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AurelienJaquierAurelienJaquier
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add tests for BPAP analysis (#21)
* add tests for BPAP analysis
1 parent 2642bee commit 400b228

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5 files changed

+504
-12
lines changed

5 files changed

+504
-12
lines changed

‎bluecellulab/analysis/analysis.py

Lines changed: 22 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -248,7 +248,7 @@ def __init__(self, cell: Cell) -> None:
248248
self.cell = cell
249249
self.dt = 0.025
250250
self.stim_start = 1000
251-
self.stim_duration = 3
251+
self.stim_duration = 5
252252
self.basal_cmap = sns.color_palette("crest", as_cmap=True)
253253
self.apical_cmap = sns.color_palette("YlOrBr_r", as_cmap=True)
254254

@@ -301,7 +301,11 @@ def amplitudes(self, recs) -> list[float]:
301301
for rec in recs.values()
302302
]
303303
features_results = efel.get_feature_values(traces, [efel_feature_name])
304-
amps = [feat_res[efel_feature_name][0] for feat_res in features_results]
304+
amps = [
305+
feat_res[efel_feature_name][0]
306+
for feat_res in features_results
307+
if feat_res[efel_feature_name] is not None
308+
]
305309

306310
return amps
307311

@@ -320,7 +324,7 @@ def distances_to_soma(self, recs) -> list[float]:
320324

321325
def get_amplitudes_and_distances(self):
322326
soma_rec, dend_rec, apic_rec = self.get_recordings()
323-
soma_amp = self.amplitudes({"soma": soma_rec})[0]
327+
soma_amp = self.amplitudes({"soma": soma_rec})
324328
dend_amps = None
325329
dend_dist = None
326330
apic_amps = None
@@ -334,20 +338,21 @@ def get_amplitudes_and_distances(self):
334338

335339
return soma_amp, dend_amps, dend_dist, apic_amps, apic_dist
336340

337-
def fit(self, soma_amp, dend_amps, dend_dist, apic_amps, apic_dist):
341+
@staticmethod
342+
def fit(soma_amp, dend_amps, dend_dist, apic_amps, apic_dist):
338343
"""Fit the amplitudes vs distances to an exponential decay function."""
339344
from scipy.optimize import curve_fit
340345

341346
popt_dend = None
342347
if dend_amps and dend_dist:
343348
dist = [0] + dend_dist # add soma distance
344-
amps = [soma_amp] + dend_amps # add soma amplitude
349+
amps = soma_amp + dend_amps # add soma amplitude
345350
popt_dend, _ = curve_fit(exp_decay, dist, amps)
346351

347352
popt_apic = None
348353
if apic_amps and apic_dist:
349354
dist = [0] + apic_dist # add soma distance
350-
amps = [soma_amp] + apic_amps # add soma amplitude
355+
amps = soma_amp + apic_amps # add soma amplitude
351356
popt_apic, _ = curve_fit(exp_decay, dist, amps)
352357

353358
return popt_dend, popt_apic
@@ -357,10 +362,18 @@ def validate(self, soma_amp, dend_amps, dend_dist, apic_amps, apic_dist):
357362
validated = True
358363
notes = ""
359364
popt_dend, popt_apic = self.fit(soma_amp, dend_amps, dend_dist, apic_amps, apic_dist)
365+
logging.warning(popt_dend)
366+
if dend_amps is not None:
367+
plt.cla()
368+
plt.plot([0], soma_amp, '.')
369+
plt.plot(dend_dist, dend_amps, '.')
370+
x = np.linspace(0, max(dend_dist), 100)
371+
plt.plot(x, exp_decay(x, *popt_dend), color='darkgreen', linestyle='--', label='Basal Dendritic Fit')
372+
plt.savefig("bad_dendritic_fit.png")
360373
if popt_dend is None:
361374
logger.debug("No dendritic recordings found.")
362375
notes += "No dendritic recordings found.\n"
363-
elif popt_dend[1] <= 0:
376+
elif popt_dend[1] <= 0 or popt_dend[0] <= 0:
364377
logger.debug("Dendritic fit is not decaying.")
365378
validated = False
366379
notes += "Dendritic fit is not decaying.\n"
@@ -369,7 +382,7 @@ def validate(self, soma_amp, dend_amps, dend_dist, apic_amps, apic_dist):
369382
if popt_apic is None:
370383
logger.debug("No apical recordings found.")
371384
notes += "No apical recordings found.\n"
372-
elif popt_apic[1] <= 0:
385+
elif popt_apic[1] <= 0 or popt_apic[0] <= 0:
373386
logger.debug("Apical fit is not decaying.")
374387
validated = False
375388
notes += "Apical fit is not decaying.\n"
@@ -395,7 +408,7 @@ def plot_amp_vs_dist(
395408

396409
outpath = pathlib.Path(output_dir) / output_fname
397410
fig, ax1 = plt.subplots(figsize=(10, 6))
398-
ax1.scatter([0], [soma_amp], marker="^", color='black', label='Soma')
411+
ax1.scatter([0], soma_amp, marker="^", color='black', label='Soma')
399412
if dend_amps and dend_dist:
400413
ax1.scatter(
401414
dend_dist,

‎tests/data/analysis/bpap_amplitude_distance.json

Lines changed: 215 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,215 @@
1+
{
2+
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3+
111.34521528672875
4+
],
5+
"dend_amps": [
6+
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7+
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23+
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24+
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25+
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26+
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27+
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28+
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29+
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30+
],
31+
"dend_dist": [
32+
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33+
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34+
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35+
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37+
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39+
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40+
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41+
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42+
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43+
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44+
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45+
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46+
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47+
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48+
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49+
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50+
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51+
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52+
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53+
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54+
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55+
200.1518994137304
56+
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57+
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58+
110.80678737727112,
59+
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60+
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61+
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62+
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63+
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64+
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65+
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66+
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68+
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70+
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136+
"apic_dist": [
137+
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]
215+
}

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