Release 0.4.2

[mcgarth]

Added

• Save full-res coherence files to disk in conv2tif step if cohmask = 1.
• Save multi-looked coherence files to disk in prepifg step if cohmask = 1.
• Additional DATA_TYPE geotiff header metadata for above coherence files.
• conv2tif and prepifg output files have a tag applied to filename dependent
  on data type, i.e. _ifg.tif, _coh.tif, _dem.tif.
• Metadata about used reference pixel is added to interferogram geotiff headers:
  lat/lon and x/y values; mean and standard deviation of reference window samples.
• Quicklook PNG and KML files are generated for the Stack Rate error map by default.

Changed

• Bugfix: ensure prepifg treats input data files as read only.
• Bugfix: fix the way that the reference phase is subtracted from interferograms
  during process step.
• Bugfix: manual entry of refx/y converted to type int.
• User supplies latitude and longitude values when specifying a reference pixel in
  the config file. Pixel x/y values are calculated and used internally.
• Move Stack Rate masking to a standalone function pyrate.core.stack.mask_rate,
  applied during the merge step and add unit tests.
• Skip Stack Rate masking if threshold parameter maxsig = 0.
• Provide log message indicating the percentage of pixels masked by
  pyrate.core.stack.mask_rate.
• Refactor pyrate.core.stack module; expose two functions in documentation:
  i) single pixel stacking algorithm, and
  ii) loop function for processing full ifg array.
• Refactor pyrate.merge script; remove duplicated code and create reusable
  generic functions.
• Colourmap used to render quicklook PNG images is calculated from min/max values of
  the geotiff band.
• Updated test and dev requirements.

Removed

• Deprecate unused functions in pyrate.core.config and corresponding tests.
• Static colourmap utils/colourmap.txt that was previously used to render
  quicklook PNG images is removed.

[codecov-commenter]

Codecov Report

❗ No coverage uploaded for pull request base (master@ceabb05). Click here to learn what that means.
The diff coverage is 95.68%.

@@            Coverage Diff            @@
##             master     #274   +/-   ##
=========================================
  Coverage          ?   93.17%           
=========================================
  Files             ?       26           
  Lines             ?     3207           
  Branches          ?      495           
=========================================
  Hits              ?     2988           
  Misses            ?      137           
  Partials          ?       82           

Impacted Files	Coverage Δ
pyrate/constants.py	100.00% <ø> (ø)
pyrate/default_parameters.py	100.00% <ø> (ø)
pyrate/core/aps.py	85.25% <83.33%> (ø)
pyrate/core/refpixel.py	91.81% <93.10%> (ø)
pyrate/core/stack.py	97.22% <93.10%> (ø)
pyrate/merge.py	92.85% <95.57%> (ø)
pyrate/core/shared.py	95.24% <96.96%> (ø)
pyrate/process.py	91.78% <97.22%> (ø)
pyrate/prepifg.py	97.61% <97.72%> (ø)
pyrate/configuration.py	100.00% <100.00%> (ø)
... and 34 more

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[chandra2ga]

Here I confirm that the changes applied to the code working as expected. In my processing I used directly GAMMA generated *tif coherence and interferogram files. So I started from prepfig step.

Following are my observations while processing:

• Multi-looked coherence files generate and saved to the out/ directory using cohmask = ON
• I noticed filenames without _ifg.tif and _coh.tif are also working alright in prepifg step but in case files have two dots (e.g., *.ifg.tif) will show error. For dem file name must ended with _dem.tif in out/ otherwise showing error.
• PNG and KML files generated for stack_error as a default.
• lat/lon of reference pixel is working fine applying manually and automatic in the processing
• reference phase removal printing for each interferograms (this shouldn't display on the screen for each interferogram instead should work on the background and show only "reference phase removal calculation" as orbital step on the processing screen)
• APS correction steps are not displaying on the processing screen.
• colormap.txt files generated for both stack_rate and stack_error files using respective min/max values.

[adeane-ga]

I tested these changes using the Mexico data binary files and default .config file with coherence mask and APS turned ON. Everything is working as expected:

• Full-res and multi-looked coherence files are saved to the /out directory.
• The respective DATA_TYPE was in the header file of both coherence file types.
• The filename tags for ifg and coh are there.
• the X/Y and lat/lon pixel values are added to the multilooked ifg header.
• the KML and quick-look PNG files are created for stack_rate and stack_error.

No changes required, but a thought on the quick-look PNG for stack_error:

• For the Mexico data, it was quite hard to see the pixels with higher sigmas because it was light-red on white. We could consider more contrast, but to be discussed.