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CHANGELOG.md

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CHANGELOG

22Jan2019

  • Switched image padding code in analysis\simpleSegmentation.m
  • Fixed select peaks tooltip string typo for HistogramPeakSlider.m
  • Added SegmentationPreprocessingTutorial.mlx
  • Images are default converted to doubles now within analysis\simpleSegmentation.m
  • Colormap in ChoroidApp.m is now pink, added colormap button to HistogramPeakSlider.m
  • Closing out of OCT\crop without specifying a crop value resets JSON crop value
  • Image alignment with analysis\alignImages.m now uses cropped raw images

7Jan2019

  • Added image reload to ChoroidApp.m and OCT\update()

6Jan2019

  • Added option to OCT class save as a .json file. This will replace the many .txt files previously used for each parameter.
  • New function alignILM.m to calculate the x-axis shift of one OCT image to match the reference image.
  • Two new plotting functions: util\plotRPE.m and util\plotILM.m

5Jan2019

  • User interface changes for HistogramPeakSlider: removed physical slider bc arrow keys were easier
  • If segmentation exists, instatiating an OCT object automatically runs OCT.doAnalysis.
  • Relative choroid ratio option for OCT.plotRatio() to compare choroid ratio to a reference OCT, if exists.
  • Fixed application of Shift property for non-relative OCT.plotRatio()

4Jan2019

  • Added refID property to OCT class for the image number of the reference OCT.

3Jan2019

  • Added scale property to OCT class and modified analysis\alignImages.m accordingly
  • Wrote ChoroidRatioView to interactively display choroid ratio while fitting boundary control points with ChoroidApp.

2Jan2019

  • Wrote HistogramSlider.m to compare 1D histograms with segmented RPE, ILM and choroid.
  • Wrote HistogramPeakSlider.m to cooperate with ChoroidApp.m for interactive identification of choroid boundary control points using the 1D histograms.
  • Reformatted ChoroidApp.m with UI layout on right side
  • Reorganized folders, adding deprecated\ and `analysis'

1Jan2019

  • Prepped ChoroidApp.m for new experiments.

20Dec2018

  • Added ChoroidApp.m, an improved version of ChoroidIdentification.m that relies on control points, not edge detection.
  • Moved ChoroidIdentification.m

16Aug2018

  • Reload and crop functions for OCT class.

8Aug2018

  • Extra visualization options for the OCT class.
  • QOD export option for getting choroid ratios into Igor Pro.
  • Added instructions to README

7Aug2018

  • Working class encompassing existing functions for individual OCT images (OCT.m).
  • General improvements to workflow while analyzing images.

6Aug2018

  • New function alignImages.m to determine rotation degree necessary to align images of the same eye from different days.
  • New function compareChoroids.m plots a comparison of two choroid thickness ratios and optionally aligns by shifting the 2nd ratio along the x-axis.
  • Updates to choroidThickness.m.
  • Utility function exportFigure.m for saving images of segmentation from ChoroidIdentification.m.

5Aug2018

  • Array format of RPE and ILM segmentation now matches Edges and Choroid. Previous code needs to account for [y;x] to [x, y] conversion.
  • Added initial analysis function choroidThickness.m. Next step is to align the signals.

4Aug2018

  • Changed ExcludeEdges function from imrect to imfreehand
  • Added fast MEX function for finding edges within polygon lib\inPolygon.c which must be compiled. For now ChoroidIdentification.m tries to compile the function if InPolygon.mexw64 isn't available, but in the future, an option to use Matlab's builtin inpolygon would be good.

3Aug2018

  • First working version of RPE, ILM segmentation and choroid fits to a parabola.