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Timestamp:
Aug 3, 2018 10:51:26 PM (3 years ago)
Author:
toby
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finish web tutorials for now

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  • Tutorials/DeterminingWavelength/DeterminingWavelength.html

    r3544 r3553  
    2727<p class="c3"><span class="c4 c2">Since the single-image calibration looks good, it is time to copy these parameters onto the rest of the images.</span></p><p class="c3"><span class="c2">Next select </span><span class="c0">Parms/Copy Selected</span><span class="c4 c2">. A text box like this will pop up:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 446.50px; height: 299.36px;"><img alt="" src="images/image7.png" style="width: 936.47px; height: 523.88px; margin-left: -321.16px; margin-top: -99.15px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Click </span><span class="c0">Set All</span><span class="c2">&nbsp;on the bottom then go back and unselect both </span><span class="c0">distance (10)</span><span class="c2">&nbsp;and</span><span class="c0">&nbsp;setdist</span><span class="c2">&nbsp;</span><span class="c0">(25)</span><span class="c2">, as below, then press</span><span class="c0">&nbsp;OK</span><span class="c4 c2">. We want to copy all parameters except for the distances because they differ for each image. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 465.50px; height: 414.40px;"><img alt="" src="images/image16.png" style="width: 902.09px; height: 506.81px; margin-left: -284.79px; margin-top: -30.32px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Another dialog box will appear for selection of the images to copy these parameters to, hit </span><span class="c0">Set All</span><span class="c2">&nbsp;and press </span><span class="c4 c0">OK</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 246.75px; height: 321.50px;"><img alt="" src="images/image23.png" style="width: 1015.29px; height: 565.44px; margin-left: -466.62px; margin-top: -106.06px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Next select </span><span class="c0">C</span><span class="c0">alibration/Recalibrate all </span><span class="c2">to recalibrate all images with the new parameters.
    2828</span></p><p class="c8"><span class="c4 c2">
    29 Do </span><span class="c0">File/Save project as...</span><span class="c2">&nbsp;and name it </span><span class="c0">Wavelength_Determination</span><span class="c4 c2">. This will create a copy of the project to use for calibration.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c2">The next step is to check to make sure the Min calib d-spacing setting value ensures that only full rings are used in each calibration. The </span><span class="c2">Min calib d-spacing restrict the set of reflections to be used in the MC/SA run</span><span class="c2">. To do this, start at the </span><span class="c0">Image Controls</span><span class="c2">&nbsp;for the first image and then go in increasing order through the images until you find one where the outer rings are cut off. For us, the first image with rings cut off is </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c4 c2">, as below.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 582.00px; height: 543.00px;"><img alt="" src="images/image21.png" style="width: 1104.29px; height: 620.82px; margin-left: -279.84px; margin-top: -21.22px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c4 c2">Start with your cursor in the center of the rings and then pan your mouse over to the right edge. Watch the Min calib d-spacing decrease as you continue to move the mouse to the right.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 488.00px;"><img alt="" src="images/image18.gif" style="width: 624.00px; height: 488.00px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Look at the dsp value at the bottom of the plot window. Look at the value when the cursor is on the edge. That will be the new Min calib d-spacing. The default value of 0.50 is allowing the outer rings to be cut off.</span><span class="c2">&nbsp;</span><span class="c2">&nbsp;We then looked at what the dsp value was when the cursor was on the edge of the image. Here it is 0.529, so we went to image controls &nbsp;for image </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c2">&nbsp;</span><span class="c2">a</span><span class="c2">nd changed </span><span class="c0">Min calib d-spacing</span><span class="c4 c2">&nbsp;to 0.53.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 637.00px; height: 394.00px;"><img alt="" src="images/image5.png" style="width: 799.07px; height: 449.01px; margin-left: -109.57px; margin-top: -14.07px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Then select </span><span class="c0">Calibration/Recalibrate</span><span class="c4 c2">&nbsp;and the image should now have all the rings intact. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 561.00px; height: 527.00px;"><img alt="" src="images/image14.png" style="width: 1070.53px; height: 602.04px; margin-left: -271.06px; margin-top: -20.58px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">After you fix the first image where the Min calib d-spacing is off you can fix the rest of the images that also have this problem. To fix this, select image controls for image </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c2">. </span><span class="c2">Then select </span><span class="c0">Parms/XFer Angles </span><span class="c4 c2">and a window will pop up.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 252.50px; height: 441.38px;"><img alt="" src="images/image20.png" style="width: 1240.63px; height: 697.85px; margin-left: -536.81px; margin-top: -107.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Select </span><span class="c0">Set All </span><span class="c2">but then </span><span class="c0">unselect</span><span class="c2">&nbsp;all the earlier images that did not have a Min calib d-spacing problem. For us, this was </span><span class="c0">images 200-350</span><span class="c2">. Then </span><span class="c0">select</span><span class="c2">&nbsp;the </span><span class="c0">Xfer scaled calib d-min </span><span class="c2">option on the bottom of the window and </span><span class="c0">unselect</span><span class="c2">&nbsp;the </span><span class="c0">Xfer scaled 2-theta max </span><span class="c4 c2">option. This takes min calibrated d-spacing from the image selected and determines the accurate d-spacing for all other images. The text box should look like the following:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 262.00px; height: 454.00px;"><img alt="" src="images/image22.png" style="width: 1277.25px; height: 717.60px; margin-left: -552.66px; margin-top: -108.