdirectory structure inside the current directory: docs docs/friends docs/friends/birthdays.txt docs/friends/messages.txt docs/cse374 docs/cse374/notes.txt
More informationTopic 2: More Shell Skills
Topic 2: More Shell Skills Sub-topics: 1 quoting 2 shell variables 3 sub-shells 4 simple shell scripts (no ifs or loops yet) 5 bash initialization files 6 I/O redirection & pipes 7 aliases 8 text file
More informationLong (or LONGMATH ) floating-point (or integer) variables (length up to 1 million, limited by machine memory, range: approx. ±10 1,000,000.
QuickCalc User Guide. Number Representation, Assignment, and Conversion Variables Constants Usage Double (or DOUBLE ) floating-point variables (approx. 16 significant digits, range: approx. ±10 308 The
More information