doowah2004's scratchpad

Public Scratchpad

Section 01:
Ok, probably more info than you want to know, but here is the full scoop:

I work as a medical physicist and as part of the job we have to verify that the radiation that we are giving to the patient is what we thought it was. How do we do this?

We plan the patient on a 3D planning system based off of a CT image set. We use the CT numbers (Hounsfield numbers) to determine the electron density in any given region, and then can determine how the radiation will be affected (attenuated) and converted into dose. When we have a plan that we like and the physician is happy with, we then take all of the parameters from the plan (beam angles, shapes…) and deliver that to a phantom. { a phantom is a device for which the makeup and geometry is well know, often it is made of solid water (a plastic with radiological properties within the range of treatment energies, 4MV ~ 20MV photons and 6MeV~22MeV electrons, nearly identical to that of water)}.

The phantom also has a CT study and we can get a 3D plan similar to the patient. In my case the phantom comes in 2 pieces, a 5cm thick piece on top, and a 5cm thick piece on the bottom. The top piece has 7 holes in the same orientation as shown in my post about the film. We put a piece of XV film between the 2 pieces of the phantom, mark the film with punctures at the holes and deliver the treatment. We can now compare the dose delivered to the film to the calculated does at the same plane as the film. To do this we have to register the film with the calculated plan. We will always align the phantom to the treatment machine, but the film has ~ .5-1cm of play, so we do not have consistency between films, so we can not assume that the points are always at the same location, but we can be fairly certain that they are in the same region. We can process up to 50 of these films a day (currently this number continues to increase).

The minimum number of points to have a good registration is 4.

What I have done so far is to write a macro for imageJ to find points that meet a certain criteria within the region of interest, and then write to a file the matching points.
ImageJ out puts it in the following format:

1    X    Y
2    X    Y
3    X    Y
.
.
.
N    X    Y
1    X    Y
2    X    Y
.
.
M    X    Y
1    -1    -1
1    X    Y
.
.
[download]

The first column describes the points, every time there is a new “1” it is in a new ROI. I will get you the ROI order with the actual data. The second and third column is self explanatory. If there is a “-1” in it, it means that no points were contained in that ROI.

I wrote a very rough/simple script to import the data (it is ugly, I was only going for expedience in writing, I always clean things up after they work…and I am not good enough to write good code first time through) Here it is if you want it:

my $i = 0;
my $toggle = -1;
my @p = qw|ROI1 ROI2 ROI3 ROI4 ROI5 ROI6 ROI7|;
my @points,%ROI;
open (POINTS, "<points.txt");
while (<POINTS>) {
    chomp $_;
    my $a,$b,$c;
    ($a,$b,$c) = split(/\t/,$_);
    if ($a == 1) {
        $toggle *= -1;
        if ($toggle < 0) {
            $i++;
            $toggle = 1;
        }
    }
    if ($b == -1) {
        $i++;
        $toggle = -1;
    } else {
        push @{$p[$i]}, [$b,$c];
    }
}
[download]

Also I wrote a script to filter the points and remove any points that can not be valid (i.e. less then 4 adequate distances). This I did not test, do not have actual data yet, will have the data today or tomorrow.

# this is sent the roi info and the distances from that point to all o
+f the other points from the template
#$index pulls in the roi info, @deltas then pulls in the distances.
#if there is a match from a point in the region in question and the re
+gion it is testing against, it stops testing against that region and 
+increments its success, if it has 4 successes, it stops checking that
+ point.  If at the end it does not have 4 successes it splices that p
+oint….. again untested.
 
