Fitting - User's Guide
Contents
1. file refresh all graphics windows and clear all the variables associated with that file Another loaded file will be set as the current file if any Quit Exit IMPSTAR and returns to the IDL IDE environment Edit Menu Undo Undo the last change This is available while smoothing image Redo Redo the last change This is available while smoothing image Restore Original Restore the original image This is available while smoothing image Smooth Image Smooth current image using one of the three smooth algorithms average smooth median smooth and noise filter Smooth Options Dialog will pop up Select one of the three smooth algorithms as smoothing type Input strength with valid value that is between 1 and 100 Input box size with valid value that is between 2 and 30 Click on Smooth to begin smoothing Click on Cancel to cancel the operation and close Smooth Options Dialog Smooth Options BAX Smoothing type Average smooth x Strength 0 100 30 of final image that will be smoothed Box Size 2 30 5 amp of adjacent pixels used to smooth Smooth Cancel Figure 2 1 Smooth Options Dialog Color Tables XLOADCT Dialog will pop up This is a predefined dialog provided by IDL It displays the current Direct Graphics color table and shows a list of available predefined color tables Clicking on the name of a color table causes that color table to become IDL s current color table Click Done to ap2. of the color table the range of the Stretch Top is now black instead of the color at the original highest index With the Intensity option you can change the slider to control the intensity instead of the index location The Stretch Bottom slider will darken the color table and the Stretch Top slider will brighten the color table The Function section allows you to place control points which you can use to change the color table with respect to the other colors in that table The color table function is shown as a straight line increasing from the lowest index 0 to the highest index 255 The x axis ranges from 0 to 255 and the y axis ranges from 0 to 255 Moving a control point in the x direction has the same effects as the previous sliders Moving a control point in the y direction changes the color of that index to another color within the color table For example if a control point is red at an index of 128 and the color table is 11 green at an index of 92 when the control point is moved in the y direction to an index of 92 the color at that x location will become green af XLoadct iof x Done Help Tables Options C Function 0 E 2 Stretch Bottom 100 E z Stretch Top 1 00000 E z I Gamma Correction Rainbow Blue Waves Rainbow white Rainbow black Magenta and White Spi Figure 2 2 XLOADCT Dialog ResetColorTables Reset current color table to the default value This is useful if you want to
3. restore the default color table after selecting a color table View Menu Channel View real imaginary magnitude and phase angle data channels selectively if current file is DAT format Brighten Brighten current image in the main window Restore Restore the brightness of current image in the main window Global Display current image according to the global scale of all the loaded images This is implemented by finding the brightest and dimmest points in the entire dataset of all loaded images and scales every image accordingly This is useful when a number of different images have to be compared at the same scale factor but if one image is significantly brighter than the rest or even has one extremely bright pixel all the other images could appear very dark 12 ROI Menu Import Import an external ROI definition file as ROI of current image You can select an external ROI definition file with the File Selection Dialog The default extension name of ROI definition file is roi Look in Ga UNB MRI PROGRAM C EJ C 3DData test data Gyacciss testcode Animator UNF esv junisort2 Dat yYanazhi etc 2 1 fitting 412 CgGradient Tables 4 3 C GRADTABLE 14 7 Qimpstar 4 8 lb HMRI small _progs_for ja ROI Song C SummerStudent Temp r SE roi v Figure 4 1 File Selection Dialog for importing ROI definition file Export Save ROI of current image as a
