1. 2012-02-021 Extension of the Excel-based Numerical Integration Calculation of the Coded Aperture Image to include mask partial-transmission and phase shift. - reminder of the calculation, including known deficiencies - issues that are apparent in the December 2011 data - addressing some deficiencies in the calculation - calibrating the model parameters - sensitivity to the model parameters - update on pinhole fitting - comparison of coded aperture with pinhole - remaining deficiencies, future improvements and calibrations Dan Peterson

2. 2012-02-022 Recall, the image calculation and fitting technique were developed in January 2011, uses an Excel spreadsheet to perform the numerical integration of the amplitudes, (1) where y is the vertical position at the plane of the optics element, r(y) is the path length from the source, through the optic, to the detector pixel, T(y) is the transmission of the optics element as a function of vertical position. Pulse height is calculated for 64 pixels of size 25μm, (half diodes). Paths are separated by Δy=0.5 μm at the optic. (Features are 10 μm. ) January 2011 version had many shortcuts: x-ray energy: mono-energetic 2.0 keV, λ=6.2 x10 -10 m, 6.2 x10 -4 microns. transmission of the gold coded aperture mask is 0 the semitransparent mask contributes to the diffraction pattern range of the integration is ±155 microns, projects to ± 0.52 mm at the detector. The integration produces the point source image at right. raw smoothed 50% n.n. E = E 0 ∑ e i 2π r(y) /λ T(y) History: calculated image

3. 2012-02-023 F = B + C / (2π) ½ ∑ J=1,12 A J / (σ J 2 + σ 2 ) ½ e -½ ( x - X 0J - X 0 ) 2 / (σ J 2 + σ 2 ) (2) The fitting function is then: The 36 function definition parameters are calculated, for beam size=0, once. These parameters are ( A J, σ J, X 0J ) J=1,12. In January 2011, there were 4 fitting parameters: C (area), X 0 (position), σ (magnified beam size), B (background ) The beam size=0 image is parameterized as a Sum Of Gaussians, SOG. The parameterization allows a simple convolution with the broadening due to beam size. History: Sum Of Gaussian fit

4. 2012-02-024 The original calculated image had systematic deviations from the data. We expected inaccuracies in the calculated image from the shortcuts: use of mono-energy and opaque mask, The side bumps, in particular, would be enhanced with the inclusion of semi-transmission. An empirical “recalibration” was applied to improve the fit. image, as calculated image, after recalibration Although stepping away from a calculation with known inputs, the recalibration provides a point-source image closer to reality. This reduces the minimum χ 2 and makes the fit more sensitive to the beam size. History: Recalibrating (fudging) the calculated image December 2010 D-line, 14ns readout

5. 2012-02-025 Performance in January 2011 Results from the 3 optics elements were similar.

6. 2012-02-026 uncover several problems 004018, BigD 004020, BigD displaced detector 004029, Norm Shown: 3 conditions, 4 turns each (3) interference dip - is lower than the fit, is lower than the background level (4) left shoulder of the primary peak - is higher and narrower than the fit (2) secondary peak - is higher than the fit (1)primary peak is OK, but is dominating the fit (5) background - does not match a flat line - is from a material property and should be a fixed contribution Attempts to fit December 2011 data.

7. 2012-02-027 Improving the image calculation in January 2012. The image shape should be calculated from characteristics of the x-ray beam and the coded aperture, without an ad-hoc recalibration. Add an x-ray energy distribution and the coded aperture mask semi-transmission. The range of integration at the plane of the mask was expanded to project beyond detector boundaries. The background is a fundamental problem with the original fit. The image fills the detector so there is not an independent measure of the background in a single pass. The floating background allows degenerate solutions; the two main peaks and the dip between them can be fit with a smaller width and larger background. It would be nice to be able to apply everything we know about the beam, filters/windows and the mask, and get the right answer. But, for example, the mask thickness specification appears to be inaccurate. The semi-transmission of the mask should be calibrated to the data. Image shape details may depend on the personality of a specific coded aperture. The semi-transmission is accompanied by a phase shift of waves passing through the mask. As will be described, the phase shift is significant, and significantly changes the image shape. For example, the dip between the two main peaks is enhanced by interference. (Someone thought about this when designing the coded aperture.) The phase shift provides an extra handle in calibrating the semi-transmission of the mask.

