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danielparthierdanielparthier
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add actionpotential default pyqt
1 parent e59a050 commit 1d73f12

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3 files changed

+223
-94
lines changed

3 files changed

+223
-94
lines changed

‎ephys/classes/action_potentials.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -377,7 +377,7 @@ def plot(
377377
align_threshold: bool = True,
378378
threshold: bool = True,
379379
save_path: str = "action_potentials.png",
380-
backend: str = "matplotlib",
380+
backend: str = "pyqt",
381381
**kwargs: Any,
382382
) -> None | ActionPotentialsPyQt:
383383
"""

‎ephys/classes/plot/plot_action_potentials.py‎

Lines changed: 134 additions & 58 deletions
Original file line numberDiff line numberDiff line change
@@ -225,6 +225,7 @@ def plot(
225225
save_path: str = "action_potentials.png",
226226
show: bool = True,
227227
save: bool = False,
228+
polar: bool = False,
228229
alpha: float | None = None,
229230
color: str = "gist_rainbow",
230231
**kwargs: Any,
@@ -249,96 +250,171 @@ def plot(
249250
ch_action_potentials = self.action_potentials.action_potentials[ch_mask]
250251
ch_sweeps = self.action_potentials.sweep_numbers[ch_mask]
251252
ch_threshold_index = self.action_potentials.threshold["index"][ch_mask]
253+
ch_action_potentials_diff = self.action_potentials.action_potentials_diff[
254+
ch_mask
255+
]
252256
channel_tmp = self.win.addPlot(row=idx, col=0) # type: ignore
253-
channel_tmp.setYRange(
254-
np.nanmin(ch_action_potentials.magnitude),
255-
np.nanmax(ch_action_potentials.magnitude),
256-
)
257-
channel_tmp.setXRange(
258-
np.nanmin(
259-
self.action_potentials.time.magnitude
260-
- self.action_potentials.time.magnitude[ch_threshold_index.min()]
261-
),
262-
np.nanmax(
263-
self.action_potentials.time.magnitude
264-
- self.action_potentials.time.magnitude[ch_threshold_index.max()]
265-
),
266-
)
257+
if polar:
258+
259+
channel_tmp.setYRange(
260+
np.nanmin(ch_action_potentials_diff.magnitude),
261+
np.nanmax(ch_action_potentials_diff.magnitude),
262+
)
263+
channel_tmp.setXRange(
264+
np.nanmin(ch_action_potentials.magnitude),
265+
np.nanmax(ch_action_potentials.magnitude),
266+
)
267+
else:
268+
channel_tmp.setYRange(
269+
np.nanmin(ch_action_potentials.magnitude),
270+
np.nanmax(ch_action_potentials.magnitude),
271+
)
272+
channel_tmp.setXRange(
273+
np.nanmin(
274+
self.action_potentials.time.magnitude
275+
- self.action_potentials.time.magnitude[
276+
ch_threshold_index.min()
277+
]
278+
),
279+
np.nanmax(
280+
self.action_potentials.time.magnitude
281+
- self.action_potentials.time.magnitude[
282+
ch_threshold_index.max()
283+
]
284+
),
285+
)
267286
if idx == 0:
268287
channel_0 = channel_tmp
269288
channel_tmp.setXLink(channel_0)
270289
for i, sweep in enumerate(sweep_numbers):
271290
sweep_index = np.where(ch_sweeps == sweep)
272291
sweep_array = ch_action_potentials[sweep_index].magnitude
273-
if align_threshold:
292+
# curve_array = CurveArray(np.array([]), np.array([]))
293+
if align_threshold and (polar is False):
274294
time_scale = np.array(
275295
[
276296
self.action_potentials.time.magnitude
277297
- self.action_potentials.time.magnitude[threshold_idx]
278298
for threshold_idx in ch_threshold_index[sweep_index]
279299
]
280300
)
281-
else:
301+
elif polar is False:
282302
time_scale = self.action_potentials.time.magnitude
303+
else:
304+
time_scale = ch_action_potentials_diff[sweep_index].magnitude
305+
306+
if polar:
307+
curve_array = CurveArray(sweep_array, time_scale)
308+
else:
309+
curve_array = CurveArray(time_scale, sweep_array)
310+
283311
sweep_color = color_picker_qcolor(
284312
len(sweep_numbers),
285313
i,
286314
color=self.params.color,
287315
alpha=self.params.alpha,
288316
)
289-
curve_array = CurveArray(time_scale, sweep_array)
317+
290318
plot_curve = pg.PlotCurveItem(
291319
curve_array.x,
292320
curve_array.y,
293321
pen=pg.mkPen(sweep_color, width=self.params.line_width),
294322
connect="finite",
295323
)
296324
channel_tmp.addItem(plot_curve)
297-
for i, sweep in enumerate(sweep_numbers):
298-
sweep_index = np.where(ch_sweeps == sweep)
299-
sweep_array = ch_action_potentials[sweep_index].magnitude
300-
if align_threshold:
301-
time_scale = np.array(
302-
[
303-
self.action_potentials.time.magnitude
304-
- self.action_potentials.time.magnitude[threshold_idx]
305-
for threshold_idx in ch_threshold_index[sweep_index]
306-
]
307-
)
308-
else:
309-
time_scale = self.action_potentials.time.magnitude
310-
sweep_color = color_picker_qcolor(
311-
len(sweep_numbers), i, color=self.params.color, alpha=0.8
312-
)
313-
if threshold:
314-
ch_threshold = self.action_potentials.threshold["threshold"][
315-
ch_mask
316-
][sweep_index]
325+
if polar is False:
326+
for i, sweep in enumerate(sweep_numbers):
327+
sweep_index = np.where(ch_sweeps == sweep)
328+
sweep_array = ch_action_potentials[sweep_index].magnitude
317329
if align_threshold:
318-
time_scale_threshold = 0.0
330+
time_scale = np.array(
331+
[
332+
self.action_potentials.time.magnitude
333+
- self.action_potentials.time.magnitude[threshold_idx]
334+
for threshold_idx in ch_threshold_index[sweep_index]
335+
]
336+
)
319337
else:
320-
time_scale_threshold = self.action_potentials.time.magnitude[
321-
ch_threshold_index[sweep_index]
322-
]
323-
plot_scatter = pg.ScatterPlotItem(
324-
x=time_scale_threshold,
325-
y=ch_threshold,
326-
pen=pg.mkPen(sweep_color, width=1),
327-
brush=pg.mkBrush(sweep_color),
328-
marker="o",
329-
markersize=2,
338+
time_scale = self.action_potentials.time.magnitude
339+
sweep_color = color_picker_qcolor(
340+
len(sweep_numbers), i, color=self.params.color, alpha=0.8
330341
)
331-
channel_tmp.addItem(plot_scatter)
342+
if threshold:
343+
ch_threshold = self.action_potentials.threshold["threshold"][
344+
ch_mask
345+
][sweep_index]
346+
if align_threshold:
347+
time_scale_threshold = 0.0
348+
else:
349+
time_scale_threshold = (
350+
self.action_potentials.time.magnitude[
351+
ch_threshold_index[sweep_index]
352+
]
353+
)
354+
plot_scatter = pg.ScatterPlotItem(
355+
x=time_scale_threshold,
356+
y=ch_threshold,
357+
pen=pg.mkPen(sweep_color, width=1),
358+
brush=pg.mkBrush(sweep_color),
359+
marker="o",
360+
markersize=2,
361+
)
362+
channel_tmp.addItem(plot_scatter)
332363

