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Commit cd1a722

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mayofaulknermayofaulkner
committed
Merge branch 'develop'
2 parents 1a2ce76 + 5c3d349 commit cd1a722

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3 files changed

+49
-17
lines changed

3 files changed

+49
-17
lines changed

‎atlaselectrophysiology/ephys_atlas_gui.py‎

Lines changed: 15 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -364,7 +364,7 @@ def save_plots(self):
364364

365365
while plot != start_plot:
366366
self.set_font(self.fig_img_cb, 'top', ptsize=15, height=ax_height + 15)
367-
exporter = pg.exporters.ImageExporter(self.fig_data_layout)
367+
exporter = pg.exporters.ImageExporter(self.fig_data_layout.scene())
368368
exporter.export(str(image_path.joinpath(sess_info + 'img_' +
369369
self.img_options_group.checkedAction()
370370
.text() + '.png')))
@@ -391,7 +391,7 @@ def save_plots(self):
391391

392392
while plot != start_plot:
393393
self.set_font(self.fig_probe_cb, 'top', ptsize=15, height=ax_height + 15)
394-
exporter = pg.exporters.ImageExporter(self.fig_data_layout)
394+
exporter = pg.exporters.ImageExporter(self.fig_data_layout.scene())
395395
exporter.export(str(image_path.joinpath(sess_info + 'probe_' +
396396
self.probe_options_group.checkedAction().
397397
text() + '.png')))
@@ -419,7 +419,7 @@ def save_plots(self):
419419
plot = None
420420
start_plot = self.line_options_group.checkedAction()
421421
while plot != start_plot:
422-
exporter = pg.exporters.ImageExporter(self.fig_data_layout)
422+
exporter = pg.exporters.ImageExporter(self.fig_data_layout.scene())
423423
exporter.export(str(image_path.joinpath(sess_info + 'line_' +
424424
self.line_options_group.checkedAction().
425425
text() + '.png')))
@@ -476,8 +476,19 @@ def save_plots(self):
476476
plot = self.slice_options_group.checkedAction()
477477

478478
# Save the brain regions image
479-
exporter = pg.exporters.ImageExporter(self.fig_hist_layout)
479+
self.set_axis(self.fig_hist_extra_yaxis, 'left')
480+
# Add labels to show which ones are aligned
481+
self.set_axis(self.fig_hist, 'bottom', label='aligned', ticks=False)
482+
self.set_font(self.fig_hist, 'bottom', ptsize=12)
483+
self.set_axis(self.fig_hist_ref, 'bottom', label='original', ticks=False)
484+
self.set_font(self.fig_hist_ref, 'bottom', ptsize=12)
485+
exporter = pg.exporters.ImageExporter(self.fig_hist_layout.scene())
480486
exporter.export(str(image_path.joinpath(sess_info + 'hist.png')))
487+
self.set_axis(self.fig_hist_extra_yaxis, 'left', pen=None)
488+
self.set_font(self.fig_hist, 'bottom', ptsize=8)
489+
self.set_axis(self.fig_hist, 'bottom', pen='w')
490+
self.set_font(self.fig_hist_ref, 'bottom', ptsize=8)
491+
self.set_axis(self.fig_hist_ref, 'bottom', pen='w')
481492

482493
make_overview_plot(image_path, sess_info)
483494

‎atlaselectrophysiology/ephys_gui_setup.py‎

Lines changed: 20 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -677,14 +677,27 @@ def init_figures(self):
677677
self.fig_hist_area.scene().sigMouseClicked.connect(self.on_mouse_double_clicked)
678678
self.fig_hist_area.scene().sigMouseHover.connect(self.on_mouse_hover)
679679

