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CHANGES.txt
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CHANGES.txt
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Version 0.8
-----------
* significant speed-up of mod contrast calc
* fixed several problems with reconstructed Fourier plots
* improved Fourier plots (window function, calibration)
* fixed mod contrast map display scaling
* ELYRA data conversion from main dialog now works
* better log info - tidied output, preparation for GUI
Version 0.9
-----------
* SI "Z variation" plugin now normalized to average values
in the image, making it more robust
* Modulation contrast calculation improved / fixed,
** so it is valid at different noise levels
** uses illumination pattern orders 1 and 2 instead of 1
** a noticeable effect is that typical mod contrast values
are halved
* intensity histogram and mismatch plugins produce stacks
* reconstructed Fourier check produces a radial profile plot
* phase calibration plugin improved,
** detects peaks from pattern order 1 and plots them
** estimates line spacing and k angle from the peaks
** produces result table for phase step analysis
* new N-SIM format converter
Version 0.9.5
-------------
* new SIMcheck Manual (using the Sphinx documentation tool)
* fixes to Phase Step calibration check (Ian Dobbie)
* switched to Apache Maven for build & dependency management
* reconstructed Fourier Plots streamlined and improved
* many of the checks have been renamed
* fixed bug in Reconstructed Intensity Histogram statistic
* code tidied and more tests added, several minor bugs fixed
* Modulation Contrast Map shows saturation in raw data (green)
* new Illumination Pattern Focus calibration check
* new Threshold and 16-bit Conversion utility
* raw data Fourier plugin now displays montage of projections
* fixes to ELYRA and N-SIM data format conversion
* implemented image-cropping utility in main SIMcheck dialog
* added option to specify camera bit depth (to identify saturation)
* Look-Up Tables displayed as overlay on results when appropriate
* the log output / report generation has been tidied up
Version 0.9.6
-------------
* new Result Table summarising key numerical stats and interpretation
* RMSE stat for MIV check implementation finished
* CIP changed to report overall intensity fluctuation statistic
Version 0.9.7
-------------
fixed many minor bugs, the most important of which are:
* preserve calibration info in all checks
* several bugs in SI to pseudo-widefield utility
* incorrect FTR radial profile scale
* show saturation in MCM if *any* raw data angle saturated (not all as before)
other updates and notable new features:
* added check for ZMV value
* reformatted and tidied log output, plot axes and titles
* added Results summary table with stat value checks
* SI to pseudo-widefield: preserve data type, scale XY x2 to match super-res
* added flicker correction routine to IPF cabliration check and PWF utility
* improved intensity profile stats, inlcluding total variation and flicker
* improved stack feature intensity estimates (now using Otsu method)
* raw fourier projection now projects all angles for 1 summary image
* increased default FFT window function size
* raw FPJ and reconstructed SAM checks default off in main dialog
* change SA mismatch calibration check back to reconstructed
Version 0.9.8
-------------
* extensive SIMcheck Manual updates, with figures for visual guide
* feature: Stack FFT 2D gamma scaling display option (reviewer request)
* add '_' to jar finalName via pom so plugin appears in IJ Plugins
* bugfix: si2wf accidental rescale
* Cal_PatternFocus change default angle def method to line
Version 0.9.9
-------------
* bugfix: Util_RescaleTo16bit incorrect minimum
* add new FFT2D display option (log-scaled, float) and refactor
* update all javadocs
Version 0.9.10
--------------
* IPS, set plot width to ensure it fits stack of plots
* report all stats to 3 sig fig, previously 2
* pattern focus, add CCW stripe rotation checkbox
* change default pattern focus angle method back to IJ degrees
* CIP bugfix: was overwriting intens array for each C (pass ref to Plot)
* 16-bit util: fix for missing subtraction of specified min
Version 0.9.11
--------------
* make reconstructed FFT gamma 0.2 display default
Version 1.0.0
-------------
* change raw MCN stat check criteria from 3,6 to 4,8
* python script for dumping binary LUT file as comma-separated text
* rescale to 16-bit in Stack FFT utility to match reconstructed FFT
* bugfix: I1l.getStatsForChannel and affected display settings
* raw FPJ: now uses 32-bit log and central mask, display min-max
* raw CIP check criteria change from 50,70 to 60,40
* CIP: improve bleach estimation, add normalised plot
* updates to allow macro recording
Version 1.1
-----------
* SI to widefield utility: add option to skip XY rescale 2x
* implement 3D FFT using Parallel FFTJ for Rec Fourier check
* "FTR" radial profile plot: fixed range 20-40 for log-scaled PS
Version 1.2
-----------
* Fix URL to online help
Version 1.3
-----------
* New "Modulation Contrast Filter" utility.
Version 1.4
-----------