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Presub #68

Merged
merged 20 commits into from
Nov 26, 2018
Merged

Presub #68

merged 20 commits into from
Nov 26, 2018

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ccluri
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@ccluri ccluri commented Nov 23, 2018

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ccluri and others added 19 commits October 24, 2018 17:44
@ccluri
new method to save pre-computed tables for efficient subsequent runs
3cc5f41
@ccluri
some efficiency related changes for error figure plot
4c412de
@ccluri
towards figures of the tutorials
d8ab8da
@ccluri
figures using grid spec and with large and small sources
2f0fb6f
@ccluri
adding tutorials and the corresponding figure scripts
f4dcc5b
@ccluri
spelling check noisy instead
17f3788
@m-kowalska @ccluri
figures for targeted basis and spectral structure investigation (#61)
4f9f818 
* Change dist:precise to dist:trusty (#56)

* Change dist:precise to dist:trusty

* Make shorter tests

* Remove incorrect part of the test

* Lower source number and spatial resolution to speed up tests

* Add docstrings

* Comment out build for ubuntu trusty because the build takes too long

* figure 5

* figure 5 with correct axis

* targeted basis with GridSpec

* targeted basis with regularization and noise

* vectors with gridspec

* legend on the separate subplot
@ccluri
adding tutorial for the broken electrodes
b7b615b
@ccluri
consolidated tutorial for the paper
81d7cf1
@ccluri
tbasis figure updated
1db177f
@m-kowalska @asiaszmek
tbasis and regularization method choice update (#62)
41afcd0 
* show tbasis with both cross-validation and l-curve in the same figure

* updated choice of regularization method
@ccluri
minor label and font improvements
48e3e99
@ccluri
stylized vectors figure
9130dd2
@ccluri
style changes
7dc8bfe
@m-kowalska @ccluri
Saved tables - changed y axis alignment (issue #63) (#65)
7464025 
* tbasis with both cross-validation and l-curve on the same figure

* updated regularization method choice
@m-kowalska @ccluri
Saved tables (#66)
7a0190b 
* tbasis with both cross-validation and l-curve on the same figure

* updated regularization method choice

* consistent documentation - solved issue #52.1

* changed name of the method recon to do_kcsd - solved issue #52.4

* refactoring of make_reconstruction method
@ccluri
pre submission branch for figure and tutorials
9edbca7
@ccluri
removing the numba enhancement
3bd60c9
@ccluri
merge issues
d800606
@ccluri ccluri closed this Nov 23, 2018
@ccluri ccluri reopened this Nov 23, 2018
@ccluri
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ccluri commented Nov 23, 2018

This was a stupid way of testing a feature.

  1. Initially I tested numba-jit (numba jit speed increase #57) and saved pickle tables (Pickles for forward model #64) both in the saved_tables branch.

  2. To this, Marta and I added the figures and tutorials as I used the features from 1 to improve speed in computations.

Now this presub branch only has the features from 2 (the numba, and pickled tables are reverted in 9edbca7 and 3bd60c9) that I wish to push to the master branch as the numba-jit and pickles are two different enhancements that need to be tested exhaustively before merger to master.

@ccluri ccluri requested a review from m-kowalska November 23, 2018 14:06
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Pull Request Test Coverage Report for Build 142

  • 7 of 22 (31.82%) changed or added relevant lines in 3 files are covered.
  • 7 unchanged lines in 4 files lost coverage.
  • Overall coverage increased (+0.5%) to 60.792%
Changes Missing Coverage Covered Lines Changed/Added Lines %
kcsd/validation/VisibilityMap.py 0 3 0.0%
kcsd/validation/ValidateKCSD.py 5 17 29.41%
Files with Coverage Reduction New Missed Lines %
kcsd/validation/ValidateKCSD.py 1 30.95%
kcsd/tests/test_loadData.py 2 98.67%
kcsd/tests/test_sKCSD.py 2 97.3%
kcsd/tests/test_sKCSDcell.py 2 96.41%
Totals Coverage Status
Change from base Build 136: 0.5%
Covered Lines: 1673
Relevant Lines: 2752
💛 - Coveralls

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Pull Request Test Coverage Report for Build 142

  • 7 of 22 (31.82%) changed or added relevant lines in 3 files are covered.
  • 7 unchanged lines in 4 files lost coverage.
  • Overall coverage increased (+0.5%) to 60.792%
Changes Missing Coverage Covered Lines Changed/Added Lines %
kcsd/validation/VisibilityMap.py 0 3 0.0%
kcsd/validation/ValidateKCSD.py 5 17 29.41%
Files with Coverage Reduction New Missed Lines %
kcsd/validation/ValidateKCSD.py 1 30.95%
kcsd/tests/test_loadData.py 2 98.67%
kcsd/tests/test_sKCSD.py 2 97.3%
kcsd/tests/test_sKCSDcell.py 2 96.41%
Totals Coverage Status
Change from base Build 136: 0.5%
Covered Lines: 1673
Relevant Lines: 2752
💛 - Coveralls

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coveralls commented Nov 23, 2018 •
edited
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Pull Request Test Coverage Report for Build 142

  • 7 of 22 (31.82%) changed or added relevant lines in 3 files are covered.
  • 7 unchanged lines in 4 files lost coverage.
  • Overall coverage increased (+0.5%) to 60.792%
Changes Missing Coverage Covered Lines Changed/Added Lines %
kcsd/validation/VisibilityMap.py 0 3 0.0%
kcsd/validation/ValidateKCSD.py 5 17 29.41%
Files with Coverage Reduction New Missed Lines %
kcsd/validation/ValidateKCSD.py 1 30.95%
kcsd/tests/test_loadData.py 2 98.67%
kcsd/tests/test_sKCSD.py 2 97.3%
kcsd/tests/test_sKCSDcell.py 2 96.41%
Totals Coverage Status
Change from base Build 136: 0.5%
Covered Lines: 1673
Relevant Lines: 2752
💛 - Coveralls

@m-kowalska m-kowalska merged commit c3c5dbd into master Nov 26, 2018
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@ccluri @coveralls @m-kowalska