8. 2012-02-028 I take an empirical, data driven, approach to calibrating the image function. Continue using Excel, which provides rapid feedback. The limitation of Excel is that the energy spectrum is limited to 5 discrete energies. 2012-02-028 004029, Norm, turn 1 calibration variables: For the current calibration, these variables are tuned without much theoretical input. (1) low energy cut-off of the x-ray spectrum (2) high energy tail of the x-ray spectrum (3) semi-transmission of the coded aperture mask (4) phase shift in passing through the gold mask The goal of the calibration is to match major features of the observed image (1) primary peak (2) secondary peak (3) interference dip (4) left shoulder of the primary peak (5) background (6) side peak at channel 7 (7) side peak at channel 31 There are still shortcuts: The transmission and phase shift are ( as yet ) energy-independent. Calibrating the image function

9. 2012-02-029 I have parameterized John’s image with 12 gaussians. Some of the smaller fine features (< 1 pixel) are smoothed out. The image is available as an alternative function in CodedAperatureFit.m You may ask, “Why not just use John’s image?”

10. 2012-02-0210 You may ask again, “ So why not just use John’s image?” The floating background is a source of uncertainty. We can use John’s image with an added, even locked, background. However, there are the shape issues described above. The apparent underestimation of the transmission indicates that the phase is incorrect. (The discussion of phase is coming… next.) The fit to the left shoulder of the primary satellite is improved, compared to the DanP original fit. The fit to the secondary peak is low. The fit at the central dip does not reach low enough. The fit does not account for the background. Note that the fit to the peak is high. (Fit to displaced detector uses beam size constrained to result from centered detector fit.) 004018, BigD 004020, BigD displaced detector

11. 2012-02-0211 transmission, phase shift, and the complex index of refraction ref. X-ray Data Booklet, LBNL/PUB-490 The expression for the complex index of refraction n = 1 - δ - iβ (3) describes the phase velocity of the wave and absorption due to atomic interactions. The phase velocity is greater than c, speed of light in a vacuum. The wave equation (1) stated in slide 2 E = E 0 ∑ e i 2π r(y) /λ T(y) (1) becomes (including the time dependence) E = E 0 ∑ e i (2π / λ) (-ct + r) e - i (2π / λ ) δ r e – ( 2π / λ ) β r (4) So far, this is simply an expression of the undisturbed wave, a phase shift, and the transmission.

12. 2012-02-0212 transmission, phase shift, and the complex index of refraction Substituting the definitions, (5) and (6) into equation (4) E = E 0 ∑ e i (2π / λ) (-ct + r) e - i 2π ( r e λ n a 1/(2π) f 1 ) r e – ( r e λ n a f 2 ) r (7) We can calculate the image shape with this equation, knowing the energy spectrum and material thicknesses (windows and coded aperture). ref. X-ray Data Booklet, LBNL/PUB-490 The transmission and phase shift terms are calculated from atomic scattering of the x-rays and expressed as δ = r e λ 2 n a / (2π) f 1 (5) iβ = i r e λ 2 n a / (2π) f 2 (6) where r e is the electron radius, n a is the atomic number density and f 1 and f 2 are unit-less form factors, which are provided in the reference in graphs. footnote: Noting the similarity of the phase shift and transmission terms, the wave equation can be expressed in a form that is dependent on a measured amplitude transmission: T = A/A 0 = e – ( r e λ n a f 2 ) r (8) then E = E 0 ∑ e i (2π / λ) (-ct + r(y) ) T(y,λ) e i 2π [ ln ( T(y,λ) ) 1/(2π) f 1 (λ) / f 2 (λ) ] (9)

