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show trace data
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@paulmueller
paulmueller committed Oct 7, 2019
1 parent 66173d6 commit 08ad760
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Showing 2 changed files with 135 additions and 54 deletions.
56 changes: 45 additions & 11 deletions shapeout2/gui/quick_view.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,8 @@ def __init__(self, *args, **kwargs):
self.on_event_scatter_update)
self.checkBox_auto_contrast.stateChanged.connect(
self.on_event_scatter_update)
self.checkBox_raw_trace.stateChanged.connect(
self.on_event_scatter_update)

# value changed signals for plot
self.signal_widgets = [self.checkBox_downsample,
Expand All @@ -74,13 +76,27 @@ def __init__(self, *args, **kwargs):
w.stateChanged.connect(self.plot)

# disable pyqtgraph controls we don't need
for vim in [self.imageView_image, self.imageView_trace]:
for vim in [self.imageView_image]:
vim.ui.histogram.hide()
vim.ui.roiBtn.hide()
vim.ui.menuBtn.hide()
# disable keyboard shortcuts
vim.keyPressEvent = lambda _: None
vim.keyReleaseEvent = lambda _: None
# Set individual plots
kw0 = dict(x=np.arange(10), y=np.arange(10))
self.trace_plots = {
"fl1_raw": pg.PlotDataItem(pen="#6EA068", **kw0), # green
"fl2_raw": pg.PlotDataItem(pen="#8E7A45", **kw0), # orange
"fl3_raw": pg.PlotDataItem(pen="#8F4D48", **kw0), # red
"fl1_median": pg.PlotDataItem(pen="#15BF00", **kw0), # green
"fl2_median": pg.PlotDataItem(pen="#BF8A00", **kw0), # orange
"fl3_median": pg.PlotDataItem(pen="#BF0C00", **kw0), # red
}

for key in self.trace_plots:
self.graphicsView_trace.addItem(self.trace_plots[key])
self.trace_plots[key].hide()

#: default parameters for the event image
self.imkw = dict(autoLevels=False,
Expand All @@ -98,10 +114,11 @@ def __getstate__(self):
"isoelastics enabled": self.checkBox_isoelastics.isChecked(),
"filters": self.filters,
}
event = {"auto contrast": self.checkBox_auto_contrast.isChecked(),
"contour": self.checkBox_contour.isChecked(),
"index": self.spinBox_event.value(),
"zoom": self.checkBox_zoom_roi.isChecked(),
event = {"index": self.spinBox_event.value(),
"image auto contrast": self.checkBox_auto_contrast.isChecked(),
"image contour": self.checkBox_contour.isChecked(),
"image zoom": self.checkBox_zoom_roi.isChecked(),
"trace raw": self.checkBox_raw_trace.isChecked(),
}
state = {"plot": plot,
"event": event,
Expand Down Expand Up @@ -140,10 +157,11 @@ def __setstate__(self, state):
for tb in self.signal_widgets:
tb.blockSignals(False)
if "event" in state:
self.checkBox_auto_contrast.setChecked(state["auto contrast"])
self.checkBox_contour.setChecked(state["contour"])
self.checkBox_auto_contrast.setChecked(state["image auto contrast"])
self.checkBox_contour.setChecked(state["image contour"])
self.checkBox_zoom_roi.setChecked(state["event"]["image zoom"])
self.spinBox_event.setValue(state["event"]["index"])
self.checkBox_zoom_roi.setChecked(state["event"]["zoom"])
self.checkBox_raw_trace.setChecked(state["event"]["trace raw"])

