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v0.6.0

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@JoepVanlier JoepVanlier released this 18 Aug 12:23
faf4929
  • Plot and return images and timestamps for scans using physical coordinate system rather than fast and slow scanning axis. In v5.0, this resulted in a failed reconstruction and Scan.pixels_per_line being defined as pixels along the x axis. Scan.pixels_per_line and Kymo.pixels_per_line now return the number of pixels along the fast axis. This fix was also applied to the timestamps. In the previous version, for a multi-frame scan where the y-axis is the fast axis, you could incorrectly get the time between pixels on the fast axis by calculating scan.timestamps[0, 0, 1] - scan.timestamps[0, 0, 0]. In the new version, this is scan.timestamps[0, 1, 0] - scan.timestamps[0, 0, 0] (note that the image array convention is [frame, height, width]). Note that this is a breaking change affecting scans with the fast axis in y direction!
  • Verify starting timestamp when reconstructing Kymo or Scan. In those cases, scans cannot be reliably reconstructed from the exported data and an error is thrown. For kymos, the first (partial) line is omitted and a warning is issued. Note that scans where the scan was initiated before the exported time window cannot be reconstructed! For kymos, the first line cannot be reconstructed if the export window does not cover the start of the kymograph.
  • Add literature page to the documentation.
  • Fix docstring for Fit.plot().
  • Optimized reconstruction algorithm for sum.