333-
channel_tmp.setLabel("left", f"Channel {ch}")
334-
channel_tmp.setLabel(
335-
"bottom",
336-
f"Time ({self.action_potentials.time.dimensionality.string})",
337-
)
338-
channel_tmp.setLabel(
339-
"right",
340-
f"Amplitude ({self.action_potentials.action_potentials.dimensionality.string})",
341-
)
364+
channel_tmp.setLabel("left", f"Channel {ch}")
365+
channel_tmp.setLabel(
366+
"bottom",
367+
f"Time ({self.action_potentials.time.dimensionality.string})",
368+
)
369+
channel_tmp.setLabel(
370+
"right",
371+
f"Amplitude ({self.action_potentials.action_potentials.dimensionality.string})",
372+
)
373+
else:
374+
for i, sweep in enumerate(sweep_numbers):
375+
sweep_index = np.where(ch_sweeps == sweep)
376+
sweep_array = ch_action_potentials[sweep_index].magnitude
377+
sweep_array_diff = ch_action_potentials_diff[sweep_index].magnitude
378+
sweep_color = color_picker_qcolor(
379+
len(sweep_numbers), i, color=self.params.color, alpha=0.8
380+
)
381+
if threshold:
382+
383+
ch_threshold_index = self.action_potentials.threshold["index"][
384+
ch_mask
385+
][sweep_index]
386+
ch_threshold = self.action_potentials.threshold["threshold"][
387+
ch_mask
388+
][sweep_index]
389+
ch_threshold_diff = [
390+
sweep_array_diff[idx, threshold_idx]
391+
for idx, threshold_idx in enumerate(ch_threshold_index)
392+
]
393+
print(
394+
ch_threshold,
395+
ch_threshold_diff,
396+
sweep_color,
397+
sweep_index,
398+
)
399+
plot_scatter = pg.ScatterPlotItem(
400+
x=ch_threshold,
401+
y=ch_threshold_diff,
402+
pen=pg.mkPen(sweep_color, width=1),
403+
brush=pg.mkBrush(sweep_color),
404+
marker="o",
405+
markersize=2,
406+
)
407+
channel_tmp.addItem(plot_scatter)
408+
409+
channel_tmp.setLabel("left", f"Channel {ch} (Polar)")
410+
channel_tmp.setLabel(
411+
"bottom",
412+
f"Amplitude ({self.action_potentials.action_potentials.dimensionality.string})",
413+
)
414+
channel_tmp.setLabel(
415+
"right",
416+
f"ΔAmplitude ({self.action_potentials.action_potentials.dimensionality.string})",
417+
)
342418

343419
def show(self) -> None:
344420
"""Show the plot window."""

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