4. similar way for example acciss fitting and unisort IDL Virtual Machine In order to run IMPSTAR and other MRI programs on a computer without IDL you will need to include a runtime version of IDL with a runtime or embedded license in your application distribution The IDL Virtual Machine M IDL VM is a free IDL runtime environment available with the release of IDL 6 3 CD which can also be downloaded from the RSI web site You can use the IDL Virtual Machine to open the sav file which is a stand alone IDL application that can be run on any Windows UNIX or Mac OS X computer containing the IDL Virtual Machine or a licensed copy of IDL Therefore in order to run IMPSTAR without IDL installed please use the IDL Virtual Machine to open the IMPSTAR sav file The Interface of IMPSTAR This section describes the functionality of each of IMPSTAR s four graphics windows The user can switch between the histogram window and the contour map windows by clicking the tabs at the top of the window The Main Window e eme N EIL Status Coordinate 102 3 6 000000 This window is used for displaying current image or associated profiles The title bar above the main window displays the version information and the name of the current file There are eight buttons at the left side of the main window The first four buttons are used to define ROI of current image The next one is used to edit ROI point by point The last t
5. 1data060710 003 4888 a Copy of slice2D a data 1 FT 4 data RAW ia recent ia slice2D a flowing 600u 7cm 13 cylinder a flowing 600u 7cm 13 cylinder ft 4 flowing 600u 7cm 13 cylinder pc 2 UNB MR 2 UNB MR 2 UNB MR 2 UNB MR I7 UNB MR la Yang 3 w 3 Save as type to be overwritten or input a new file name You can also save the statistics data as TEXT format After clicking on Statistics menu item a File Selection Dialog dat DAT x Figure 1 2 File Selection Dialog for writing file will be available to select a file to be overwritten or input a new file name The integral values of all the loaded files can be saved into a text file After clicking on Integrations menu item a File Selection Dialog will be available to select a file to be overwritten or input a new file name Print Print the histogram or contour map of all loaded files depending on which is currently displayed Print Dialog will pop up with default layout You can select the number of columns to change the layout The default scale factor is 1 Click on _Cancel_ Invert button to perform black white inversion Click on Print to print out the histograms or contour maps a Contourmap Print Window BAX Number of columns 2 Scale factor 1 Invert Print f 10 20 30 40 CONTOURMAP data 1 FT dat Figure 1 3 Print Dialog Close Close the current
6. 2 3 aood la static_6 ue ChenXH itj h mt 48 Copy of dataExcell02 E hist jTi ia Copy of slice2D Hist 4 T2 My Documents a data 1 FT la recent T7 4 data JRAW ijs Ka jui My Network File name Places Files of type dat csv jpg jpeg tif tiff Figure 1 1 File Selection Dialog for reading file Save This sub menu contains commands to save current image current ROI histogram statistics data and integral values If you click on Current Image menu item File Selection Dialog will pop up Please select a file to be overwritten or input a new file name The current file will then be saved in DAT format Note that DAT format is the default file format for IMPSTAR 2 1 and it can be handled by all other IDL programs in MRI Center Please Select a File for Writing My Recent Documents 2 Desktop My Documents 98 My Computer My Network Places Similarly you can also save the ROI portion of the image in DAT format You can save the histogram of the current image as TIFF or JPEG format by selecting appropriate menu item File Selection Dialog will be available to select a file Save in ug MRI PROGRAM 4 c Eg r C3 3DData Cjacciss c Animator cv Dat c Etc fitting CQ Gradient Tables C GRADTABLE impstar liib small_progs_for Song iC summerStudent Temp sal test data testcode UNIF junisort2 YangZhi 4
7. IMPSTAR 2 1 User s Guide Last Update July 2006 by Biao Wang Table of Contents iQ UID MI Functionality Sumilary 2 pnr toon e eor ros euo aane ses senes iae o ee by Ege e e Sao ORE ER TREES CS saeensssesssseuscssnesssabegoneesbessssossssesesseseD Running IMPSTAR oerte aeree neve see a esee peces eesstereessupeseeveseseesseueseessesveenesvexess sec S reedis e eer aug 4 The Interface of IMPSTAR 5 roseo re tritt nues ano soa ee sean og es ora evo se esee pee eee ps desee esee uses rece tegess tope eese 4 Th Main WindOw 29 deepest rece t e NEEE ENIS A eae es oinessvecsU sepes vr e Usvbossese eU ssi ee ege e UR SE Us PbeS Qe S 4 Th Histogram Wind Wers iire eere eoi so sides oo Y yov a paises Exe vec sab dle nie vert esi deb pet eckuesu veo o Eee sabe E TY E e ees ree aas 6 Th Contour Map WindOWw ese rees eee nassa enses tess edeseoveeseccsesss pases cdesessbeceteesseaseeseted ENEE Enin nansa ses 7 Whe Stat Wind OW 5 035 oes deseck vs oy cewek ees oe etree ls oh obese Sok aes oe eke vhs oben es bade dea TIRER AEAEE sets 7 The Menu Commands sseccccsscicscsdecsescscoescecedsccescuscgesdes odes secevscdeensedesscescecescsscbacdovecuseceseseveeseeecewessesees 8 File MENMU E 8 lb MENU mr 19 Image Ca