13. footnote: Alternatively, the transmission can be calculated from the macroscopic description: T = ( I / I 0 ) ½ = e - ½ μ ρ r μ is taken from the plot in the reference: 2.8 x 10 3 cm 2 /g T (2.4 keV) = e -1.891 = 0.151 Thus, the mass absorption coefficient, μ, is related to the form factor, f 2, by μ = 2 r e N/A au λ f 2 2012-02-0213 calculation of transmission and phase shift: what is reasonable for the specification gold thickness Amplitude transmission and phase shift can be calculated from equation (7): E = E 0 ∑ e i (2π / λ) (-ct + r) e - i 2π ( r e λ n a 1/(2π) f 1 ) r e – ( r e λ n a ρ f 2 ) r (7) I express the phase shift as a fraction of 2π. Again, referring to equation (7): θ = - ( r e λ n a 1/(2π) f 1 ) r = - ( r e λ N/A Au ρ 1/(2π) f 1 ) r f 1 is taken from the plot: 52 at 2.4 keV, λ=5.17 x10-8 cm 50 at 2.0 keV, λ=6.20 x10-8 cm θ (2.4 keV) = -0.50 θ (2.4 keV) = -0.57 f2f2 μ (cm 2 /g) The amplitude transmission is thus T = e – ( r e λ n a f 2 ) r = e – ( r e λ N/A Au ρ f 2 ) r where r is the thickness of the gold: specification: 0.7 x 10 -4 cm r e is the electron radius: 2.818 x 10 -13 cm N is Avogadro’s number 6.022 x 10 +23 /g A Au is the atomic weight of gold: 197 ρ is the density of gold, 19.3 g/cm 3 f 2 is taken from the plot: 31 at 2.4 keV, λ=5.17 x10 -8 cm 10 at 2.0 keV, λ=6.20 x10 -8 cm T (2.4 keV) = e -1.865 = 0.155 and T (2.0 keV)= = 0.49 ( the simple average is 0.32 ) phase shifttransmission

14. 2012-02-0214 The plots at the right, show the transmission and phase shift for 0.5 micron gold thickness. Loosely averaging {1.7 to 4.0 keV} leads to an expected average amplitude transmission of ~0.43 and average phase shift of ~ -0.35 x 2π. The specification gold thickness, 0.7 micron, leads to an average transmission that does not account for the large background under the coded aperture image. The data indicates a lower gold thickness, ~0.5 micron, approximating with an energy-independent transmission and phase. (As described earlier, the current calibration uses average values for the transmission and the phase.) for illustration, this actually corresponds to ~0.8 micron gold thickness. (the gold thickness issue) Calculation of transmission and phase shift: what is reasonable for the observed background

15. 2012-02-0215 Other material in the beam line are 2.5 microns of Silicon in the Coded Aperture substrate, ~6 ??? microns of Carbon in the diamond window, and 0.16 microns Si 3 N 4 in the diode passivation layer, which I ignore. I would like to express this in terms of equivalent carbon because I have a spread sheet. Using the mass absorption coefficient, μ, T = ( I / I 0 ) ½ = e - ½ μ ρ r Mass absorption coefficient are shown in the graphs at right. The ratio for Silicon to Carbon is: μ Si ρ Si / μ C ρ C = ( 995 x 2.33) / (105 x 3.52 ) = 6.27 at 2.5 keV ( the slopes are similar ) Ignoring the Silicon K-edge, 2.5 microns of silicon has roughly the absorption equivalent of 16 microns of carbon. μCμC μ Si Input Energy distribution: other material in the beamline

16. 2012-02-0216 The power distribution is calculated (at upper right) with 6 micron and 22 micron carbon filtering. (Aaron Lyndaker) The combined diamond window and silicon is represented by the 22 micron line (ignoring the 1.839 keV Silicon K-edge). (6 micron line represents the diamond window used for the pinhole.) Brian Heltsley is improving the power distribution to include the silicon and gold K-edges. Future calculations should include the more realistic power distribution, and energy dependent gold transmission and phase shift. But, for now… The numerical integration includes 5 discrete energy values (lower right). In the red distribution, the 5 delta functions are spread into equal-area blocks centered on the discrete energies. This is the energy distribution used in the current calculation, along with energy-independent gold amplitude transmission and energy-independent phase shift. Input Energy distribution, what I use

17. 2012-02-0217 2012-01-27 calculate image with photon energy distribution, 1.9, 2.0, 2.2, 2.5, 2.9, (ave=2.30), scaled to average energy=2.40 amplitude transmission of mask = 0.450 phase shift = -0.31 ( x 2π ) “pulse height uncertainty” = 351.48 The current coded aperture image and Sum Of Gaussians (this stuff is for my records)

