Neuroinflab / kCSD-python / 257
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ccluri 
Add sKCSD tutorial (#88)

* Introduction to sKCSD tutorial

* Add description for load data

* Add example how to add morphology to empty data

* Better description of assign function

* Update test files.

Update files for tests (and test_loadData.py to account for change
filenames). Add segment lengths and membrane currents for
sKCSD tutorial. Fix a bug in checking branching points in test_sKCSDcell.py.

* Delete unused test data files.

* Fix typo in the name of the file with electrode positions

* Fix error in skcsd calculation

skcsd is current density, no need to divide by segment length.

* Add test data generation

* Shorter simulation for test data

* Make data plot of ground truth current density

* Even shorter data (using a smaller morphology) for the skcsd tutorial

* First description of values()

* Add a comparison fig to the tutorial

* Clean up dataset

Increase number of used electrodes from 16 to 100. Record soma voltage,
so it can be shown in tutorials.

* Remove unused morphology file

* New morphology file

This actually is the same morphology file as before, only with a
filename corresponding to the simulation parameters, which have been
changed, because now 10x10 electrode grid is used.

* Save array with timestamps to file

* Add soma voltage plot

* Fix small errors

* Add some morphology transformations

* Comment out L-curve for speed

* Add savefig

Switch to plotting with imshow, remove plt.show(), add a few tweaks.

* Do not draw circles for morphology

* Provide extent in meters not in microns.

For compatibility with the rest of KCSD, which is implemented in SI
units.

* Remove obsolete figure

* Remove unnecessary print

* Move sKCSDcell.distribute_srcs_3D_morph() to init

* Rewrite calculation of 2D morphology for images

Rewrite calculation of 2D morphology for drawing images to use only
code used for finding indices for CSD and potential t... (continued)

1808 of 2898 relevant lines covered (62.39%)

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Jobs
ID Job ID Ran Files Coverage
1 257.1 (DISTRIB="conda" PYTHON_VERSION="2.7" NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1" SIX_VERSION="1.10.0" COVERAGE="true") 0
62.18
 Travis Job 257.1
2 257.2 (DISTRIB="conda" PYTHON_VERSION="3.5" NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1" SIX_VERSION="1.10.0" COVERAGE="true") 0
62.35
 Travis Job 257.2
3 257.3 (DISTRIB="conda_min" PYTHON_VERSION="2.7" SIX_VERSION="1.10.0" NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1" COVERAGE="true") 0
62.18
 Travis Job 257.3
4 257.4 (DISTRIB="conda_min" PYTHON_VERSION="3.4" SIX_VERSION="1.10.0" NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1" COVERAGE="true") 0
62.35
 Travis Job 257.4
Source Files on build 257
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