8. g image calculator Smooth image Select color table Reset color table Print histograms or contour maps Save image histogram or statistics data Running IMPSTAR 2 1 IMPSTAR is developed under Research Systems Inc s IDL 6 3 Integration Developing Environment IDE Normally IDL 6 3 needs to be installed with a valid license first and then you can run IMPSTAR at the IDL command line The detail information on how to run IMPSTAR on Windows and Mac computers is described below How to run IDL and IMPSTAR on Windows 1 Start IDL 6 3 by double clicking IDL 6 3 icon on the desktop 2 If you want to run IMPSTAR simply enter the command impstar at the IDL command line Note that each MRI program should have a main program name which can be entered in the command input window in a similar way for example acciss fitting and unisort How to run IDL and IMPSTAR on MAC OS X 1 Start X11 typically by clicking a button on the application toolbar or by running the program called X11 in the Applications folder The X11 program is an emulator made by Apple to allow you to run graphical UNIX programs on Mac OS X 2 Select the option Application gt IDLDE from the menu bar of X11 at the top of the screen to start IDL 6 3 3 If you want to run IMPSTAR simply enter the command acciss at the IDL command line Note that each MRI program should have a main program name which can be entered in the command input window in a
9. hree buttons are used to extract a profile from the image along different directions There are hints if you move the cursor over these buttons There are two non editable textboxes below the main window One is used to display system status Aonthser is used to display the coordinates of the current point and its associated intensity The Histogram Window Histogram Contour 10 15 25 25 420 Intensity 100 0 AM data 1 FT dat Intensity 15 Numbers 27 30 4 2 gt This window displays the associated histogram of the current image There are two non editable textboxes below this window One is for intensity value another is for corresponding number of points When you move cursor within the histogram window using mouse the current intensity that the cursor stands for is displayed in the intensity textbox and the corresponding number of points that have this intensity value is displayed in the number textbox This will help to analyze the histogram There are also two sliders below these two textboxes which are used to define the scope of the histogram i e the maximum and minimum values to be considered The Contour Map Window Histogram Contour 30 data 1 FT dat Thils window displays the associaated contour map of the current image The Stat Window Area 4096 Area Min Mean Variance Integral over ROI 17591 8 This window displays the statistics data of the current i
10. le Men ee eee see seesessve see a eu ues ae ce detache dees sssed dee sleacveevevesewete ed V vk SSES ENTE ta e aereo 19 hana m 20 Introduction IMPSTAR IMage Processing STatistics And ROI is a program that allows users to perform image analysis At first many researchers at the MRI Centre used two IDL programs by David Axelson called II pro and II zoom pro as image analysis tools which are the basis for Impstar Impstar 1 0 was written by James Rioux in 2003 The current version is Impstar 2 1 which was written by Biao Wang in 2005 This document outlines the basic functionality of Impstar and all the menu commands and dialog boxes available to the user For more information on how IMPSTAR itself operates please consult the IDL source code on one of the data analysis computers in Room 110 Functionality Summary IMPSTAR is meant to provide various image statistics and analysis functions It can currently do the following Read DAT BYTE format and Bruker files generated by other programs such as Acciss Define ROI by various methods Display ROI in one of three modes Edit ROI point by point View or export ROI portion of an image Calculate integral over ROI Convert to any image conveniently View real imaginary magnitude and phase angle data channels selectively Display an image either in brightened mode or normal mode Perform image calculation usin
