place fields #126
place fields #126
Conversation
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@MRScheid can you also make sure speed gating is used for the 1D rate maps? |
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@MRScheid could you allow the widget to optionally take as input a TimeSeries of velocity? Sometimes that is provided separately. |
- Checkbox for normalize added in last commit
I'm not sure I fully understand what you have in mind--would it be a TimeSeries of velocity in place of the position in the SpatialSeries? Would I then need to derive approximate position from the TimeSeries of velocity? |
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Also, what would be the file extension of the TimeSeries input? .nwb? Maybe this will be good to discuss during our meeting today |
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Sometimes velocity is calculated separately with special smoothing function or something and I want to be able to use this in the widget if it is available. The |
Co-authored-by: Ben Dichter <[email protected]>
Co-authored-by: Ben Dichter <[email protected]>
Co-authored-by: Ben Dichter <[email protected]>
Co-authored-by: Ben Dichter <[email protected]>
nwbwidgets/placefield.py
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| fig, ax = plt.subplots() |
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| fig, ax = plt.subplots() | |
| fig, ax = plt.subplots(figsize=(7,7)) |
* figure size
# Conflicts: # nwbwidgets/placefield.py
…se from caching the calls in placefields.py with numpy arrays im the cache keys. Incorporated an additional input in the widget to specify the width of the gaussian kernel independently for x and y respectively. Built a wrapper function around the 2D place field calculation call so that the place field calculation function calls could be properly cached without the "unhashable key" errors.
Re-factor position and widget controls to make the PlaceFieldWidget class more easily extensible for the towers task place field widget
Refactored placefield to take separate pixel_widths. for x and y dimension. Modified placefields to reflect this change.
Modifications: - Disabled velocity button when not in use - Modified both compute_2d_occupancy and compute_2d_n_spikes to recognize when the towers task place field widget is calling it so that speed is computed on just the x-dim. - Modified compute_speed to work with 1-dim input - Fixed the order of inputs to np.histogram2d. Previously the x and y input were reversed from the order expected by the function. - Refactored the pixel_width instance atrribute definition to be separate for x and y. This allows the towers task place field widget extension to overwrite this method.
Made modifications to: - NaN out any unexplored areas in the place field - Add the ability to control the number of bins in the place field calculation.
Codecov Report
@@ Coverage Diff @@
## master #126 +/- ##
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- Coverage 63.25% 60.10% -3.16%
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Files 47 49 +2
Lines 3013 3181 +168
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+ Hits 1906 1912 +6
- Misses 1107 1269 +162
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.gitignore
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| nwbwidgets/controllers/group_and_sort_controllers_multi_select.py | ||
| nwbwidgets/placefield_group_and_sort.py | ||
| nwbwidgets/towers_task_placefield.py |
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@MRScheid what are these files? Why are you gitignoring them?
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@bendichter I removed all these from the git ignore file--they were modules that I was developing with but weren't quite ready to be committed, I thought I'd get back around to them but I never did. They're irrelevant now.
Removed outdated files being ignored
Creating place field class