sub filter1
{
    my $i = $j = $k = 0;
    my $index = shift;
    my @deltas = @_;
    foreach my $testreg (@{$p[$index]}) {
        my ($testX,$testY) = @$testreg;
        foreach my $region (@p) {
            do {
                if ($i == $index) {$i++}
                else {
                    $k = 0;
                    foreach my $points(@{$region}) {
                        do {
                            my ($X,$Y) = @$points;
                            my $distance = sqrt(abs(($testX - $X)**2 +
+ ($testY - $Y)**2));
                            if (($deltas[$i] - $precision) <= $distanc
+e) && ($deltas[$i] + $precision) >= $distance)){
                                $k++;
                                $j++;
                            }
                        } unless ($k == 1);
                    }
                }
            } unless ($j == 4);
        }
        if ($j < 4) {
            splice (@{$p[$index]},$i,1);
        } else {
            $i++;
        }
    }
}
[download]

I think that after this first filter, the total number of points should be much more manageable.

Let me know if you have any questions.

Here is the data:

1    599    377    
2    829    410    
3    643    465    
4    522    511    
5    626    552    
6    762    575    
7    577    597    
8    699    618    
1    1474    13    
2    1507    14    
3    1882    15    
4    1912    15    
5    1704    16    
6    1573    17    
7    1685    21    
8    1709    21    
9    1795    90    
10    1668    107    
11    1732    131    
12    1819    144    
13    1755    159    
14    1692    163    
15    1936    213    
16    1708    218    
17    1808    227    
18    1704    221    
19    1747    229    
20    1744    293    
1    2673    619    
2    2765    620    
3    2839    638    
4    2729    659    
5    2779    688    
6    2681    703    
7    2744    729    
8    2821    738    
9    2807    788    
10    2740    808    
11    2560    822    
12    2570    821    
1    3308    1800    
2    3371    1828    
3    3280    1854    
4    3412    1856    
5    3274    1934    
6    3360    1986    
7    3308    1998    
8    3366    2046    
1    2235    2522    
2    2408    2541    
3    2335    2547    
4    2267    2580    
5    2383    2602    
6    2296    2630    
7    2214    2627    
8    2426    2652    
9    2425    2657    
10    2228    2678    
11    2364    2684    
12    2283    2726    
13    2358    2764    
1    1768    2505    
2    1696    2527    
3    1800    2567    
4    1650    2586    
5    1733    2624    
6    1835    2632    
7    1621    2675    
8    1689    2677    
9    1650    2730    
10    1770    2738    
1    29    1746    
2    30    1764    
3    78    1781    
4    30    1783    
5    30    1806    
6    320    1897    
7    231    1944    
8    31    1938    
9    30    1968    
10    376    1965    
11    206    2013    
12    260    2068    
13    193    2096    
14    401    2097    
15    350    2133    
16    32    2166    
17    257    2187    
18    32    2258    

____________________

1    585    600
1    1715    280
1    2745    815
1    3240    2090
1    2280    2770
1    1715    2770
1    190    2090
[download]

The first set are from a film that I just created with a lot of noise, and 2 regions do not contain any true points. The second set are from the template, and the order for the roi's are the same and follow:



        ----------------------------------
       |                                  |
       |                2                 |
       |                                  |
       |      1                           |
       |                          3       |
       |                                  |
       |                                  |
       |    7                       4     |
       |                                  |
       |                                  |
       |                 6     5          |
       |                                  |
        ----------------------------------
[download]

Film has a lattace of silver (a molecule containing silver) When the film is exposed to light/x-rays (photons), the silver which has a high probability of interaction becomes ionized. Then when the fixer is used the ionized portion remains and the rest is washed away. This is why in an xray, bone looks white. Compared to other tissue the photons are heavily attenuated by the bone, so most of the silver is washed away. When you damage film, i.e. punture or even just by pressure, it damages the lattace, and when the film is developed, even if it wasn't exposed, the damage can be seen.

As far as the template goes...Think of 2 blocks of styrofoam with dimensions 25cm x 25cm x 5cm, if you drilled holes in one block such that went completely though the 5cm thickness, and the holes were grouped in a known pattern, then when you placed the film between the 2 blocks, you can gain access to the film through the holes. So if you cause damage to the film at the locatoion of the holes, then you will always be able to maintain the alignment of the film to the blocks at the time of the exposure.

