BeamSchemeV1: A Pascal repository from alanphys

1) Introduction
Welcome to BeamScheme

BeamScheme is an analysis tool for 2D datasets. It will assist you in extracting 1D profiles from 2D datasets and can calculate over 90 different parameters. BeamScheme can open various image and 2D array file formats such as SNC MapCheck, PTW 720, IBA Matrix and StarTrack, Eclipse, XiO, BrainLab, DICOM, jpg, etc.

Parameters include field size, field centre, penumbra, flatness and symmetry. FFF beams are supported with both maximum slope and sigmoid fit parameters available. Profiles can be taken at any angle, offset or thickness. Profiles can be exported to a text file or clipboard for further processing. Results can be exported to PDF.

BeamScheme is not intended to replace the commercial software available with 2D arrays, but to complement it.

2) Licence
Please read the file Licence.txt. This means that if as a result of using this program you fry your patients, trash your linac, nuke the cat, blow the city power in a ten block radius and generally cause global thermonuclear meltdown! Sorry, you were warned!

3) Installation
BeamScheme V1.00 is not compatible with previous versions of BeamScheme. While it is not necessary to uninstall previous versions all data in the program executable directory and the program configuration directory will be deleted before installing the new version.

To install BeamScheme run the BSSetup.exe file.

From version 1.01 BeamScheme features a USB disk install where the files can be extracted to a directory of your choosing and run.

4) Use
Run the program by double clicking the desktop icon, selecting the "BeamScheme" menu option or double clicking the BeamScheme.exe file in Windows explorer

Open a file by clicking the Open button or selecting "File,Open". If you don't see any files make sure the correct file type is selected.

Use the Offset, Width and Angle boxes to manipulate the profiles.

Windows can be maximised and restored by clicking the arrow in the top right hand corner of the window.

5) Validation
BeamScheme features extensive internal and external validation against commercial and open source software. Please see the unit tests directory for more information.

6) Notes on using 2D Array files
For correct field sizes the detector plane of the 2D array must be at 100cm SSD.

There will be small differences between the flatness and symmetry reported by BeamScheme and your 2D Array. This is due to differences in the algorithms. The differences should not be more than 0.05%.

7) Notes on using EPID images
No correction for SSD is made. You will have to apply corrections yourselves at this stage.

It is recommended that an EPID calibration be done before acquiring images to get the best image quality.

If you have an integrated imaging mode, use this as it will give you a better image.

DICOM images will usually need to be inverted (by clicking the Invert button) and then normalised (by clicking the normalise button).

8) Notes on normalising
The program uses the normalised, corrected 2D array data. No normalisation should be necessary for the 2D arrays if they have been calibrated and zeroed correctly.

There are three normalisation modes. None, CAX or maximum. Normalisation places the minimum of the image at 0 and the CAX or maximum value at 100. If the image contains dead pixels, burn markers or other strange artifacts it is possible for the normalisation to fail and give you strange results. This is not the fault of the program but of the image. See the previous comment about calibration. Normalisation acts on the windowed data and is non-destructive.

9) Release notes
These detail new or changed functionality in BeamScheme. Please see the History for bug fixes.

Version 1.01
FFF parameters according to NCS-70 have been included. Extensive testing of the maths functions has been added. Additional protocol validation has been added. The help web server has been removed. Help is now served directly from file. This version can be run from a single directory such as a usb disk.

Version 1.00
BeamScheme v1.00 is virtually a complete rewrite of BeamScheme featuring a new parameter calculation engine. The code has been extensively modularised making it easy to add new parameters. New algorithms have been implemented with individual parameter calculation. Extensive unit testing has been implemented. The GUI has been updated. The expression parser has been dropped and all parameters are calculated in the code. Efficiency is achieved by only calculating needed parameters.

Version 0.54
This is a bug fix release.

Version 0.53
Normalisation is now modal, i.e. non destructive. The normalisation modes are none, norm_cax and norm_max. In mode none the dataset is unnormalised and not grounded with the reference value taken at CAX. For norm_cax the data is grounded and normalised to 100% at the CAX value. For norm_max the data is grounded and normalised to 100% at the profile maximum value. The normalisation modes are enabled by the appropriate toolbar button.

Version 0.52
This version adds support for FFF beams. A Hill function is fitted to the penumbra region to determine the inflection point. Clipboard functionality has been added. Profile and results can be exported to the clipboard. The profiles and results now have context menus giving direct access to this functionality. The online help has been updated.

