LAUEGEN - Initial Stages of Laue Data Processing

Lauegen Montage

Version Number: 6.0

John W. Campbell, CCLRC Daresbury Laboratory

CONTENTS

CHAPTER 1: OVERVIEW

1.1  INTRODUCTION
1.2  Introduction to XDL_VIEW
1.3  Running the Program
1.4  Screen Layout
1.5  Some Basic Concepts
1.6  Outline of the Main Options
1.7  Command Line Input
1.8  Cylindrical Cameras
1.9  References

CHAPTER 2: THE 'READ PARAMETERS FILE' OPTION

2.1  INTRODUCTION

CHAPTER 3: THE 'WRITE PARAMETERS FILE' OPTION

3.1  INTRODUCTION

CHAPTER 4: THE 'LAUE SIMULATIONS' OPTION

4.1  INTRODUCTION
4.2  Colour Coded Displays
4.3  Interactive Displays
4.4  Gnomonic Projections
4.5  Set Direction

CHAPTER 5: THE 'DISPLAY/MEASURE IMAGE' OPTION

5.1  INTRODUCTION
5.2  Measure Image
     5.2.1    Introduction
     5.2.2    Cursor In Centre
     5.2.3    Find Conics Centre
     5.2.4    Gnomonic Centre
     5.2.5    Reset x_cen_f, y_cen_f
     5.2.6    Input Spot Positions
     5.2.7    Read Spots File
     5.2.8    Write Spots File
     5.2.9    Clear Spots List
     5.2.10   Get Background Image
5.3  Show Predicted Pattern
     5.3.1    Introduction
     5.3.2    Display All Predicted
     5.3.3    Display Nodals Only
5.4  X-Distortion Image
5.5  Y-Distortion Image
5.6  Re-Display Normal Image
5.7  Spot Input Parameter Table

CHAPTER 6: THE 'FIND ORIENTATION' OPTION

6.1  INTRODUCTION
6.2  Spot Selection
     6.2.1    Introduction
     6.2.2    Read Spots File
     6.2.3    Measure Spots on Image
     6.2.4    Use Current Spots
6.3  The Auto-indexing
     6.3.1    Introduction
     6.3.2    The Procedure

CHAPTER 7: THE 'PROCESS' OPTION

7.1  INTRODUCTION
7.2  Processing Options
7.3  Logging Parameter Value Changes
7.4  Changing Parameter Values in Process Mode
7.5  Integration Status

CHAPTER 8: THE 'DETERMINE SPOT SIZE' PROCESSING OPTION

8.1  INTRODUCTION
8.2  Spotsize Options Menu
8.3  Control Parameters
8.4  The Procedure
8.5  Looking at the Results
     8.5.1    Introduction
     8.5.2    Show Spots on Image
     8.5.3    Spot Length Histogram
     8.5.4    Spot Width Histogram
     8.5.5    Accept New Spot Size
     8.5.6    Input Another Limit

CHAPTER 9: THE 'REFINE ORIENTATION' PROCESSING OPTION

9.1  INTRODUCTION
9.2  Refinement Options Menu
9.3  Match Spots and Refine
     9.3.1    Introduction
     9.3.2    The Match Spots Option Menu
     9.3.3    Display All Predicted
     9.3.4    Display Nodals Only
     9.3.5    Clear Matches List
     9.3.6    Input Matches
     9.3.7    Delete Matches
     9.3.8    Read Matches File
     9.3.9    Write Matches File
9.4  Select, Search and Refine
     9.4.1    Introduction
     9.4.2    Select Reflections Menu
     9.4.3    Display All Predicted
     9.4.4    Display Nodals Only
     9.4.5    Select by Nodal Index
     9.4.6    Select by Nodal h,k,l
     9.4.7    Clear Reflections List
     9.4.8    Input Reflections
     9.4.9    Delete Reflections
     9.4.10   Read Reflections File
     9.4.11   Write Reflections File
9.5  Nodals Search and Refine
9.6  The Spot Search
9.7  The Refinement Procedure
     9.7.1    Introduction
     9.7.2    Start of the Procedure
     9.7.3    Selecting Parameters to Refine and Refinement Method
     9.7.4    Completion of the Procedure
9.8  Auto-refine Plate or Auto-refine Pack
9.9  Writing '.ge' Files