Does this help?

Ok...You are very close on many things. I think that you have the problem figure and understood. The geometric consistency IS there, but it is not a perfect 1:1. The jig is fine. The "plunger fits very snug into the holes, BUT there is no way to determine how the damage to the film will be represented (shape) when the film is processed/scanned. I have seen the full range of:



      ______                  __________
     /      \                / --      /
    |   --   |     to        | --     |
    |   --   |                |      /
     \_______/                 \____/
[download]

where the outside ring represents the darkening of the film due to the damage, and the in side marks represent the actual puncture. The resolution that we scan at is 89 microns per pixel, and the average darking per puncture is ~ 3mm across => 33 pixels. The digital processing that I do on the film after scanning finds the points, then it asigns the X,Y value to that point by way of center of mass. So in the first exampl above we would have a near perfect match, but we could be off by 10-15 pixels in the second example.

After getting some prelim. results I checked them against the film. here are the real points +/- 2 pixels:

ROI          X          Y
1           464        642
2           157        1756
3           687        2779
4
5           2631       2296
6           2625       1732
7
[download]

Notice that the X/Y are flipped from the input data, that is because the data given after points are found versus the software where the analysis is done call the columns/rows differently. So reverse the order to find the closest pair which would be:

ROI 1
3    643    465

ROI 2
13    1755    159

ROI 3
5    2779    688

ROI 4
None

ROI 5
6    2296    2630

ROI 6
5    1733    2624

ROI 7
None
[download]

If we look at distance beween points:


True Point Distances for ROI1.

ROI2
Distance = 1153.33429672407
ROI3
Distance = 2147.60913576004
ROI5
Distance = 2723.90051213329
ROI6
Distance = 2418.54935860321

Template Point Distances for ROI1.

ROI2
Distance = 1174.4360348695
ROI3
Distance = 2170.67385850569
ROI5
Distance = 2753.52955313721
ROI6
Distance = 2446.58946290545


True Point Distances for ROI2.

ROI1
Distance = 1153.33429672407
ROI3
Distance = 1152.56973758641
ROI5
Distance = 2529.5299958688
ROI6
Distance = 2465.09817248725

Template Point Distances for ROI2.

ROI1
Distance = 1174.4360348695
ROI3
Distance = 1160.65714145048
ROI5
Distance = 2553.29688833868
ROI6
Distance = 2490


True Point Distances for ROI3.

ROI1
Distance = 2147.60913576004
ROI2
Distance = 1152.56973758641
ROI5
Distance = 2001.16291190897
ROI6
Distance = 2200.50266984614

Template Point Distances for ROI3.

ROI1
Distance = 2170.67385850569
ROI2
Distance = 1160.65714145048
ROI5
Distance = 2009.53974830059
ROI6
Distance = 2209.73414690546


True Point Distances for ROI5.

ROI1
Distance = 2723.90051213329
ROI2
Distance = 2529.5299958688
ROI3
Distance = 2001.16291190897
ROI6
Distance = 563.031970673069

Template Point Distances for ROI5.

ROI1
Distance = 2753.52955313721
ROI2
Distance = 2553.29688833868
ROI3
Distance = 2009.53974830059
ROI6
Distance = 565


True Point Distances for ROI6.

ROI1
Distance = 2418.54935860321
ROI2
Distance = 2465.09817248725
ROI3
Distance = 2200.50266984614
ROI5
Distance = 563.031970673069

Template Point Distances for ROI6.

ROI1
Distance = 2446.58946290545
ROI2
Distance = 2490
ROI3
Distance = 2209.73414690546
ROI5
Distance = 565
[download]

We can see fairly good agreement, but it does appear to be +/- 30

Well I am going to work further, and will start to implement some of your code for testing....