def on_event_scatter_clicked(self, plot, point):
"""User clicked on scatter plot
Expand Down Expand Up @@ -199,7 +217,7 @@ def show_event(self, event):
with dclab.new_dataset(state["plot"]["path"]) as ds:
if "image" in ds:
cellimg = ds["image"][event]
if state["event"]["auto contrast"]:
if state["event"]["image auto contrast"]:
imkw["levels"] = cellimg.min(), cellimg.max()
# convert to RGB
cellimg = cellimg.reshape(
Expand All @@ -210,14 +228,14 @@ def show_event(self, event):
# might run into trouble displaying random contours.
if "mask" in ds and len(ds["mask"]) > event:
mask = ds["mask"][event]
if state["event"]["contour"]:
if state["event"]["image contour"]:
# compute contour image from mask
cont = mask ^ binary_erosion(mask)
# set red contour pixel values in original image
cellimg[cont, 0] = int(imkw["levels"][1]*.7)
cellimg[cont, 1] = 0
cellimg[cont, 2] = 0
if state["event"]["zoom"]:
if state["event"]["image zoom"]:
xv, yv = np.where(mask)
idminx = xv.min() - 5
idminy = yv.min() - 5
Expand All @@ -234,6 +252,22 @@ def show_event(self, event):

self.imageView_image.setImage(cellimg, **imkw)

if "trace" in ds:
for key in dclab.dfn.FLUOR_TRACES:
if key.count("raw") and not state["event"]["trace raw"]:
# hide raw trace data if user decided so
show = False
else:
show = True
if (key in ds["trace"] and show):
# show the trace information
tracey = ds["trace"][key][event]
tracex = np.arange(tracey.size)
self.trace_plots[key].setData(tracex, tracey)
self.trace_plots[key].show()
else:
self.trace_plots[key].hide()

def on_tool(self):
"""Show and hide tools when the user selected a tool button"""
# show extra data
Expand Down
133 changes: 90 additions & 43 deletions shapeout2/gui/quick_view.ui
View file
Original file line number Diff line number Diff line change
Expand Up @@ -295,55 +295,97 @@
</layout>
</item>
<item>
<layout class="QGridLayout" name="gridLayout_3">
<property name="topMargin">
<number>0</number>
<widget class="QGroupBox" name="groupBox">
<property name="title">
<string>Brightfield image</string>
</property>
<item row="0" column="0">
<widget class="QCheckBox" name="checkBox_contour">
<property name="text">
<string>Show contour</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QCheckBox" name="checkBox_zoom_roi">
<property name="text">
<string>Zoom to ROI</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QCheckBox" name="checkBox_auto_contrast">
<property name="text">
<string>Auto contrast</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
<layout class="QGridLayout" name="gridLayout_3">
<property name="topMargin">
<number>0</number>
</property>
<item row="0" column="0">
<widget class="QCheckBox" name="checkBox_contour">
<property name="text">
<string>Show contour</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="1">
<widget class="QCheckBox" name="checkBox_zoom_roi">
<property name="text">
<string>Zoom to ROI</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QCheckBox" name="checkBox_auto_contrast">
<property name="text">
<string>Auto contrast</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="ImageView" name="imageView_image">
<property name="minimumSize">
<size>
<width>300</width>
<height>200</height>
</size>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="ImageView" name="imageView_image">
<property name="minimumSize">
<size>
<width>300</width>
<height>0</height>
</size>
<widget class="QGroupBox" name="groupBox_2">
<property name="title">
<string>Fluorescence traces</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout_2">
<item>
<layout class="QGridLayout" name="gridLayout_4">
<property name="topMargin">
<number>0</number>
</property>
<item row="0" column="0">
<widget class="QCheckBox" name="checkBox_raw_trace">
<property name="text">
<string>Show raw data</string>
</property>
<property name="checked">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="PlotWidget" name="graphicsView_trace">
<property name="minimumSize">
<size>
<width>0</width>
<height>200</height>
</size>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item>
<widget class="ImageView" name="imageView_trace"/>
</item>
</layout>
</widget>
</item>
Expand All @@ -361,6 +403,11 @@
<extends>QGraphicsView</extends>
<header>pyqtgraph</header>
</customwidget>
<customwidget>
<class>PlotWidget</class>
<extends>QGraphicsView</extends>
<header>pyqtgraph</header>
</customwidget>
</customwidgets>
<resources/>
<connections/>
Expand Down

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