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Then select</span><span class="c0">&nbsp;OK</span><span class="c4 c2">&nbsp;and the rest of the Min calib d-spacing will be adjusted for the rest of the images.</span></p><p class="c3"><span class="c2">Now it&rsquo;s time to recalibrate all of the images with the new Min calib d-spacing values. Go to any image controls window and select </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">and select </span><span class="c4 c0">Set All. </span></p><p class="c3"><span class="c4 c2">This will take a bit of time as each image is being recalibrated. </span></p><p class="c3"><span class="c2">After the recalibration, all the images should only have full intact rings. Once the process is complete go to the bottom of the data tree and select </span><span class="c0">Sequential image calibration results </span><span class="c4 c2">and a table should appear. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 605.50px; height: 376.16px;"><img alt="" src="images/image17.png" style="width: 757.18px; height: 425.91px; margin-left: -103.14px; margin-top: -12.13px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">In </span><span class="c0">Sequential Image Calibration results</span><span class="c2">, a table should appear with a column labeled dep containing detector penetration depths (</span><span class="c0">dep</span><span class="c2">). As we look over the table we need to make sure that the detector penetration depths have roughly the same values except for the first few rows (these will be off due to the close distances). As we look at our data we notice that the last few values are inconsistent with the rest. To investigate we select the </span><span class="c0">IMG Si_free_dc1250_1</span><span class="c0">-00000.tif</span><span class="c0">/ Image Controls</span><span class="c2">&nbsp;and view the second to last image.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 537.50px; height: 503.19px;"><img alt="" src="images/image15.png" style="width: 1019.45px; height: 573.44px; margin-left: -258.13px; margin-top: -17.97px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c4 c2">We can see from the image that there is a fake (or fragmented) fourth ring that should not actually be there (the last &ldquo;1300&rdquo; image does not have this issue of the fake fourth ring). In order to fix this we will pan the mouse over to the space in between the last full ring and the fake ring as shown below.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 577.33px;"><img alt="" src="images/image26.gif" style="width: 624.00px; height: 577.33px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">We found a value of the dsp to be 1.592 and changed the Min calib d-spacing to that value under </span><span class="c0">Image controls </span><span class="c4 c2">for the &ldquo;1250&rdquo; image. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 620.00px; height: 383.00px;"><img alt="" src="images/image2.png" style="width: 776.56px; height: 436.77px; margin-left: -106.78px; margin-top: -12.44px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">We then selected </span><span class="c0">Calibration/Recalibrate</span><span class="c4 c2">&nbsp;and our image now excludes the fake fourth ring.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 497.50px; height: 464.33px;"><img alt="" src="images/image3.png" style="width: 940.73px; height: 529.16px; margin-left: -236.69px; margin-top: -16.58px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Continue to go through the i</span><span class="c2">mages in decreasing distance from</span><span class="c2">&nbsp;the detector and check to see whether there is a phantom ring and adjust the Min calib d-spacing accordingly. However once you get to an image where there is another full ring outside of the phantom ring, there is no need to adjust the Min calib d-spacing. We adjusted the Min calib d-spacing value to </span><span class="c0">1.59</span><span class="c2">&nbsp;for images </span><span class="c0">IMG Si_free_dc1200_1</span><span class="c0">-00000.tif</span><span class="c0">&nbsp;</span><span class="c2">and </span><span class="c0">IMG Si_free_dc1150_1</span><span class="c0">-00000.tif</span><span class="c4 c2">. The &ldquo;1100&rdquo; image had a fifth full ring that we did not want to exclude.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c2">After completing this process select </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">once again. Continue calibrating until the dep values</span><span class="c2">&nbsp;</span><span class="c2">converge. After a few recalibrations, the table under </span><span class="c0">Sequential image calibration results</span><span class="c2 c4">&nbsp;shows our dep values converge the detector distances are further from the sample.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 636.00px; height: 395.00px;"><img alt="" src="images/image25.png" style="width: 796.57px; height: 447.24px; margin-left: -109.51px; margin-top: -12.74px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Our new values have improved quite a bit. If the any </span><span class="c2">&nbsp;detector penetration depth (dep) </span><span class="c2">values are negative then go to </span><span class="c0">Image Controls </span><span class="c2">for the images with negative dep values. You will see that the penetration values for those images are also negative. As this should not be possible, change the value of </span><span class="c0">Penetration </span><span class="c2">to </span><span class="c0">zero</span><span class="c2">&nbsp;and then did </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">once again and the penetration values should become positive.