Version 0.51
BeamScheme now uses Form2PDF to render results to PDF. This has several advantages, the image is printed with the results, considerably less mouse clicks are required to save results and the results are printed as the form itself. The hard copy functionality has been removed. The PDF can, of course, still be printed by any PDF viewer.

Version 0.50
Help has been updated

Parameters are no longer auto normalised. Eg. the field edge or 50% value was calculated on the 50% value between the maximum and minimum of the profile. Now it is calculated on 50% of the maximum of the profile only. The user must explictly normalise the data if the normalised value is required. This is to bring BeamScheme in line with other programs.

Added an expression parser. This allows different parameter sets to be defined. The user can also define parameter sets. Expression editing has been included. Output has been updated to provide for mulitpage output.

Version 0.42
Added new About unit detailing readme, licence and credits.

Version 0.41
Added Average and Standard Deviation parameters over the flattened region of the profiles

Version 0.40
Profiles can now be positioned by clicking on the image with the mouse.

10) Known issues
Windows does not automatically focus the control under the mouse cursor therefore the context sensitive help may return the wrong help page.

11) History
22/07/2008 version 0.1
3/09/2009 added DICOM unit
22/8/2011 Fix field centre error,
Fix Y resolution error for MapCheck 2
28/09/2011 removed MultiDoc
added invert
added normalise
added windowing
fixed profile display
fixed symmetry calculation
cleaned up printout
Version 0.2 released 1/8/2011
22/8/2011 Fix field centre error,
Fix Y resolution error for MapCheck 2
15/2/2012 Fix CAX normalisation error,
2/4/2013 Add read for XiO Dose plane file
20/6/2014 Removed redundant DICOM read code causing memory bug
24/6/2014 Fixed XiO read offset by 1
Fixed MapCheck read if dose cal file not present
Included Min/Max as part of beam class
Fixed panel maximise to form area
21/5/2015 combine open dialog and DICOM dialog
20/7/2015 add messaging system
Version 0.3 released 20/7/2015
26/8/2016 Add normalise to max
28/6/2016 Support PTW 729 mcc
29/9/2016 Fix PTW 729 memory error
21/10/2016 Add PowerPDF for output
24/10/2016 Fix Profile event misfire
15/8/2017 Fix image integer conversion
13/10/2017 Support IBA Matrix and StartTrack opg
16/10/2017 Fix Diff divide by zero error
Fix profile offset limit error
18/11/2017 Fix even number of detectors offset
15/12/2017 Support Brainlab iPlan Dose plane format
Add text file format identification
8/1/2018 Add help system
Fix windowing error on normalise to CAX
25/1/2018 QT5 version must be compiled on Lazarus 1.9 r57132 for correct image display
26/1/2018 Fix panel maximise under QT5
Fix window level control size under max/min
30/1/2018 Fix area symmetry off by 1
Fix CAX for even no of detectors
1/2/2018 Add mouse control for profiles
2/2/2018 Fix off by 1 error profile limits
Version 0.4 released 2/2/2018
27/3/2018 Fix regional settings decimal separator
3/4/2018 Add mean and standard deviation
Fix profile increment
30/4/2019 Fix DTrackbar if image max = maxlongint
3/5/2019 Fix DICOM off by one and pointer conversion
17/7/2019 Update about unit
18/7/2019 Update status bar
23/7/2019 Add expression parser
30/7/2019 Add multipage output
31/7/2019 Fix profile export dirs
1/8/2019 Add expression editor
14/8/2019 Remove auto normalisation of profile values.
Fix previous image and profile display on open image cancel
11/9/2019 Fix prompt for overwrite results
Fix protocol list unsorted on reload
Add Quit Edit menu item
16/9/2019 Fix Y axis swapped for IBA files
10/10/2019 Change BitButtons to SpeedButtons on protocol edit toolbar
Fix cancel on protocol save
Fix edit flag on protocol edit exit
Correct result window title on edit
23/10/2019 Updated help
Fix click on empty Image pane crash
25/10/2019 Fix user protocol path
Version 0.5 released 25/10/2019
16/4/2020 Fix various memory leaks
6/8/2020 use Form2PDf for printing PDF
fix SaveDialog titles
remove results unit and PowerPDF
24/8/2020 add get correct resolution for tiff images
18/9/2020 fix range check error in calcparams
add inflection points
neaten filename display
22/9/2020 support raw text file
29/9/2020 shift maths routines to unit mathsfuncs
30/9/2020 shift types and constants to unit bstypes
use Hill function non linear regression to determine inflection points
add copy profiles to clipboard