18. 2012-02-0218 Fits of the resulting function to beam various conditions The background basically follows the shape of the data, but now may be slightly high and may require wider shape. Features in the very low beam size data mainly fit well, but the dip in the fit may be too low. 004018, BigD ~18 micron 004020, BigD displaced detector 004029, Norm ~13 micron 021442 Coup8 ~23 micron

19. 2012-02-0219 Image contributions from the 5 energies. 1.98 keV3.03 keV2.61 keV2.30 keV2.09 keV 4.0 keV 1.98, 2.09, 2.3, 2.61, 3.03 keV with average= 2.4 keV 1.6 keV In each case, the red line is the parameterization of the sum. And, the possible contribution from lower and higher energies with -0.31 x 2π phase, at all energies with 0.45 amplitude transmission, at all energies

20. 2012-02-0220 variation with phase phase = -0.1 phase = 0 phase = -0.2phase = -0.4phase = -0.3 phase = -0.6 phase = -0.5phase = -0.9 phase = -0.7 phase = -0.8 all with 0.45 amplitude transmission, at all energies

21. 2012-02-0221 variation with gold mask thickness Gold thickness ~ 0.2 micron Gold thickness ~ 0.7 micron Gold thickness ~ 0.3 micron Gold thickness ~ 1.0 micron Gold thickness ~ 0.5 micron 0.2 0.3 0.5 0.7 1.0 micron gold all with standard energy distribution, transmission ~ e -thickness phase ~ thickness In each case, the red line is the parameterization of the standard image, artificially shifted to match the background. Gold thickness ~ 0.55 micron

22. 2012-02-0222 compare pinhole and CA on coup 8 scan With smaller beam size in the December 2011 running, a non-gaussian component to the diffraction pattern became visible. A 2 nd wide gaussian component was added to the fit. This changes the fitted width of the main component. sigma rms back with 20% wide 0.8824 0.879 0.092 without 0.9905 1.034 0.132 The current pinhole subtractor is 16 microns. What would the subtractor be with the 2011 fit: single gaussian with floating background ? (20 x 0.8824) 2 -16 2 = (20 x 9905) 2 –S 2 S = 18.4 So, the reduction of the subtractor from 21 to 16 is half due to the function change. pinhole fit: compare with/without added wide part

23. 2012-02-0223 subtractor = 16 microns compare pinhole and CA on coupling-8 scan

24. 2012-02-0224 summary, future improvements, calibrations The new coded aperture function has only 3 free parameters, no floating background. It provides stable fits up to 55 micron beam size. The main features have sizes of about 8 micron (referred to the source), which should provide stable beam size measurements to about 6 microns. (The pixel size will be a significant effect below 6 microns.) Even though this is currently using average values, the transmission and phase of the resultant calculated image match the expectations of the averages better than might be expected. The calculated image was “fit” to the data before investigating the range of reasonable values for the amplitude transmission and the phase. We plan to input a detailed energy spectrum seen by the coded aperture, add energy-dependent transmission and phase shift, geared to a variable input gold thickness. Various experiment can be done to understand the transmission and phase: take measurements with various filters, measure the details of the image from the “box” on the optics chip, take offset images (moving the detector) to efficiently place the major peaks and sufficient background. Daily monitoring the image must be performed to test for changes in the transmission.

25. 2012-02-0225 variation with phase; energy distribution as in current image calculation all with 0.45 amplitude transmission, 0.20 intensity transmission phase = -0.1 phase = 0 phase = -0.2phase = -0.4phase = -0.3 phase = -0.6 phase = -0.5phase = -0.9 phase = -0.7 phase = -0.8 Calibration with the “box” on the optic chip

26. 2012-02-0226 backup

27. 2012-02-0227 No tweak With tweak (+.5, x2.5), (+0, x0.5), (+1.5, x1.5) In each case, the blue line is the new image, 2012-01-27. The red line is the SoG of the January 2011 image (narrow and smoothed) Added 1200 background, scaled by 0.9, for the overlay

28. 2012-01-31 Set up function CodedAperatureFit.m with JohnF2 (gaussian background in parameterization) DanP6 (.45 trans, -.31phase(on each wavelength) ) Both have ZERO added background. DanP6, 2 events each, 4029, 21442 get also 004018 JohnF2, 2 events each, 4029, 21442 put this in backup