CHAPTER 10: THE 'IMPROVE SOFT LIMITS' PROCESSING OPTION

10.1  INTRODUCTION
10.2  Soft Limits Options Menu
10.3  Determining 'dmin' or 'lambda-min'
10.4  Looking at the Results
      10.4.1   Introduction
      10.4.2   Normalised Histogram
      10.4.3   Un-normalised Histogram
      10.4.4   Show Results on Image
      10.4.5   Accept New Soft Limit
      10.4.6   Input Another Limit

CHAPTER 11: THE 'INTEGRATE SPOTS' PROCESSING OPTION

11.1  INTRODUCTION
11.2  Integration Options Menu
11.3  The Integration Parameters
11.4  The Integration Procedure
11.5  The 'Integrate Plate' Option
11.6  The 'Examine Last Integration' Option
      11.6.1   Introduction
      11.6.2   Examine Profiles
      11.6.3   Examine Individual Spots
      11.6.4   Integration Statistics
11.7  Auto-integrate Pack
11.8  Write Intensities File
11.9  Integration Status
11.10 Bad Spots

CHAPTER 12: COMMAND LINE PROCESSING OPTIONS

12.1  INTRODUCTION
12.2  The Processing Options
12.3  General Principles
12.4  The LG_SPOTSIZE Command
12.5  The LG_REFINE Command
12.6  The LG_DMIN Command
12.7  The LG_LMIN Command
12.8  The LG_INTEGRATE Command
12.9  The LG_WRITEINT Command
12.10 The LG_CLEARINT Command
12.11 The LG_READLDM Command
12.12 The LG_WRITELDM Command
12.13 Example of a Processing Command File

APPENDIX 1: SETTING UP THE PROGRAM

1.1  INTRODUCTION
1.2  Symmetry Operators File
1.3  Fonts
1.4  Program Modes
1.5  Automatic Parameter Updates
1.6  Compiling and Linking LAUEGEN

APPENDIX 2: THE PARAMETERS

2.1  INTRODUCTION
2.2  The Crystallographic/Pack Parameters
2.3  The Current Plate Parameters
2.4  The Extended Integration Related Parameters

APPENDIX 3: FILE FORMATS

3.1  INTRODUCTION
3.2  The Parameters File
3.3  The Spot Positions File
3.4  The Spot Matches File
3.5  The Reflections List File
3.6  The Image Files
3.7  The .ge Files
3.8  The Output Intensities File

APPENDIX 4: COORDINATE SYSTEMS

4.1  INTRODUCTION
4.2  Scanner Axes for Image Plate
4.3  Scanner Coordinates for Film
4.4  Camera Constants
4.5  Transformations

APPENDIX 5: DISTORTION CORRECTIONS

5.1  INTRODUCTION
5.2  Standard Distortion Correction
5.3  Distortion Correction for Radially Scanned Plates
5.4  Polynomial Based Spatial Distortion Correction
5.5  Addition of Centre and Conversion to Rasters

APPENDIX 6: THE PLATE CENTRE

6.1  INTRODUCTION

APPENDIX 7: FINDING FIDUCIAL POSITIONS

7.1  INTRODUCTION

APPENDIX 8: IMAGE BACKGROUND HANDLING

8.1  INTRODUCTION

APPENDIX 9: NODAL SPOTS

9.1  INTRODUCTION

APPENDIX 10: DETERMINING SPOT POSITIONS

10.1  INTRODUCTION

APPENDIX 11: SPATIALLY OVERLAPPED SPOTS

11.1  INTRODUCTION

APPENDIX 12: REFINEMENT METHODS

12.1  INTRODUCTION
12.2  The Least Squares Refinement Method
12.3  Powell Minimisation
12.4  The Automatic Refinement Protocol

APPENDIX 13: OPENING IMAGE FILES

13.1  INTRODUCTION

APPENDIX 14: RADIAL MASKING OPTION

14.1  INTRODUCTION

APPENDIX 15: INTEGRATION STATUS WARNINGS

15.1  INTRODUCTION
15.2  Integration Status Check Points
15.3  Exit From Processing Mode
15.4  Quit The Program
15.5  Reset the Program Defaults
15.6  Read a New Parameters File
15.7  Enter the Processing Mode

