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--- jvs:fscan:manual:chapter2:align [2013/01/04 17:07]
voyvodic
+++ jvs:fscan:manual:chapter2:align [2023/02/23 18:43] (current)
@@ Line 5: / Line 5: @@
 =====  =====
-ALIGN superimposes the data set to be aligned onto the current (reference) data set and then adjusts the alignment data set to optimize its registration with the reference data set.  The adjustment is done by stepping through several possible alignment settings and calculating a "mutual information" index for each step. The parameter settings that can be adjusted are Translation, Rotation, and Scaling along each of the 3 cardinal image axes (X, Y, and Z). For each parameter being adjusted, ALIGN tests NSTEPS values (default=5), with NSTEPS/2 values on either side of the starting value. It performs NCYCLES of adjustment (default=3) of all parameters, decreasing the step size on each cycle.
+ALIGN superimposes the data set to be aligned (DATASET) onto the current data set (reference) and then adjusts the alignment data set to optimize its registration with the reference data set. If the current data set has another image data set overlaid on it, then DATASET will default to that overlay data set. Otherwise, if DATASET is omitted it is assumed to be the image data set in the previous active window.
+Adjustment is done by stepping through several possible alignment settings and calculating a "mutual information" index for each step. The parameter settings that can be adjusted are Translation, Rotation, and Scaling along each of the 3 cardinal image axes (X, Y, and Z). The FLAG option can be used to control which parameters are to be adjusted.
+FLAG (octal values in parenthesis -- combine options by adding values):
+  * 1 (1) - Fine adjustment
+  * 2 (2) - Coarse adjustment (if combined with Fine, Coarse runs first)
+  * 4 (4) - open and display dynamic MutualInformation window
+  * 8 (010) - Adjust Offset (translation along axis)
+  * 16 (020) - Adjust Rotation (around axis)
+  * 32 (040) - Adjust Scaling (along axis)
+  * 64 (0100) - Do X axis adjustments
+  * 128 (0200) - Do Y axis adjustments
+  * 256 (0400) - Do Z axis adjustments
+  * 512 (01000) - Mask flag -- ignore voxels in current dataset that have low-bit zero
+  * 1024 (02000) - Use current image overlay as alignment data set (default if DATASET omitted)
+  * 2048 (04000) - Debug flag -- display mutual information values and single step through alignment
+Default FLAG is 0737: Adjust X,Y,Z axes for Coarse and Fine Offset and Rotation (not Scaling), displaying progress window.
+For each parameter being adjusted, ALIGN tests NSTEPS values (default=5), with NSTEPS/2 values on either side of the starting value. It performs NCYCLES of adjustment (default=3) of all parameters, decreasing the step size on each cycle.
 The adjustment stepsize is specified by a combination of the FLAG, NCYCLES, DOFF, DROT, and DSCALE parameters. The finest adjustment step for the last adjustment cycle is (assuming no Coarse FLAG option):
@@ Line 11: / Line 31: @@
   * DROT - rotation step (default=0.25 degrees)
   * DSCALE - scale step (default=1.0)
-FLAG (combine options by adding values):
-  * 1 -
-  * 2 -
-  * 4 -
-  * 8 -
 **See Also:**\\
 [[jvs:fscan:manual:chapter1:overlay_and_alignment|Overlay and Alignment]],
-[[jvs:fscan:manual:chapter3:overlay|Overlay]]
+[[jvs:fscan:manual:chapter3:imagekeys:overlay|Overlay]]
 [[jvs:fscan|fScan Home]],

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