     29Do </span><span class="c0">File/Save project as...</span><span class="c2">&nbsp;and name it </span><span class="c0">Wavelength_Determination</span><span class="c4 c2">. This will create a copy of the project to use for calibration.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c2">The next step is to check to make sure the Min calib d-spacing setting value ensures that only full rings are used in each calibration. The </span><span class="c2">Min calib d-spacing restrict the set of reflections to be used. </span><span class="c2">To do this, start at the </span><span class="c0">Image Controls</span><span class="c2">&nbsp;for the first image and then go in increasing order through the images until you find one where the outer rings are cut off. For us, the first image with rings cut off is </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c4 c2">, as below.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 582.00px; height: 543.00px;"><img alt="" src="images/image21.png" style="width: 1104.29px; height: 620.82px; margin-left: -279.84px; margin-top: -21.22px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c4 c2">Start with your cursor in the center of the rings and then pan your mouse over to the right edge. Watch the Min calib d-spacing decrease as you continue to move the mouse to the right.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 488.00px;"><img alt="" src="images/image18.gif" style="width: 624.00px; height: 488.00px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Look at the dsp value at the bottom of the plot window. Look at the value when the cursor is on the edge. That will be the new Min calib d-spacing. The default value of 0.50 is allowing the outer rings to be cut off.</span><span class="c2">&nbsp;</span><span class="c2">&nbsp;We then looked at what the dsp value was when the cursor was on the edge of the image. Here it is 0.529, so we went to image controls &nbsp;for image </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c2">&nbsp;</span><span class="c2">a</span><span class="c2">nd changed </span><span class="c0">Min calib d-spacing</span><span class="c4 c2">&nbsp;to 0.53.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 637.00px; height: 394.00px;"><img alt="" src="images/image5.png" style="width: 799.07px; height: 449.01px; margin-left: -109.57px; margin-top: -14.07px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Then select </span><span class="c0">Calibration/Recalibrate</span><span class="c4 c2">&nbsp;and the image should now have all the rings intact. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 561.00px; height: 527.00px;"><img alt="" src="images/image14.png" style="width: 1070.53px; height: 602.04px; margin-left: -271.06px; margin-top: -20.58px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">After you fix the first image where the Min calib d-spacing is off you can fix the rest of the images that also have this problem. To fix this, select image controls for image </span><span class="c0">IMG Si_free_dc400_1</span><span class="c0">-00000.tif</span><span class="c2">. </span><span class="c2">Then select </span><span class="c0">Parms/XFer Angles </span><span class="c4 c2">and a window will pop up.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 252.50px; height: 441.38px;"><img alt="" src="images/image20.png" style="width: 1240.63px; height: 697.85px; margin-left: -536.81px; margin-top: -107.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Select </span><span class="c0">Set All </span><span class="c2">but then </span><span class="c0">unselect</span><span class="c2">&nbsp;all the earlier images that did not have a Min calib d-spacing problem. For us, this was </span><span class="c0">images 200-350</span><span class="c2">. Then </span><span class="c0">select</span><span class="c2">&nbsp;the </span><span class="c0">Xfer scaled calib d-min </span><span class="c2">option on the bottom of the window and </span><span class="c0">unselect</span><span class="c2">&nbsp;the </span><span class="c0">Xfer scaled 2-theta max </span><span class="c4 c2">option. This takes min calibrated d-spacing from the image selected and determines the accurate d-spacing for all other images. The text box should look like the following:</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 262.00px; height: 454.00px;"><img alt="" src="images/image22.png" style="width: 1277.25px; height: 717.60px; margin-left: -552.66px; margin-top: -108.36px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Then select</span><span class="c0">&nbsp;OK</span><span class="c4 c2">&nbsp;and the rest of the Min calib d-spacing will be adjusted for the rest of the images.</span></p><p class="c3"><span class="c2">Now it&rsquo;s time to recalibrate all of the images with the new Min calib d-spacing values. Go to any image controls window and select </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">and select </span><span class="c4 c0">Set All. </span></p><p class="c3"><span class="c4 c2">This will take a bit of time as each image is being recalibrated. </span></p><p class="c3"><span class="c2">After the recalibration, all the images should only have full intact rings. Once the process is complete go to the bottom of the data tree and select </span><span class="c0">Sequential image calibration results </span><span class="c4 c2">and a table should appear. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 605.50px; height: 376.16px;"><img alt="" src="images/image17.png" style="width: 757.18px; height: 425.91px; margin-left: -103.14px; margin-top: -12.13px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">In </span><span class="c0">Sequential Image Calibration results</span><span class="c2">, a table should appear with a column labeled dep containing detector penetration depths (</span><span class="c0">dep</span><span class="c2">). As we look over the table we need to make sure that the detector penetration depths have roughly the same values except for the first few rows (these will be off due to the close distances). As we look at our data we notice that the last few values are inconsistent with the rest. To investigate we select the </span><span class="c0">IMG Si_free_dc1250_1</span><span class="c0">-00000.tif</span><span class="c0">/ Image Controls</span><span class="c2">&nbsp;and view the second to last image.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 537.50px; height: 503.19px;"><img alt="" src="images/image15.png" style="width: 1019.45px; height: 573.44px; margin-left: -258.13px; margin-top: -17.97px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c4 c2">We can see from the image that there is a fake (or fragmented) fourth ring that should not actually be there (the last &ldquo;1300&rdquo; image does not have this issue of the fake fourth ring). In order to fix this we will pan the mouse over to the space in between the last full ring and the fake ring as shown below.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 624.00px; height: 577.33px;"><img alt="" src="images/image26.gif" style="width: 624.00px; height: 577.33px; margin-left: 0.00px; margin-top: 0.00px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">We found a value of the dsp to be 1.592 and changed the Min calib d-spacing to that value under </span><span class="c0">Image controls </span><span class="c4 c2">for the &ldquo;1250&rdquo; image. </span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 620.00px; height: 383.00px;"><img alt="" src="images/image2.png" style="width: 776.56px; height: 436.77px; margin-left: -106.78px; margin-top: -12.44px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">We then selected </span><span class="c0">Calibration/Recalibrate</span><span class="c4 c2">&nbsp;and our image now excludes the fake fourth ring.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 497.50px; height: 464.33px;"><img alt="" src="images/image3.png" style="width: 940.73px; height: 529.16px; margin-left: -236.69px; margin-top: -16.58px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Continue to go through the i</span><span class="c2">mages in decreasing distance from</span><span class="c2">&nbsp;the detector and check to see whether there is a phantom ring and adjust the Min calib d-spacing accordingly. However once you get to an image where there is another full ring outside of the phantom ring, there is no need to adjust the Min calib d-spacing. We adjusted the Min calib d-spacing value to </span><span class="c0">1.59</span><span class="c2">&nbsp;for images </span><span class="c0">IMG Si_free_dc1200_1</span><span class="c0">-00000.tif</span><span class="c0">&nbsp;</span><span class="c2">and </span><span class="c0">IMG Si_free_dc1150_1</span><span class="c0">-00000.tif</span><span class="c4 c2">. The &ldquo;1100&rdquo; image had a fifth full ring that we did not want to exclude.</span></p><p class="c1"><span class="c4 c2"></span></p><p class="c3"><span class="c2">After completing this process select </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">once again. Continue calibrating until the dep values</span><span class="c2">&nbsp;</span><span class="c2">converge. After a few recalibrations, the table under </span><span class="c0">Sequential image calibration results</span><span class="c2 c4">&nbsp;shows our dep values converge the detector distances are further from the sample.</span></p><p class="c3"><span style="overflow: hidden; display: inline-block; margin: 0.00px 0.00px; border: 0.00px solid #000000; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px); width: 636.00px; height: 395.00px;"><img alt="" src="images/image25.png" style="width: 796.57px; height: 447.24px; margin-left: -109.51px; margin-top: -12.74px; transform: rotate(0.00rad) translateZ(0px); -webkit-transform: rotate(0.00rad) translateZ(0px);" title=""></span></p><p class="c3"><span class="c2">Our new values have improved quite a bit. If the any </span><span class="c2">&nbsp;detector penetration depth (dep) </span><span class="c2">values are negative then go to </span><span class="c0">Image Controls </span><span class="c2">for the images with negative dep values. You will see that the penetration values for those images are also negative. As this should not be possible, change the value of </span><span class="c0">Penetration </span><span class="c2">to </span><span class="c0">zero</span><span class="c2">&nbsp;and then did </span><span class="c0">Calibration/Recalibrate all </span><span class="c2">once again and the penetration values should become positive.
    3030If required, turn off refinement of Penetration with a value of 0.0 if that is the only way to keep
    3131the value from becoming negative. </span></p>
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