new multi-SEM layer offset process (part D)#225
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…mageProcessorWithMasks behavior is to drop the mask with just a System.err.println statement.
…e size matches the tile spec size so that rendered image dimensions remain consistent with mask specifications.
…oid incorrectly matching SFOV edges within MFOV-as-tile images of areas that have very little tissue. One example of a pair that gets incorrectly connected with 48 matches at render scale 0.3 is w60_s360_r00_gc MFOV 13 in z 1 and 2.
…montage minNumInliers 100 for both passes, make cross minNumInliers 150 for both passes, increase matchMaxEpsilonFullScale to 20
… for new problem area
…alignTask instance constructor, explicitly log layerMfovDevString in run method to workaround missing context in Google Logs Explorer, remove try block from run method and let exceptions bubble out
…nfo as JavaRenderTilesClientInfoForLayerMfov, increase Spark parallelism for alignAndIntensityCorrectMfovAsTileStacks and buildRenderedMfovAsTileStacks
…computing mean, add elapsedSeconds to run log
…0.0,0.0) for MFOV-as-tile test H
…ad of just one point
…st option, remove no longer needed renameMatchCollectionAlignStackAndRoughStack method
…ach MFOV-as-tile stack
… return removal tile pair information instead of just a count for improved logging on the driver, rename RemoveMatchClient as RemoveMatchPairClient
… Spark parallelism for MfovPrealignTask jobs
…and add a few more utility scripts there
…ction MFOV prealign and intensity correction
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follow-up work to #224