Sue test #3
Sue test #3
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| """Example.""" | ||
| data_dir = Path(os.path.dirname(__file__)).parent.parent | ||
| nwbfile = os.path.join( | ||
| data_dir, "tests\\data\\689514_2024-02-01_18-06-43.nwb" |
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Could you change all \\s in the path to / so that they work for both Windows and Linux? I get an error when I run this in Code Ocean.
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Thank you for the tip! Also changed other cases in the code.
| leftLicks = nwb.acquisition["left_lick_time"].timestamps[:] | ||
| rightLicks = nwb.acquisition["right_lick_time"].timestamps[:] | ||
| allLicks = np.sort(np.concatenate((rightLicks, leftLicks))) | ||
| sortInd = np.argsort(np.concatenate((rightLicks, leftLicks))) | ||
| allLicksID = np.concatenate( | ||
| (np.ones_like(rightLicks), np.zeros_like(leftLicks)) | ||
| ) | ||
| allLicksID = allLicksID[sortInd] | ||
| allLickDiffs = np.diff(allLicks) |
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Ideally we should separate the code that extracts data from nwb and the code that generates plots for a better modularity.
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(don't have to make this change if integrating the code is more urgent)
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This is separated in the new commits.
| class lickMetrics: | ||
| """calculate lick quantiles""" | ||
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| def __init__(self, nwb): | ||
| """Input: nwb of behavior data""" | ||
| self.sessionID = nwb.session_id | ||
| self.tblTrials = nwb.trials.to_dataframe() | ||
| self.leftLicks = nwb.acquisition["left_lick_time"].timestamps[:] | ||
| self.rightLicks = nwb.acquisition["right_lick_time"].timestamps[:] | ||
| self.allLicks = np.sort( | ||
| np.concatenate((self.rightLicks, self.leftLicks)) | ||
| ) | ||
| self.lickLat = ( | ||
| self.tblTrials["reward_outcome_time"] | ||
| - self.tblTrials["goCue_start_time"] | ||
| ) | ||
| self.lickLatR = self.lickLat[self.tblTrials["animal_response"] == 1] | ||
| self.lickLatL = self.lickLat[self.tblTrials["animal_response"] == 0] | ||
| self.thresh = [0.05, 0.5, 1.0] | ||
| self.kernel = norm.pdf(np.arange(-2, 2.1, 0.5)) | ||
| self.binWidth = 0.2 | ||
| self.binSteps = np.arange(0, 1.5, 0.02) | ||
| self.lickMet = None | ||
| self.winGo = [self.thresh[0], 1.0] | ||
| self.winBl = [-1, 0] |
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For the same reason, in general, we discourage the use of classes in the shared repo. For example, this class can be refactored as:
- a function that extracts data from nwb (could be the same as the one mentioned at Lines 29~37) and returns
tblTrials,leftLicksandrightLicksetc - a function
calMetricsthat works on the extracted data and returns the dictionarylickMet - a plot function that receives
lickMetand does the plotting.
But if you think it is unlikely that someone will reuse the functions independently of the class, we can leave them as they are.
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The original version was indeed three separate functions, they were later combined because they share a lot of inputs. It's easy to split them!
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| lickSum = lickMetrics(nwb) | ||
| lickSum.calMetrics() | ||
| fig = lickSum.plot() |
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this should be
| fig = lickSum.plot() | |
| fig, _ = lickSum.plot() |
as lickSum.plot() returns two variables.
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Thank you! I also corrected other similar cases.
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Have you pushed your latest changes for review? |
I added some new figures and also merged main branch in. It is ready for review now! |
Added two lick-focused analysis:
plotLickAnalysis: plot lick rasters and lick rates aligned to the time of go cueslickMetrics: calculate lick metrics and plot summary plots.Both of them take nwb as input and generate a figure and a string for sessionID.
Example plots can be found here:
plots
Example usage is here:
https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-basic-analysis/blob/sueTest/src/aind_dynamic_foraging_basic_analysis/lickAnalysis.py