Updated pixels analysis #1
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| def significance_extraction(CI): | |||
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It seems that the functions in this module are duplicated elsewhere in one of your own scripts. What's the difference between them?
| #First sort the data into long form for both datasets, by percentile | ||
| CIs_long = CIs.reset_index().melt("percentile").sort_values("value", ascending= dir_ascending) | ||
| CIs_long = CIs_long.reset_index() | ||
| CIs_long["index"] = pd.Series(range(0, CIs_long.shape[0]))#reset the index column to allow ordered plotting | ||
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| CIs_long_sig = sig_CIs.reset_index().melt("percentile").sort_values("value", ascending=dir_ascending) | ||
| CIs_long_sig = CIs_long_sig.reset_index() | ||
| CIs_long_sig["index"] = pd.Series(range(0, CIs_long_sig.shape[0])) | ||
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| #Now select if we want only significant values plotted, else raise an error. | ||
| if sig_only is True: | ||
| data = CIs_long_sig | ||
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| elif sig_only is False: | ||
| data = CIs_long |
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Maybe move the dataframe wrangling into the if statement? That way CIs_long_sig won't need to be generated when sig_only is False and vice versa
| noise_tests = Experiment( | ||
| ["noisetest1"], | ||
| NoBehaviour, | ||
| "~/duguidlab/visuomotor_control/neuropixels", | ||
| ) | ||
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| noise_test_unchanged = Experiment( | ||
| ["noisetest_unchanged"], | ||
| NoBehaviour, | ||
| "~/duguidlab/visuomotor_control/neuropixels", | ||
| ) | ||
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| noise_test_nopi = Experiment( | ||
| ["noisetest_nopi"], | ||
| NoBehaviour, | ||
| "~/duguidlab/visuomotor_control/neuropixels", | ||
| ) | ||
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| noise_test_no_caps = Experiment( | ||
| "VR50", | ||
| Reach, | ||
| "~/duguidlab/visuomotor_control/neuropixels", | ||
| ) | ||
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| # This contains the list of experiments we want to plot noise for, here only interested in the reaching task | ||
| # Remember to change this in base.py |
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pixtools should be general functions that anyone could use - this code here is not general, it's using specific experiments for something
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Likewise the sys.path stuff at the top, which is incidental to your setup
to local space to stop spamming the repo
…rst phase of dissertation work
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| #Now determine the optimal number of clusters to use in the K-means analysis by producing elbow plots | ||
| def elbowplot(data, myexp): |
| from pixels import Experiment | ||
| from pixels.behaviours.leverpush import LeverPush | ||
| from pixels.behaviours.pushpull import PushPull | ||
| from pixels.behaviours.reach import Reach | ||
| from pixels.behaviours.no_behaviour import NoBehaviour | ||
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| import numpy as np | ||
| import pandas as pd | ||
| import seaborn as sns | ||
| import datetime | ||
| import matplotlib.pyplot as plt | ||
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| from pixtools import clusters | ||
| from pixtools import utils | ||
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can you remove imports that are not needed in this file? None of those behaviour classes are needed
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| # Unlike other noiseplot file (by channel) this file will cluster the SDs, allowing for a mean square analysis | |||
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Please could you move this module into a new folder pixtools/noise/ rather than pixtools/clusters/? 'clusters' here refers to clusters of spikes as determined by kilosort, not clustering analyses.
| random_state=42, # The random number seed for centroid generation, can really be anything for our purposes | ||
| ) | ||
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| df2 = data |
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It looks like this variable is redundant, why not just use data for the rest of the function?
| plt.ylabel("Channel Noise (SD)") | ||
| plt.title(f"{name} Channel Noise k-Mean Clustering Analysis") | ||
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| plt.show() |
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I think it would be nice if users of this module aren't locked into using plt.show() and accessing generated plots exclusively via opened windows. Perhaps we could just pass a single session into this function, make the plot, then return the axis used that contains the plot? Then client code can create a figure/axis, or alternatively make a bunch of subplots (i.e. per sesssion) then do this inner loop themselves if that's how they wanted to plot.
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Same for the elbow plot function above
| from turtle import fd | ||
| from channeldepth import * | ||
| from channeldepth import * |
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Please could you remove this turtle import? It isn't used in this module, and in any case isn't a dependency of pixels so it would be good to keep those limited to what is already needed.
Also what is channeldepth here? I dont see the module
… files containing fano factor analyses
Have updated my fork to include analysis scripts and figures. Changes confined to my projects folder with the exception of a k-means clustering script added to pixtools/clusters/.