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Integrate your bugfixes with nauralcodinglab/openscope_surround #6

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23d1c42
Add object oriented skeleton for datasets
efharkin Jul 1, 2020
b54d2cb
Add density plot for EyeTracking position
efharkin Jul 2, 2020
6fd956c
Add .ipynb_checkpoints to gitignore
efharkin Jul 2, 2020
8899cf6
Add fluorescence objects
efharkin Jul 3, 2020
96d1247
Add RawFluorescence to read_data factory functions
efharkin Jul 3, 2020
8ebfc1b
Break up read_data and introduce CenterSurround classes
efharkin Jul 6, 2020
1237f0b
Bugfixes in CenterSurroundStimulus and factory
efharkin Jul 6, 2020
c1d4db0
Implement hashing for CenterSurroundStimulus
efharkin Jul 6, 2020
e538236
Implement slicing RawFluorescence into TrialFluorescence
efharkin Jul 6, 2020
3b5eeff
Fix bugs with plotting fluorescence
efharkin Jul 6, 2020
9cc637f
Update python and dep requirements
efharkin Jul 7, 2020
1153caf
Add read_data import to oscopetools init
efharkin Jul 7, 2020
7e8a209
Add sphinx docs
efharkin Jul 7, 2020
93536d9
Add sphinx dependencies to requirements.txt
efharkin Jul 7, 2020
43db06d
Improve performance of copy operations
efharkin Jul 7, 2020
0dedcdd
Add subsetting by cell to Fluorescence objects
efharkin Jul 8, 2020
7ef8dbd
Autoformat and add summary stats to TrialFluorescence
efharkin Jul 8, 2020
de9e0d6
Add trial and cell iterators for TrialFluorescence
efharkin Jul 8, 2020
e10ca0c
TrialFluorescence.plot() produces lineplot if only one cell
efharkin Jul 8, 2020
12c82c2
Change behaviour of Orientation(None)
efharkin Jul 8, 2020
25d41ad
Implement Orientation arithmetic
efharkin Jul 8, 2020
045b408
Implement len for _NamedOrderedSet
efharkin Jul 8, 2020
37a9303
Add Orientation.radians property
efharkin Jul 8, 2020
57075ca
Remove guard against getting negative time window
efharkin Jul 8, 2020
26f4743
Add script for diagnostic plots of orientation tuning
efharkin Jul 8, 2020
842b5df
Add `data` attribute to `Dataset`s
efharkin Jul 9, 2020
2c0f1b1
Switch to np.squeeze() for data matrices
efharkin Jul 9, 2020
81d18fe
Add xlabel to Eyetracking plot
efharkin Jul 9, 2020
f4182ca
Implement RunningSpeed Dataset
efharkin Jul 9, 2020
fc07c9a
Add robust_range for robust dataset visualization
efharkin Jul 9, 2020
5d35638
Add RunningSpeed to do.__all__ and make factories open files in r mode
efharkin Jul 9, 2020
3db8f01
Robust range tweaks
efharkin Jul 9, 2020
fcbf792
Add script for generating behavioural plots
efharkin Jul 9, 2020
c1c31d4
Set eye position plot to 180 deg range by default
efharkin Jul 10, 2020
c86730c
Autoformat dataset_objects.py
efharkin Jul 10, 2020
97c2a49
Change position markeredgecolor to improve clarity
efharkin Jul 10, 2020
c351cea
Add jupyter notebook for inspecting eyetracking
efharkin Jul 10, 2020
9e25334
Added both_ends_baseline to cut_by_trials.
kt1524 Jul 24, 2020
0531075
LSN analysis and RF plotting
kt1524 Jul 24, 2020
400a400
LSN analysis and RF plotting
kt1524 Jul 24, 2020
fade678
Merge branch 'doc' into dev
efharkin Jul 28, 2020
2776d57
Modified with Emerson's suggestions.
kt1524 Jul 30, 2020
5cea92a
Added TrialEyeTracking
kt1524 Jul 30, 2020
543ab4e
Add files via upload
kt1524 Jul 30, 2020
fa01801
Merge branch 'master' into master
efharkin Jul 30, 2020
5938fb9
Merge pull request #1 from kt1524/master
efharkin Jul 30, 2020
d944b42
Replaced _is_trial with issubclass().
kt1524 Jul 30, 2020
26d9000
Replaced_is_trial with issubclass().
kt1524 Jul 30, 2020
7292630
Merge pull request #3 from kt1524/master
efharkin Jul 30, 2020
aac88a9
Added greedy pixelwise RF
kt1524 May 4, 2021
df97113
Modified get_metadata
kt1524 May 4, 2021
2c34809
Added greedy pixelwise RF
kt1524 May 4, 2021
e8264a4
Corrected overlapping index equation
kt1524 May 4, 2021
35271c1
Merge pull request #7 from kt1524/master
efharkin May 4, 2021
b7c18ec
Merge 'saskiad/master' into master
efharkin May 4, 2021
0714569
Corrected overlapping index equation
kt1524 May 4, 2021
0326cd7
Merge pull request #8 from kt1524/master
efharkin May 4, 2021
987b17e
Merging PR from kt1524: Added gag and save_data (#9)
kt1524 May 5, 2021
5faf45d
Squashed merge of PR #12 from kt1524
efharkin May 19, 2021
a04c4c8
Add autoformat script
efharkin May 19, 2021
5d124ef
Merge Saskia's stim_table.py updates into oscopetools
efharkin May 19, 2021
0520bf2
Remove duplicate RunningData.py
efharkin May 19, 2021
6aaa1eb
Remove duplicate get_eye_tracking.py
efharkin May 20, 2021
05960f7
Remove commented duplicate of align_eye_tracking
efharkin May 20, 2021
d4702c4
Autoformat analysis/get_all_data.py
efharkin May 20, 2021
01c1703
Clean up oscopetools/get_all_data.py to prepare for removal
efharkin May 20, 2021
1bd20d8
Remove oscopetools/get_all_data.py
efharkin May 20, 2021
446cfcc
Remove get_all_data import in oscopetools/__init__.py
efharkin May 25, 2021
b641ee6
Add Saskia's WIP from 2021-06-03
efharkin Jun 16, 2021
e27ba01
Clean up Saskia's working directory
efharkin Jun 16, 2021
3746c81
Strip trailing whitespace from all .py files
efharkin Jun 16, 2021
5784709
Resolve merge conflicts from ad507cd
efharkin Jun 16, 2021
59b2ddf
Upgrade to python3
efharkin Jun 16, 2021
201717f
Autoformat using black
efharkin Jun 16, 2021
eb26c5c
Remove duplicate get_eye_tracking.py
efharkin Jun 16, 2021
2a7871b
Merge 'nauralcodinglab/consolidate' into cleanup
efharkin Jun 16, 2021
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,6 @@
*.pyc
__pycache__
*.egg-info
.ipynb_checkpoints
plots/
_build/
11 changes: 11 additions & 0 deletions Makefile
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
.PHONY : doc
doc :
mkdir -p _build/docsource
cp index.rst _build/docsource/
sphinx-apidoc -f -o _build/docsource oscopetools **/test_*.py
sphinx-build _build/docsource _build/html -c .
open _build/html/index.html

.PHONY : clean
clean :
rm -rf _build/*
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