DEMONSTRATION 1: DEMONSTRATION FOR FIRST TIME USERS

1.1  INTRODUCTION
1.2  Preparation
1.3  Section 1: Setting Up (/Saving) Parameters
     1.3.1    Introduction
     1.3.2    Changing Values in Parameter Table 1
     1.3.3    Reading in a Parameters File
     1.3.4    Writing a Parameters File
     1.3.5    Resetting the Defaults
     1.3.6    Other Suggestions
1.4  Section 2: Laue Simulations
     1.4.1    Introduction
     1.4.2    Colour Coded Display
     1.4.3    Interactive Display
     1.4.4    Other Suggestions
1.5  Section 3: Displaying/Measuring an Image
     1.5.1    Introduction
     1.5.2    Inputting Parameters and Displaying the Image
     1.5.3    Manipulating the Image
     1.5.4    Measuring the Image
     1.5.5    Showing a Predicted Pattern
     1.5.6    Other Suggestions
1.6  Section 4: Find the Crystal Orientation (Auto-indexing)
     1.6.1    Introduction
     1.6.2    Preparation
     1.6.3    The Auto-indexing
     1.6.4    Other Suggestions
1.7  Section 5: Refining the Crystal Orientation
     1.7.1    Introduction
     1.7.2    Preparation
     1.7.3    The Refinement
     1.7.4    Writing the '.ge' Files
     1.7.5    Other Suggestions
1.8  Other Program Options

DEMONSTRATION 2: DEMONSTRATION USING TEST DATA SETS

2.1  INTRODUCTION
2.2  Preparation
2.3  Proflavin Test
     2.3.1    Introduction
     2.3.2    Setting/Saving the Parameters
     2.3.3    Laue Simulations
     2.3.4    Display/Measure Image
     2.3.5    Find the Crystal Orientation
     2.3.6    Refine the Crystal Orientation
     2.3.7    Write the '.ge' Files
     2.3.8    Improving the Soft Limits
     2.3.9    Integrate Spots
2.4  Lysozyme Test
     2.4.1    Introduction
     2.4.2    Setting/Saving the Parameters
     2.4.3    Laue Simulations
     2.4.4    Display/Measure Image
     2.4.5    Find the Crystal Orientation
     2.4.6    Refine the Crystal Orientation
     2.4.7    Writing the '.ge' Files
     2.4.8    Improving the Soft Limits
     2.4.9    Integrate Spots

FIGURES: CHAPTER 1

1.1  Main Screen of LAUEGEN

FIGURES: CHAPTER 4

4.1  Example of a Colour Laue Simulation
4.2  Example of an Interactive Rotation Simulation
4.3  Example of a Colour Gnomonic Projection

FIGURES: CHAPTER 5

5.1  Example of an Image Display (Lysozyme)

FIGURES: CHAPTER 6

6.1  Example of an auto-indexing results screen from LAUEGEN

FIGURES: CHAPTER 8

8.1  Proflavin Spot Length Histogram
8.2  Proflavin Width Length Histogram

FIGURES: CHAPTER 9

9.1  Example of a pop-up frame for selecting refinement parameters

FIGURES: CHAPTER 10

10.1  Example of a normalised histogram for a 'dmin' determination

FIGURES: CHAPTER 11

11.1  Example of a profile details window
11.2  Example of a scaled pixels plot
11.3  Example of a background subtracted pixels plot
11.4  Example of a scaled spot profile plot
11.5  Example of an integration statistics table

FIGURES: APPENDIX 4

4.1  Laboratory and Detector Axes
4.2  Ideal and Detector Axes and Camera Constants
4.3  Film Fiducial Positions

FIGURES: APPENDIX 8

8.1  Example of a background image for a Proflavin film, using the 2-Dbackground method

FIGURES: APPENDIX 12

12.1  Outline of Automatic Refinement Protocol
12.2  Flowchart of Initial Refinement Phase

FIGURES: DEMONSTRATION 2

2.1  Plot of the Proflavin film image
2.2  Plot of the Lysozyme image-plate image