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jvs:fscan:manual:chapter2:align [2011/03/31 14:49] 127.0.0.1 external edit |
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**fScan Reference Manual, Chapter 2 (CmdLineOptions): | **fScan Reference Manual, Chapter 2 (CmdLineOptions): | ||
===== Align -- Auto align images by optimizing mutual information ===== | ===== Align -- Auto align images by optimizing mutual information ===== | ||
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**usage:** -align dataset flag ncycles nsteps nbits imin shift1 shift2 doff drot dscale | **usage:** -align dataset flag ncycles nsteps nbits imin shift1 shift2 doff drot dscale | ||
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===== ===== | ===== ===== | ||
- | ALIGN superimposes the data set to be aligned onto the current (reference) | + | ALIGN superimposes the data set to be aligned |
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+ | Adjustment | ||
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+ | 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 | ||
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+ | Default FLAG is 0737: Adjust X,Y,Z axes for Coarse and Fine Offset and Rotation (not Scaling), displaying progress window. | ||
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+ | For each parameter being adjusted, ALIGN tests NSTEPS values (default=5), | ||
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): | 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): | ||
* DOFF - translation offset step (default=0.25 mm) | * DOFF - translation offset step (default=0.25 mm) | ||
* DROT - rotation step (default=0.25 degrees) | * DROT - rotation step (default=0.25 degrees) | ||
- | * DSALE - scale step (default=1.0) | + | * DSCALE |
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- | + | ||
- | FLAG (combine options by adding values): | + | |
- | * 1 - | + | |
- | * 2 - | + | |
- | * 4 - | + | |
- | * 8 - | + | |
**See Also:**\\ | **See Also:**\\ | ||
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