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Contents
Contents
The STXM V User's Manual
Holger Fleckenstein, Benjamin Hornberger, Mirna Lerotic, Chris Jacobsen, Michael Feser
Contents
List of Tables
List of Figures
User Information
STXM Principle and Overview
STXM Principle
STXM 5 Coordinate System
Scan Devices
Detectors
Outboard Detectors
Inboard Detectors
Running STXM V: The Essentials
Overview
Brief
SM_GUI
Overview
Using the Visible Light Microscope (VLM)
Exchanging specimens
Changing specimen mounts (
e.g.
, wet cell)
Taking Scans
Moving the Sample and other Scan Devices
How to find and record the X-ray focus
Changing the photon energy
Acquiring point spectra
Recording defocused point spectra
Acquisition of spectromicroscopy ``stacks''
Short and Simple
In Detail
Running STXM V: Inboard Particularities
Taking Care of the Segmented Silicon Detector
Filling the chamber with helium
Venting from helium to atmosphere
Using the helium flow system
Wet Cell
The
SM_GUI
Graphical User Interface
Starting
SM_GUI
Starting
SM_GUI
in a licensed IDL session
Starting the precompiled version on the Virtual Machine
More options to choose the program mode
GUI overview
The Draw Windows
Display Parameters Area
The Histogram Display
Spectra Settings Area
Signal Type, Detector and Display Area
The Display Information Area
Marking rectangles in an image
Fitting spectral peaks
The "Move Scan Devices to Mouse" button
The "Recenter Piezos" button
The Microscope Control Area
Shutter Control
Beamline Control
Silicon Detector -- Calibrate Now
The File Menu
Opening and Saving Data Files
Data Export
Printing
Additional Entries
The Alignment Menu
The Scan Menu
The Move Menu
The Extra Menu
Change Colortable
Use Nearest Neighbor Sampling on Zoom (no Interpolation)
Display Crosshair on Mouseclick Position
Plot Noise per Line in iTool
Image Processing
Edit Pointlist
Statistics
Zoom In, Zoom Out
Set up Stack
Start Stack
STXM 4 Display Settings File
Re-read Config File
APS File Read Settings
The Advanced Menu
Use Laser Positions
Homing
Track ZSTG in Spectra
Adjust Feedback Parameters
Monitor ADC Signal
Calibrate SGM
The Help Menu
The Toolbar
STXM 4 Support
APS Data File Support
Restrictions
Availability of Signal Types and Meaning of Data Values
APS File Read Settings
The
SM_GUI
config file
Running STXM V: Problems and Frequently Asked Questions (FAQ)
Help! I can't see my sample, the image is all black! (Or white)
Help! What's the difference between opening / saving data files files on the server and locally?
Help! I want to take a scan, but I have only one scan type to choose from in the scan menu!
Help! How can I print directly to the printer on Unix machines, rather than to a file?
Help! My scans on the inboard STXM look very noisy!
The scanning program (sm_gui) can't connect at startup
sm_server has crashed
Another client is connected
Your connection settings are wrong
The scanning program (sm_gui) get's stuck at startup
How do I remount the
data
folder?
What to do if the computer window seems locked up
Rebooting the computers
Rebooting the client computer (Linux)
Rebooting the server computer (Windows)
Beamline EPICS motors:
x1a_mot_server
Beamline printer problems
After a crash
Advanced information
The Scan Process in more Detail
Scan Types in the Scan Menu
The Scan Setup Window
Detector channels to record
The Scan Process
Scanning the Monochromator (EV)
Scan Direction
Linearity in Monochromator Scans
Scan Directions and the Orientation of the Image
Obtaining Data Files for later Analysis
File Naming Conventions
Downloading Data Files from the Web
Burning Data Files to CD / DVD
Accessing Recent Data Files
Directly in the microscope control program
From the thumbnail website
From the file system in the
X1A
network
Which Data STXM 5 Records -- STXM 5 Display Concept
The 3-dimensional Dataset
Which Signals are read by Default
Signal Types ("Flavors")
Raw Integers (
image_data_intraw
)
Raw Counts / mVolts (
image_data_raw
)
Calibrated kHz (
image_data_khz
)
Predefined Combinations
Custom (User-defined) Display Combinations in
SM_GUI
Choosing Different Signals in
SM_GUI
and
read_stxm5.pro
Choosing the Display in
SM_GUI
Choosing the Display in
read_stxm5.pro
Predefined Combinations
Reading and Understanding STXM 5 Data Files
The Contents of STXM 5 Data Files
Viewing Data Files in
SM_GUI
Reading Data Files on the IDL Command Line
Reading Point Spectra
The
sm_par
Structure
Writing STXM 5 Data files with
write_stxm5.pro
Changing / Overwriting Data Files
Silicon Detector Calibration
Calibration Model
Calibrating the Detector
The Structure of the netCDF File
Data File Format Changelog
Client-Server Concept and Networking How-To
Client-Server Concept
X1A and NSLS/BNL Network Structure
Microscope Remote Control
x1a
subnet
BNL intranet
Outside world
Tunnelling the VLM
Access to Data Files "Locally" and "On the Server"
Alignment of STXM V
Homing of stepping motor stages
Initial alignment
Visible light microscope (VLM) setup
Detector prealignment
Beam into the chamber
Aligning microscope components
Correcting the tilt of the ZSTG axis with respect to the beam axis
Determining the drift parameters
Software correction
Hardware correction
Aligning the laser interferometer
Aligning the mirrors
Adjusting the receiver gain
Aligning inboard STXM to the Nitrogen edge
Mounting of ZP and/or OSA on glass cones
Configuration and alignment files
The alignment file
The configuration file
The silicon detector calibration file
The beamline slitsettings file
The NSLS ring parameters file
Moving Motors with the XPS Controller
Web Interface
Remote Control
Bibliography
About this document ...
Holger Fleckenstein 2008-07-08