1/10/2020 use parser.SetVariable for performance enhancement
fix status warning display
add FFF params inflection point, 0.4*InfP (20%) and 1.6*InfP (80%)
7/10/2020 add copy results to clipboard
make Protocol read only while not in edit mode
add context menus for X Y profiles and results
8/10/2020 fix duplicate text file open
fix RAWOpen range check error
add sigmoid slope for penumbra
add position of max
fix protocol name change on edit
add profile points for FFF
14/10/2020 add app version
20/10/2020 fix file extensions
5/11/2020 update help
17/11/2020 fix resolution for tiff files
7/12/2020 add normalisation to max for calcs
11/12/2020 make normalisation modal, i.e. non destructive
change toolbar panel to TToolBar
14/12/2020 select default protocol on startup
3/3/2021 fix FFF penumbra slope
11/9/2021 fix recognise files with tiff extension
4/10/2021 fix ShowProfile and refactor
fix initialise vars
profile draw on trackbar change
14/10/2021 Remove sExePath in file Open
22/10/2021 move DisplayBeam into Beam class
create drawfuncs unit
create import unit
shift toolbar to form, resize form
fix profile position on mouse click
29/10/2021 redesign GUI with new icons
2/11/2021 add settings unit
add return error code from form2pdf to status bar
3/11/2021 add paramfuncs test unit
4/11/2021 add bstypes test unit
5/11/2021 refactor drawprofile
17/11/2021 rename paramfuncs unit to param1Dfuncs
18/11/2021 implement param2Dfuncs unit
19/11/2021 split PArr array of TProfilePoint into two arrays of double
22/11/2021 move beam min max into TBeam class and refactor
change XiO distance units to cm for consistency
fix windows bitmap default resolution
add import unit tests
add 2D param unit tests
25/11/2021 fix Beam Min initialisation
fix profile left edge find
2/12/2021 change Beam.Display to procedure
add show parameters
fix bug in DTrackbar.UpdateTicks integer overflow causing infinite loop
add scale display on normalisation
10/12/2021 add MaxPosNan and MinPosNan to mathsfuncs as LMath does not handle Nans
fix profile bug in MaxNorm and CAXNorm
17/1/2022 create IFA data types and add to settings unit
19/1/2022 create circular IFA
create TBasicBeam data class, derive TBeam and define IFA as TBasicBeam
20/1/2022 fix SingeProfile IFA if edges not found
move Invert to TBasicbeam and create test
finally remove 2x col offset in Data from legacy MapCheck
move Centre to TBeam and create test
fix invert and centre crash with no file open
24/1/2022 show full file name in cImage hint
fix display file name correctly on image maximise
27/1/2022 set profile angle limits to corners of image
create TSingleProfile.ToSeries and refactor
28/1/2022 shift Limit and LimitL to mathsfuncs
split calcprofile into drawing and calculation routines
shift to bstypes and refactor, delete drawfuncs
31/1/2022 remove overlimit compensation in CreateProfile
1/2/2022 fix profile grounding bug in param1Dfuncs
add TSingleProfile.ToString and refactor
2/2/2022 fix rounding error on profile increment
create TBasicProfile, derive TSingleProfile and define IFA as TBasicProfile
14/2/2022 add definable precision
9/3/2022 add show/hide profile points
add peak params to TSingleProfile, refactor
14/3/2022 fix window limit on normalise to centre
2/6/2022 add relative centering to peak and absolute to detector to IFA
24/6/2022 make maxposnan bidirectional, add differential params
20/7/2022 add sigmoid function and params
16/8/2022 fix infinite loop error with small floats, add rescale
4/11/2022 add field centre and size for sigmoid and derivative functions
7/11/2022 fix infinite loop for small dynamic range images
8/11/2022 add penumbra for sigmoid function
15/11/2022 add normalise function to TSingleProfile and refactor
16/11/2022 fix TSingleProfile.Res initalisation and range check errors
add dose points
13/1/2023 add ShowPoints to View menu
fix dangling ShowParameters in View menu
fix Invert toggle
3/2/2023 update help
6/2/2023 fix config directory creation
fix formatting issues in Windows
7/2/2023 fix protocol save path under Windows
change protocol dir from exe or program config to both
fix protocol save errors
fix memory leak in buildprotocol
fix crash on protocol edit exit
Version 1.00 released 7/2/2023
22/9/2023 add status history to settings unit
28/9/2023 add test unit for maths funcs
14/12/2023 add top and peak slope to FFF params
18/12/2023 look for config file in program dir as well
remove web server for help
5/1/2024 fix max pos 1D param
fix behaviour on invalid protocol

alanphys/BeamSchemeV1