11. mage There is a non editable textbox below the stat window which is used to display the summary of intensities of all the points within ROI The Menu Commands This section provides a brief overview of the functions performed by the menu commands available in IMPSTAR 2 1 More information on the details of these commands may be found in other sections of this User s Guide File Menu Open Load files of DAT Bruker CSV JPEG or TIFF format into the program Select the files to be loaded using the File Selection Dialog Please change File of type to if you want to open a Bruker file so that it will be listed On most operating systems you can use the Ctrl and or Shift keys to select multiple files The image of the current file will then be displayed in the main window The file name of the current image is displayed in the bar above the main window You click on the Images menu to select another file as current file Note that only 2D data is supported by IMPSTAR 2 1 Select Image file s to read in X I 600x800 Ij data 6 Esi t 800 Bexcello fj Sample 1 My Recent 4 ass amp Excello2 E Samplez Documents al VExcello7 itj Sample 3 irj aa S amp Excellos Scan aa 3 amp Excelloo screen Desktop Chen 170x170 i4 flowing_600u_7cm_13_cylinder 4 slice2D Chen256x256 la flowing_600u_7cm_13_cylinder_ft SliceGro ee Chen512x256 a flowing 600u 7cm 13 cylinder pc 4 static_6 Chen512x51
12. n external ROI definition file File Selection Dialog will be available to select a file to be overwritten or input a new file name The default extension name of ROI definition file is roi test data O testcode CQUNIFIT CQunisort2 Co Yanazhi lia 1 lia 2 E Gradient_Tables 4 3 C GRADTABLE a7 Qimpstar 4 a Bib 4 MRI C3small progs for 4 ROI song Cj SummerStudent Temp Figure 4 2 File Selection Dialog for exporting ROI definition file Display Select one of the three ROI display modes Fill Outline and Hide The default ROI display mode is Fill mode Figure 4 3 ROI display mode Fill 15 Figure 4 4 ROI display mode Outline Figure 4 5 ROI display mode Hide View ROI Only Only ROI portion of the image is displayed Figure 4 6 View ROI portion only Invert ROI Clear current ROI and convert the rest portion of current image as ROI Figure 4 7 Invert ROI Clear ROI Clear current ROI and the whole image is regard as ROI Apply ROI to All Apply ROI of current image to all loaded files Images Menu Select a file as current file from a list of loaded files and refresh all the graphical windows ImageCalc Menu Perform image calculation with Image Calculator Dialog Build an equation from the images and operations below and press calculate HAAA Gem Calculate Finished Figure 4 8 Image Calculator Dialog Help Menu Contents Display this use
13. ply the selected color table The Stretch Bottom slider in the XLOADCT Dialog increases the range of the lowest color index For example if black was the color of the lowest index and you increased the bottom stretch by 50 percent the lower half of the color table would become all black The remaining part of the color table will contain a scaled version of all the previous color ranges The Stretch Top slider in the XLOADCT Dialog increases the range of the highest color index For example if white was the color of the highest index and you increased the top stretch by 50 percent the higher half of the color table would become all white The remaining part of the color table will contain a scaled version of all the previous color ranges You can change the contrast within the color table using the Gamma Correction slider in the XLOADCT Dialog A value of 1 0 indicates a linear ramp no gamma correction Values other than 1 0 indicate a logarithmic ramp Higher values of gamma give more contrast Values less than 1 0 yield lower contrast XLOADCT Dialog also contains two other sections Options and Function The Options section allows you to change what the sliders represent and how they are used When the Gang option is selected the sliders become dependent upon each other When either the Stretch Bottom or Stretch Top sliders are moved the other ones reset to their default values 0 or 100 respectively With the Chop option you can chop off the top
14. r manual in a pop up window About Impstar Display version information in a pop up window IMPSTAR IMage Processing STatistics And ROI program Version2 1 Author Biao Wang Based on codes of David Axelson amp James Rioux Supervisor Dr Bruce Balcom amp Dr Bryce MacMillan Modified by Biao Wang Date August 30 2006 20
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