680+
self.fig_hist_extra_yaxis = pg.PlotItem()
681+
self.fig_hist_extra_yaxis.setMouseEnabled(x=False, y=False)
682+
self.fig_hist_extra_yaxis.setMaximumWidth(2)
683+
self.fig_hist_extra_yaxis.setYRange(min=self.probe_tip - self.probe_extra,
684+
max=self.probe_top + self.probe_extra,
685+
padding=self.pad)
686+
687+
self.set_axis(self.fig_hist_extra_yaxis, 'bottom', pen='w')
688+
self.ax_hist2 = self.set_axis(self.fig_hist_extra_yaxis, 'left', pen=None)
689+
self.ax_hist2.setWidth(10)
690+
680691
self.fig_hist_layout = pg.GraphicsLayout()
681-
self.fig_hist_layout.addItem(self.fig_scale_cb, 0, 0, 1, 3)
682-
self.fig_hist_layout.addItem(self.fig_hist, 1, 0)
683-
self.fig_hist_layout.addItem(self.fig_scale, 1, 1)
684-
self.fig_hist_layout.addItem(self.fig_hist_ref, 1, 2,)
685-
self.fig_hist_layout.layout.setColumnStretchFactor(0, 4)
686-
self.fig_hist_layout.layout.setColumnStretchFactor(1, 1)
687-
self.fig_hist_layout.layout.setColumnStretchFactor(2, 4)
692+
self.fig_hist_layout.addItem(self.fig_scale_cb, 0, 0, 1, 4)
693+
self.fig_hist_layout.addItem(self.fig_hist_extra_yaxis, 1, 0)
694+
self.fig_hist_layout.addItem(self.fig_hist, 1, 1)
695+
self.fig_hist_layout.addItem(self.fig_scale, 1, 2)
696+
self.fig_hist_layout.addItem(self.fig_hist_ref, 1, 3)
697+
self.fig_hist_layout.layout.setColumnStretchFactor(0, 1)
698+
self.fig_hist_layout.layout.setColumnStretchFactor(1, 4)
699+
self.fig_hist_layout.layout.setColumnStretchFactor(2, 1)
700+
self.fig_hist_layout.layout.setColumnStretchFactor(3, 4)
688701
self.fig_hist_layout.layout.setRowStretchFactor(0, 1)
689702
self.fig_hist_layout.layout.setRowStretchFactor(1, 10)
690703
self.fig_hist_area.addItem(self.fig_hist_layout)

‎atlaselectrophysiology/plot_data.py‎

Lines changed: 14 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -113,17 +113,25 @@ def get_depth_data_scatter(self):
113113
A_BIN = 10
114114
amp_range = np.quantile(self.spikes['amps'][self.spike_idx][self.kp_idx], [0, 0.9])
115115
amp_bins = np.linspace(amp_range[0], amp_range[1], A_BIN)
116-
colour_bin = np.linspace(0.0, 1.0, A_BIN)
116+
colour_bin = np.linspace(0.0, 1.0, A_BIN + 1)
117117
colours = (cm.get_cmap('BuPu')(colour_bin)[np.newaxis, :, :3][0]) * 255
118118
spikes_colours = np.empty(self.spikes['amps'][self.spike_idx][self.kp_idx].size,
119119
dtype=object)
120120
spikes_size = np.empty(self.spikes['amps'][self.spike_idx][self.kp_idx].size)
121-
for iA in range(amp_bins.size - 1):
122-
idx = np.where((self.spikes['amps'][self.spike_idx][self.kp_idx] > amp_bins[iA]) &
123-
(self.spikes['amps'][self.spike_idx][self.kp_idx] <=
124-
amp_bins[iA + 1]))[0]
121+
for iA in range(amp_bins.size):
122+
if iA == (amp_bins.size - 1):
123+
idx = np.where((self.spikes['amps'][self.spike_idx][self.kp_idx] >
124+
amp_bins[iA]))[0]
125+
# Make saturated spikes a very dark purple
126+
spikes_colours[idx] = QtGui.QColor('#400080')
127+
else:
128+
idx = np.where((self.spikes['amps'][self.spike_idx][self.kp_idx] >
129+
amp_bins[iA]) &
130+
(self.spikes['amps'][self.spike_idx][self.kp_idx] <=
131+
amp_bins[iA + 1]))[0]
132+
133+
spikes_colours[idx] = QtGui.QColor(*colours[iA])
125134

126-
spikes_colours[idx] = QtGui.QColor(*colours[iA])
127135
spikes_size[idx] = iA / (A_BIN / 4)
128136

129137
data_scatter = {

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